Evolution of Karyotypes in Chameleons

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Michail Rovatsos

2017-12-01

Full Text Available The reconstruction of the evolutionary dynamics of karyotypes and sex determining systems in squamate reptiles is precluded by the lack of data in many groups including most chameleons (Squamata: Acrodonta: Chamaeleonidae. We performed cytogenetic analysis in 16 species of chameleons from 8 genera covering the phylogenetic diversity of the family and also phylogenetic reconstruction of karyotype evolution in this group. In comparison to other squamates, chameleons demonstrate rather variable karyotypes, differing in chromosome number, morphology and presence of interstitial telomeric signal (ITS. On the other hand, the location of rDNA is quite conserved among chameleon species. Phylogenetic analysis combining our new results and previously published data tentatively suggests that the ancestral chromosome number for chameleons is 2n = 36, which is the same as assumed for other lineages of the clade Iguania, i.e., agamids and iguanas. In general, we observed a tendency for the reduction of chromosome number during the evolution of chameleons, however, in Rieppeleon brevicaudatus, we uncovered a chromosome number of 2n = 62, very unusual among squamates, originating from a number of chromosome splits. Despite the presence of the highly differentiated ZZ/ZW sex chromosomes in the genus Furcifer, we did not detect any unequivocal sexual differences in the karyotypes of any other studied species of chameleons tested using differential staining and comparative genomic hybridization, suggesting that sex chromosomes in most chameleons are only poorly differentiated.

Congenital heart disease and chromossomopathies detected by the karyotype

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Patrícia Trevisan

2014-06-01

Full Text Available OBJECTIVE: To review the relationship between congenital heart defects and chromosomal abnormalities detected by the karyotype.DATA SOURCES: Scientific articles were searched in MEDLINE database, using the descriptors "karyotype" OR "chromosomal" OR "chromosome" AND "heart defects, congenital". The research was limited to articles published in English from 1980 on.DATA SYNTHESIS: Congenital heart disease is characterized by an etiologically heterogeneous and not well understood group of lesions. Several researchers have evaluated the presence of chromosomal abnormalities detected by the karyotype in patients with congenital heart disease. However, most of the articles were retrospective studies developed in Europe and only some of the studied patients had a karyotype exam. In this review, only one study was conducted in Latin America, in Brazil. It is known that chromosomal abnormalities are frequent, being present in about one in every ten patients with congenital heart disease. Among the karyotype alterations in these patients, the most important is the trisomy 21 (Down syndrome. These patients often have associated extra-cardiac malformations, with a higher risk of morbidity and mortality, which makes heart surgery even more risky.CONCLUSIONS: Despite all the progress made in recent decades in the field of cytogenetic, the karyotype remains an essential tool in order to evaluate patients with congenital heart disease. The detailed dysmorphological physical examination is of great importance to indicate the need of a karyotype.

Congenital heart disease and chromossomopathies detected by the karyotype

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Trevisan, Patrícia; Rosa, Rafael Fabiano M.; Koshiyama, Dayane Bohn; Zen, Tatiana Diehl; Paskulin, Giorgio Adriano; Zen, Paulo Ricardo G.

2014-01-01

OBJECTIVE: To review the relationship between congenital heart defects and chromosomal abnormalities detected by the karyotype. DATA SOURCES: Scientific articles were searched in MEDLINE database, using the descriptors "karyotype" OR "chromosomal" OR "chromosome" AND "heart defects, congenital". The research was limited to articles published in English from 1980 on. DATA SYNTHESIS: Congenital heart disease is characterized by an etiologically heterogeneous and not well understood group of lesions. Several researchers have evaluated the presence of chromosomal abnormalities detected by the karyotype in patients with congenital heart disease. However, most of the articles were retrospective studies developed in Europe and only some of the studied patients had a karyotype exam. In this review, only one study was conducted in Latin America, in Brazil. It is known that chromosomal abnormalities are frequent, being present in about one in every ten patients with congenital heart disease. Among the karyotype alterations in these patients, the most important is the trisomy 21 (Down syndrome). These patients often have associated extra-cardiac malformations, with a higher risk of morbidity and mortality, which makes heart surgery even more risky. CONCLUSIONS: Despite all the progress made in recent decades in the field of cytogenetic, the karyotype remains an essential tool in order to evaluate patients with congenital heart disease. The detailed dysmorphological physical examination is of great importance to indicate the need of a karyotype. PMID:25119760

Bivariate discrete beta Kernel graduation of mortality data.

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Mazza, Angelo; Punzo, Antonio

2015-07-01

Various parametric/nonparametric techniques have been proposed in literature to graduate mortality data as a function of age. Nonparametric approaches, as for example kernel smoothing regression, are often preferred because they do not assume any particular mortality law. Among the existing kernel smoothing approaches, the recently proposed (univariate) discrete beta kernel smoother has been shown to provide some benefits. Bivariate graduation, over age and calendar years or durations, is common practice in demography and actuarial sciences. In this paper, we generalize the discrete beta kernel smoother to the bivariate case, and we introduce an adaptive bandwidth variant that may provide additional benefits when data on exposures to the risk of death are available; furthermore, we outline a cross-validation procedure for bandwidths selection. Using simulations studies, we compare the bivariate approach proposed here with its corresponding univariate formulation and with two popular nonparametric bivariate graduation techniques, based on Epanechnikov kernels and on P-splines. To make simulations realistic, a bivariate dataset, based on probabilities of dying recorded for the US males, is used. Simulations have confirmed the gain in performance of the new bivariate approach with respect to both the univariate and the bivariate competitors.

PCR-based karyotyping of Anopheles gambiae inversion 2Rj identifies the BAMAKO chromosomal form

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Conway David J

2007-10-01

Full Text Available Abstract Background The malaria vector Anopheles gambiae is polymorphic for chromosomal inversions on the right arm of chromosome 2 that segregate nonrandomly between assortatively mating populations in West Africa. One such inversion, 2Rj, is associated with the BAMAKO chromosomal form endemic to southern Mali and northern Guinea Conakry near the Niger River. Although it exploits a unique ecology and both molecular and chromosomal data suggest reduced gene flow between BAMAKO and other A. gambiae populations, no molecular markers exist to identify this form. Methods To facilitate study of the BAMAKO form, a PCR assay for molecular karyotyping of 2Rj was developed based on sequences at the breakpoint junctions. The assay was extensively validated using more than 700 field specimens whose karyotypes were determined in parallel by cytogenetic and molecular methods. As inversion 2Rj also occurs in SAVANNA populations outside the geographic range of BAMAKO, samples were tested from Senegal, Cameroon and western Guinea Conakry as well as from Mali. Results In southern Mali, where 2Rj polymorphism in SAVANNA populations was very low and most of the 2Rj homozygotes were found in BAMAKO karyotypes, the molecular and cytogenetic methods were almost perfectly congruent. Elsewhere agreement between the methods was much poorer, as the molecular assay frequently misclassified 2Rj heterozygotes as 2R+j standard homozygotes. Conclusion Molecular karyotyping of 2Rj is robust and accurate on 2R+j standard and 2Rj inverted homozygotes. Therefore, the proposed approach overcomes the lack of a rapid tool for identifying the BAMAKO form across developmental stages and sexes, and opens new perspectives for the study of BAMAKO ecology and behaviour. On the other hand, the method should not be applied for molecular karyotyping of j-carriers within the SAVANNA chromosomal form.

Main trends of karyotype evolution in the superfamily Chalcidoidea (Hymenoptera

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Vladimir Gokhman

2009-08-01

Full Text Available An overview of karyotype evolution in the superfamily Chalcidoidea is given. Structural types of chromosome sets in the superfamily are listed. Main pathways of karyotypic change in the Chalcidoidea are outlined. The chromosome set containing eleven subtelo- or acrocentrics is considered as an ancestral karyotype for the superfamily. Multiple independent reductions in n values through chromosomal fusions presumably occurred in various groups of chalcid families.

Updating the maize karyotype by chromosome DNA sizing

Science.gov (United States)

2018-01-01

The karyotype is a basic concept regarding the genome, fundamentally described by the number and morphological features of all chromosomes. Chromosome class, centromeric index, intra- and interchromosomal asymmetry index, and constriction localization are important in clinical, systematic and evolutionary approaches. In spite of the advances in karyotype characterization made over the last years, new data about the chromosomes can be generated from quantitative methods, such as image cytometry. Therefore, using Zea mays L., this study aimed to update the species’ karyotype by supplementing information on chromosome DNA sizing. After adjustment of the procedures, chromosome morphometry and class as well as knob localization enabled describing the Z. mays karyotype. In addition, applying image cytometry, DNA sizing was unprecedentedly measured for the arms and satellite of all chromosomes. This way, unambiguous identification of the chromosome pairs, and hence the assembly of 51 karyograms, were only possible after the DNA sizing of each chromosome, their arms and satellite portions. These accurate, quantitative and reproducible data also enabled determining the distribution and variation of DNA content in each chromosome. From this, a correlation between DNA amount and total chromosome length evidenced that the mean DNA content of chromosome 9 was higher than that of chromosome 8. The chromosomal DNA sizing updated the Z. mays karyotype, providing insights into its dynamic genome with regards to the organization of the ten chromosomes and their respective portions. Considering the results and the relevance of cytogenetics in the current scenario of comparative sequencing and genomics, chromosomal DNA sizing should be incorporated as an additional parameter for karyotype definition. Based on this study, it can be affirmed that cytogenetic approaches go beyond the simple morphological description of chromosomes. PMID:29293613

Normal karyotype mosaicism in adult AML patients with adverse-risk and undefined karyotype: preliminary report of treatment outcomes after hematopoietic stem cell transplantation.

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Yoon, Jae-Ho; Kim, Hee-Je; Shin, Seung-Hwan; Yahng, Seung-Ah; Cho, Byung-Sik; Eom, Ki-Seong; Kim, Yoo-Jin; Lee, Seok; Min, Chang-Ki; Cho, Seok-Goo; Kim, Dong-Wook; Lee, Jong-Wook; Min, Woo-Sung; Park, Chong-Won

2013-06-01

Karyotype analysis in acute myeloid leukemia (AML) is one of the powerful prognostic factors for complete remission (CR), relapse, and overall survival (OS). Cytogenetic mosaicism is considered to be one of the important characteristics in expression of phenotypic manifestations. However, it has not come into focus due to emerging molecular biological approaches and the results of a number of mutation studies. Clinical correlates and prognostic relevance of mosaicism were evaluated in 163 AML patients [adverse-risk karyotypes (n = 72) and undefined karyotypes (n = 91)]. All patients were treated by induction and consolidation chemotherapies and finally went on hematopoietic stem cell transplantations (HSCT). Patients were divided into two subgroups, either with or without normal karyotype (NK) mosaicism. Seventy patients exhibited NK mosaicism and 93 did not. There were no significant differences in age, gender, chemotherapy cycles to achieve CR, HSCT donor type, source or intensity properties between the two subgroups. We found that NK mosaicism remaining in adverse-risk and undefined karyotype at diagnosis significantly correlates with better OS (p = 0.001) and lower CIR (p = 0.021) rate after HSCT. Our data show that the poor prognostic properties of unfavorable risk karyotype can be overcome to a great extent by allogeneic HSCT and chronic GVHD, especially in the subgroup with NK mosaicism. Cytogenetic mosaicism at initial diagnosis can be an influential factor for survival outcomes, even after HSCT.

Karyotype of some Thai Hypoxidaceae species

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Ladda Eksomtramage

2013-08-01

Full Text Available Somatic chromosome numbers and karyotypes of nine species in three genera of Thai Hypoxidaceae were determinedin root tips. All species are diploid with 2n = 18 and asymmetrical karyotypes including metacentric (m submetacentric (smsubtelocentric (st and also telocentric (t in some species. Satellite chromosomes (SAT were observed in all species studiedexcept in C. latifolia. The karyotypes of Curculigo ensifolia 4m+8sm+6st(2SAT, C. latifolia 2m+14sm+2st, C. megacarpa2m+12sm+4st(2SAT, C. villosa 4m+10sm(2SAT+4st, Hypoxis aurea 2m+8sm+8st(2SAT, Molineria capitulata 2m+10sm+2st (2SAT+4t, M. trichocarpa 2m+10sm+6st(2SAT, M. gracilis and M. latifolia 4m+8sm+4st (2SAT+2t are reported forthe first time. The chromosome relative length of Curculigo, Hypoxis and Molineria range between 3.44-9.55, 4.03-8.12 and3.64-8.97, respectively.

Karyotypic characterization of Ramphastidae (Piciformes, Aves

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Castro Márcio Siqueira

2002-01-01

Full Text Available The karyotypes of nine species of the family Ramphastidae were determined and compared with that of the toco toucan (Ramphastos toco, the only ramphastid karyotype so far reported in the literature. Differences in the morphology of the largest chromosomes allowed to identify three karyotype groups. The first group included the species R. toco, Baillonius bailloni, Pteroglossus castanotis, P. aracari and Selenidera maculirostris, in which only the first pair of chromosomes was metacentric. The second group included four Ramphastos species (R. dicolorus, R. ariel, R. vitellinus, R. tucanus cuvieri with two pairs of metacentric macrochromosomes (the first and the seventh. The third group was represented by a single species, A. laminirostris, in which all the autosomal chromosomes were telocentric. All of the species had subtelocentric Z chromosomes, similar in size to homologues of the first pair. Sex chromosome W was a small chromosome. The chromosome number ranged from 2n = 62 in P. aracari to 114 in R. toco. The cytotaxonomic relationships among toucan species are discussed, based on chromosome analysis.

Karyotype diversity and genome size variation in Neotropical Maxillariinae orchids.

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Moraes, A P; Koehler, S; Cabral, J S; Gomes, S S L; Viccini, L F; Barros, F; Felix, L P; Guerra, M; Forni-Martins, E R

2017-03-01

Orchidaceae is a widely distributed plant family with very diverse vegetative and floral morphology, and such variability is also reflected in their karyotypes. However, since only a low proportion of Orchidaceae has been analysed for chromosome data, greater diversity may await to be unveiled. Here we analyse both genome size (GS) and karyotype in two subtribes recently included in the broadened Maxillariinea to detect how much chromosome and GS variation there is in these groups and to evaluate which genome rearrangements are involved in the species evolution. To do so, the GS (14 species), the karyotype - based on chromosome number, heterochromatic banding and 5S and 45S rDNA localisation (18 species) - was characterised and analysed along with published data using phylogenetic approaches. The GS presented a high phylogenetic correlation and it was related to morphological groups in Bifrenaria (larger plants - higher GS). The two largest GS found among genera were caused by different mechanisms: polyploidy in Bifrenaria tyrianthina and accumulation of repetitive DNA in Scuticaria hadwenii. The chromosome number variability was caused mainly through descending dysploidy, and x=20 was estimated as the base chromosome number. Combining GS and karyotype data with molecular phylogeny, our data provide a more complete scenario of the karyotype evolution in Maxillariinae orchids, allowing us to suggest, besides dysploidy, that inversions and transposable elements as two mechanisms involved in the karyotype evolution. Such karyotype modifications could be associated with niche changes that occurred during species evolution. © 2016 German Botanical Society and The Royal Botanical Society of the Netherlands.

The Karyotype of Alstroemeria diluta Ehr. Bayer subsp. chrysantha (Alstroemeriaceae Karyotype of Alstroemeria diluta Ehr. Bayer subsp. chrysantha (Alstroemeriaceae

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Carlos M Baeza

2010-12-01

Full Text Available The karyotype of Alstroemeria diluta subsp. chrysantha Ehr. Bayer from Chile was examined. The species has 2n = 2x = 16 chromosomes, with 4m + 4sm + 2st-sat + 4t + 2t-sat. The reported karyotype is very asymmetrical (AsK % = 71.4 and Syi = 40.0%. This karyotype is similar to that published previously for Alstroemeria graminea Phil.Alstroemeria diluta subsp. chrysantha Ehr. Bayer (Alstroemeriaceae fue examinada citológicamente. Esta especie presenta un número cromosómico somático de 2n = 2x = 16 cromosomas, con una fórmula haploide constituida por 4m + 4sm + 2st-sat + 4t + 2t-sat cromosomas. El cariotipo es muy asimétrico, con valores de AsK % = 71,4 y Syi = 40,0%. Estos resultados se compararon con los de Alstroemeria graminea Phil., especie que presenta un cariotipo muy similar.

Is the Karyotype of Neotropical Boid Snakes Really Conserved? Cytotaxonomy, Chromosomal Rearrangements and Karyotype Organization in the Boidae Family.

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Patrik F Viana

Full Text Available Boids are primitive snakes from a basal lineage that is widely distributed in Neotropical region. Many of these species are both morphologically and biogeographically divergent, and the relationship among some species remains uncertain even with evolutionary and phylogenetic studies being proposed for the group. For a better understanding of the evolutionary relationship between these snakes, we cytogenetically analysed 7 species and 3 subspecies of Neotropical snakes from the Boidae family using different chromosomal markers. The karyotypes of Boa constrictor occidentalis, Corallus hortulanus, Eunectes notaeus, Epicrates cenchria and Epicrates assisi are presented here for the first time with the redescriptions of the karyotypes of Boa constrictor constrictor, B. c. amarali, Eunectes murinus and Epicrates crassus. The three subspecies of Boa, two species of Eunectes and three species of Epicrates exhibit 2n = 36 chromosomes. In contrast, C. hortulanus presented a totally different karyotype composition for the Boidae family, showing 2n = 40 chromosomes with a greater number of macrochromosomes. Furthermore, chromosomal mapping of telomeric sequences revealed the presence of interstitial telomeric sites (ITSs on many chromosomes in addition to the terminal markings on all chromosomes of all taxa analysed, with the exception of E. notaeus. Thus, we demonstrate that the karyotypes of these snakes are not as highly conserved as previously thought. Moreover, we provide an overview of the current cytotaxonomy of the group.

A new karyotype of Calomys (Rodentia, Sigmodontinae

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Lima J. Fernando de S.

2001-01-01

Full Text Available The genus Calomys Waterhouse, 1837 is widely distributed within South America, being found in Venezuela, Colombia, Peru, Bolivia, Brazil, Paraguay, Uruguay and Argentina. Specimens of Calomys were collected in Formoso do Araguaia, Tocantins, Brazil. For chromosome characterization standard staining techniques and as G-banding and nucleolar organizer region were used. The karyotype was 2n=46 and AN=66. The X chromosome is a medium metacentric and the Y chromosome a small acrocentric chromosome. Chromosome homologies with other species were observed. Probably, karyotype differences were basically due to Robertsonian rearrangements.

Bivariate Kumaraswamy Models via Modified FGM Copulas: Properties and Applications

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Indranil Ghosh

2017-11-01

Full Text Available A copula is a useful tool for constructing bivariate and/or multivariate distributions. In this article, we consider a new modified class of FGM (Farlie–Gumbel–Morgenstern bivariate copula for constructing several different bivariate Kumaraswamy type copulas and discuss their structural properties, including dependence structures. It is established that construction of bivariate distributions by this method allows for greater flexibility in the values of Spearman’s correlation coefficient, ρ and Kendall’s τ .

An Affine Invariant Bivariate Version of the Sign Test.

Science.gov (United States)

1987-06-01

words: affine invariance, bivariate quantile, bivariate symmetry, model,. generalized median, influence function , permutation test, normal efficiency...calculate a bivariate version of the influence function , and the resulting form is bounded, as is the case for the univartate sign test, and shows the...terms of a blvariate analogue of IHmpel’s (1974) influence function . The latter, though usually defined as a von-Mises derivative of certain

Flow cytogenetics: progress toward chromosomal aberration detection

International Nuclear Information System (INIS)

Carrano, A.V.; Gray, J.W.; Van Dilla, M.A.

1977-01-01

Using clonal derivatives of the Chinese hamster M3-1 cell line, we demonstrate the potential of flow systems to karyotype homogeneous aberrations (aberrations which are identical and present in every cell) and to detect heterogeneous aberrations (aberrations which occur randomly in a population and are not identical in every cell). Flow cytometry (FCM) of ethidium bromide stained isolated chromosomes from clone 650A of the M3-1 cells distinguishes nine chromosome types from the fourteen present in the actual karyotype. X-irradiation of this parent 650A clone produced two sub-clones with an altered flow karyotype, that is, their FCM distributions were characterized by the addition of new peaks and alterations in area under existing peaks. From the relative DNA content and area for each peak, as determined by computer analysis, we predicted that each clone had undergone a reciprocal translocation involving chromosomes from two peaks. This prediction was confirmed by Giemsa-banding the metaphase cells. Heterogeneous aberrations are reflected in the flow karyotype as an increase in background, that is, an increase in area underlying the chromosome peaks. This increase is dose dependent but, as yet, the sample variability has been too large for quantitative analysis. Flow sorting of the valleys between chromosome peaks produces enriched fractions of aberrant chromosomes for visual analysis. These approaches are potentially applicable to the analysis of chromsomal aberrations induced by environmental contaminants

Karyotype asymmetry in Cynodon Rich. (Poaceae) accessions.

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Chiavegatto, R B; Paula, C M P; Souza Sobrinho, F; Benites, F R G; Techio, V H

2016-12-02

Cynodon is a genus of plants with forage potential that has attracted the interest of breeders. These species have high morphological variability in a large number of varieties and cytotypes, hampering identification. This study aimed to determine the karyotype asymmetry index among accessions of Cynodon to discriminate between them. Karyotype symmetry was based on three estimates, which were compared. The basic number for the genus is x = 9. The results of the chromosome count and DNA quantification, respectively, were as follows: two diploid accessions (2n = 2x = 18 and 1.08 ± 0.094 to 1.17 ± 0.036 pg DNA and ± standard deviation), one triploid accession (2n = 3x = 27 and 1.63 ± 0.017 pg DNA), four tetraploid accessions (2n = 4x = 36 and 1.88 ± 0.069 to 2.10 ± 0.07 pg DNA), and one pentaploid accession (2n = 5x = 45 and 2.55 ± 0.098 pg DNA). C. incompletus var. hirsutus had the longest total length of the haploid lot (29.05 µm), with chromosomes that ranged from 1.7 to 6.2 µm in length. On the basis of the karyotype asymmetry indices, the accessions were divided into two groups: 1) C. dactylon var. dactylon, C. transvaalensis, C. dactylon var. polevansii, three accessions of Cynodon sp, and C. nlemfuensis; and 2) C. incompletus var. hirsutus. This is the first description of tetraploidy in C. transvaalensis. The karyotypic data facilitated a determination of the degree of proximity between the accessions.

STUDI PERBANDINGAN ANTARA ALGORITMA BIVARIATE MARGINAL DISTRIBUTION DENGAN ALGORITMA GENETIKA

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Chastine Fatichah

2006-01-01

Full Text Available Bivariate Marginal Distribution Algorithm is extended from Estimation of Distribution Algorithm. This heuristic algorithm proposes the new approach for recombination of generate new individual that without crossover and mutation process such as genetic algorithm. Bivariate Marginal Distribution Algorithm uses connectivity variable the pair gene for recombination of generate new individual. Connectivity between variable is doing along optimization process. In this research, genetic algorithm performance with one point crossover is compared with Bivariate Marginal Distribution Algorithm performance in case Onemax, De Jong F2 function, and Traveling Salesman Problem. In this research, experimental results have shown performance the both algorithm is dependence of parameter respectively and also population size that used. For Onemax case with size small problem, Genetic Algorithm perform better with small number of iteration and more fast for get optimum result. However, Bivariate Marginal Distribution Algorithm perform better of result optimization for case Onemax with huge size problem. For De Jong F2 function, Genetic Algorithm perform better from Bivariate Marginal Distribution Algorithm of a number of iteration and time. For case Traveling Salesman Problem, Bivariate Marginal Distribution Algorithm have shown perform better from Genetic Algorithm of optimization result. Abstract in Bahasa Indonesia : Bivariate Marginal Distribution Algorithm merupakan perkembangan lebih lanjut dari Estimation of Distribution Algorithm. Algoritma heuristik ini mengenalkan pendekatan baru dalam melakukan rekombinasi untuk membentuk individu baru, yaitu tidak menggunakan proses crossover dan mutasi seperti pada Genetic Algorithm. Bivariate Marginal Distribution Algorithm menggunakan keterkaitan pasangan variabel dalam melakukan rekombinasi untuk membentuk individu baru. Keterkaitan antar variabel tersebut ditemukan selama proses optimasi berlangsung. Aplikasi yang

Karyotype evolution in Rhinolophus bats (Rhinolophidae, Chiroptera) illuminated by cross-species chromosome painting and G-banding comparison.

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Mao, Xiuguang; Nie, Wenhui; Wang, Jinhuan; Su, Weiting; Ao, Lei; Feng, Qing; Wang, Yingxiang; Volleth, Marianne; Yang, Fengtang

2007-01-01

Rhinolophus (Rhinolophidae) is the second most speciose genus in Chiroptera and has extensively diversified diploid chromosome numbers (from 2n = 28 to 62). In spite of many attempts to explore the karyotypic evolution of this genus, most studies have been based on conventional Giemsa staining rather than G-banding. Here we have made a whole set of chromosome-specific painting probes from flow-sorted chromosomes of Aselliscus stoliczkanus (Hipposideridae). These probes have been utilized to establish the first genome-wide homology maps among six Rhinolophus species with four different diploid chromosome numbers (2n = 36, 44, 58, and 62) and three species from other families: Rousettus leschenaulti (2n = 36, Pteropodidae), Hipposideros larvatus (2n = 32, Hipposideridae), and Myotis altarium (2n = 44, Vespertilionidae) by fluorescence in situ hybridization. To facilitate integration with published maps, human paints were also hybridized to A. stoliczkanus chromosomes. Our painting results substantiate the wide occurrence of whole-chromosome arm conservation in Rhinolophus bats and suggest that Robertsonian translocations of different combinations account for their karyotype differences. Parsimony analysis using chromosomal characters has provided some new insights into the Rhinolophus ancestral karyotype and phylogenetic relationships among these Rhinolophus species so far studied. In addition to Robertsonian translocations, our results suggest that whole-arm (reciprocal) translocations involving multiple non-homologous chromosomes as well could have been involved in the karyotypic evolution within Rhinolophus, in particular those bats with low and medium diploid numbers.

Karyotype analysis of three Solanum plants using combined PI-DAPI ...

African Journals Online (AJOL)

The chromosomes were distinguished by combined PI-DAPI (CPD) staining and double fluorescence in situ hybridization (FISH) with 45S and 5S rDNA probes and their molecular cytogenetic karyotypes were established. Although, the karyotype of S. surattense Burm. and S. photeinocarpum Nakam was first established, ...

Comparison of Model Reliabilities from Single-Step and Bivariate Blending Methods

DEFF Research Database (Denmark)

Taskinen, Matti; Mäntysaari, Esa; Lidauer, Martin

2013-01-01

Model based reliabilities in genetic evaluation are compared between three methods: animal model BLUP, single-step BLUP, and bivariate blending after genomic BLUP. The original bivariate blending is revised in this work to better account animal models. The study data is extracted from...... be calculated. Model reliabilities by the single-step and the bivariate blending methods were higher than by animal model due to genomic information. Compared to the single-step method, the bivariate blending method reliability estimates were, in general, lower. Computationally bivariate blending method was......, on the other hand, lighter than the single-step method....

Evolution of Karyotypes in Chameleons

Czech Academy of Sciences Publication Activity Database

Rovatsos, M.; Altmanová, M.; Johnson Pokorná, Martina; Velenský, P.; Baca, A. S.; Kratochvíl, L.

2017-01-01

Roč. 8, č. 12 (2017), č. článku 382. ISSN 2073-4425 Institutional support: RVO:67985904 Keywords : karyotype evolution * ITS * rDNA Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Genetics and heredity (medical genetics to be 3) Impact factor: 3.600, year: 2016

Karyotypes of Saccharomyces sensu lato species

DEFF Research Database (Denmark)

Petersen, Randi Føns; Nilsson-Tilgren, Torsten; Piskur, Jure

1999-01-01

An improved pulsed-field electrophoresis program was developed to study differently sized chromosomes within the genus Saccharomyces. The number of chromosomes in the type strains was shown to be nine in Saccharomyces castellii and Saccharomyces dairenensis, 12 in Saccharomyces servazzii...... and Saccharomyces unisporus, 16 in Saccharomyces exiguus and seven in Saccharomyces kluyveri. The sizes of individual chromosomes were resolved and the approximate genome sizes were determined by the addition of individual chromosomes of the karyotypes. Apparently. the genome of S. exiguus, which is the only...... Saccharomyces sensu late yeast to contain small chromosomes, is larger than that of Saccharomyces cerevisiae. On the other hand, other species exhibited genome sizes that were 10-25% smaller than that of S. cerevisiae. Well-defined karyotypes represent the basis for future genome mapping and sequencing projects...

Multidirectional cross-species painting illuminates the history of karyotypic evolution in Perissodactyla.

Science.gov (United States)

Trifonov, Vladimir A; Stanyon, Roscoe; Nesterenko, Anastasia I; Fu, Beiyuan; Perelman, Polina L; O'Brien, Patricia C M; Stone, Gary; Rubtsova, Nadezhda V; Houck, Marlys L; Robinson, Terence J; Ferguson-Smith, Malcolm A; Dobigny, Gauthier; Graphodatsky, Alexander S; Yang, Fengtang

2008-01-01

The order Perissodactyla, the group of odd-toed ungulates, includes three extant families: Equidae, Tapiridae, and Rhinocerotidae. The extremely rapid karyotypic diversification in perissodactyls has so far prevented the establishment of genome-wide homology maps between these three families by traditional cytogenetic approaches. Here we report the first genome-wide comparative chromosome maps of African rhinoceroses, four tapir species, four equine species, and humans. These maps were established by multidirectional chromosome painting, with paint probes derived from flow-sorted chromosomes of Equus grevyi, Tapirus indicus, and Ceratotherium simum as well as painting probes from horse and human. The Malayan tapir (Tapirus indicus), Baird's tapir (T. bairdii), mountain tapir (T. pinchaque), lowland tapir (T. terrestris), and onager (E. hemionus onager), were studied by cross-species chromosome painting for the first time. Our results, when integrated with previously published comparative chromosome maps of the other perissodactyl species, have enabled the reconstruction of perissodactyl, ceratomorph, and equid ancestral karyotypes, and the identification of the defining evolutionary chromosomal rearrangements along each lineage. Our results allow a more reliable estimate of the mode and tempo of evolutionary chromosomal rearrangements, revealing a striking switch between the slowly evolving ceratomorphs and extremely rapidly evolving equids.

Dynamic karyotype evolution and unique sex determination systems in Leptidea wood white butterflies.

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Šíchová, Jindra; Voleníková, Anna; Dincă, Vlad; Nguyen, Petr; Vila, Roger; Sahara, Ken; Marec, František

2015-05-19

Chromosomal rearrangements have the potential to limit the rate and pattern of gene flow within and between species and thus play a direct role in promoting and maintaining speciation. Wood white butterflies of the genus Leptidea are excellent models to study the role of chromosome rearrangements in speciation because they show karyotype variability not only among but also within species. In this work, we investigated genome architecture of three cryptic Leptidea species (L. juvernica, L. sinapis and L. reali) by standard and molecular cytogenetic techniques in order to reveal causes of the karyotype variability. Chromosome numbers ranged from 2n = 85 to 91 in L. juvernica and 2n = 69 to 73 in L. sinapis (both from Czech populations) to 2n = 51 to 55 in L. reali (Spanish population). We observed significant differences in chromosome numbers and localization of cytogenetic markers (rDNA and H3 histone genes) within the offspring of individual females. Using FISH with the (TTAGG) n telomeric probe we also documented the presence of multiple chromosome fusions and/or fissions and other complex rearrangements. Thus, the intraspecific karyotype variability is likely due to irregular chromosome segregation of multivalent meiotic configurations. The analysis of female meiotic chromosomes by GISH and CGH revealed multiple sex chromosomes: W1W2W3Z1Z2Z3Z4 in L. juvernica, W1W2W3Z1Z2Z3 in L. sinapis and W1W2W3W4Z1Z2Z3Z4 in L. reali. Our results suggest a dynamic karyotype evolution and point to the role of chromosomal rearrangements in the speciation of Leptidea butterflies. Moreover, our study revealed a curious sex determination system with 3-4 W and 3-4 Z chromosomes, which is unique in the Lepidoptera and which could also have played a role in the speciation process of the three Leptidea species.

Karyotype characterization and comparison of three hexaploid species of Bromus Linnaeus, 1753 (Poaceae

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Leonardo Luís Artico

2017-04-01

Full Text Available Chromosome morphometry and nuclear DNA content are useful data for cytotaxonomy and to understand the evolutionary history of different taxa. For the genus Bromus Linnaeus, 1753, distinct ploidy levels have been reported, occurring from diploid to duodecaploid species. The geographic distribution of Bromus species has been correlated with chromosome number and ploidy level. In this study, the aims were to determine the nuclear genome size and characterize the karyotype of the South American Bromus species: Bromus auleticus Trinius ex Nees, 1829, Bromus brachyanthera Döll, 1878 and Bromus catharticus Vahl, 1791. The mean nuclear 2C value ranged from 2C = 12.64 pg for B. catharticus to 2C = 17.92 pg for B. auleticus, meaning a maximum variation of 2C = 5.28 pg, equivalent to 41.70%. Despite this significant difference in 2C value, the three species exhibit the same chromosome number, 2n = 6x = 42, which confirms their hexaploid origin. Corroborating the genome size, the chromosome morphometry (total, short- and long-arm length and, consequently, the class differed among the karyotypes of the species. Based on the first karyograms for these Bromus species, some morphologically similar and several distinct chromosome pairs were found. Therefore, the karyotype characterization confirmed the hexaploid origin of the studied Bromus species, which differ in relation to the karyogram and the nuclear 2C value. Considering this, cytogenetics and flow cytometry can be used to discriminate Bromus species, contributing to taxonomy and systematic studies and providing information on the evolutionary history of this taxa.

Karyotype characterization and comparison of three hexaploid species of Bromus Linnaeus, 1753 (Poaceae).

Science.gov (United States)

Artico, Leonardo Luís; Mazzocato, Ana Cristina; Ferreira, Juliano Lino; Carvalho, Carlos Roberto; Clarindo, Wellington Ronildo

2017-01-01

Chromosome morphometry and nuclear DNA content are useful data for cytotaxonomy and to understand the evolutionary history of different taxa. For the genus Bromus Linnaeus, 1753, distinct ploidy levels have been reported, occurring from diploid to duodecaploid species. The geographic distribution of Bromus species has been correlated with chromosome number and ploidy level. In this study, the aims were to determine the nuclear genome size and characterize the karyotype of the South American Bromus species: Bromus auleticus Trinius ex Nees, 1829, Bromus brachyanthera Döll, 1878 and Bromus catharticus Vahl, 1791. The mean nuclear 2C value ranged from 2C = 12.64 pg for B. catharticus to 2C = 17.92 pg for B. auleticus , meaning a maximum variation of 2C = 5.28 pg, equivalent to 41.70%. Despite this significant difference in 2C value, the three species exhibit the same chromosome number, 2n = 6x = 42, which confirms their hexaploid origin. Corroborating the genome size, the chromosome morphometry (total, short- and long-arm length) and, consequently, the class differed among the karyotypes of the species. Based on the first karyograms for these Bromus species, some morphologically similar and several distinct chromosome pairs were found. Therefore, the karyotype characterization confirmed the hexaploid origin of the studied Bromus species, which differ in relation to the karyogram and the nuclear 2C value. Considering this, cytogenetics and flow cytometry can be used to discriminate Bromus species, contributing to taxonomy and systematic studies and providing information on the evolutionary history of this taxa.

Covariate analysis of bivariate survival data

Energy Technology Data Exchange (ETDEWEB)

Bennett, L.E.

1992-01-01

The methods developed are used to analyze the effects of covariates on bivariate survival data when censoring and ties are present. The proposed method provides models for bivariate survival data that include differential covariate effects and censored observations. The proposed models are based on an extension of the univariate Buckley-James estimators which replace censored data points by their expected values, conditional on the censoring time and the covariates. For the bivariate situation, it is necessary to determine the expectation of the failure times for one component conditional on the failure or censoring time of the other component. Two different methods have been developed to estimate these expectations. In the semiparametric approach these expectations are determined from a modification of Burke's estimate of the bivariate empirical survival function. In the parametric approach censored data points are also replaced by their conditional expected values where the expected values are determined from a specified parametric distribution. The model estimation will be based on the revised data set, comprised of uncensored components and expected values for the censored components. The variance-covariance matrix for the estimated covariate parameters has also been derived for both the semiparametric and parametric methods. Data from the Demographic and Health Survey was analyzed by these methods. The two outcome variables are post-partum amenorrhea and breastfeeding; education and parity were used as the covariates. Both the covariate parameter estimates and the variance-covariance estimates for the semiparametric and parametric models will be compared. In addition, a multivariate test statistic was used in the semiparametric model to examine contrasts. The significance of the statistic was determined from a bootstrap distribution of the test statistic.

Reliability for some bivariate beta distributions

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Nadarajah Saralees

2005-01-01

Full Text Available In the area of stress-strength models there has been a large amount of work as regards estimation of the reliability R=Pr( Xbivariate distribution with dependence between X and Y . In particular, we derive explicit expressions for R when the joint distribution is bivariate beta. The calculations involve the use of special functions.

Reliability for some bivariate gamma distributions

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Nadarajah Saralees

2005-01-01

Full Text Available In the area of stress-strength models, there has been a large amount of work as regards estimation of the reliability R=Pr( Xbivariate distribution with dependence between X and Y . In particular, we derive explicit expressions for R when the joint distribution is bivariate gamma. The calculations involve the use of special functions.

Implementation of molecular karyotyping in clinical genetics

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Luca Lovrecic

2013-11-01

Full Text Available Rapid development of technologies for the study of the human genome is an expected step after the discovery and sequencing of the entire human genome. Chromosomal microarrays, which allow us to perform tens of thousands of previously individual experiments simultaneously, are being utilized in all areas of human genetics and genomics. Initially, this was applicable only for research purposes, but in the last few years their clinical diagnostic purposes are becoming more and more relevant. Using molecular karyotyping (also chromosomal microarray, comparative genomic hybridization with microarray, aCGH, one can analyze microdeletions / microduplications in the whole human genome at once. It is a first-tier cytogenetic diagnostic test instead of G-banded karyotyping in patients with developmental delay and/or congenital anomalies. Molecular karyotyping is used as a diagnostic test in patients with unexplained developmental delay and/or idiopathic intellectual disability and/or dysmorphic features and/or multiple congenital anomalies (DD/ID/DF/MCA. In addition, the method is used in prenatal diagnostics and in some centres also in preimplantation genetic diagnosis.The aim of this paper is to inform the professional community in the field about this new diagnostic method and its implementation in Slovenia, and to define the clinical situations where the method is appropriate.

Karyotype Learning Center: A Software For Teaching And Learning Cytogenetics

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Joelma Freire De Mesquita

2004-05-01

Full Text Available The in vitro cultivation of human cells is an essential part of the work of every diagnostic cytoge-netics laboratory. Almost all human cytogenetic studies involve the examination of dividing bloodcell population by blocking cell division at metaphase with subsequent processing and staining bybanding techniques. The chromosome constitution is described as Karyotype that states the totalnumber of chromosomes and the sex chromosome constitution. Karyotypes are prepared by cuttingup a photograph of the spread metaphase chromosomes, matching up homologous chromosomes andsticking them back down on a card or nowadays more often by getting an image analysis computerto do the job. Chromosomes are identied by their size, centromere position and banding pattern.Teaching a student how to detect and interpret even the most common chromosome abnormaliti-es is a major challenge: mainly, in a developing country where the laboratorial facilities are notalways available for a big number of students. Therefore, in this work we present an educationalsoftware for teaching undergraduate students of Medical and Life Sciences Courses how to arrangenormal and abnormal chromosomes in the form of karyotype. The user, using drag-and-drop, is da-red to match up homologous chromosome. For that, we have developed a free full access web site(http://www.biomol.net/cariotipo/ for hosting the software. The latter has proved to be light andfast even under slow dial-up connections. This web site also oers a theoretical introductory sectionwith basic concepts about karyotype. Up to now the software has been successfully applied to un-dergraduate courses at the University of Rio de Janeiro (UNIRIO. The students have approved thesoftware; to them the similarities with the well-known game solitaire turns the exercise more excitingand provides additional stimulus to learn and understand karyotype. Professors have also used thesoftware as complementary material in their regular classes

Karyotypes of some medium-sized Dytiscidae (Agabinae and Colymbetinae (Coleoptera

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Robert Angus

2013-06-01

Full Text Available An account is given of the karyotypes of 29 species of medium sized Dytiscidae (Coleoptera. Of the 20 species of Agabus Leach, 1817, 18 have karyotypes comprising 21 pairs of autosomes and sex chromosomes which are either X0(♂ or XX (♀. These species are A. serricornis (Paykull, 1799, A. labiatus (Brahm, 1791, A. congener (Thunberg, 1794, A. lapponicus (Thomson, 1867, A. thomsoni (J. Sahlberg, 1871, A. confinis (Gyllenhal, 1808, A. sturmii (Gyllenhal, 1808, A. bipustulatus (Linnaeus, 1767, A. nevadensis Håkan Lindberg, 1939, A. wollastoni Sharp, 1882, A. melanarius Aubé, 1837, A. biguttatus (Olivier, 1795, A. binotatus Aubé, 1837, A. affinis (Paykull, 1798, A. unguicularis (Thomson, 1867, A. ramblae Millan & Ribera, 2001, A. conspersus (Marsham, 1802 and A. nebulosus (Forster, 1771. However two species, A. infuscatus Aubé, 1838 and A. adpressus Aubé, 1837, have developed a neo-XY system, with karyotypes comprising 21 pairs of autosomes and XY sex chromosomes (♂. No chromosomal differences have been detected between typical A. bipustulatus and A. bipustulatus var. solieri Aubé, 1837, nor have any been found between the three species of the A. bipustulatus complex (A. bipustulatus, A. nevadensis and A. wollastoni. The four species of Colymbetes Clairville, 1806, C. fuscus (Linnaeus, 1758, C. paykulli Erichson, 1837, C. piceus Klug, 1834 and C. striatus (Linnaeus, 1758 have karyotypes comprising 20 pairs of autosomes and sex chromosomes which are X0 (♂, XX (♀. Two of the species of Rhantus Dejean, 1833, R. exsoletus (Forster, 1771 and R. suturellus (Harris, 1828 have karyotypes comprising 20 pairs of autosomes and X0/XX sex chromosomes, but the other three species, R. grapii (Gyllenhal, 1808, R. frontalis (Marsham, 1802 and R. suturalis (Macleay, 1825 have 22 pairs of autosomes and X0/XX sex chromosomes. Agabus congener and Rhantus suturellus may have one B-chromosome. Nine of the species have previously published karyotype data but

Evolutionary dynamics of mammalian karyotypes

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Carlo Alberto Redi

2012-12-01

Full Text Available This special volume of Cytogenetic and Genome Research (edited by Roscoe Stanyon, University of Florence and Alexander Graphodatsky, Siberian division of the Russian Academy of Sciences is dedicated to the fascinating long search of the forces behind the evolutionary dynamics of mammalian karyotypes, revealed after the hypotonic miracle of the 1950s....

Ordinal bivariate inequality

DEFF Research Database (Denmark)

Sonne-Schmidt, Christoffer Scavenius; Tarp, Finn; Østerdal, Lars Peter Raahave

This paper introduces a concept of inequality comparisons with ordinal bivariate categorical data. In our model, one population is more unequal than another when they have common arithmetic median outcomes and the first can be obtained from the second by correlationincreasing switches and/or median......-preserving spreads. For the canonical 2x2 case (with two binary indicators), we derive a simple operational procedure for checking ordinal inequality relations in practice. As an illustration, we apply the model to childhood deprivation in Mozambique....

Spectral Karyotyping for identification of constitutional chromosomal abnormalities at a national reference laboratory

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Anguiano Arturo

2012-01-01

Full Text Available Abstract Spectral karyotyping is a diagnostic tool that allows visualization of chromosomes in different colors using the FISH technology and a spectral imaging system. To assess the value of spectral karyotyping analysis for identifying constitutional supernumerary marker chromosomes or derivative chromosomes at a national reference laboratory, we reviewed the results of 179 consecutive clinical samples (31 prenatal and 148 postnatal submitted for spectral karyotyping. Over 90% of the cases were requested to identify either small supernumerary marker chromosomes (sSMCs or chromosomal exchange material detected by G-banded chromosome analysis. We also reviewed clinical indications of those cases with marker chromosomes in which chromosomal origin was identified by spectral karyotyping. Our results showed that spectral karyotyping identified the chromosomal origin of marker chromosomes or the source of derivative chromosomal material in 158 (88% of the 179 clinical cases; the identification rate was slightly higher for postnatal (89% compared to prenatal (84% cases. Cases in which the origin could not be identified had either a small marker chromosome present at a very low level of mosaicism (

Ordinal Bivariate Inequality

DEFF Research Database (Denmark)

Sonne-Schmidt, Christoffer Scavenius; Tarp, Finn; Østerdal, Lars Peter Raahave

2016-01-01

This paper introduces a concept of inequality comparisons with ordinal bivariate categorical data. In our model, one population is more unequal than another when they have common arithmetic median outcomes and the first can be obtained from the second by correlation-increasing switches and....../or median-preserving spreads. For the canonical 2 × 2 case (with two binary indicators), we derive a simple operational procedure for checking ordinal inequality relations in practice. As an illustration, we apply the model to childhood deprivation in Mozambique....

Karyotype relationships among Anastrepha bistrigata, A. striata and A. serpentina (Diptera, Tephritidae

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Denise Selivon

2007-01-01

Full Text Available The species of Anastrepha are arranged into 17 intrageneric groups. Recently, it was proposed that two species of the striata group, Anastrepha striata and A. bistrigata, might be realocated to serpentina group. Anastrepha bistrigata and A. serpentina have an X1X2Y/X1X1 X2X2 sex chromosome system while A. striata has a XY/XX system. It was previously proposed that the karyotype of A. bistrigata could be derived from that of A. striata by an Y:A fusion, and that the karyotype of A. serpentina would be derived from another, hypothetical karyotype. In the present report sequential staining with DAPI and chromomycin A3 (CMA3, followed by C-banding, revealed that the C-banded heterochromatic blocks of the sex chromosomes of A. bistrigata have different affinities to fluorochromes in comparison to the chromosomes of A. striata, from which they have hypothetically derived. The chromosomes of A. serpentina show substantial differences in their cytochemical properties compared to their A. bistrigata and A. striata counterparts. The FISH technique showed that the ribosomal gene sequences are located in DAPI- or DAPI/CMA3-positive heterochromatic blocks of the sex chromosomes, one site on the Y chromosome and one site on the X chromosome (X1 in A. bistrigata and A. serpentina. The data suggest that the karyotype of A. striata and A. bistrigata could be derived from a common ancestral karyotype, while the A. serpentina karyotype probably has a distinct origin.

Study of karyotypes in Case of Recurrent Abortions in Gujarat

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N. Parikh

2015-06-01

Full Text Available Introduction: - The biological definition of miscarriage is the expulsion of the conceptus before viability has been achieved. The definition of recurrent miscarriage is three or more consecutive spontaneous abortions. The risk factors for recurrent miscarriage are epidemiological, genetic, anatomical disorders, endocrinal, reproductive tract infections, thrombophilic disorders, disorders of materno-fetal alloimmune relationships, environmental effects and psychological causes. About 50% to 60% of all first trimester abortions are associated with derangement of one or more chromosomal complements. Aim: - The aim of this study was to assess frequency and increasing the awareness of physician about the nature of chromosomal aberration that contribute to the occurrence of repeated abortions. Material & Methods: - Patient of recurrent abortion was investigated by history taking, examination and investigations. For present study 20 women having two or more consecutive spontaneous abortions, who attended outdoor & indoor patient department, were selected and karyotyping was done. In 10 of the above cases karyotype study of both partners was done. So in total 30 individuals (20 females & 10 males were selected for Cytogenetic study. In all cases relevant history and clinical findings and other investigations were noted. Blood samples were obtained and karyotype study was performed at Genetic Laboratory, B. J. Medical College, Ahmedabad. Results and Conclusions: - Cytogenetic evaluation by karyotypes revealed robertsonian translocation in one (5% female; this patient had a history of 2 spontaneous abortions and two times IVF failure, she had history of chocolate cyst of ovary and family history of infertility. No numerical anomaly; mosaicism or inversions were found in this study; 23 cases had normal karyotype and remaining 6 cases came out inconclusive.

Bivariate copula in fitting rainfall data

Science.gov (United States)

Yee, Kong Ching; Suhaila, Jamaludin; Yusof, Fadhilah; Mean, Foo Hui

2014-07-01

The usage of copula to determine the joint distribution between two variables is widely used in various areas. The joint distribution of rainfall characteristic obtained using the copula model is more ideal than the standard bivariate modelling where copula is belief to have overcome some limitation. Six copula models will be applied to obtain the most suitable bivariate distribution between two rain gauge stations. The copula models are Ali-Mikhail-Haq (AMH), Clayton, Frank, Galambos, Gumbel-Hoogaurd (GH) and Plackett. The rainfall data used in the study is selected from rain gauge stations which are located in the southern part of Peninsular Malaysia, during the period from 1980 to 2011. The goodness-of-fit test in this study is based on the Akaike information criterion (AIC).

Karyotypic evolution in the Galliformes: an examination of the process of karyotypic evolution by comparison of the molecular cytogenetic findings with the molecular phylogeny.

Science.gov (United States)

Shibusawa, M; Nishibori, M; Nishida-Umehara, C; Tsudzuki, M; Masabanda, J; Griffin, D K; Matsuda, Y

2004-01-01

To define the process of karyotypic evolution in the Galliformes on a molecular basis, we conducted genome-wide comparative chromosome painting for eight species, i.e. silver pheasant (Lophura nycthemera), Lady Amherst's pheasant (Chrysolophus amherstiae), ring-necked pheasant (Phasianus colchicus), turkey (Meleagris gallopavo), Western capercaillie (Tetrao urogallus), Chinese bamboo-partridge (Bambusicola thoracica) and common peafowl (Pavo cristatus) of the Phasianidae, and plain chachalaca (Ortalis vetula) of the Cracidae, with chicken DNA probes of chromosomes 1-9 and Z. Including our previous data from five other species, chicken (Gallus gallus), Japanese quail (Coturnix japonica) and blue-breasted quail (Coturnix chinensis) of the Phasianidae, guinea fowl (Numida meleagris) of the Numididae and California quail (Callipepla californica) of the Odontophoridae, we represented the evolutionary changes of karyotypes in the 13 species of the Galliformes. In addition, we compared the cytogenetic data with the molecular phylogeny of the 13 species constructed with the nucleotide sequences of the mitochondrial cytochrome b gene, and discussed the process of karyotypic evolution in the Galliformes. Comparative chromosome painting confirmed the previous data on chromosome rearrangements obtained by G-banding analysis, and identified several novel chromosome rearrangements. The process of the evolutionary changes of macrochromosomes in the 13 species was in good accordance with the molecular phylogeny, and the ancestral karyotype of the Galliformes is represented. Copyright 2004 S. Karger AG, Basel

Bivariable analysis of ventricular late potentials in high resolution ECG records

International Nuclear Information System (INIS)

Orosco, L; Laciar, E

2007-01-01

In this study the bivariable analysis for ventricular late potentials detection in high-resolution electrocardiographic records is proposed. The standard time-domain analysis and the application of the time-frequency technique to high-resolution ECG records are briefly described as well as their corresponding results. In the proposed technique the time-domain parameter, QRSD and the most significant time-frequency index, EN QRS are used like variables. A bivariable index is defined, that combines the previous parameters. The propose technique allows evaluating the risk of ventricular tachycardia in post-myocardial infarct patients. The results show that the used bivariable index allows discriminating between the patient's population with ventricular tachycardia and the subjects of the control group. Also, it was found that the bivariable technique obtains a good valuation as diagnostic test. It is concluded that comparatively, the valuation of the bivariable technique as diagnostic test is superior to that of the time-domain method and the time-frequency technique evaluated individually

Description of karyotype in Hypostomus regani (Ihering, 1905 (Teleostei, Loricariidae from the Piumhi river in Brazil with comments on karyotype variation found in Hypostomus

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Ernani de Oliveira Mendes-Neto

2011-07-01

Full Text Available The paper represents a comparative cytogenetic analysis of three populations of Hypostomus regani in Brazil. Two populations belong to the Upper Paraná River Basin and the third one, the karyotype of which is described for the first time, was probably introduced into the São Francisco River Basin through transposition from the Piumhi River. Karyotype features of populations of H. regani from the Piracicaba and Tietê River Basins are also discussed. The occurrence of H. regani in the São Francisco River Basin is reported for the first time here. The study also revealed distinct differences in the location of the Ag-NORs between the analyzed populations that enable individuals from the Piumhi River, Mogi-Guaçu River and Tietê River to be distinguished from one another. Thus, the data obtained indicate the possibility of geographic variation fixing different karyotypes even in the same basin of origin.

Karyotype variability in neotropical catfishes of the family Pimelodidae (Teleostei: Siluriformes

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Américo Moraes Neto

Full Text Available Karyotypic data are presented for four species of fish belonging to the Pimelodidae family. These species show a conserved diploid number, 2n = 56 chromosomes, with different karyotypic formulae. The analyzed species showed little amount of heterochromatin located preferentially in the centromeric and telomeric regions of some chromosomes. The nucleolus organizer regions activity (Ag-NORs and the chromosomal location of ribosomal genes by fluorescent in situ hybridization (FISH, with 18S and 5S probes, showing only one chromosome pair marked bearer of ribosomal genes, the only exception was Pimelodus britskii that presented multiple NORs and syntenic location of the 18S and 5S probes. Non-Robertsonian events, as pericentric inversion and NORs duplication are requested to explain the karyotype diversification in Pseudoplatystoma from the rio Paraguay (MS, Pimelodus from the rio Iguaçu (PR, Sorubim from the rio Paraguay (MS and Steindachneridion from the rio Paraíba do Sul (SP. The obtained data for the karyotype macrostructure of these species corroborates a conserved pattern observed in Pimelodidae. On the other hand, interspecific variations detected by molecular cytogenetics markers made possible cytotaxonomic inferences and differentiation of the species here analyzed.

Karyotypic relationships among Equus grevyi, Equus burchelli and domestic horse defined using horse chromosome arm-specific probes.

Science.gov (United States)

Musilova, P; Kubickova, S; Zrnova, E; Horin, P; Vahala, J; Rubes, J

2007-01-01

Using laser microdissection we prepared a set of horse chromosome arm-specific probes. Most of the probes were generated from horse chromosomes, some of them were derived from Equus zebra hartmannae. The set of probes were hybridized onto E. grevyi chromosomes in order to establish a genome-wide chromosomal correspondence between this zebra and horse. The use of arm-specific probes provided us with more information on the mutual arrangement of the genomes than we could obtain by means of whole-chromosome paints generated by flow sorting, even if we used reciprocal painting with probe sets from both species. By comparison of our results and results of comparative mapping in E. burchelli, we also established the chromosomal correspondence between E. grevyi and E. burchelli, providing evidence for a very close karyotypic relationship between these two zebra species. Establishment of the comparative map for E. grevyi contributes to the knowledge of the karyotypic phylogeny in the Equidae family.

Building Bivariate Tables: The compareGroups Package for R

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Isaac Subirana

2014-05-01

Full Text Available The R package compareGroups provides functions meant to facilitate the construction of bivariate tables (descriptives of several variables for comparison between groups and generates reports in several formats (LATEX, HTML or plain text CSV. Moreover, bivariate tables can be viewed directly on the R console in a nice format. A graphical user interface (GUI has been implemented to build the bivariate tables more easily for those users who are not familiar with the R software. Some new functions and methods have been incorporated in the newest version of the compareGroups package (version 1.x to deal with time-to-event variables, stratifying tables, merging several tables, and revising the statistical methods used. The GUI interface also has been improved, making it much easier and more intuitive to set the inputs for building the bivariate tables. The ?rst version (version 0.x and this version were presented at the 2010 useR! conference (Sanz, Subirana, and Vila 2010 and the 2011 useR! conference (Sanz, Subirana, and Vila 2011, respectively. Package compareGroups is available from the Comprehensive R Archive Network at http://CRAN.R-project.org/package=compareGroups.

The relative performance of bivariate causality tests in small samples

NARCIS (Netherlands)

Bult, J..R.; Leeflang, P.S.H.; Wittink, D.R.

1997-01-01

Causality tests have been applied to establish directional effects and to reduce the set of potential predictors, For the latter type of application only bivariate tests can be used, In this study we compare bivariate causality tests. Although the problem addressed is general and could benefit

Modeling animal-vehicle collisions using diagonal inflated bivariate Poisson regression.

Science.gov (United States)

Lao, Yunteng; Wu, Yao-Jan; Corey, Jonathan; Wang, Yinhai

2011-01-01

Two types of animal-vehicle collision (AVC) data are commonly adopted for AVC-related risk analysis research: reported AVC data and carcass removal data. One issue with these two data sets is that they were found to have significant discrepancies by previous studies. In order to model these two types of data together and provide a better understanding of highway AVCs, this study adopts a diagonal inflated bivariate Poisson regression method, an inflated version of bivariate Poisson regression model, to fit the reported AVC and carcass removal data sets collected in Washington State during 2002-2006. The diagonal inflated bivariate Poisson model not only can model paired data with correlation, but also handle under- or over-dispersed data sets as well. Compared with three other types of models, double Poisson, bivariate Poisson, and zero-inflated double Poisson, the diagonal inflated bivariate Poisson model demonstrates its capability of fitting two data sets with remarkable overlapping portions resulting from the same stochastic process. Therefore, the diagonal inflated bivariate Poisson model provides researchers a new approach to investigating AVCs from a different perspective involving the three distribution parameters (λ(1), λ(2) and λ(3)). The modeling results show the impacts of traffic elements, geometric design and geographic characteristics on the occurrences of both reported AVC and carcass removal data. It is found that the increase of some associated factors, such as speed limit, annual average daily traffic, and shoulder width, will increase the numbers of reported AVCs and carcass removals. Conversely, the presence of some geometric factors, such as rolling and mountainous terrain, will decrease the number of reported AVCs. Published by Elsevier Ltd.

Is routine karyotyping required in prenatal samples with a molecular or metabolic referral?

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Kooper Angelique JA

2012-01-01

Full Text Available Abstract As a routine, karyotyping of invasive prenatal samples is performed as an adjunct to referrals for DNA mutation detection and metabolic testing. We performed a retrospective study on 500 samples to assess the diagnostic value of this procedure. These samples included 454 (90.8% chorionic villus (CV and 46 (9.2% amniocenteses specimens. For CV samples karyotyping was based on analyses of both short-term culture (STC and long-term culture (LTC cells. Overall, 19 (3.8% abnormal karyotypes were denoted: four with a common aneuploidy (trisomy 21, 18 and 13, two with a sex chromosomal aneuploidy (Klinefelter syndrome, one with a sex chromosome mosaicism and twelve with various autosome mosaicisms. In four cases a second invasive test was performed because of an abnormal finding in the STC. Taken together, we conclude that STC and LTC karyotyping has resulted in a diagnostic yield of 19 (3.8% abnormal cases, including 12 cases (2.4% with an uncertain significance. From a diagnostic point of view, it is desirable to limit uncertain test results as secondary test findings. Therefore, we recommend a more targeted assay, such as e.g. QF-PCR, as a replacement of the STC and to provide parents the autonomy to choose between karyotyping and QF-PCR.

The distribution of chromosome aberrations among chromosomes of karyotype in exposed human lymphocyte

International Nuclear Information System (INIS)

Que Tran; Tien Hoang Hung

1997-01-01

Induced chromosome aberrations (ch. ab.) in exposed Human peripheral blood lymphocyte have been used to assay radio.bio.doses, because of their characters such as: the maintaining Go phase in cell cycle in body, the distribution of cell in blood system and the distribution of ch. ab. in exposed cells of body and among chromosomes of karyotype. The frequency of ch. ab. reflected the quantity of radiation dose, dose rate and radiation energy. The dependence between radiation dose and frequency of ch. ab. was illustrated by the mathematic equations. The distribution of induced ch. ab. among the cells exposed to uniform radiation fields was Poisson's, but the distribution of ch. ab. among chromosomes in karyotype depended on radiation field and mononucleotid sequence of DNA molecular of each chromosome. The minimum influence of mononucleotid sequence of DNA molecular in inform ch. ab. will be advantageous state for dose-assessments. The location of induced ch. ab. in exposed Human lymphocyte had been determined by karyotype analyses. The data of statistic analyse had improved that the number of ch. ab. depended on the size of chromosomes in karyotype. The equal distribution of ch. ab.among chromosomes in karyotype provided the objectiveness and the accuracy of using the chromosomal aberrant analysis technique on bio-dosimetry. (author)

Clinical disease characteristics according to karyotype in Turner syndrome

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Chae Young Yeo

2010-02-01

Full Text Available Purpose : Turner syndrome (TS is a disorder in which various anomalies can be accompanied, especially cardiovascular, renal, thyroid and auditory problems. The aim of this study is to identify the incidence of these disorders in patients with TS according to karyotype. Methods : We reviewed medical records of 90 patients with TS diagnosed by chromosomal analysis in 4 hospitals from Jan 1998 to Dec 2007. We evaluated these cases by prepared protocol of 4 medical problems. Results : The distribution of karyotype was 45,X (47.8%, mosaic pattern (34.4% and structural aberration group (17.8 %. Renal anomalies, cardiovascular anomalies, thyroid disorders and auditory problems are accompanied in 4.4%, 10.0 %, 11.1% and 5.6%, respectively. 45,X group had renal anomalies (7.0%, cardiovascular anomalies (18.6%, thyroid disorders (9.3% and auditory problems (11.6%. Mosaic group had renal anomalies (3.2%, thyroid disorders (12.9%, no cardiovascular anomalies and auditory problems. Structural aberration group had cardiovascular anomalies (6.3%, thyroid disorders (12.5% and no other 2 problems. Patients with 45,X group had a significant higher incidence of cardiovascular anomalies (P=0.025. Conclusion : Our results indicate that there are differences clinically according to karyotype of TS, especially in incidence of cardiovascular anomalies.

Karyotypes and heterochromatin variation (C-bands in Melipona species (Hymenoptera, Apidae, Meliponinae

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Rocha Marla Piumbini

1998-01-01

Full Text Available We describe the karyotypes of eight bee species of the genus Melipona and compare them in terms of heterochromatin content and location (C-banding technique. All species had 2n = 18 (females and n = 9 (males chromosomes, but a wide variation in heterochromatin content was detected among karyotypes. On the basis of these differences, the species were divided into two functional groups, one of them comprising species with a karyotype having a low heterochromatin content (M. bicolor bicolor, M. quadrifasciata, M. marginata, and M. asilvai, and the other species with a high heterochromatin content (M. seminigra fuscopilosa, M. capixaba, M. scutellaris, and M. captiosa. In the species with high heterochromatin content, heterochromatin occupied practically the entire extent of all chromosomes, with euchromatin being limited to the extremities, a fact that prevented observation of the centromere. In contrast, in the species with karyotypes having a low heterochromatin content, heterochromatin was visualized only in some chromosomes. In the chromosomes in which it was present, heterochromatin was located in the centromere or on the short arm. M. bicolor bicolor had the smallest heterochromatin content with only three chromosome pairs presenting heterochromatin in females. Increased heterochromatin content may be explained by interstitial and pericentromeric growth.

Flow karyotyping and flow instrumentation development. Final report

Energy Technology Data Exchange (ETDEWEB)

GEngh, G.J. van den

1997-11-01

The project had three major aims: improvement of technology for high-speed cell and chromosome sorting; the use of such instrumentation in genome analysis; applying the principles developed and the lessons learned to automated processes for the genome program. The work was a continuation of studies that were started at the Lawrence Livermore National Laboratory before the PI moved to the University of Washington. At Livermore, a high-speed sorter for the selection of human chromosomes was built. The instrument incorporated Livermore`s advanced sorter technology. The engineering focused on improving robustness and reliability so that the full potential of high-speed sorting would become available to the biological research laboratory. The new instrument, dubbed MoFlo for modular flow cytometer, proved to be a very practical and efficient tool during the chromosome isolation phase of the gene-library project. Its reliability and ease of operation exceeded that of the commercial instruments. The technology was licensed to two companies.

[Rapid karyotyping in the 2nd and 3rd trimester: results and experiences].

Science.gov (United States)

Claussen, U; Voigt, H J; Ulmer, R; Beinder, E

1995-01-01

Rapid karyotyping in the second and third trimester is an increasing field of collaboration between women's hospitals and human genetics. Techniques available for rapid karyotyping are: 1. Amniocentesis; to obtain amniotic fluid cells for culturing and subsequent chromosome harvesting using the pipette method or the "in situ" technique. The average time between preparation of the amniotic fluid and the verbal notification of the analysed karyotype is 4.65 days for the pipette method and 5.97 days for the "in situ" technique. The major advantages are that amniocentesis can be handled safely by many gynaecologist, and the amniotic fluid samples can be posted easily to cytogenetic units familiar with rapid karyotyping. The main disadvantage is that currently only a few laboratories are able to handle the pipette method or the "in situ" technique for rapid karyotyping. 2. Fetal blood sampling (cordocentesis); and subsequent chromosome analysis on cultivated fetal lymphocytes leading to results within 2 to 4 days. The main advantage of this procedure is the reliability of the results obtained. Fetal blood sampling, however, is restricted to specialists; this may involve scheduling delays. 3. Placental biopsy; with subsequent direct preparation and long term culturing. In comparison to both other techniques this procedure is faster if direct preparation is used. Results can be obtained even on the same day. The main disadvantage, however, is the problem with the reliability of the direct preparation results. They must be confirmed by time-consuming long-term culturing. Data are presented on the likelihood of abnormal ultrasound findings being caused by chromosomal aberrations.(ABSTRACT TRUNCATED AT 250 WORDS)

Spectral Karyotyping. An new method for chromosome analysis

International Nuclear Information System (INIS)

Zhou Liying; Qian Jianxin; Guo Xiaokui; Dai Hong; Liu Yulong; Zhou Jianying

2006-01-01

Spectral Karyotyping (SKY) can reveal fine changes in Chromosome structure which could not be detected by G, R, Q banding before, has become an accurate, sensitive and reliable method for karyotyping, promoted the development of cell genetics to molecular level and has been used in medicine and radiological injury research. It also has the ability of analyzing 24 chromosomes on its once test run and, find implicated structure of chromosome changes, such as metathesis, depletion, amplification, rearrangement, dikinetochore, equiarm and maker-body, detect the abnormal change of stable Chromosome and calculate the bio-dose curve; The abnormal Chromosome detected by SKY can be adopted as early diagnosis, effective indexes of minor remaining changes for use of monitor of treatment and in the duration of follow up. This technique provides us a more advanced and effective method for relative gene cloning and the study of pathological mechanism of cancer. (authors)

The genome diversity and karyotype evolution of mammals

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Trifonov Vladimir A

2011-10-01

Full Text Available Abstract The past decade has witnessed an explosion of genome sequencing and mapping in evolutionary diverse species. While full genome sequencing of mammals is rapidly progressing, the ability to assemble and align orthologous whole chromosome regions from more than a few species is still not possible. The intense focus on building of comparative maps for companion (dog and cat, laboratory (mice and rat and agricultural (cattle, pig, and horse animals has traditionally been used as a means to understand the underlying basis of disease-related or economically important phenotypes. However, these maps also provide an unprecedented opportunity to use multispecies analysis as a tool for inferring karyotype evolution. Comparative chromosome painting and related techniques are now considered to be the most powerful approaches in comparative genome studies. Homologies can be identified with high accuracy using molecularly defined DNA probes for fluorescence in situ hybridization (FISH on chromosomes of different species. Chromosome painting data are now available for members of nearly all mammalian orders. In most orders, there are species with rates of chromosome evolution that can be considered as 'default' rates. The number of rearrangements that have become fixed in evolutionary history seems comparatively low, bearing in mind the 180 million years of the mammalian radiation. Comparative chromosome maps record the history of karyotype changes that have occurred during evolution. The aim of this review is to provide an overview of these recent advances in our endeavor to decipher the karyotype evolution of mammals by integrating the published results together with some of our latest unpublished results.

Identification of a structural chromosomal rearrangement in the karyotype of a root vole from Chernobyl

International Nuclear Information System (INIS)

Nadzhafova, R.S.; Bulatova, N.Sh.; Kozlovskii, A.I.; Ryabov, I.N.

1994-01-01

Karyological studies of rodents within a 30-km radius of the Chernobyl nuclear power plant revealed one female root vole (Microtus oeconomus) with an abnormal karyotype. The use of C, G, and AgNOR banding methods allowed determination that morphological changes in two nonhomologous autosomes, which were accompanied by rearrangements in distribution of G bands, heterochromatin, and NOR, are the result of a reciprocal translocation. Chromosomal aberrations were probably inherited or appeared in embryogenesis, since none of the analyzed cells of the studied vole had a normal karyotype. It is important to note that this rearrangement was detected five years after the meltdown. Both breaks and reunions of the chromosomes that participate in this rearrangement are probably located in regions that are not important for functioning of these chromosomes. Thus, it can be supposed that the detected rearrangement did not influence the viability of the vole. This karyotype was compared to a standard karyotype of a root vole from another area of the species range. The heteromorphism of the first pair of chromosomes in both voles, which was detected for the first time, is probably normal for the karyotype of M. oeconomus and is not linked with any radiation-induced intrachromosomal aberrations

A generalized right truncated bivariate Poisson regression model with applications to health data.

Science.gov (United States)

Islam, M Ataharul; Chowdhury, Rafiqul I

2017-01-01

A generalized right truncated bivariate Poisson regression model is proposed in this paper. Estimation and tests for goodness of fit and over or under dispersion are illustrated for both untruncated and right truncated bivariate Poisson regression models using marginal-conditional approach. Estimation and test procedures are illustrated for bivariate Poisson regression models with applications to Health and Retirement Study data on number of health conditions and the number of health care services utilized. The proposed test statistics are easy to compute and it is evident from the results that the models fit the data very well. A comparison between the right truncated and untruncated bivariate Poisson regression models using the test for nonnested models clearly shows that the truncated model performs significantly better than the untruncated model.

Evaluation of an automated karyotyping system for chromosome aberration analysis

International Nuclear Information System (INIS)

Prichard, H.M.

1987-01-01

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

Karyotypic differences and evolutionary tendencies of some species ...

Indian Academy of Sciences (India)

The established karyotype differences have been helpful in clarifying the taxonomic position of these two species. The cytological analyses of other related clonal cultures suggest an evolutionary transition from S. pectinatus towards S. regularis through S. pectinatus f. regularis, which correlates with the morphological data ...

A comparison of bivariate and univariate QTL mapping in livestock populations

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Sorensen Daniel

2003-11-01

Full Text Available Abstract This study presents a multivariate, variance component-based QTL mapping model implemented via restricted maximum likelihood (REML. The method was applied to investigate bivariate and univariate QTL mapping analyses, using simulated data. Specifically, we report results on the statistical power to detect a QTL and on the precision of parameter estimates using univariate and bivariate approaches. The model and methodology were also applied to study the effectiveness of partitioning the overall genetic correlation between two traits into a component due to many genes of small effect, and one due to the QTL. It is shown that when the QTL has a pleiotropic effect on two traits, a bivariate analysis leads to a higher statistical power of detecting the QTL and to a more precise estimate of the QTL's map position, in particular in the case when the QTL has a small effect on the trait. The increase in power is most marked in cases where the contributions of the QTL and of the polygenic components to the genetic correlation have opposite signs. The bivariate REML analysis can successfully partition the two components contributing to the genetic correlation between traits.

Karyotype in secondary hematologic disorders after treatment for Hodgkin's disease. A study of 19 patients

International Nuclear Information System (INIS)

Iurlo, A.; Mecucci, C.; Van Orshoven, A.; Michaux, J.L.; Boogaerts, M.; Van den Berghe, H.

1988-01-01

In 19 cases of secondary hematologic disorders in patients previously treated for Hodgkin's disease, chromosome aberrations were analyzed in relation to the type of previous chemo- and/or radiotherapy, age of the patients, histopathologic features of the Hodgkin's disease at diagnosis, time interval between the treatment and the occurrence of the secondary disorder, and survival. The karyotype was of significant prognostic value when three cytogenetic groups were considered: patients with normal karyotypes; patients with aberrations of chromosome 7 as the sole anomaly; and patients with complex rearrangements and translocations. The last group showed the lowest rate of survival. Bone marrow transplantation was successful in two patients with a normal karyotype

Comparative Chromosome Map and Heterochromatin Features of the Gray Whale Karyotype (Cetacea).

Science.gov (United States)

Kulemzina, Anastasia I; Proskuryakova, Anastasia A; Beklemisheva, Violetta R; Lemskaya, Natalia A; Perelman, Polina L; Graphodatsky, Alexander S

2016-01-01

Cetacean karyotypes possess exceptionally stable diploid numbers and highly conserved chromosomes. To date, only toothed whales (Odontoceti) have been analyzed by comparative chromosome painting. Here, we studied the karyotype of a representative of baleen whales, the gray whale (Eschrichtius robustus, Mysticeti), by Zoo-FISH with dromedary camel and human chromosome-specific probes. We confirmed a high degree of karyotype conservation and found an identical order of syntenic segments in both branches of cetaceans. Yet, whale chromosomes harbor variable heterochromatic regions constituting up to a third of the genome due to the presence of several types of repeats. To investigate the cause of this variability, several classes of repeated DNA sequences were mapped onto chromosomes of whale species from both Mysticeti and Odontoceti. We uncovered extensive intrapopulation variability in the size of heterochromatic blocks present in homologous chromosomes among 3 individuals of the gray whale by 2-step differential chromosome staining. We show that some of the heteromorphisms observed in the gray whale karyotype are due to distinct amplification of a complex of common cetacean repeat and heavy satellite repeat on homologous autosomes. Furthermore, we demonstrate localization of the telomeric repeat in the heterochromatin of both gray and pilot whale (Globicephala melas, Odontoceti). Heterochromatic blocks in the pilot whale represent a composite of telomeric and common repeats, while heavy satellite repeat is lacking in the toothed whale consistent with previous studies. © 2016 S. Karger AG, Basel.

Comparison between two bivariate Poisson distributions through the ...

African Journals Online (AJOL)

These two models express themselves by their probability mass function. ... To remedy this problem, Berkhout and Plug proposed a bivariate Poisson distribution accepting the correlation as well negative, equal to zero, that positive.

Bivariate value-at-risk

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Giuseppe Arbia

2007-10-01

Full Text Available In this paper we extend the concept of Value-at-risk (VaR to bivariate return distributions in order to obtain measures of the market risk of an asset taking into account additional features linked to downside risk exposure. We first present a general definition of risk as the probability of an adverse event over a random distribution and we then introduce a measure of market risk (b-VaR that admits the traditional b of an asset in portfolio management as a special case when asset returns are normally distributed. Empirical evidences are provided by using Italian stock market data.

Two new bivariate zero-inflated generalized Poisson distributions with a flexible correlation structure

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Chi Zhang

2015-05-01

Full Text Available To model correlated bivariate count data with extra zero observations, this paper proposes two new bivariate zero-inflated generalized Poisson (ZIGP distributions by incorporating a multiplicative factor (or dependency parameter λ, named as Type I and Type II bivariate ZIGP distributions, respectively. The proposed distributions possess a flexible correlation structure and can be used to fit either positively or negatively correlated and either over- or under-dispersed count data, comparing to the existing models that can only fit positively correlated count data with over-dispersion. The two marginal distributions of Type I bivariate ZIGP share a common parameter of zero inflation while the two marginal distributions of Type II bivariate ZIGP have their own parameters of zero inflation, resulting in a much wider range of applications. The important distributional properties are explored and some useful statistical inference methods including maximum likelihood estimations of parameters, standard errors estimation, bootstrap confidence intervals and related testing hypotheses are developed for the two distributions. A real data are thoroughly analyzed by using the proposed distributions and statistical methods. Several simulation studies are conducted to evaluate the performance of the proposed methods.

Chromosomal Diversity and Karyotype Evolution in South American Macaws (Psittaciformes, Psittacidae.

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Ivanete de Oliveira Furo

Full Text Available Most species of macaws, which represent the largest species of Neotropical Psittacidae, characterized by their long tails and exuberant colours, are endangered, mainly because of hunting, illegal trade and habitat destruction. Long tailed species seem to represent a monophyletic group within Psittacidae, supported by cytogenetic data. Hence, these species show karyotypes with predominance of biarmed macrochromosomes, in contrast to short tailed species, with a predominance of acro/telocentric macrochromosomes. Because of their similar karyotypes, it has been proposed that inversions and translocations may be the main types of rearrangements occurring during the evolution of this group. However, only one species of macaw, Ara macao, that has had its genome sequenced was analyzed by means of molecular cytogenetics. Hence, in order to verify the rearrangements, we analyzed the karyotype of two species of macaws, Ara chloropterus and Anodorhynchus hyacinthinus, using cross-species chromosome painting with two different sets of probes from chicken and white hawk. Both intra- and interchromosomal rearrangements were observed. Chicken probes revealed the occurrence of fusions, fissions and inversions in both species, while the probes from white hawk determined the correct breakpoints or chromosome segments involved in the rearrangements. Some of these rearrangements were common for both species of macaws (fission of GGA1 and fusions of GGA1p/GGA4q, GGA6/GGA7 and GGA8/GGA9, while the fissions of GGA 2 and 4p were found only in A. chloropterus. These results confirm that despite apparent chromosomal similarity, macaws have very diverse karyotypes, which differ from each other not only by inversions and translocations as postulated before, but also by fissions and fusions.

Karyotype variation in cultivars and spontaneous cocoa mutants (Theobroma cacao L.).

Science.gov (United States)

Figueiredo, G S F; Melo, C A F; Souza, M M; Araújo, I S; Zaidan, H A; Pires, J L; Ahnert, D

2013-10-18

Four mutant cocoa accessions with morphological changes and a cultivar sample were karyomorphologically characterized. Slides were prepared by enzymatic digestion of the root meristem and squashed in 45% acetic acid, followed by 2% Giemsa staining. The chromosome number of 2n = 20 was seen in all accessions. The karyotype formula for Cacau Comum and Cacau Rui was 2n = 20m. Submetacentric chromosomes were observed in Cacau Pucala and Cacau Jaca, both with 2n = 18m + 2sm, but the karyotype formula for Cacau Sem Vidro was 2n = 16m + 4sm. Satellites were located on the long arm of the 1st and 2nd chromosome pairs of Cacau Comum, whereas Cacau Pucala had satellites on the 6th chromosome pair. Greater karyotypic variation in Cacau Sem Vidro was found, whose 1st and 2nd chromosome pairs had satellites on the long arm and 6th and 10th pairs had satellites on the short arm. Analysis revealed a lower average chromosome length in Cacau Comum (1.53 ± 0.026 µm) and a higher length in Cacau Sem Vidro (2.26 ± 0.038 µm). ANOVA revealed significant difference (P Theobroma cacao.

Digital karyotyping reveals probable target genes at 7q21.3 locus in hepatocellular carcinoma

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Wang Shengyue

2011-07-01

Full Text Available Abstract Background Hepatocellular carcinoma (HCC is a worldwide malignant liver tumor with high incidence in China. Subchromosomal amplifications and deletions accounted for major genomic alterations occurred in HCC. Digital karyotyping was an effective method for analyzing genome-wide chromosomal aberrations at high resolution. Methods A digital karyotyping library of HCC was constructed and 454 Genome Sequencer FLX System (Roche was applied in large scale sequencing of the library. Digital Karyotyping Data Viewer software was used to analyze genomic amplifications and deletions. Genomic amplifications of genes detected by digital karyotyping were examined by real-time quantitative PCR. The mRNA expression level of these genes in tumorous and paired nontumorous tissues was also detected by real-time quantitative RT-PCR. Results A total of 821,252 genomic tags were obtained from the digital karyotyping library of HCC, with 529,162 tags (64% mapped to unique loci of human genome. Multiple subchromosomal amplifications and deletions were detected through analyzing the digital karyotyping data, among which the amplification of 7q21.3 drew our special attention. Validation of genes harbored within amplicons at 7q21.3 locus revealed that genomic amplification of SGCE, PEG10, DYNC1I1 and SLC25A13 occurred in 11 (21%, 11 (21%, 11 (21% and 23 (44% of the 52 HCC samples respectively. Furthermore, the mRNA expression level of SGCE, PEG10 and DYNC1I1 were significantly up-regulated in tumorous liver tissues compared with corresponding nontumorous counterparts. Conclusions Our results indicated that subchromosomal region of 7q21.3 was amplified in HCC, and SGCE, PEG10 and DYNC1I1 were probable protooncogenes located within the 7q21.3 locus.

Karyotypic similarities between two species of Rhamphichthys (Rhamphichthyidae, Gymnotiformes from the Amazon basin

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Patrícia Silva

2013-10-01

Full Text Available The family Rhamphichthyidae includes three genera: Rhamphichthys Müller et Troschel, 1846, Gymnorhamphichthys M. M. Ellis, 1912 and Iracema Triques, 1996. From this family, only the species Rhamphichthys hanni Meinken, 1937 has had its karyotype described. Here, we describe the karyotypes of two additional Rhamphichthys species: R. marmoratus Castelnau, 1855 from the Reserva de Desenvolvimento Sustentável Mamirauá, Amazonas state and R. prope rostratus Linnaeus, 1766 from Pará state, both in Brazil. Our karyotypic analyses demonstrated that the diploid number is conserved for the genus (2n = 50, but the karyotypic formulas (KFs differed between R. marmoratus (44m/sm+6a and R. prope rostratus (42m/sm+8a. In both species, the constitutive heterochromatin (CH was located in the centromeric region of most chromosomes. Large heterochromatic blocks were found on the long arms of pairs 4 and 14 in R. marmoratus and on chromosomes 3, 4 and 19 in R. prope rostratus, which also has a heteromorphism in chromosome pair 1. The CH was DAPI positive, indicating that it is rich in AT base pairs. The Nucleolus Organizer Region (NOR showed staining at a single location in both species: the long arm of pair 1 in R. marmoratus and the long arm of pair 12 in R. prope rostratus, where it showed a size heteromorphism. CMA3 staining coincided with that of Ag-NOR, indicating that the ribosomal genes contain interspaced GC-rich sequences. FISH with an 18S rDNA probe confirmed that there is only one NOR site in each species. These results can be used as potential cytogenetic markers for fish populations, and comparative analysis of the karyotypes of Hypopygus Hoedman, 1962, Rhamphichthys and Steatogenys Boulenger, 1898 suggests that the first two genera diverged later that the third.

FISH with whole chromosome and telomeric probes demonstrates huge karyotypic reorganization with ITS between two species of Oryzomyini (Sigmodontinae, Rodentia): Hylaeamys megacephalus probes on Cerradomys langguthi karyotype.

Science.gov (United States)

Nagamachi, Cleusa Yoshiko; Pieczarka, Julio Cesar; O'Brien, Patricia Caroline Mary; Pinto, Jamilly Amaral; Malcher, Stella Miranda; Pereira, Adenilson Leão; Rissino, Jorge das Dores; Mendes-Oliveira, Ana Cristina; Rossi, Rogério Vieira; Ferguson-Smith, Malcolm Andrew

2013-04-01

Rodentia comprises 42 % of living mammalian species. The taxonomic identification can be difficult, the number of species currently known probably being underestimated, since many species show only slight morphological variations. Few studies surveyed the biodiversity of species, especially in the Amazon region. Cytogenetic studies show great chromosomal variability in rodents, with diploid numbers ranging from 10 to 102, making it difficult to find chromosomal homologies by comparative G banding. Chromosome painting is useful, but only a few species of rodents have been studied by this technique. In this study, we sorted whole chromosome probes by fluorescence-activated cell sorting from two Hylaeamys megacephalus individuals, an adult female (2n = 54) and a fetus (2n = 50). We made reciprocal chromosome painting between these karyotypes and cross-species hybridization on Cerradomys langguthi (2n = 46). Both species belong to the tribe Oryzomyini (Sigmodontinae), which is restricted to South America and were collected in the Amazon region. Twenty-four chromosome-specific probes from the female and 25 from the fetus were sorted. Reciprocal chromosome painting shows that the karyotype of the fetus does not represent a new cytotype, but an unbalanced karyotype with multiple rearrangements. Cross-species hybridization of H. megacephalus probes on metaphases of C. langguthi shows that 11 chromosomes of H. megacephalus revealed conserved synteny, 10 H. megacephalus probes hybridized to two chromosomal regions and three hybridized to three regions. Associations were observed on chromosomes pairs 1-4 and 11. Fluorescence in situ hybridization with a telomeric probe revealed interstitial regions in three pairs (1, 3, and 4) of C. langguthi chromosomes. We discuss the genomic reorganization of the C. langguthi karyotype.

Causal networks clarify productivity-richness interrelations, bivariate plots do not

Science.gov (United States)

Grace, James B.; Adler, Peter B.; Harpole, W. Stanley; Borer, Elizabeth T.; Seabloom, Eric W.

2014-01-01

Perhaps no other pair of variables in ecology has generated as much discussion as species richness and ecosystem productivity, as illustrated by the reactions by Pierce (2013) and others to Adler et al.'s (2011) report that empirical patterns are weak and inconsistent. Adler et al. (2011) argued we need to move beyond a focus on simplistic bivariate relationships and test mechanistic, multivariate causal hypotheses. We feel the continuing debate over productivity–richness relationships (PRRs) provides a focused context for illustrating the fundamental difficulties of using bivariate relationships to gain scientific understanding.

A bivariate model for analyzing recurrent multi-type automobile failures

Science.gov (United States)

Sunethra, A. A.; Sooriyarachchi, M. R.

2017-09-01

The failure mechanism in an automobile can be defined as a system of multi-type recurrent failures where failures can occur due to various multi-type failure modes and these failures are repetitive such that more than one failure can occur from each failure mode. In analysing such automobile failures, both the time and type of the failure serve as response variables. However, these two response variables are highly correlated with each other since the timing of failures has an association with the mode of the failure. When there are more than one correlated response variables, the fitting of a multivariate model is more preferable than separate univariate models. Therefore, a bivariate model of time and type of failure becomes appealing for such automobile failure data. When there are multiple failure observations pertaining to a single automobile, such data cannot be treated as independent data because failure instances of a single automobile are correlated with each other while failures among different automobiles can be treated as independent. Therefore, this study proposes a bivariate model consisting time and type of failure as responses adjusted for correlated data. The proposed model was formulated following the approaches of shared parameter models and random effects models for joining the responses and for representing the correlated data respectively. The proposed model is applied to a sample of automobile failures with three types of failure modes and up to five failure recurrences. The parametric distributions that were suitable for the two responses of time to failure and type of failure were Weibull distribution and multinomial distribution respectively. The proposed bivariate model was programmed in SAS Procedure Proc NLMIXED by user programming appropriate likelihood functions. The performance of the bivariate model was compared with separate univariate models fitted for the two responses and it was identified that better performance is secured by

Approximation of bivariate copulas by patched bivariate Fréchet copulas

KAUST Repository

Zheng, Yanting; Yang, Jingping; Huang, Jianhua Z.

2011-01-01

Bivariate Fréchet (BF) copulas characterize dependence as a mixture of three simple structures: comonotonicity, independence and countermonotonicity. They are easily interpretable but have limitations when used as approximations to general dependence structures. To improve the approximation property of the BF copulas and keep the advantage of easy interpretation, we develop a new copula approximation scheme by using BF copulas locally and patching the local pieces together. Error bounds and a probabilistic interpretation of this approximation scheme are developed. The new approximation scheme is compared with several existing copula approximations, including shuffle of min, checkmin, checkerboard and Bernstein approximations and exhibits better performance, especially in characterizing the local dependence. The utility of the new approximation scheme in insurance and finance is illustrated in the computation of the rainbow option prices and stop-loss premiums. © 2010 Elsevier B.V.

Approximation of bivariate copulas by patched bivariate Fréchet copulas

KAUST Repository

Zheng, Yanting

2011-03-01

Bivariate Fréchet (BF) copulas characterize dependence as a mixture of three simple structures: comonotonicity, independence and countermonotonicity. They are easily interpretable but have limitations when used as approximations to general dependence structures. To improve the approximation property of the BF copulas and keep the advantage of easy interpretation, we develop a new copula approximation scheme by using BF copulas locally and patching the local pieces together. Error bounds and a probabilistic interpretation of this approximation scheme are developed. The new approximation scheme is compared with several existing copula approximations, including shuffle of min, checkmin, checkerboard and Bernstein approximations and exhibits better performance, especially in characterizing the local dependence. The utility of the new approximation scheme in insurance and finance is illustrated in the computation of the rainbow option prices and stop-loss premiums. © 2010 Elsevier B.V.

Sex Determination, Sex Chromosomes, and Karyotype Evolution in Insects.

Science.gov (United States)

Blackmon, Heath; Ross, Laura; Bachtrog, Doris

2017-01-01

Insects harbor a tremendous diversity of sex determining mechanisms both within and between groups. For example, in some orders such as Hymenoptera, all members are haplodiploid, whereas Diptera contain species with homomorphic as well as male and female heterogametic sex chromosome systems or paternal genome elimination. We have established a large database on karyotypes and sex chromosomes in insects, containing information on over 13000 species covering 29 orders of insects. This database constitutes a unique starting point to report phylogenetic patterns on the distribution of sex determination mechanisms, sex chromosomes, and karyotypes among insects and allows us to test general theories on the evolutionary dynamics of karyotypes, sex chromosomes, and sex determination systems in a comparative framework. Phylogenetic analysis reveals that male heterogamety is the ancestral mode of sex determination in insects, and transitions to female heterogamety are extremely rare. Many insect orders harbor species with complex sex chromosomes, and gains and losses of the sex-limited chromosome are frequent in some groups. Haplodiploidy originated several times within insects, and parthenogenesis is rare but evolves frequently. Providing a single source to electronically access data previously distributed among more than 500 articles and books will not only accelerate analyses of the assembled data, but also provide a unique resource to guide research on which taxa are likely to be informative to address specific questions, for example, for genome sequencing projects or large-scale comparative studies. © The American Genetic Association 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Ovotesticular disorder of sexual development and a rare 46,XX/47,XXY karyotype.

Science.gov (United States)

Ozsu, Elif; Mutlu, Gul Yesiltepe; Cizmecioglu, Filiz M; Ekingen, Gülsen; Muezzinoglu, Bahar; Hatun, Sukru

2013-01-01

Ovotesticular disorder of sexual development (DSD) is characterized by the presence of both ovarian and testicular tissues in the same individual. The most common karyotype is 46,XX. Here, we report the case of a boy with a 46,XX/47,XXY karyotype diagnosed as ovotesticular DSD by gonadal biopsy. A 5-month-old boy presented with hypospadias, unilateral cryptorchidism, and a micropenis. Pelvic magnetic resonance imaging revealed a suspicious gonad tissue that is solid in structure in the right scrotum and a suspicious gonad that is cystic in structure in the left inguinal canal. He underwent a diagnostic laparoscopy. Cytogenetic analysis of peripheral blood revealed a 46,XX/47,XXY karyotype. Histopathologic examination of the left gonad showed ovarian tissue containing primordial follicles with ipsilateral undifferentiated tuba uterina. The right gonad showed immature testis tissue. He underwent left gonadectomy and hypospadias repair, and was raised as a male. Through this rare case, we highlight the importance of histological and cytogenetic investigation in DSD.

Association of electrophoretic karyotype of Candida stellatoidea with virulence for mice

International Nuclear Information System (INIS)

Kwon-Chung, K.J.; Wickes, B.L.; Merz, W.G.

1988-01-01

Seven isolates of Candida stellatoidea were studied for their electrophoretic karyotype, virulence for mice, sensitivity to UV radiation, growth rate in vitro, reaction on cycloheximide-indicator medium, and proteinase activity. The isolates exhibited one of two distinct electrophoretic karyotypes as determined by orthogonal field alternating gel electrophoresis (OFAGE). Four isolates, including the type culture of C. stellatoidea, belonged to electrophoretic karyotype type I by OFAGE, showing eight to nine bands of which at least two bands were less than 1,000 kilobases in size as estimated by comparison with the DNA bands of Saccharomyces cerevisiae. These isolates failed to produce fatal infection in mice within 20 days when 5 X 10(5) cells were injected intravenously. The yeasts were cleared from the kidneys of two of three mice tested by day 30. Type I showed proteinase activity on bovine serum albumin agar at pH 3.8 and produced a negative reaction on cycloheximide-bromcresol green medium within 48 h. The three grouped in type II by OFAGE showed banding patterns similar to those of a well-characterized isolate of Candida albicans. The isolates of type II had an electrophoretic karyotype of six to seven bands approximately 1,200 kilobases or greater in size. All three type II isolates were highly virulent for mice, producing fatality curves similar to those of a previously studied C. albicans isolate. From 80 to 90% of the mice injected with 5 X 10(5) cells intravenously died within 20 days. The type II isolates produced a positive reaction on cycloheximide-bromcresol green agar and showed no proteinase activity on bovine serum albumin agar at the low pH. In addition, the type II isolates grew faster and were significantly more resistant to UV irradiation than the type I isolates

First Description of the Karyotype and Sex Chromosomes in the Komodo Dragon (Varanus komodoensis).

Science.gov (United States)

Johnson Pokorná, Martina; Altmanová, Marie; Rovatsos, Michail; Velenský, Petr; Vodička, Roman; Rehák, Ivan; Kratochvíl, Lukáš

2016-01-01

The Komodo dragon (Varanus komodoensis) is the largest lizard in the world. Surprisingly, it has not yet been cytogenetically examined. Here, we present the very first description of its karyotype and sex chromosomes. The karyotype consists of 2n = 40 chromosomes, 16 macrochromosomes and 24 microchromosomes. Although the chromosome number is constant for all species of monitor lizards (family Varanidae) with the currently reported karyotype, variability in the morphology of the macrochromosomes has been previously documented within the group. We uncovered highly differentiated ZZ/ZW sex microchromosomes with a heterochromatic W chromosome in the Komodo dragon. Sex chromosomes have so far only been described in a few species of varanids including V. varius, the sister species to Komodo dragon, whose W chromosome is notably larger than that of the Komodo dragon. Accumulations of several microsatellite sequences in the W chromosome have recently been detected in 3 species of monitor lizards; however, these accumulations are absent from the W chromosome of the Komodo dragon. In conclusion, although varanids are rather conservative in karyotypes, their W chromosomes exhibit substantial variability at the sequence level, adding further evidence that degenerated sex chromosomes may represent the most dynamic genome part. © 2016 S. Karger AG, Basel.

All males do not have 46 xy karyotype: A rare case report

Directory of Open Access Journals (Sweden)

Ritesh Kumar Agrawala

2013-01-01

Full Text Available The sex of an embryo is determined by genetic sex due to presence or absence of Y chromosome, but it may not be true in all. We hereby report an interesting case of a phenotypic male carrying a female karyotype (46 XX. A 26-year-old male presented with bilateral gynecomastia, poor development of secondary sexual characters and azospermia. On evaluation patient had hypergonadotrophic hypogonadism and chromosomal analysis revealed 46 XX karyotype. The ultrasound revealed no Mullerian structures. Fluorescent in situ hybridization (FISH showed sex determining region of Y chromosome (SRY gene locus on X chromosome.

[X tetrasomy (48,XXXX karyotype) in a girl with altered behavior].

Science.gov (United States)

Rodado, Maria José; Manchón Trives, Irene; Lledó Bosch, Belén; Galán Sánchez, Francisco

2010-07-01

We report the case of a 14-year-old girl with mental retardation and dysmorphic features referred to child psychiatry because of altered behavior at school. Karyotyping (GTG banding), in situ fluorescent hybridization (FISH) and molecular study of parental origin by polymorphic STS were performed. Genetic study revealed a 48,XXXX karyotype with a maternal origin of the X-tetrasomy. The mechanism was successive non-dysjunction at meiosis I and II. The interest of this case lies in the rarity of the chromosomal anomaly and its late diagnosis, leading to a failure to adapt the girl's education to her needs, with consequences for her psyche. Copyright © 2010 SEP y SEPB. Published by Elsevier Espana. All rights reserved.

OneD: increasing reproducibility of Hi-C samples with abnormal karyotypes.

Science.gov (United States)

Vidal, Enrique; le Dily, François; Quilez, Javier; Stadhouders, Ralph; Cuartero, Yasmina; Graf, Thomas; Marti-Renom, Marc A; Beato, Miguel; Filion, Guillaume J

2018-05-04

The three-dimensional conformation of genomes is an essential component of their biological activity. The advent of the Hi-C technology enabled an unprecedented progress in our understanding of genome structures. However, Hi-C is subject to systematic biases that can compromise downstream analyses. Several strategies have been proposed to remove those biases, but the issue of abnormal karyotypes received little attention. Many experiments are performed in cancer cell lines, which typically harbor large-scale copy number variations that create visible defects on the raw Hi-C maps. The consequences of these widespread artifacts on the normalized maps are mostly unexplored. We observed that current normalization methods are not robust to the presence of large-scale copy number variations, potentially obscuring biological differences and enhancing batch effects. To address this issue, we developed an alternative approach designed to take into account chromosomal abnormalities. The method, called OneD, increases reproducibility among replicates of Hi-C samples with abnormal karyotype, outperforming previous methods significantly. On normal karyotypes, OneD fared equally well as state-of-the-art methods, making it a safe choice for Hi-C normalization. OneD is fast and scales well in terms of computing resources for resolutions up to 5 kb.

The Influence of Single Nucleotide Polymorphism Microarray-Based Molecular Karyotype on Preimplantation Embryonic Development Potential.

Directory of Open Access Journals (Sweden)

Gang Li

Full Text Available In order to investigate the influence of the molecular karyotype based on single nucleotide polymorphism (SNP microarray on embryonic development potential in preimplantation genetic diagnosis (PGD, we retrospectively analyzed the clinical data generated by PGD using embryos retrieved from parents with chromosome rearrangements in our center. In total, 929 embryos from 119 couples had exact diagnosis and development status. The blastocyst formation rate of balanced molecular karyotype embryos was 56.6% (276/488, which was significantly higher than that of genetic imbalanced embryos 24.5% (108/441 (P35 respectively. Blastocyst formation rates of male and female embryos were 44.5% (183/411 and 38.8% (201/518 respectively, with no significant difference between them (P>0.05. The rates of balanced molecular karyotype embryos vary from groups of embryos with different cell numbers at 68 hours after insemination. The blastocyst formation rate of embryos with 6-8 cells (48.1% was significantly higher than that of embryos with 8 cells (42.9% (P8 cells, embryos with 6-8 blastomeres have higher rate of balanced molecular karyotype and blastocyst formation.

Karyotype evolution in harvestmen of the suborder Cyphophthalmi (Opiliones)

Czech Academy of Sciences Publication Activity Database

Svojanovská, H.; Nguyen, Petr; Hiřman, M.; Tuf, I. H.; Wahab, R. A.; Haddad, C. R.; Šťáhlavský, F.

2016-01-01

Roč. 148, 2-3 (2016), s. 227-236 ISSN 1424-8581 R&D Projects: GA ČR(CZ) GP14-35819P Institutional support: RVO:60077344 Keywords : 18S rDNA * FISH * karyotype evolution Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.354, year: 2016

The karyotype and taxonomic status of Cryptomys hottentotus darlingi

African Journals Online (AJOL)

hypotonic solution. The animals were injecled subcutane- ously with yeasl for three consecutive days before colchicine injection to increase the mitotic rate in the bone marrow cells (Lee & Elder 1980). C-banded karyotypes were prepared by the barium hydroxide lechnique of. Sumner (1972). Nomenclalure for centromeric ...

Karyotype studies in some species of the family annonaceae ...

African Journals Online (AJOL)

A pair of satellited chromosomes was observed in the genome of Greenwayodendron suaveolens and Cleistopholis patens. The centromeric positions in the species of ... The karyotypic patterns suggest that there is no evidence of chromosome rearrangement in their evolution. IFE Journal of Science Vol. 9 (2) 2007 pp.

Dynamics of Tumor Heterogeneity Derived from Clonal Karyotypic Evolution

Directory of Open Access Journals (Sweden)

Ashley M. Laughney

2015-08-01

Full Text Available Numerical chromosomal instability is a ubiquitous feature of human neoplasms. Due to experimental limitations, fundamental characteristics of karyotypic changes in cancer are poorly understood. Using an experimentally inspired stochastic model, based on the potency and chromosomal distribution of oncogenes and tumor suppressor genes, we show that cancer cells have evolved to exist within a narrow range of chromosome missegregation rates that optimizes phenotypic heterogeneity and clonal survival. Departure from this range reduces clonal fitness and limits subclonal diversity. Mapping of the aneuploid fitness landscape reveals a highly favorable, commonly observed, near-triploid state onto which evolving diploid- and tetraploid-derived populations spontaneously converge, albeit at a much lower fitness cost for the latter. Finally, by analyzing 1,368 chromosomal translocation events in five human cancers, we find that karyotypic evolution also shapes chromosomal translocation patterns by selecting for more oncogenic derivative chromosomes. Thus, chromosomal instability can generate the heterogeneity required for Darwinian tumor evolution.

Probability distributions with truncated, log and bivariate extensions

CERN Document Server

Thomopoulos, Nick T

2018-01-01

This volume presents a concise and practical overview of statistical methods and tables not readily available in other publications. It begins with a review of the commonly used continuous and discrete probability distributions. Several useful distributions that are not so common and less understood are described with examples and applications in full detail: discrete normal, left-partial, right-partial, left-truncated normal, right-truncated normal, lognormal, bivariate normal, and bivariate lognormal. Table values are provided with examples that enable researchers to easily apply the distributions to real applications and sample data. The left- and right-truncated normal distributions offer a wide variety of shapes in contrast to the symmetrically shaped normal distribution, and a newly developed spread ratio enables analysts to determine which of the three distributions best fits a particular set of sample data. The book will be highly useful to anyone who does statistical and probability analysis. This in...

Exploring karyotype diversity of Argentinian Guaraní maize landraces: Relationship among South American maize.

Directory of Open Access Journals (Sweden)

María Florencia Realini

Full Text Available In Argentina there are two different centers of maize diversity, the Northeastern (NEA and the Northwestern (NWA regions of the country. In NEA, morphological studies identified 15 landraces cultivated by the Guaraní communities in Misiones Province. In the present study we analyzed the karyotype diversity of 20 populations of Guaraní maize landraces through classical and molecular cytogenetic analyses. Our results demonstrate significant intra and inter-populational variation in the percentage, number, size, chromosome position and frequencies of the heterochromatic blocks, which are called knobs. Knob sequence analysis (180-bp and TR-1 did not show significant differences among Guaraní populations. B chromosomes were not detected, and abnormal 10 (AB10 chromosomes were found with low frequency (0.1≥f ≤0.40 in six populations. Our results allowed karyotypic characterization of each analyzed population, defining for the first time the chromosomal constitution of maize germplasm from NEA. The multivariate analysis (PCoA and UPGMA of karyotype parameters allowed the distinction between two populations groups: the Popcorn and the Floury maize populations. These results are in agreement with previously published microsatellite and morphological/phenological studies. Finally, we compared our karyotype results with those previously reported for NWA and Central Region of South America maize. Our data suggest that there are important differences between maize from NEA and NWA at the karyotype level, supporting the hypothesis that there are two pathways of input of South America maize. Our results also confirm the existence of two centers of diversification of Argentinian native maize, NWA and NEA. This work contributes new knowledge about maize diversity, which is relevant for future plans to improve commercial maize, and for conservation of agrobiodiversity.

Care of women with XY karyotype

DEFF Research Database (Denmark)

Jorgensen, Pernille Bach; Kjartansdóttir, Kristín Rós; Fedder, Jens

2010-01-01

OUTCOME MEASURE(S): Evaluation of etiology, diagnosis, treatment, and associated disorders in XY women. RESULT(S): Many gene mutations can cause abnormal fetal development leading to androgen insensitivity syndrome or gonadal dysgenesis disorders. Females with these disorders have an XY karyotype but look...... like girls. They are mostly diagnosed at puberty, and the condition will often lead to serious psychological problems. Increased risk of malignancies and problems with pregnancy and infertility are other aspects that should be considered. This guideline will aid doctors in caring for XY females...

Karyotype and nuclear DNA content of Trichomycterus areolatus (Siluriformes, Trichomycteridae

Directory of Open Access Journals (Sweden)

Nelson Colihueque

2006-01-01

Full Text Available Cytogenetic analysis of Trichomycterus areolatus, collected from the Tijeral and Huilma Rivers in southern Chile has shown a diploid chromosome number of 2n = 54, a fundamental number of FN = 106, and a karyotypic formula of 44m + 8sm + 2st. Intra-individual polymorphism of chromosome number (2n = 54, 55 and 56 in specimens from the Huilma River has also been documented, providing further evidence of the occurrence of this phenomenon in Trichomycterus. The karyotype exhibited large chromosome pairs: metacentric pairs 1 (relative length 7.54%, 2 (5.75% and 3 (5.09%, submetacentric pair 23 (5.25%, and subtelocentic pair 27 (5.28%. Nuclear DNA content analysis showed an average value of 5.04 ± 1.09 pg/nucleus. This DNA content is higher than the mean value described for other species in this genus.

46,XX Karyotype in a Male with Ambigious Genitalia: A Case Report

Directory of Open Access Journals (Sweden)

Mahmut Balkan

2004-01-01

Full Text Available 40 days old case who were diagnosed with ambigious genitalia were sentto laboratory of cytogenetics. Mother was 26 years old and have to alivechildren and case were the second child and applied to Child SurgeryDepartment due to continiously vomiting and uneasy conditions. Sexualdevelopment were as male on physical examinations. Cell culture wasapplied for chromosomal analysis. Slides were stained with GiemsaBanding Staining (GTG and 100 cells were totaly counted and karyotypingwere done with 15 metaphase. Chromosome with 46,XX karyotype. Casewere taken under consideration of congenital adrenel hyperplasia afterevalution of karyotype. Case were discussed according to by information ofpresents literatures.

Genomicus 2018: karyotype evolutionary trees and on-the-fly synteny computing.

Science.gov (United States)

Nguyen, Nga Thi Thuy; Vincens, Pierre; Roest Crollius, Hugues; Louis, Alexandra

2018-01-04

Since 2010, the Genomicus web server is available online at http://genomicus.biologie.ens.fr/genomicus. This graphical browser provides access to comparative genomic analyses in four different phyla (Vertebrate, Plants, Fungi, and non vertebrate Metazoans). Users can analyse genomic information from extant species, as well as ancestral gene content and gene order for vertebrates and flowering plants, in an integrated evolutionary context. New analyses and visualization tools have recently been implemented in Genomicus Vertebrate. Karyotype structures from several genomes can now be compared along an evolutionary pathway (Multi-KaryotypeView), and synteny blocks can be computed and visualized between any two genomes (PhylDiagView). © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Subchromosomal karyotype evolution in Equidae.

Science.gov (United States)

Musilova, P; Kubickova, S; Vahala, J; Rubes, J

2013-04-01

Equidae is a small family which comprises horses, African and Asiatic asses, and zebras. Despite equids having diverged quite recently, their karyotypes underwent rapid evolution which resulted in extensive differences among chromosome complements in respective species. Comparative mapping using whole-chromosome painting probes delineated genome-wide chromosome homologies among extant equids, enabling us to trace chromosome rearrangements that occurred during evolution. In the present study, we performed subchromosomal comparative mapping among seven Equidae species, representing the whole family. Region-specific painting and bacterial artificial chromosome probes were used to determine the orientation of evolutionarily conserved segments with respect to centromere positions. This allowed assessment of the configuration of all fusions occurring during the evolution of Equidae, as well as revealing discrepancies in centromere location caused by centromere repositioning or inversions. Our results indicate that the prevailing type of fusion in Equidae is centric fusion. Tandem fusions of the type telomere-telomere occur almost exclusively in the karyotype of Hartmann's zebra and are characteristic of this species' evolution. We revealed inversions in segments homologous to horse chromosomes 3p/10p and 13 in zebras and confirmed inversions in segments 4/31 in African ass, 7 in horse and 8p/20 in zebras. Furthermore, our mapping results suggested that centromere repositioning events occurred in segments homologous to horse chromosomes 7, 8q, 10p and 19 in the African ass and an element homologous to horse chromosome 16 in Asiatic asses. Centromere repositioning in chromosome 1 resulted in three different chromosome types occurring in extant species. Heterozygosity of the centromere position of this chromosome was observed in the kiang. Other subtle changes in centromere position were described in several evolutionary conserved chromosomal segments, suggesting that tiny

Karyotype differentiation in Chromaphyosemion killifishes (Cyprinodontiformes, Nothobranchiidae)II: Cytogenetic and mitochondrial DNA analyses demostrate karyotype differentiation and its evolutionary direction in C. riggenbachi

Czech Academy of Sciences Publication Activity Database

Völker, M.; Sonnenberg, R.; Ráb, Petr; Kullmann, H.

2006-01-01

Roč. 115, 1 (2006), s. 70-83 ISSN 1424-8581 Grant - others:DFG Ku-1469/2-1; DFG Mi-649/2-1; DAAD D/03/44465 Institutional research plan: CEZ:AV0Z50450515 Keywords : karyotype differentiation Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.993, year: 2006

Karyotyping, dermatoglyphic, and sweat pore analysis of five families affected with ectodermal dysplasia.

Science.gov (United States)

Sidhu, Manpreet; Kale, Alka D; Kotrashetti, Vijayalakshmi S

2012-09-01

Hereditary ectodermal dysplasia is a genetic recessive trait characterized by hypohydrosis, hypotrichosis, and hypodontia. The affected individual show characteristic physiognomy like protruded forehead, depressed nasal bridge, periorbital wrinkling, protruded lips, etc. There is marked decrease in sweat and salivary secretion. Due to skin involvement palm and sole ridge patterns are disrupted. In this study an attempt has been made to classify the affected members according to the degree of penetrance by pedigree analysis and also study karyotyping for cytogenetics, dermatoglyphic analysis for the various ridge patterns and variations in the number of sweat glands by sweat pore analysis in affected individuals. A total of five families who were affected with ectodermal dysplasia were considered. Pedigree analysis was drawn up to three generation by obtaining history. Dermatoglyphics and sweat pore analysis was done by obtaining palm and finger print impression using stamp pad ink. Karyotyping was done by collecting 3-5 ml peripheral blood. Karyotyping was prepared using lymphocyte culture. Chromosomes were examined at 20 spreads selected randomly under ×100 magnification. Results were analyzed by calculating mean values and percentage was obtained. Karyotyping did not show any abnormalities, dermatoglyphic analysis and sweat pore counts showed marked variations when compared with normal. Moreover, pedigree analysis confirmed the status of the disease as that of the recessive trait. Large number of affected patients needs to be evaluated for dermatoglypic analysis. Genetic aspect of the disease needs to be looked into the molecular level in an attempt to locate the gene locus responsible for ectodermal dysplasia and its manifestation.

Chromosome Mis-segregation Generates Cell-Cycle-Arrested Cells with Complex Karyotypes that Are Eliminated by the Immune System.

Science.gov (United States)

Santaguida, Stefano; Richardson, Amelia; Iyer, Divya Ramalingam; M'Saad, Ons; Zasadil, Lauren; Knouse, Kristin A; Wong, Yao Liang; Rhind, Nicholas; Desai, Arshad; Amon, Angelika

2017-06-19

Aneuploidy, a state of karyotype imbalance, is a hallmark of cancer. Changes in chromosome copy number have been proposed to drive disease by modulating the dosage of cancer driver genes and by promoting cancer genome evolution. Given the potential of cells with abnormal karyotypes to become cancerous, do pathways that limit the prevalence of such cells exist? By investigating the immediate consequences of aneuploidy on cell physiology, we identified mechanisms that eliminate aneuploid cells. We find that chromosome mis-segregation leads to further genomic instability that ultimately causes cell-cycle arrest. We further show that cells with complex karyotypes exhibit features of senescence and produce pro-inflammatory signals that promote their clearance by the immune system. We propose that cells with abnormal karyotypes generate a signal for their own elimination that may serve as a means for cancer cell immunosurveillance. Copyright © 2017 Elsevier Inc. All rights reserved.

Karyotype and nucleic acid content in Zantedeschia aethiopica Spr ...

African Journals Online (AJOL)

DR. NJ TONUKARI

2012-07-03

Jul 3, 2012 ... Analysis of karyotype, nucleic deoxyribonucleic acid (DNA) content and sodium dodecyl sulfate polyacrylamide ... base pairs) for Z. aethiopica and 1144.26 ± 0.05 picograms (equivalent to 1144.26 mega base pairs) for Z. elliottiana. ... ml ice-cold nuclei-isolation buffer A of the Partec high resolution. DNA kit ...

GIS-Based bivariate statistical techniques for groundwater potential ...

Indian Academy of Sciences (India)

24

This study shows the potency of two GIS-based data driven bivariate techniques namely ... In the view of these weaknesses , there is a strong requirement for reassessment of .... Font color: Text 1, Not Expanded by / Condensed by , ...... West Bengal (India) using remote sensing, geographical information system and multi-.

Canine osteosarcoma karyotypes from an original tumor, its metastasis, and tumor cells in tissue culture

International Nuclear Information System (INIS)

Taylor, N.; Shifrine, M.; Wolf, H.G.; Trommershausen-Smith, A.

1975-01-01

Radiation-induced osteosarcoma, its metastasis, and cells grown in tissue culture were karyotyped. Both hypodiploid and hyperdiploid stem lines were observed. The hypodiploid line contained 45-55 chromosomes with 10 to 15 abnormal metacentric and submetacentric chromosomes and one subtelocentric marker. The hyperdiploid line contained 90 to 105 chromosomes with 20 to 30 abnormal metacentric and submetacentric chromosomes with two subtelocentric markers. Karyotypic analysis can be used to monitor osteosarcomas maintained in tissue culture

Assessing the copula selection for bivariate frequency analysis ...

Indian Academy of Sciences (India)

58

Copulas are applied to overcome the restriction of traditional bivariate frequency ... frequency analysis methods cannot describe the random variable properties that ... In order to overcome the limitation of multivariate distributions, a copula is a ..... The Mann-Kendall (M-K) test is a non-parametric statistical test which is used ...

Karyotype in Pediatric Acute Lymphoblastic Leukemia: Impact On Clinical Presentation and Duration of First Remission

International Nuclear Information System (INIS)

Khairy, A.M.D.; EL-SISSY, M.D.

2003-01-01

In this study we are aiming at investigating the correlation between karyotype and the clinico pathologic features of pediatric acute lymphoblastic leukemia, duration of first remission and outcome of patients. Material and Methods: A total of 40 pediatric patients with the diagnosis of acute ]lymphoblastic leukemia (ALL) were included in this study. The patients were treated according to ALL P.NCI III/98 protocol used at the Pediatric Oncology Unit, National Cancer Institute, Cairo University. Analyzing the patients with respect to their chromosomal pattern; the majority of patients (17/40, 42.5%) showed a pseudo diploid karyotype. Their mean age was 10.2±4.8 years, M/F ratio 2.4: I. Massive hepatosplenomegaly (HSM) was encountered in 64.7%. The mean total leucocyte count (TLC) was 66.53±5.2 cells per μl. Their mean first complete remission (CR]) was 11.05±2.3 months, EFS was 40% at 12 months and 17.78% at 24 months. Patients with normal karyotype came next, representing ]3/40 (32.5%). Their mean age was 8.4±1.8 years, M/F 0.8: I. Massive HSM was found in 62.5%. The mean TLC was 78.74±3.8 cells per μl. Their mean CR 1 was I I.62±1.2 months, EFS was 41.67% at 12 months and 33.33% at 24 months. The third group represented patients with hyper diploidy (8/40; 20%). Their mean age was 8. 8±3. I years, M/F 7: I. Massive HSM was found in 50%. The mean TLC was 45.16±3.1 cells per μl], their mean CR I was 18.] 0±3.4 months, EFS was 75% at 12 months and 62.5% at 24 months. The least group showed a hypo diploid pattern (5/40; 12.5%). Their mean age was] 3±2.6 years, all were males. Massive HSM was encountered in 100%. The mean TLC was 20.00±2.9 cells per Ill. Their mean CRI was 10±2.8 months. Egyptian patients with childhood ALL who have hyper diploid karyotype, specially those having >50 chromosomes carry a better prognosis than patients with other chromosomal abnormalities. Pseudo diploid karyotype is the most frequent among Egyptian ALL cases and this could

Karyotype Reorganization in the Hokou Gecko (Gekko hokouensis, Gekkonidae): The Process of Microchromosome Disappearance in Gekkota

OpenAIRE

Srikulnath, Kornsorn; Uno, Yoshinobu; Nishida, Chizuko; Ota, Hidetoshi; Matsuda, Yoichi

2015-01-01

The Hokou gecko (Gekko hokouensis: Gekkonidae, Gekkota, Squamata) has the chromosome number 2n = 38, with no microchromosomes. For molecular cytogenetic characterization of the gekkotan karyotype, we constructed a cytogenetic map for G. hokouensis, which retains the ancestral karyotype of Gekkota, with 86 functional genes, and compared it with cytogenetic maps for four Toxicofera species that have many microchromosomes (Elaphe quadrivirgata, Varanus salvator macromaculatus, Leiolepis reevesii...

Karyotype analyses of the species of the genus Jurinea Cass ...

African Journals Online (AJOL)

In this study, karyotype analyses of 13 species belonging to the genus Jurinea Cass. (Compositae) and grown naturally in Turkey were conducted. These taxa include Jurinea alpigena C. Koch, Jurinea ancyrensis Bornm., Jurinea aucherana DC., Jurinea cadmea Boiss., Jurinea cataonica Boiss. and Hausskn., Jurinea ...

Karyotype analyses of the species of the genus Jurinea Cass ...

African Journals Online (AJOL)

user

2011-01-31

Jan 31, 2011 ... 1Selcuk University, Education Faculty, Department of Science Education, Konya, Turkey. 2Selcuk University, Education .... at the KNYA and Selcuk University Faculty of Education herbaria. (Appendix). For karyotypes, root tips ..... numbers of phanerogams from Morocco and Algeria. Bot. Not. 131: 391-406.

About some properties of bivariate splines with shape parameters

Science.gov (United States)

Caliò, F.; Marchetti, E.

2017-07-01

The paper presents and proves geometrical properties of a particular bivariate function spline, built and algorithmically implemented in previous papers. The properties typical of this family of splines impact the field of computer graphics in particular that of the reverse engineering.

Karyotype analysis of three Solanum plants using combined PI-DAPI ...

African Journals Online (AJOL)

ajl yemi

2011-12-19

Dec 19, 2011 ... OLYMPUS epifluorescence microscope, and their images were captured with a CoolSNAP-CCD video camera using Meta Imaging. Series software. In this study, Adobe Photoshop software was used to take photos of the chromosomes, and karyotype analysis was studied by Li and. Chen (1985) methods.

Optimizing an objective function under a bivariate probability model

NARCIS (Netherlands)

X. Brusset; N.M. Temme (Nico)

2007-01-01

htmlabstractThe motivation of this paper is to obtain an analytical closed form of a quadratic objective function arising from a stochastic decision process with bivariate exponential probability distribution functions that may be dependent. This method is applicable when results need to be

A New Measure Of Bivariate Asymmetry And Its Evaluation

International Nuclear Information System (INIS)

Ferreira, Flavio Henn; Kolev, Nikolai Valtchev

2008-01-01

In this paper we propose a new measure of bivariate asymmetry, based on conditional correlation coefficients. A decomposition of the Pearson correlation coefficient in terms of its conditional versions is studied and an example of application of the proposed measure is given.

Spectrum-based estimators of the bivariate Hurst exponent

Czech Academy of Sciences Publication Activity Database

Krištoufek, Ladislav

2014-01-01

Roč. 90, č. 6 (2014), art. 062802 ISSN 1539-3755 R&D Projects: GA ČR(CZ) GP14-11402P Institutional support: RVO:67985556 Keywords : bivariate Hurst exponent * power- law cross-correlations * estimation Subject RIV: AH - Economics Impact factor: 2.288, year: 2014 http://library.utia.cas.cz/separaty/2014/E/kristoufek-0436818.pdf

Analyses of karyotypes and comparative physical locations of the ...

African Journals Online (AJOL)

The frequencies of signal detection of the marker, RG556 and the BAC clone, 44B4, were 8.0 and 41.3% in O. sativa, while 9.0 and 42.3% in O. officinalis, respectively. Based on a comparative RFLP map of a wild rice, O. officinalis and O. sativa, comparative analyses of karyotypes of O. officinalis were demonstrated firstly ...

Resolution and evolution of the duck-billed platypus karyotype with an X1Y1X2Y2X3Y3X4Y4X5Y5 male sex chromosome constitution.

Science.gov (United States)

Rens, Willem; Grützner, Frank; O'brien, Patricia C M; Fairclough, Helen; Graves, Jennifer A M; Ferguson-Smith, Malcolm A

2004-11-16

The platypus (2n = 52) has a complex karyotype that has been controversial over the last three decades. The presence of unpaired chromosomes and an unknown sex-determining system especially has defied attempts at conventional analysis. This article reports on the preparation of chromosome-specific probes from flow-sorted chromosomes and their application in the identification and classification of all platypus chromosomes. This work reveals that the male karyotype has 21 pairs of chromosomes and 10 unpaired chromosomes (E1-E10), which are linked by short regions of homology to form a multivalent chain in meiosis. The female karyotype differs in that five of these unpaired elements (E1, E3, E5, E7, and E9) are each present in duplicate, whereas the remaining five unpaired elements (E2, E4, E6, E8, and E10) are absent. This finding indicates that sex is determined by the alternate segregation of the chain of 10 during spermatogenesis so that equal numbers of sperm bear either one of the two groups of five elements, i.e., five X and five Y chromosomes. Chromosome painting reveals that these X and Y chromosomes contain pairing (XY shared) and differential (X- or Y-specific) segments. Y differential regions must contain male-determining genes, and X differential regions should be dosage-compensated in the female. Two models for the evolution of the sex-determining system are presented. The resolution of the longstanding debate over the platypus karyotype is an important step toward the understanding of mechanisms of sex determination, dosage compensation, and karyotype evolution.

Phenotype in girls and women with Turner syndrome: Association between dysmorphic features, karyotype and cardio-aortic malformations.

Science.gov (United States)

Noordman, Iris; Duijnhouwer, Anthonie; Kapusta, Livia; Kempers, Marlies; Roeleveld, Nel; Schokking, Michiel; Smeets, Dominique; Freriks, Kim; Timmers, Henri; van Alfen-van der Velden, Janiëlle

2018-06-01

Turner syndrome (TS) is a genetic disorder characterized by the (partial) absence or a structural aberration of the second sex chromosome and is associated with a variety of phenotypes with specific physical features and cardio-aortic malformations. The objective of this study was to gain a better insight into the differences in dysmorphic features between girls and women with TS and to explore the association between these features, karyotype and cardio-aortic malformations. This prospective study investigated 14 dysmorphic features of TS girls and women using a checklist. Three major phenotypic patterns were recognized (severe phenotype, lymphatic phenotype and skeletal phenotype). Patient data including karyotype and cardio-aortic malformations (bicuspid aortic valve (BAV) and aortic coarctation (COA)) were collected. Associations between the prevalence of dysmorphic features, karyotype and cardio-aortic malformations were analysed using chi 2 -test and odds ratios. A total of 202 patients (84 girls and 118 women) were analysed prospectively. Differences in prevalence of dysmorphic features were found between girls and women. A strong association was found between monosomy 45,X and the phenotypic patterns. Furthermore, an association was found between COA and lymphatic phenotype, but no association was found between karyotype and cardio-aortic malformations. This study uncovered a difference in dysmorphic features between girls and women. Monosomy 45,X is associated with a more severe phenotype, lymphatic phenotype and skeletal phenotype. All patients with TS should be screened for cardio-aortic malformations, because in contrast to previous reports, karyotype and cardio-aortic malformations showed no significant association. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

FSH, LH, inhibin B and estradiol levels in Turner syndrome depend on age and karyotype: longitudinal study of 70 Turner girls with or without spontaneous puberty

DEFF Research Database (Denmark)

Hagen, Casper P; Main, Katharina M; Kjaergaard, Susanne

2010-01-01

Ovarian function in Turner syndrome (TS) patients depends on the specific karyotype. This retrospective clinical study evaluates the pituitary-gonadal axis during infancy, childhood and adolescence in TS patients according to karyotype and ovarian function.......Ovarian function in Turner syndrome (TS) patients depends on the specific karyotype. This retrospective clinical study evaluates the pituitary-gonadal axis during infancy, childhood and adolescence in TS patients according to karyotype and ovarian function....

Bivariate generalized Pareto distribution for extreme atmospheric particulate matter

Science.gov (United States)

Amin, Nor Azrita Mohd; Adam, Mohd Bakri; Ibrahim, Noor Akma; Aris, Ahmad Zaharin

2015-02-01

The high particulate matter (PM10) level is the prominent issue causing various impacts to human health and seriously affecting the economics. The asymptotic theory of extreme value is apply for analyzing the relation of extreme PM10 data from two nearby air quality monitoring stations. The series of daily maxima PM10 for Johor Bahru and Pasir Gudang stations are consider for year 2001 to 2010 databases. The 85% and 95% marginal quantile apply to determine the threshold values and hence construct the series of exceedances over the chosen threshold. The logistic, asymmetric logistic, negative logistic and asymmetric negative logistic models areconsidered as the dependence function to the joint distribution of a bivariate observation. Maximum likelihood estimation is employed for parameter estimations. The best fitted model is chosen based on the Akaike Information Criterion and the quantile plots. It is found that the asymmetric logistic model gives the best fitted model for bivariate extreme PM10 data and shows the weak dependence between two stations.

Bivariational calculations for radiation transfer in an inhomogeneous participating media

International Nuclear Information System (INIS)

El Wakil, S.A.; Machali, H.M.; Haggag, M.H.; Attia, M.T.

1986-07-01

Equations for radiation transfer are obtained for dispersive media with space dependent albedo. Bivariational bound principle is used to calculate the reflection and transmission coefficients for such media. Numerical results are given and compared. (author)

Karyotypic evolution and phylogenetic relationships in the order Chiroptera as revealed by G-banding comparison and chromosome painting.

Science.gov (United States)

Ao, Lei; Mao, Xiuguang; Nie, Wenhui; Gu, Xiaoming; Feng, Qing; Wang, Jinhuan; Su, Weiting; Wang, Yingxiang; Volleth, Marianne; Yang, Fengtang

2007-01-01

Bats are a unique but enigmatic group of mammals and have a world-wide distribution. The phylogenetic relationships of extant bats are far from being resolved. Here, we investigated the karyotypic relationships of representative species from four families of the order Chiroptera by comparative chromosome painting and banding. A complete set of painting probes derived from flow-sorted chromosomes of Myotis myotis (family Vespertilionidae) were hybridized onto metaphases of Cynopterus sphinx (2n = 34, family Pteropodidae), Rhinolophus sinicus (2n=36, family Rhinolophidae) and Aselliscus stoliczkanus (2n=30, family Hipposideridae) and delimited 27, 30 and 25 conserved chromosomal segments in the three genomes, respectively. The results substantiate that Robertsonian translocation is the main mode of chromosome evolution in the order Chiroptera, with extensive conservation of whole chromosomal arms. The use of M. myotis (2n=44) probes has enabled the integration of C. sphinx, R. sinicus and A. stoliczkanus chromosomes into the previously established comparative maps between human and Eonycteris spelaea (2n=36), Rhinolophus mehelyi (2n=58), Hipposideros larvatus (2n=32), and M. myotis. Our results provide the first cytogenetic signature rearrangement that supports the grouping of Pteropodidae and Rhinolophoidea in a common clade (i.e. Pteropodiformes or Yinpterochiroptera) and thus improve our understanding on the karyotypic relationships and genome phylogeny of these bat species.

Spectral density regression for bivariate extremes

KAUST Repository

Castro Camilo, Daniela

2016-05-11

We introduce a density regression model for the spectral density of a bivariate extreme value distribution, that allows us to assess how extremal dependence can change over a covariate. Inference is performed through a double kernel estimator, which can be seen as an extension of the Nadaraya–Watson estimator where the usual scalar responses are replaced by mean constrained densities on the unit interval. Numerical experiments with the methods illustrate their resilience in a variety of contexts of practical interest. An extreme temperature dataset is used to illustrate our methods. © 2016 Springer-Verlag Berlin Heidelberg

The ancestral chromosomes of Dromiciops gliroides (Microbiotheridae), and its bearings on the karyotypic evolution of American marsupials

OpenAIRE

Su?rez-Villota, Elkin Y.; Haro, Ronie E.; Vargas, Rodrigo A.; Gallardo, Milton H.

2016-01-01

Background The low-numbered 14-chromosome karyotype of marsupials has falsified the fusion hypothesis claiming ancestrality from a 22-chromosome karyotype. Since the 14-chromosome condition of the relict Dromiciops gliroides is reminecent of ancestrality, its interstitial traces of past putative fusions and heterochromatin banding patterns were studied and added to available marsupials? cytogenetic data. Fluorescent in situ hybridization (FISH) and self-genomic in situ hybridization (self-GIS...

Bivariate extreme value with application to PM10 concentration analysis

Science.gov (United States)

Amin, Nor Azrita Mohd; Adam, Mohd Bakri; Ibrahim, Noor Akma; Aris, Ahmad Zaharin

2015-05-01

This study is focus on a bivariate extreme of renormalized componentwise maxima with generalized extreme value distribution as a marginal function. The limiting joint distribution of several parametric models are presented. Maximum likelihood estimation is employed for parameter estimations and the best model is selected based on the Akaike Information Criterion. The weekly and monthly componentwise maxima series are extracted from the original observations of daily maxima PM10 data for two air quality monitoring stations located in Pasir Gudang and Johor Bahru. The 10 years data are considered for both stations from year 2001 to 2010. The asymmetric negative logistic model is found as the best fit bivariate extreme model for both weekly and monthly maxima componentwise series. However the dependence parameters show that the variables for weekly maxima series is more dependence to each other compared to the monthly maxima.

Karyotypic evolution in family Hipposideridae (Chiroptera, Mammalia) revealed by comparative chromosome painting, G- and C-banding.

Science.gov (United States)

Mao, Xiu-Guang; Wang, Jin-Huan; Su, Wei-Ting; Wang, Ying-Xiang; Yang, Feng-Tang; Nie, Wen-Hui

2010-10-01

Comparing to its sister-family (Rhinolophidae), Hipposideridae was less studied by cytogenetic approaches. Only a few high-resolution G-banded karyotypes have been reported so far, and most of the conclusions on the karyotypic evolution in Hipposideridae were based on conventional Giemsa-staining. In this study, we applied comparative chromosome painting, a method of choice for genome-wide comparison at the molecular level, and G- and C-banding to establish comparative map between five hipposiderid species from China, using a whole set of chromosome-specific painting probes from one of them (Aselliscus stoliczkanus). G-band and C-band comparisons between homologous segments defined by chromosome painting revealed that Robertsonian translocations, paracentric inversions and heterochromatin addition could be the main mechanism of chromosome evolution in Hipposideridae. Comparative analysis of the conserved chromosomal segments among five hipposiderid species and outgroup species suggests that bi-armed chromosomes should be included into the ancestral karyotype of Hipposideridae, which was previously believed to be exclusively composed of acrocentric chromosomes.

Karyotypes of Akodon orophilus Osgood 1913 and Thomasomys sp. (Rodentia: Sigmodontinae from Huánuco, Peru

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Víctor Pacheco

2012-10-01

Full Text Available Conventional chromosomal preparations were made of three native mice from Huánuco, Peru: a male and a female of Thomasomys sp., and a male of Akodon orophilus. Thomasomys sp. had a karyotype of 2n = 42, XY (n = 21, meanwhile A. orophilus presented 2n = 22, XY (n = 11. Comparisons between chromosomal pairs from the existent literature indicate that both are new karyotypes. Thomasomys sp. has a distinct sexual Y chromosome, the only metacentric (m reported for the genus. The chromosomes X and Y of A. orophilus are acrocentrics (a; and the length of chromosome Y (2/3 of the length of X distinguishes A. orophilus from other congeneric. Because the structural differences between the sexual chromosomes usually generates mechanism of reproductive isolation at intraspecific level and are bigger still in interspecific crosses, we concluded that the karyotypes reported here support the validity of the species A. orophilus and suggest that Thomasomys sp. represents a new species to science.

Karyotypic characterization of Trachemys dorbigni (Testudines: Emydidae) and Chelonoidis (Geochelone) donosobarrosi (Testudines: Testudinidae), two species of Cryptodiran turtles from Argentina.

Science.gov (United States)

Martinez, Pablo A; Boeris, Juan M; Sánchez, Julieta; Pastori, María C; Bolzán, Alejandro D; Ledesma, Mario A

2009-12-01

We describe for the first time the karyotypes of two species of Cryptodiran turtles from Argentina, namely, Trachemys dorbigni (Emydidae) and Chelonoidis (Geochelone) donosobarrosi (Testudinidae). The karyotype of T. dorbigni (2n = 50) consists of 13 pairs of macrochromosomes and 12 pairs of microchromosomes, whereas the karyotype of C. donosobarrosi (2n = 52) consists of 11 pairs of macrochromosomes and 15 pairs of microchromosomes. Fluorescence in situ hybridization (FISH) with a (TTAGGG)n telomeric probe showed that the chromosomes of these species have four telomeric signals, two at each end, indicating that none of the chromosomes of T. dorbigni and C. donosobarrosi are telocentric. The fact that no interstitial telomeric signals were observed after FISH, suggests that interstitial telomeric sequences did not have a major role in the chromosomal evolution of these species. Additional data will be needed to elucidate if interstitial telomeric sequences have a major role in the karyotypic evolution of Testudines.

Bivariate Rayleigh Distribution and its Properties

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Ahmad Saeed Akhter

2007-01-01

Full Text Available Rayleigh (1880 observed that the sea waves follow no law because of the complexities of the sea, but it has been seen that the probability distributions of wave heights, wave length, wave induce pitch, wave and heave motions of the ships follow the Rayleigh distribution. At present, several different quantities are in use for describing the state of the sea; for example, the mean height of the waves, the root mean square height, the height of the “significant waves” (the mean height of the highest one-third of all the waves the maximum height over a given interval of the time, and so on. At present, the ship building industry knows less than any other construction industry about the service conditions under which it must operate. Only small efforts have been made to establish the stresses and motions and to incorporate the result of such studies in to design. This is due to the complexity of the problem caused by the extensive variability of the sea and the corresponding response of the ships. Although the problem appears feasible, yet it is possible to predict service conditions for ships in an orderly and relatively simple manner Rayleigh (1980 derived it from the amplitude of sound resulting from many independent sources. This distribution is also connected with one or two dimensions and is sometimes referred to as “random walk” frequency distribution. The Rayleigh distribution can be derived from the bivariate normal distribution when the variate are independent and random with equal variances. We try to construct bivariate Rayleigh distribution with marginal Rayleigh distribution function and discuss its fundamental properties.

Karyotype characterization and nucleolar organizer regions of marsupial species (Didelphidae from areas of Cerrado and Atlantic Forest in Brazil

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Núbia P. Pereira

2008-01-01

Full Text Available The karyotypes of 23 specimens belonging to 16 species from nine genera of Brazilian marsupials (family Didelphidae were studied. The animals were collected in eight localities of Cerrado or Atlantic Forest biomes in the states of Goiás, Tocantins and São Paulo. The karyotypes were analyzed after conventional Giemsa staining and silver staining of the nucleolus organizer regions (Ag-NORs. New karyotypic data were obtained for Gracilinanus microtarsus (2n = 14, FN = 24, Marmosops paulensis (2n = 14, FN = 24 , Micoreus paraguayanus (2n = 14, FN = 20 and Monodelphis rubida (2n = 18, FN = 32 and are discussed in detail. The karyotypes of G. microtarsus , M. paulensis and M. paraguayanus include three large pairs of submetacentrics (pairs 1, 2 and 3 and a medium-sized metacentric or submetacentric pair 4. Pairs 5 and 6 are small submetacentrics in G. microtarsus and M. paulensis and acrocentrics in M. paraguayanus . M. paulensis presented a single Ag-NOR in pair 6 (6p6p, while M. paraguayanus exhibited multiple Ag-NORs in pairs 5 and 6 (5pq5pq6p6p. There was variation in size and morphology of the sex chromosomes among these species. Monodelphis rubida presented a karyotype with 2n = 18 and FN = 32 composed of a large submetacentric pair 1, a medium-sized metacentric pair 2 and six pairs of submetacentrics (pairs 3 through 8. The X was a small acrocentric and the Y was dot-like. A single Ag-NOR bearing pair (5p5p characterized M. rubida. Relevant karyotypic information was obtained for 19 specimens belonging to 12 species collected in areas sampled for the first time [ Caluromys lanatus and C. philander (2n = 14, FN = 20, Gracilinanus emiliae (2n = 14, FN = 24, Marmosa murina , Metachirus nudicaudatus and Micoureus demerarae (2n = 14, FN = 20, Monodelphis americana (2n = 18, FN = 32 and M. domestica (2n = 18, FN = 20, and Didelphis marsupialis, Philander frenata, P. opossum and P. sp (2n = 22, FN = 20]. Although the karyotypes were relatively

Meta-analysis of studies with bivariate binary outcomes: a marginal beta-binomial model approach.

Science.gov (United States)

Chen, Yong; Hong, Chuan; Ning, Yang; Su, Xiao

2016-01-15

When conducting a meta-analysis of studies with bivariate binary outcomes, challenges arise when the within-study correlation and between-study heterogeneity should be taken into account. In this paper, we propose a marginal beta-binomial model for the meta-analysis of studies with binary outcomes. This model is based on the composite likelihood approach and has several attractive features compared with the existing models such as bivariate generalized linear mixed model (Chu and Cole, 2006) and Sarmanov beta-binomial model (Chen et al., 2012). The advantages of the proposed marginal model include modeling the probabilities in the original scale, not requiring any transformation of probabilities or any link function, having closed-form expression of likelihood function, and no constraints on the correlation parameter. More importantly, because the marginal beta-binomial model is only based on the marginal distributions, it does not suffer from potential misspecification of the joint distribution of bivariate study-specific probabilities. Such misspecification is difficult to detect and can lead to biased inference using currents methods. We compare the performance of the marginal beta-binomial model with the bivariate generalized linear mixed model and the Sarmanov beta-binomial model by simulation studies. Interestingly, the results show that the marginal beta-binomial model performs better than the Sarmanov beta-binomial model, whether or not the true model is Sarmanov beta-binomial, and the marginal beta-binomial model is more robust than the bivariate generalized linear mixed model under model misspecifications. Two meta-analyses of diagnostic accuracy studies and a meta-analysis of case-control studies are conducted for illustration. Copyright © 2015 John Wiley & Sons, Ltd.

Analysis of Blood Transfusion Data Using Bivariate Zero-Inflated Poisson Model: A Bayesian Approach.

Science.gov (United States)

Mohammadi, Tayeb; Kheiri, Soleiman; Sedehi, Morteza

2016-01-01

Recognizing the factors affecting the number of blood donation and blood deferral has a major impact on blood transfusion. There is a positive correlation between the variables "number of blood donation" and "number of blood deferral": as the number of return for donation increases, so does the number of blood deferral. On the other hand, due to the fact that many donors never return to donate, there is an extra zero frequency for both of the above-mentioned variables. In this study, in order to apply the correlation and to explain the frequency of the excessive zero, the bivariate zero-inflated Poisson regression model was used for joint modeling of the number of blood donation and number of blood deferral. The data was analyzed using the Bayesian approach applying noninformative priors at the presence and absence of covariates. Estimating the parameters of the model, that is, correlation, zero-inflation parameter, and regression coefficients, was done through MCMC simulation. Eventually double-Poisson model, bivariate Poisson model, and bivariate zero-inflated Poisson model were fitted on the data and were compared using the deviance information criteria (DIC). The results showed that the bivariate zero-inflated Poisson regression model fitted the data better than the other models.

Parameter estimation and statistical test of geographically weighted bivariate Poisson inverse Gaussian regression models

Science.gov (United States)

Amalia, Junita; Purhadi, Otok, Bambang Widjanarko

2017-11-01

Poisson distribution is a discrete distribution with count data as the random variables and it has one parameter defines both mean and variance. Poisson regression assumes mean and variance should be same (equidispersion). Nonetheless, some case of the count data unsatisfied this assumption because variance exceeds mean (over-dispersion). The ignorance of over-dispersion causes underestimates in standard error. Furthermore, it causes incorrect decision in the statistical test. Previously, paired count data has a correlation and it has bivariate Poisson distribution. If there is over-dispersion, modeling paired count data is not sufficient with simple bivariate Poisson regression. Bivariate Poisson Inverse Gaussian Regression (BPIGR) model is mix Poisson regression for modeling paired count data within over-dispersion. BPIGR model produces a global model for all locations. In another hand, each location has different geographic conditions, social, cultural and economic so that Geographically Weighted Regression (GWR) is needed. The weighting function of each location in GWR generates a different local model. Geographically Weighted Bivariate Poisson Inverse Gaussian Regression (GWBPIGR) model is used to solve over-dispersion and to generate local models. Parameter estimation of GWBPIGR model obtained by Maximum Likelihood Estimation (MLE) method. Meanwhile, hypothesis testing of GWBPIGR model acquired by Maximum Likelihood Ratio Test (MLRT) method.

A case of premature ovarian failure (POF) in a 31-year-old woman with a 47,XXX karyotype.

Science.gov (United States)

Skałba, Piotr; Cygal, Anna; Gierzyńska, Zuzanna

2010-01-01

A case of POF in a 31-year-old woman with karyotype 47,XXX. The aim of the study was to discuss a case of POF in a 31-year-old patient with polysomy 47,XXX. The described karyotype is not usually associated with this characteristic physical phenotype. In some rare cases, menstrual disorders, sterility, secondary amenorrhoea, premature menopause, and low intelligence are found. Our observations revealed the necessity for cytogenetic examination in all women at reproductive age with symptoms of premature ovarian failure. According to the data found in literature, patients with POF and karyotype disorders belong to the risk group of premature death, mostly for cardiological reasons. Raising patient awareness about the risk may have a positive effect on quality of life and regularity of check-ups.

Univariate and Bivariate Empirical Mode Decomposition for Postural Stability Analysis

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Jacques Duchêne

2008-05-01

Full Text Available The aim of this paper was to compare empirical mode decomposition (EMD and two new extended methods of  EMD named complex empirical mode decomposition (complex-EMD and bivariate empirical mode decomposition (bivariate-EMD. All methods were used to analyze stabilogram center of pressure (COP time series. The two new methods are suitable to be applied to complex time series to extract complex intrinsic mode functions (IMFs before the Hilbert transform is subsequently applied on the IMFs. The trace of the analytic IMF in the complex plane has a circular form, with each IMF having its own rotation frequency. The area of the circle and the average rotation frequency of IMFs represent efficient indicators of the postural stability status of subjects. Experimental results show the effectiveness of these indicators to identify differences in standing posture between groups.

Genetics of Obesity Traits: A Bivariate Genome-Wide Association Analysis

DEFF Research Database (Denmark)

Wu, Yili; Duan, Haiping; Tian, Xiaocao

2018-01-01

Previous genome-wide association studies on anthropometric measurements have identified more than 100 related loci, but only a small portion of heritability in obesity was explained. Here we present a bivariate twin study to look for the genetic variants associated with body mass index and waist......-hip ratio, and to explore the obesity-related pathways in Northern Han Chinese. Cholesky decompositionmodel for 242monozygotic and 140 dizygotic twin pairs indicated a moderate genetic correlation (r = 0.53, 95%CI: 0.42–0.64) between body mass index and waist-hip ratio. Bivariate genome-wide association.......05. Expression quantitative trait loci analysis identified rs2242044 as a significant cis-eQTL in both the normal adipose-subcutaneous (P = 1.7 × 10−9) and adipose-visceral (P = 4.4 × 10−15) tissue. These findings may provide an important entry point to unravel genetic pleiotropy in obesity traits....

Second-trimester IL-15 and IL-18 levels in the amniotic fluid of fetuses with normal karyotypes and with chromosome abnormalities.

Science.gov (United States)

Klimkiewicz-Blok, Dominika; Florjański, Jerzy; Zalewski, Jerzy; Blok, Radosław

2012-01-01

Little is known about the behavior of interleukin 15 (IL-15) and 18 (IL-18) in the amniotic fluid in the second trimester of gestations complicated by chromosomal defects in the fetus. Likewise, it has not yet been established whether a fetus with chromosome abnormalities creates its immunity mechanisms in the same way as a fetus with a normal karyotype. The aim of this work was to assess the concentration of IL-15 and IL-18 in the amniotic fluid in the second trimester of gestation in fetuses with normal karyotypes and with chromosome abnormalities. The material consisted of 51 samples of amniotic fluid obtained from genetic amniocenteses carried out between the 15th and the 19th weeks of gestation. On the basis of cytogenetic screening, two groups were singled out: Group I--45 fetuses with normal karyotypes, and Group II--6 fetuses with abnormal karyotypes. The concentrations of IL-15 and IL-18 in the amniotic fluid were assessed with ready-made assays and analyzed, and the results from both groups were compared. The differences between the IL-15 levels in the amniotic fluid from Groups I and II proved to be statistically insignificant (p = 0.054). However, the average IL-18 levels in the amniotic fluid of the fetuses with normal karyotypes were significantly higher than in the amniotic fluid of the fetuses with chromosome abnormalities (p = 0.032). Some defense mechanisms in the second trimester of gestation in fetuses with chromosome abnormalities may develop in a different way than in fetuses with normal karyotypes.

Karyotype with 210 chromosomes in guaraná (Paullinia cupana 'Sorbilis').

Science.gov (United States)

de Freitas, Danival Vieira; Carvalho, Carlos Roberto; Filho, Firmino José do Nascimento; Astolfi-Filho, Spartaco

2007-05-01

The genus Paullinia includes the economically important P. cupana, known as guaraná in Brazil and more recently in the world market. Native Americans of the Maué and Andirá tribes cultivated P. cupana 'Sorbilis' in central Amazon, and the Barés cultivated the 'Typica' variety in the upper Negro River (Brazil). Cytological studies in the Sapindaceae family have concentrated on the diversity in number (from 2n = 14 to 96) and size of the chromosomes. In Paullinia, seven species have been karyotyped and all show 2n = 24. Meristem maceration, cellular dissociation and air-drying techniques were used for cytogenetic preparations and DNA content was determined by flow cytometry. Chromosome characterization and DNA content of Paullinia cupana Kunth 'Sorbilis' (Mart.) Ducke (Sapindaceae) were studied. The high chromosome number (2n = 210) fall into two cytomorphological groups: (a) a metacentric and submetacentric group showing 25 sets of three pairs of chromosomes (2-76); (b) a group containing only acrocentric showing 12 sets of two pairs of chromosomes (82-105), a homologous submetacentric pair (1) and an acrocentric pair (81). Mean nuclear DNA content of guaraná was 2C = 22.8 pg. A karyogram was set up showing a high chromosome number complement.

COMPARISON OF IMAGE ENHANCEMENT METHODS FOR CHROMOSOME KARYOTYPE IMAGE ENHANCEMENT

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Dewa Made Sri Arsa

2017-02-01

Full Text Available The chromosome is a set of DNA structure that carry information about our life. The information can be obtained through Karyotyping. The process requires a clear image so the chromosome can be evaluate well. Preprocessing have to be done on chromosome images that is image enhancement. The process starts with image background removing. The image will be cleaned background color. The next step is image enhancement. This paper compares several methods for image enhancement. We evaluate some method in image enhancement like Histogram Equalization (HE, Contrast-limiting Adaptive Histogram Equalization (CLAHE, Histogram Equalization with 3D Block Matching (HE+BM3D, and basic image enhancement, unsharp masking. We examine and discuss the best method for enhancing chromosome image. Therefore, to evaluate the methods, the original image was manipulated by the addition of some noise and blur. Peak Signal-to-noise Ratio (PSNR and Structural Similarity Index (SSIM are used to examine method performance. The output of enhancement method will be compared with result of Professional software for karyotyping analysis named Ikaros MetasystemT M . Based on experimental results, HE+BM3D method gets a stable result on both scenario noised and blur image.

Morphological and karyotypic contributions for a better taxonomic definition of the frog ischnocnema ramagii (Boulenger, 1888) (anura, brachycephalidae)

OpenAIRE

Napoli, Marcelo Felgueiras; Ananias, Fernando; Fonseca, Patricia M.; Silva, Ana Paula Z.

2009-01-01

Acesso restrito. Texto completo disponível no PORTAL de PERIÓDICOS da CAPES. p. 164-172. In this study we describe the morphological variation of Ischnocnema ramagii from a population sample within the Municipality of Salvador, Bahia State, Brazil, and characterize two extremely distinct morphotypes within this taxon (striped vs. non-striped dorsum); we describe its karyotype, and compare the karyotypic structure of the distinct morphotypes recognized herein. Specimens with str...

Applied Statistics: From Bivariate through Multivariate Techniques [with CD-ROM

Science.gov (United States)

Warner, Rebecca M.

2007-01-01

This book provides a clear introduction to widely used topics in bivariate and multivariate statistics, including multiple regression, discriminant analysis, MANOVA, factor analysis, and binary logistic regression. The approach is applied and does not require formal mathematics; equations are accompanied by verbal explanations. Students are asked…

Repetitive DNA: A Versatile Tool for Karyotyping in Festuca pratensis Huds

Czech Academy of Sciences Publication Activity Database

Křivánková, Anna; Kopecký, David; Stočes, Štěpán; Doležel, Jaroslav; Hřibová, Eva

2017-01-01

Roč. 151, č. 2 (2017), s. 96-105 ISSN 1424-8581 R&D Projects: GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : Fluorescence in situ hybridization * Karyotyping * Meadow fescue * Repetitive DNA * Tandem organized repeats Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany Impact factor: 1.354, year: 2016

Comparison of the Giemsa C-banded and N-banded karyotypes of two Elymus species, E. dentatus and E. glaucescens (Poaceae; Triticeae)

DEFF Research Database (Denmark)

Linde-Laursen, I.; Seberg, O.; Salomon, B.

1994-01-01

The karyotypes of Elymus dentatus from Kashmir and E. glaucescens from Tierra del Fuego, both carrying genomes S and H, were investigated by C- and N-banding. Both taxa had 2n = 4x = 28. The karyotype of E. dentatus was symmetrical with large chromosomes. It had 18 metacentric, four submetacentric...

Gender role behavior in children with XY karyotype and disorders of sex development.

Science.gov (United States)

Jürgensen, Martina; Hiort, Olaf; Holterhus, Paul-Martin; Thyen, Ute

2007-03-01

Children exhibit gender-typical preferences in play, toys, activities and interests, and playmates. Several studies suggest that high concentrations of pre- and postnatal androgens contribute to male-typical behavior development, whereas female-typical behavior develops in the absence of high androgens levels. This study aims to explore the consequences of hypoandrogenization on gender-typical behavior in children who have an XY karyotype and disorder of sex development (DSD). Participants included 33 children (ages 2-12 years) with an XY karyotype and DSD; 21 reared as girls and 12 reared as boys. Children's preferred activities and interests and playmate preferences were assessed with parent report questionnaires, a structured free-play task, and choice of a toy to keep as a gift. Participant's responses were compared to those of children recruited in a pre-school and elementary school survey (N=166). In this study, the degree of hypoandrogenization as indicated by genital stage and diagnosis showed a significant relationship to nearly all of the gender-related behaviors assessed, supporting the hypothesis that masculinization of gender role behavior is a function of prenatal androgen exposure. Despite the fact that children with partial androgen effects reared as girls showed increased "boyish" behaviors, they did not show increased signs of gender identity confusion or instability on a group level. We conclude that androgen exposure plays a decisive role in the development of gender-typical behavior in children with XY karyotype and DSD conditions.

Synchrony of oculocutaneous albinism, the Prader-Willi syndrome, and a normal karyotype.

Science.gov (United States)

Wallis, C E; Beighton, P H

1989-01-01

A Chinese girl with oculocutaneous albinism has the Prader-Willi syndrome and a normal karyotype. This association emphasises the importance of further molecular study of the 15(q12) region of the genome in the search for the locus of an albinism gene. Images PMID:2732995

Electroclinical findings in four patients with karyotype 47,XYY.

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Torniero, Claudia; Bernardina, Bernardo Dalla; Fontana, Elena; Darra, Francesca; Danesino, Cesare; Elia, Maurizio

2011-05-01

47,XYY karyotype is a Y chromosome aneuploidy characterized by an extra copy of the Y chromosome in each of the male cells, with an incidence of 1/1000 males. Most studies about 47,XYY have focused on growth, cognitive development, academic performance, behavioural problems, speech and language skills and neuromuscular status. Up-to-date reports on seizures and EEG characteristics concerning 47,XYY men have been sporadic and poorly detailed. The aim of this study is to describe the particular electroclinical patterns in a group of four subjects with 47,XYY karyotype. We performed neurological examinations, psychometric tests, brain MRIs, prolonged EEG recordings during awake and sleep on four unselected males 47,XYY. All four patients presented various degrees of neuropsychological impairment. An incidence of familial antecedents for epilepsy was confirmed by three families. When present, seizures were very similar to that of benign epilepsy with central-temporal spikes, (BECTS), for age of onset, clinical picture, evolution and good response to antiepileptic drugs. EEG recordings in all four subjects showed normal background activity and sleep organization, particular focal spikes and sharp-waves localized mostly over the vertex and/or central-temporal regions, which increased during sleep. In our opinion, these 47,XYY patients present a particular electroclinical pattern. Copyright © 2010 The Japanese Society of Child Neurology. Published by Elsevier B.V. All rights reserved.

Fluorescence In Situ Hybridization (FISH-Based Karyotyping Reveals Rapid Evolution of Centromeric and Subtelomeric Repeats in Common Bean (Phaseolus vulgaris and Relatives

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Aiko Iwata-Otsubo

2016-04-01

Full Text Available Fluorescence in situ hybridization (FISH-based karyotyping is a powerful cytogenetics tool to study chromosome organization, behavior, and chromosome evolution. Here, we developed a FISH-based karyotyping system using a probe mixture comprised of centromeric and subtelomeric satellite repeats, 5S rDNA, and chromosome-specific BAC clones in common bean, which enables one to unambiguously distinguish all 11 chromosome pairs. Furthermore, we applied the karyotyping system to several wild relatives and landraces of common bean from two distinct gene pools, as well as other related Phaseolus species, to investigate repeat evolution in the genus Phaseolus. Comparison of karyotype maps within common bean indicates that chromosomal distribution of the centromeric and subtelomeric satellite repeats is stable, whereas the copy number of the repeats was variable, indicating rapid amplification/reduction of the repeats in specific genomic regions. In Phaseolus species that diverged approximately 2–4 million yr ago, copy numbers of centromeric repeats were largely reduced or diverged, and chromosomal distributions have changed, suggesting rapid evolution of centromeric repeats. We also detected variation in the distribution pattern of subtelomeric repeats in Phaseolus species. The FISH-based karyotyping system revealed that satellite repeats are actively and rapidly evolving, forming genomic features unique to individual common bean accessions and Phaseolus species.

Karyotype characterization and ZZ/ZW sex chromosome heteromorphism in two species of the catfish genus Ancistrus Kner, 1854 (Siluriformes: Loricariidae from the Amazon basin

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Renildo R. de Oliveira

Full Text Available We present karyotypic characteristics and report on the occurrence of ZZ/ZW sex chromosomes in Ancistrus ranunculus (rio Xingu and Ancistrus sp. "Piagaçu" (rio Purus, of the Brazilian Amazon. Ancistrus ranunculus has a modal number of 2n=48 chromosomes, a fundamental number (FN of 82 for both sexes, and the karyotypic formula was 20m+8sm+6st+14a for males and 19m+9sm+6st+14a for females. Ancistrus sp. "Piagaçu" presented 2n=52 chromosomes, FN= 78 for males and FN= 79 for females. The karyotypic formula was 16m+8sm+2st+26a for males and 16m+9sm+2st+25a for females. The high number of acrocentric chromosomes in karyotype of Ancistrus sp. "Piagaçu" differs from the majority of Ancistrini genera studied so far, and may have resulted from pericentric inversions and translocations. The lower number of chromosomes in A. ranunculus indicates that centric fusions also occurred in the evolution of Ancistrus karyotypes. We conclude that karyotypic characteristics and the presence of sex chromosomes can constitute important cytotaxonomic markers to identify cryptic species of Ancistrus. However, sex chromosomes apparently arose independently within the genus and thus do not constitute a reliable character to analyze phylogenetic relations among Ancistrus species.

On the matched pairs sign test using bivariate ranked set sampling ...

African Journals Online (AJOL)

BVRSS) is introduced and investigated. We show that this test is asymptotically more efficient than its counterpart sign test based on a bivariate simple random sample (BVSRS). The asymptotic null distribution and the efficiency of the test are derived.

Karyotypes, heterochromatin, and physical mapping of 18S-26S rDNA in Cactaceae.

Science.gov (United States)

Las Peñas, M L; Urdampilleta, J D; Bernardello, G; Forni-Martins, E R

2009-01-01

Karyotype analyses in members of the four Cactaceae subfamilies were performed. Numbers and karyotype formula obtained were: Pereskioideae = Pereskiaaculeata(2n = 22; 10 m + 1 sm), Maihuenioideae = Maihuenia patagonica (2n = 22, 9 m + 2 sm; 2n = 44, 18 m + 4 sm), Opuntioideae = Cumulopuntia recurvata(2n = 44; 20 m + 2 sm), Cactoideae = Acanthocalycium spiniflorum (2n = 22; 10 m + 1 sm),Echinopsis tubiflora (2n = 22; 10 m + 1 sm), Trichocereus candicans (2n = 22, 22 m). Chromosomes were small, the average chromosome length was 2.3 mum. Diploid species and the tetraploid C. recurvata had one terminal satellite, whereas the remaining tetraploid species showed four satellited chromosomes. Karyotypes were symmetrical. No CMA(-)/DAPI(+) bands were detected, but CMA(+)/DAPI(-) bands associated with NOR were always found. Pericentromeric heterochromatin was found in C. recurvata, A. spiniflorum, and the tetraploid cytotype of M. patagonica. The locations of the 18S-26S rDNA sites in all species coincided with CMA(+)/DAPI(-) bands; the same occurred with the sizes and numbers of signals for each species. This technique was applied for the first time in metaphase chromosomes in cacti. NOR-bearing pair no.1 may be homeologous in all species examined. In Cactaceae, the 18S-26S loci seem to be highly conserved. Copyright 2009 S. Karger AG, Basel.

The karyotype and 5S rRNA genes from Spanish individuals of the bat species Rhinolophus hipposideros (Rhinolophidae; Chiroptera).

Science.gov (United States)

Puerma, Eva; Acosta, Manuel J; Barragán, Maria José L; Martínez, Sergio; Marchal, Juan Alberto; Bullejos, Mónica; Sánchez, Antonio

2008-11-01

The karyotype of individuals of the species Rhinolophus hipposideros from Spain present a chromosome number of 2n = 54 (NFa = 62). The described karyotype for these specimens is very similar to another previously described in individual from Bulgaria. However, the presence of one additional pair of autosomal acrocentric chromosomes in the Bulgarian karyotype and the differences in X chromosome morphology indicated that we have described a new karyotype variant in this species. In addition, we have analyzed several clones of 1.4 and 1 kb of a PstI repeated DNA sequence from the genome of R. hipposideros. The repeated sequence included a region with high identity with the 5S rDNA genes and flanking regions, with no homology with GenBank sequences. Search for polymerase III regulatory elements demonstrated the presence of type I promoter elements (A-box, Intermediate Element and C-box) in the 5S rDNA region. In addition, upstream regulatory elements, as a D-box and Sp1 binding sequences, were present in flanking regions. All data indicated that the cloned repeated sequences are the functional rDNA genes from this species. Finally, FISH demonstrated the presence of rDNA in nine chromosome pairs, which is surprising as most mammals have only one carrier chromosome pair.

Chromosome radiosensitivity and kinetics of proliferation of peripheral lymphocytes in individuals with aneuploid karyotype

Energy Technology Data Exchange (ETDEWEB)

Konecna, H; Kalina, I; Ondrussekova, A

1988-08-01

Experimentally investigated was the radiosensitivity of chromosomes and the kinetics of the proliferation of peripheral lymphocytes in patients with aneuploid (DS and TS) and normal karyotype irradiated in vitro in the G/sub o/ stage of the cell cycle. Trisomic lymphocytes were found to proliferate more rapidly in the in vitro culture and to be more sensitive than diploid cell populations. In monosomic lymphocytes in Turner syndrome patients, the proliferation and incidence of chromosomal abberations was similar to the disomic lines in Down's syndrome patients and in Turner syndrome patients, and to that found in persons with a normal karyotype. The results of the experiment show that there is a relationship between the proliferation rate of peripheral lymphocytes cultures in vitro and the radiosensivity of chromosomes. (author). 1 tab., 3 figs., 11 refs.

Chromosome radiosensitivity and kinetics of proliferation of peripheral lymphocytes in individuals with aneuploid karyotype

International Nuclear Information System (INIS)

Konecna, H.; Kalina, I.; Ondrussekova, A.

1988-01-01

Experimentally investigated was the radiosensitivity of chromosomes and the kinetics of the proliferation of peripheral lymphocytes in patients with aneuploid (DS and TS) and normal karyotype irradiated in vitro in the G o stage of the cell cycle. Trisomic lymphocytes were found to proliferate more rapidly in the in vitro culture and to be more sensitive than diploid cell populations. In monosomic lymphocytes in Turner syndrome patients, the proliferation and incidence of chromosomal abberations was similar to the disomic lines in Down's syndrome patients and in Turner syndrome patients, and to that found in persons with a normal karyotype. The results of the experiment show that there is a relationship between the proliferation rate of peripheral lymphocytes cultures in vitro and the radiosensivity of chromosomes. (author). 1 tab., 3 figs., 11 refs

Smoothing of the bivariate LOD score for non-normal quantitative traits.

Science.gov (United States)

Buil, Alfonso; Dyer, Thomas D; Almasy, Laura; Blangero, John

2005-12-30

Variance component analysis provides an efficient method for performing linkage analysis for quantitative traits. However, type I error of variance components-based likelihood ratio testing may be affected when phenotypic data are non-normally distributed (especially with high values of kurtosis). This results in inflated LOD scores when the normality assumption does not hold. Even though different solutions have been proposed to deal with this problem with univariate phenotypes, little work has been done in the multivariate case. We present an empirical approach to adjust the inflated LOD scores obtained from a bivariate phenotype that violates the assumption of normality. Using the Collaborative Study on the Genetics of Alcoholism data available for the Genetic Analysis Workshop 14, we show how bivariate linkage analysis with leptokurtotic traits gives an inflated type I error. We perform a novel correction that achieves acceptable levels of type I error.

Karyotypes versus Genomes: The Nymphalid Butterflies Melitaea cinxia, Danaus plexippus, and D. chrysippus.

Science.gov (United States)

Traut, Walther; Ahola, Virpi; Smith, David A S; Gordon, Ian J; Ffrench-Constant, Richard H

2017-01-01

The number of sequenced lepidopteran genomes is increasing rapidly. However, the corresponding assemblies rarely represent whole chromosomes and generally also lack the highly repetitive W sex chromosome. Knowledge of the karyotypes can facilitate genome assembly and further our understanding of sex chromosome evolution in Lepidoptera. Here, we describe the karyotypes of the Glanville fritillary Melitaea cinxia (n = 31), the monarch Danaus plexippus (n = 30), and the African queen D. chrysippus (2n = 60 or 59, depending on the source population). We show by FISH that the telomeres are of the (TTAGG)n type, as found in most insects. M. cinxia and D. plexippus have "conventional" W chromosomes which are heterochromatic in meiotic and somatic cells. In D. chrysippus, the W is inconspicuous. Neither telomeres nor W chromosomes are represented in the published genomes of M. cinxia and D. plexippus. Representation analysis in sequenced female and male D. chrysippus genomes detected an evolutionarily old autosome-Z chromosome fusion in Danaus. Conserved synteny of whole chromosomes, so called "macro synteny", in Lepidoptera permitted us to identify the chromosomes involved in this fusion. An additional and more recent sex chromosome fusion was found in D. chrysippus by karyotype analysis and classical genetics. In a hybrid population between 2 subspecies, D. c. chrysippus and D. c. dorippus, the W chromosome was fused to an autosome that carries a wing colour locus. Thus, cytogenetics and the present state of genome data complement one another to reveal the evolutionary history of the species. © 2017 S. Karger AG, Basel.

Molecular and cytogenetic analyses of cryptic species within the Synbranchus marmoratus Bloch, 1795 (Synbranchiformes: Synbranchidae grouping: species delimitations, karyotypic evolution and intraspecific diversification

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Ricardo Utsunomia

Full Text Available The fish species Synbranchus marmoratushas been reported to exist as a species complex due to high intraspecific karyotypic variability in spite of the difficulty or impossibility to distinguish them using morphological traits alone. The goal of this work was to use cytogenetic and molecular methods to determine the species delimitations and understand the karyoevolution ofS. marmoratususing samples collected from distinct Brazilian localities. Among the analyzed specimens, a large degree of cytogenetic variation related to diploid numbers and karyotype structure was observed, with karyotypes showing 2n=42, 44 and 46 chromosomes. In addition, using sequences of three mitochondrial genes, the phylogenetic relationships between every sample with a known karyotype were determined, which revealed significant nucleotide divergence among the karyomorphs. Also, the analyses indicate that chromosomal rearrangements occurred independently within the distinct lineages of S. marmoratuscomplex, which resulted in the appearance of distinct karyotypic variants in a non-linear fashion related to diploid numbers and in the appearance of similar non-homologous chromosomes. Finally, the integration of both molecular cytogenetic and phylogenetic approaches allowed the determination of specific chromosomes possibly involved in rearrangements and a better understanding about the evolutionary processes involved in the differentiation ofSynbranchusgenus.

The Ancestral Carnivore Karyotype As Substantiated by Comparative Chromosome Painting of Three Pinnipeds, the Walrus, the Steller Sea Lion and the Baikal Seal (Pinnipedia, Carnivora.

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Violetta R Beklemisheva

Full Text Available Karyotype evolution in Carnivora is thoroughly studied by classical and molecular cytogenetics and supplemented by reconstructions of Ancestral Carnivora Karyotype (ACK. However chromosome painting information from two pinniped families (Odobenidae and Otariidae is noticeably missing. We report on the construction of the comparative chromosome map for species from each of the three pinniped families: the walrus (Odobenus rosmarus, Odobenidae-monotypic family, near threatened Steller sea lion (Eumetopias jubatus, Otariidae and the endemic Baikal seal (Pusa sibirica, Phocidae using combination of human, domestic dog and stone marten whole-chromosome painting probes. The earliest karyological studies of Pinnipedia showed that pinnipeds were characterized by a pronounced karyological conservatism that is confirmed here with species from Phocidae, Otariidae and Odobenidae sharing same low number of conserved human autosomal segments (32. Chromosome painting in Pinnipedia and comparison with non-pinniped carnivore karyotypes provide strong support for refined structure of ACK with 2n = 38. Constructed comparative chromosome maps show that pinniped karyotype evolution was characterized by few tandem fusions, seemingly absent inversions and slow rate of genome rearrangements (less then one rearrangement per 10 million years. Integrative comparative analyses with published chromosome painting of Phoca vitulina revealed common cytogenetic signature for Phoca/Pusa branch and supports Phocidae and Otaroidea (Otariidae/Odobenidae as sister groups. We revealed rearrangements specific for walrus karyotype and found the chromosomal signature linking together families Otariidae and Odobenidae. The Steller sea lion karyotype is the most conserved among three studied species and differs from the ACK by single fusion. The study underlined the strikingly slow karyotype evolution of the Pinnipedia in general and the Otariidae in particular.

Testing independence of bivariate interval-censored data using modified Kendall's tau statistic.

Science.gov (United States)

Kim, Yuneung; Lim, Johan; Park, DoHwan

2015-11-01

In this paper, we study a nonparametric procedure to test independence of bivariate interval censored data; for both current status data (case 1 interval-censored data) and case 2 interval-censored data. To do it, we propose a score-based modification of the Kendall's tau statistic for bivariate interval-censored data. Our modification defines the Kendall's tau statistic with expected numbers of concordant and disconcordant pairs of data. The performance of the modified approach is illustrated by simulation studies and application to the AIDS study. We compare our method to alternative approaches such as the two-stage estimation method by Sun et al. (Scandinavian Journal of Statistics, 2006) and the multiple imputation method by Betensky and Finkelstein (Statistics in Medicine, 1999b). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Bivariate return period for levee failure monitoring

Science.gov (United States)

Isola, M.; Caporali, E.

2017-12-01

Levee breaches are strongly linked with the interaction processes among water, soil and structure, thus many are the factors that affect the breach development. One of the main is the hydraulic load, characterized by intensity and duration, i.e. by the flood event hydrograph. On the magnitude of the hydraulic load is based the levee design, generally without considering the fatigue failure due to the load duration. Moreover, many are the cases in which the levee breach are characterized by flood of magnitude lower than the design one. In order to implement the strategies of flood risk management, we built here a procedure based on a multivariate statistical analysis of flood peak and volume together with the analysis of the past levee failure events. Particularly, in order to define the probability of occurrence of the hydraulic load on a levee, a bivariate copula model is used to obtain the bivariate joint distribution of flood peak and volume. Flood peak is the expression of the load magnitude, while the volume is the expression of the stress over time. We consider the annual flood peak and the relative volume. The volume is given by the hydrograph area between the beginning and the end of event. The beginning of the event is identified as an abrupt rise of the discharge by more than 20%. The end is identified as the point from which the receding limb is characterized by the baseflow, using a nonlinear reservoir algorithm as baseflow separation technique. By this, with the aim to define warning thresholds we consider the past levee failure events and the relative bivariate return period (BTr) compared with the estimation of a traditional univariate model. The discharge data of 30 hydrometric stations of Arno River in Tuscany, Italy, in the period 1995-2016 are analysed. The database of levee failure events, considering for each event the location as well as the failure mode, is also created. The events were registered in the period 2000-2014 by EEA

Analysis of the karyotype of Callisia elegans Alexand. (Commelinaceae including differential staining of chromosomes

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Elżbieta Weryszko-Chmielewska

2014-01-01

Full Text Available The number and morphology of Callisia elegans Alexand. chromosomes were studied employing staining with acetic carmine and differential Giemsa staining. It was found that its karyotype was 2n = 12 chromosomes, whose lengths fell in the range of 16.8 to 8.8 µm. The chomosomes, arranged in order of length, were classified respectively to types: sm, t, t, t, t, st. The distribution of C-banding is given for this karyotype. The presence of microsatellites on the long and short arms was found in the chromosomes of the second pair. Frequently there were 4 nucleoli of unequal size in interphase nuclei. In many cells, lower numbers of nucleoli (3-1 were seen which was -probably due to their fusion. The maximum number of nucleoli corresponded to the number of nucleolar organizers accompanying the satellites.

Robust bivariate error detection in skewed data with application to historical radiosonde winds

KAUST Repository

Sun, Ying

2017-01-18

The global historical radiosonde archives date back to the 1920s and contain the only directly observed measurements of temperature, wind, and moisture in the upper atmosphere, but they contain many random errors. Most of the focus on cleaning these large datasets has been on temperatures, but winds are important inputs to climate models and in studies of wind climatology. The bivariate distribution of the wind vector does not have elliptical contours but is skewed and heavy-tailed, so we develop two methods for outlier detection based on the bivariate skew-t (BST) distribution, using either distance-based or contour-based approaches to flag observations as potential outliers. We develop a framework to robustly estimate the parameters of the BST and then show how the tuning parameter to get these estimates is chosen. In simulation, we compare our methods with one based on a bivariate normal distribution and a nonparametric approach based on the bagplot. We then apply all four methods to the winds observed for over 35,000 radiosonde launches at a single station and demonstrate differences in the number of observations flagged across eight pressure levels and through time. In this pilot study, the method based on the BST contours performs very well.

Robust bivariate error detection in skewed data with application to historical radiosonde winds

KAUST Repository

Sun, Ying; Hering, Amanda S.; Browning, Joshua M.

2017-01-01

The global historical radiosonde archives date back to the 1920s and contain the only directly observed measurements of temperature, wind, and moisture in the upper atmosphere, but they contain many random errors. Most of the focus on cleaning these large datasets has been on temperatures, but winds are important inputs to climate models and in studies of wind climatology. The bivariate distribution of the wind vector does not have elliptical contours but is skewed and heavy-tailed, so we develop two methods for outlier detection based on the bivariate skew-t (BST) distribution, using either distance-based or contour-based approaches to flag observations as potential outliers. We develop a framework to robustly estimate the parameters of the BST and then show how the tuning parameter to get these estimates is chosen. In simulation, we compare our methods with one based on a bivariate normal distribution and a nonparametric approach based on the bagplot. We then apply all four methods to the winds observed for over 35,000 radiosonde launches at a single station and demonstrate differences in the number of observations flagged across eight pressure levels and through time. In this pilot study, the method based on the BST contours performs very well.

Chain Plot: A Tool for Exploiting Bivariate Temporal Structures

OpenAIRE

Taylor, CC; Zempeni, A

2004-01-01

In this paper we present a graphical tool useful for visualizing the cyclic behaviour of bivariate time series. We investigate its properties and link it to the asymmetry of the two variables concerned. We also suggest adding approximate confidence bounds to the points on the plot and investigate the effect of lagging to the chain plot. We conclude our paper by some standard Fourier analysis, relating and comparing this to the chain plot.

Bivariate tensor product ( p , q $(p, q$ -analogue of Kantorovich-type Bernstein-Stancu-Schurer operators

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Qing-Bo Cai

2017-11-01

Full Text Available Abstract In this paper, we construct a bivariate tensor product generalization of Kantorovich-type Bernstein-Stancu-Schurer operators based on the concept of ( p , q $(p, q$ -integers. We obtain moments and central moments of these operators, give the rate of convergence by using the complete modulus of continuity for the bivariate case and estimate a convergence theorem for the Lipschitz continuous functions. We also give some graphs and numerical examples to illustrate the convergence properties of these operators to certain functions.

Optimasi Penambahan Colcemid pada Karyotyping Kultur Mecenchymal Stem Cells (MSC Mencit

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Ratih Rinendyaputri

2016-02-01

Full Text Available AbstractControl of the genetic stability of stem cells prior to the conduct of therapy is essential to prevent effects such as stem cell transformation. Karyotyping is a conventional technique to conduct an analysis of the number and structure of chromosomes. The analysis can only be performed on metaphase stage that needs to be optimized to get the cell at that stage because the length of the cell cycle are different in the each cell types. This study aims to obtain an optimal time to get MSC at metaphase stage. The study was conducted at the stem cell laboratory of Center for Biomedical and Basic Technology of Health. The event begins with isolation using flushing technique at the femur and tibia of mice. Furthermore, the culture in vitro and induction colcemid 0,25μg/ml for 8,16 and 24 hours to get the MSC at metaphase stage. KCl solution with a concentration of 0.075 M and 0,045 M used as a solvent hipotonis. Results showed that 16 hours of induction colcemid 0,25μg/ml in 0.075 M KCl solution usage percentage of MSC who are at metaphase stage and do the highest analysis (p<0.05. In this study 16 hours induction colcemid 0,25μg/ml is the optimal time to obtain metaphase stage of the MSC from bone marrow of mice.Keywords: mecenchymal stem cell, karyotyping, colcemidAbstrakKontrol terhadap stabilitas genetik pada sel punca sebelum pelaksanan terapi merupakan hal yang penting untuk mencegah efek seperti transformasi sel punca yang dapat terjadi. Secara konvensional dapat dilakukan karyotyping untuk melakukan analisis terhadap jumlah dan struktur kromosom. Analisis hanya dapat dilakukan pada tahap metafase sehingga perlu dilakukan optimasi untuk mendapatkan sel pada tahap tersebut mengingat panjang siklus sel setiap jenis sel berbeda. Penelitian ini bertujuan untuk memperoleh waktu yang optimal untuk mendapatkan MSC pada tahap metafase. Penelitian dilakukan di Laboratorium stem cell Pusat Biomedis dan Teknologi Dasar Kesehatan Badan Litbangkes

47,XYY karyotype and normal SRY in a patient with a female phenotype.

Science.gov (United States)

Benasayag, S; Rittler, M; Nieto, F; Torres de Aguirre, N; Reyes, M; Copelli, S

2001-06-01

A rare case of a female patient with a 47,XYY karyotype is described. She had normal female external genitalia, bilateral testes, rudimentary Fallopian tubes and no uterus. Molecular analysis revealed a normal SRY encoding sequence. The possible events in the etiology of this sex reversal entity are discussed.

Karyotype Patterns of Hypsolebias antenori (Cyprinodontiformes: Rivulidae: An Endangered Killifish of the Semiarid Region of Brazil

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Wallace Silva do Nascimento

2014-01-01

Full Text Available Annual fish which belong to the order Cyprinodontiformes constitute an excellent model for evolutionary studies. their short life cycle, distribution in ecologically dynamic environments, and low agility make them favorable for genetic analyses. The species Hypsolebias antenori (Rivulidae, encountered in seasonal pools located in the semiarid region of Northeastern Brazil, has been the object of surveys with a view to study its ecological and behavioral aspects. This study reports on the karyotype patterns of this species, which represents the first contribution to the cytogenetics of this genus. The karyotype of this species is composed of 2n = 48 chromosomes (6m + 4sm + 36st; NF = 96; the heterochromatic regions are located in centromeric or pericentromeric position and are more pronounced in the nucleolar organizer regions. Two sites Ag-NORs/CMA+/DAPI were identified in the short arms of pairs 2 (metacentric and 21 (subtelocentric. Unlike the other species of this family which show an evolution modulated by events of centric fusions, H. antenori shows the maintenance of a basal diploid number and the large number of bibrachial elements indicates karyotypic diversification derived by pericentric inversions. Cytogenetic analyzes in this species will provide new taxonomic markers capable of being utilized in conservation issues and systematics.

Karyotype evolution and phylogenetic relationships of hamsters (Cricetidae, Muroidea, Rodentia) inferred from chromosomal painting and banding comparison.

Science.gov (United States)

Romanenko, Svetlana A; Volobouev, Vitaly T; Perelman, Polina L; Lebedev, Vladimir S; Serdukova, Natalya A; Trifonov, Vladimir A; Biltueva, Larisa S; Nie, Wenhui; O'Brien, Patricia C M; Bulatova, Nina Sh; Ferguson-Smith, Malcolm A; Yang, Fengtang; Graphodatsky, Alexander S

2007-01-01

The evolutionary success of rodents of the superfamily Muroidea makes this taxon the most interesting for evolution studies, including study at the chromosomal level. Chromosome-specific painting probes from the Chinese hamster and the Syrian (golden) hamster were used to delimit homologous chromosomal segments among 15 hamster species from eight genera: Allocricetulus, Calomyscus, Cricetulus, Cricetus, Mesocricetus, Peromyscus, Phodopus and Tscherskia (Cricetidae, Muroidea, Rodentia). Based on results of chromosome painting and G-banding, comparative maps between 20 rodent species have been established. The integrated maps demonstrate a high level of karyotype conservation among species in the Cricetus group (Cricetus, Cricetulus, Allocricetulus) with Tscherskia as its sister group. Species within the genera Mesocricetus and Phodopus also show a high degree of chromosomal conservation. Our results substantiate many of the conclusions suggested by other data and strengthen the topology of the Muroidea phylogenetic tree through the inclusion of genome-wide chromosome rearrangements. The derivation of the muroids karyotypes from the putative ancestral state involved centric fusions, fissions, addition of heterochromatic arms and a great number of inversions. Our results provide further insights into the karyotype relationships of all species investigated.

Improving risk estimates of runoff producing areas: formulating variable source areas as a bivariate process.

Science.gov (United States)

Cheng, Xiaoya; Shaw, Stephen B; Marjerison, Rebecca D; Yearick, Christopher D; DeGloria, Stephen D; Walter, M Todd

2014-05-01

Predicting runoff producing areas and their corresponding risks of generating storm runoff is important for developing watershed management strategies to mitigate non-point source pollution. However, few methods for making these predictions have been proposed, especially operational approaches that would be useful in areas where variable source area (VSA) hydrology dominates storm runoff. The objective of this study is to develop a simple approach to estimate spatially-distributed risks of runoff production. By considering the development of overland flow as a bivariate process, we incorporated both rainfall and antecedent soil moisture conditions into a method for predicting VSAs based on the Natural Resource Conservation Service-Curve Number equation. We used base-flow immediately preceding storm events as an index of antecedent soil wetness status. Using nine sub-basins of the Upper Susquehanna River Basin, we demonstrated that our estimated runoff volumes and extent of VSAs agreed with observations. We further demonstrated a method for mapping these areas in a Geographic Information System using a Soil Topographic Index. The proposed methodology provides a new tool for watershed planners for quantifying runoff risks across watersheds, which can be used to target water quality protection strategies. Copyright © 2014 Elsevier Ltd. All rights reserved.

Acute myeloid leukemia in a patient with constitutional 47,XXY karyotype

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Marla M. Jalbut

2015-01-01

Full Text Available Klinefelter syndrome (KS, a 47,XXY chromosomal abnormality, has been shown to be associated with a number of malignancies, but has not been linked to acute leukemias to date. We present a case of a 54-year-old male diagnosed with acute myeloid leukemia (AML with monocytic differentiation, whose cytogenetic and subsequent FISH analyses revealed a constitutional 47,XXY karyotype. We also review and discuss relevant prior literature.

Acute myeloid leukemia in a patient with constitutional 47,XXY karyotype.

Science.gov (United States)

Jalbut, Marla M; Sohani, Aliyah R; Dal Cin, Paola; Hasserjian, Robert P; Moran, Jenna A; Brunner, Andrew M; Fathi, Amir T

2015-01-01

Klinefelter syndrome (KS), a 47,XXY chromosomal abnormality, has been shown to be associated with a number of malignancies, but has not been linked to acute leukemias to date. We present a case of a 54-year-old male diagnosed with acute myeloid leukemia (AML) with monocytic differentiation, whose cytogenetic and subsequent FISH analyses revealed a constitutional 47,XXY karyotype. We also review and discuss relevant prior literature.

A first glimpse of wild lupin karyotype variation as revealed by comparative cytogenetic mapping

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Karolina Susek

2016-07-01

Full Text Available Insight into plant genomes at the cytomolecular level provides useful information about their karyotype structure, enabling inferences about taxonomic relationships and evolutionary origins. The Old World lupins demonstrate a high level of genomic diversification involving variation in chromosome numbers (2n=32-52, basic chromosome numbers (x=5-7, 9, 13 and in nuclear genome size (2C DNA=0.97-2.68 pg. Lupins comprise both crop and wild species and provide an intriguing system to study karyotype evolution.In order to investigate lupin chromosome structure, heterologous FISH was used. Sixteen BACs that had been generated as chromosome markers for the reference species, Lupinus angustifolius, were used to identify chromosomes in the wild species and explore karyotype variation. While all ‘single-locus’ in L. angustifolius, in the wild lupins these clones proved to be ‘single-locus’, ‘single-locus’ with additional signals, ‘repetitive’ or had no detectable BAC-FISH signal. The diverse distribution of the clones in the targeted genomes suggests a complex evolution history, which possibly involved multiple chromosomal changes such as fusions/fissions and repetitive sequence amplification. Twelve BACs were sequenced and we found numerous transposable elements including DNA transposons as well as LTR and non-LTR retrotransposons with varying quantity and composition among the different lupin species. However, at this preliminary stage, no correlation was observed between the pattern of BAC-FISH signals and the repeat content in particular BACs. Here, we describe the first BAC-based chromosome-specific markers for the wild species: L. cosentinii, L. cryptanthus, L. pilosus, L. micranthus and one New World lupin, L. multiflorus. These BACs could constitute the basis for an assignment of the chromosomal and genetic maps of other lupins, e.g. L. albus and L. luteus. Moreover, we identified karyotype variation that helps illustrate the

Comparative karyotype analysis and chromosome evolution in the genus Aplastodiscus (Cophomantini, Hylinae, Hylidae

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Gruber Simone

2012-04-01

Full Text Available Abstract Background The frogs of the Tribe Cophomantini present, in general, 2n = 24 karyotype, but data on Aplastodiscus showed variation in diploid number from 2n = 24 to 2n = 18. Five species were karyotyped, one of them for the first time, using conventional and molecular cytogenetic techniques, with the aim to perform a comprehensive comparative analysis towards the understanding of chromosome evolution in light of the phylogeny. Results Aplastodiscus perviridis showed 2n = 24, A. arildae and A. eugenioi, 2n = 22, A. callipygius, 2n = 20, and A. leucopygius, 2n = 18. In the metaphase I cells of two species only bivalents occurred, whereas in A. arildae, A. callipygius, and A. leucopygius one tetravalent was also observed besides the bivalents. BrdU incorporation produced replication bands especially in the largest chromosomes, and a relatively good banding correspondence was noticed among some of them. Silver impregnation and FISH with an rDNA probe identified a single NOR pair: the 11 in A. perviridis and A. arildae; the 6 in A. eugenioi; and the 9 in A. callipygius and A. leucopygius. C-banding showed a predominantly centromeric distribution of the heterochromatin, and in one of the species distinct molecular composition was revealed by CMA3. The telomeric probe hybridised all chromosome ends and additionally disclosed the presence of telomere-like sequences in centromeric regions of three species. Conclusions Based on the hypothesis of 2n = 24 ancestral karyotype for Aplastodiscus, and considering the karyotype differences and similarities, two evolutionary pathways through fusion events were suggested. One of them corresponded to the reduction of 2n = 24 to 22, and the other, the reduction of 2n = 24 to 20, and subsequently to 18. Regarding the NOR, two conditions were recognised: plesiomorphy, represented by the homeologous small-sized NOR-bearing pairs, and derivation, represented by the NOR in

Cytokine expression patterns and mesenchymal stem cell karyotypes from the bone marrow microenvironment of patients with myelodysplastic syndromes

Energy Technology Data Exchange (ETDEWEB)

Xiong, H.; Yang, X.Y.; Han, J.; Wang, Q.; Zou, Z.L. [Department of Hematology, Shanghai Clinical Research Center, Chinese Academy of Sciences, Shanghai Xuhui District Central Hospital, Shanghai (China)

2015-01-20

The purpose of this study was to explore cytokine expression patterns and cytogenetic abnormalities of mesenchymal stem cells (MSCs) from the bone marrow microenvironment of Chinese patients with myelodysplastic syndromes (MDS). Bone marrow samples were obtained from 30 cases of MDS (MDS group) and 30 healthy donors (control group). The expression pattern of cytokines was detected by customized protein array. The karyotypes of MSCs were analyzed using fluorescence in situ hybridization. Compared with the control group, leukemia inhibitory factor, stem cell factor (SCF), stromal cell-derived factor (SDF-1), bone morphogenetic protein 4, hematopoietic stem cell (HSC) stimulating factor, and transforming growth factor-β in the MDS group were significantly downregulated (P<0.05), while interferon-γ (IFN-γ), tumor necrosis factor-α (TNF-α), and programmed death ligand (B7-H1) were significantly upregulated (P<0.05). For chromosome abnormality analysis, the detection rate of abnormal karyotypes (+8, -8, -20, 20q-, -Y, -7, 5q-) was 30% in the MDS group and 0% in the control group. In conclusion, the up- and downregulated expression of these cytokines might play a key role in the pathogenesis of MDS. Among them, SCF and SDF-1 may play roles in the apoptosis of HSCs in MDS; and IFN-γ, TNF-α, and B7-H1 may be associated with apoptosis of bone marrow cells in MDS. In addition, the abnormal karyotypes might be actively involved in the pathogenesis of MDS. Further studies are required to determine the role of abnormal karyotypes in the occurrence and development of MDS.

Cytokine expression patterns and mesenchymal stem cell karyotypes from the bone marrow microenvironment of patients with myelodysplastic syndromes

International Nuclear Information System (INIS)

Xiong, H.; Yang, X.Y.; Han, J.; Wang, Q.; Zou, Z.L.

2015-01-01

The purpose of this study was to explore cytokine expression patterns and cytogenetic abnormalities of mesenchymal stem cells (MSCs) from the bone marrow microenvironment of Chinese patients with myelodysplastic syndromes (MDS). Bone marrow samples were obtained from 30 cases of MDS (MDS group) and 30 healthy donors (control group). The expression pattern of cytokines was detected by customized protein array. The karyotypes of MSCs were analyzed using fluorescence in situ hybridization. Compared with the control group, leukemia inhibitory factor, stem cell factor (SCF), stromal cell-derived factor (SDF-1), bone morphogenetic protein 4, hematopoietic stem cell (HSC) stimulating factor, and transforming growth factor-β in the MDS group were significantly downregulated (P<0.05), while interferon-γ (IFN-γ), tumor necrosis factor-α (TNF-α), and programmed death ligand (B7-H1) were significantly upregulated (P<0.05). For chromosome abnormality analysis, the detection rate of abnormal karyotypes (+8, -8, -20, 20q-, -Y, -7, 5q-) was 30% in the MDS group and 0% in the control group. In conclusion, the up- and downregulated expression of these cytokines might play a key role in the pathogenesis of MDS. Among them, SCF and SDF-1 may play roles in the apoptosis of HSCs in MDS; and IFN-γ, TNF-α, and B7-H1 may be associated with apoptosis of bone marrow cells in MDS. In addition, the abnormal karyotypes might be actively involved in the pathogenesis of MDS. Further studies are required to determine the role of abnormal karyotypes in the occurrence and development of MDS

FSH, LH, inhibin B and estradiol levels in Turner syndrome depend on age and karyotype: longitudinal study of 70 Turner girls with or without spontaneous puberty

DEFF Research Database (Denmark)

Hagen, Casper P; Main, Katharina M; Kjaergaard, Susanne

2010-01-01

Ovarian function in Turner syndrome (TS) patients depends on the specific karyotype. This retrospective clinical study evaluates the pituitary-gonadal axis during infancy, childhood and adolescence in TS patients according to karyotype and ovarian function....

Evolutionary dynamics of the karyotype of the wasp Trypoxylon (Trypargilum nitidum (Hymenoptera, Sphecidae from the Rio Doce State Park, Minas Gerais, Brazil

Directory of Open Access Journals (Sweden)

Ricardo Scher

2003-01-01

Full Text Available Cytogenetic analysis based on the distribution of C-bands showed two groups of karyotypes in a Trypoxylon nitidum population from the Rio Doce Park, State of Minas Gerais, Brazil. One of these groups, that was identical to a previously described karyotype (n = 15; 2n = 30, had a stable chromosome number and was rich in acrocentric chromosomes, whereas the other had a variable chromosome number (n = 12 to 14; 2n = 25 to 28 and was rich in pseudo-acrocentric chromosomes. We propose a hypothesis explaining the dynamics of the modifications which occurred in the karyotype of this species, based on the minimum interaction theory of Imai et al. (1986, 1988, 1994 and on the chromosome rearrangements and heteromorphisms observed by us.

Chromosome Evolution in the Free-Living Flatworms: First Evidence of Intrachromosomal Rearrangements in Karyotype Evolution of Macrostomum lignano (Platyhelminthes, Macrostomida)

Science.gov (United States)

Zadesenets, Kira S.; Ershov, Nikita I.; Berezikov, Eugene; Rubtsov, Nikolay B.

2017-01-01

The free-living flatworm Macrostomum lignano is a hidden tetraploid. Its genome was formed by a recent whole genome duplication followed by chromosome fusions. Its karyotype (2n = 8) consists of a pair of large chromosomes (MLI1), which contain regions of all other chromosomes, and three pairs of small metacentric chromosomes. Comparison of MLI1 with metacentrics was performed by painting with microdissected DNA probes and fluorescent in situ hybridization of unique DNA fragments. Regions of MLI1 homologous to small metacentrics appeared to be contiguous. Besides the loss of DNA repeat clusters (pericentromeric and telomeric repeats and the 5S rDNA cluster) from MLI1, the difference between small metacentrics MLI2 and MLI4 and regions homologous to them in MLI1 were revealed. Abnormal karyotypes found in the inbred DV1/10 subline were analyzed, and structurally rearranged chromosomes were described with the painting technique, suggesting the mechanism of their origin. The revealed chromosomal rearrangements generate additional diversity, opening the way toward massive loss of duplicated genes from a duplicated genome. Our findings suggest that the karyotype of M. lignano is in the early stage of genome diploidization after whole genome duplication, and further studies on M. lignano and closely related species can address many questions about karyotype evolution in animals. PMID:29084138

Karyotypic diversity and evolutionary trends in the Neotropical catfish genus Hypostomus Lacépède, 1803 (Teleostei, Siluriformes, Loricariidae

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Anderson Alves

2012-12-01

Full Text Available The family Loricariidae with 813 nominal species is one of the largest fish families of the world. Hypostominae, its more complex subfamily, was recently divided into five tribes. The tribe Hypostomini is composed of a single genus, Hypostomus Lacépède, 1803, which exhibits the largest karyotypic diversity in the family Loricariidae. With the main objective of contributing to a better understanding of the relationship and the patterns of evolution among the karyotypes of Hypostomus species, cytogenetic studies were conducted in six species of the genus from Brazil and Venezuela. The results show a great chromosome variety with diploid numbers ranging from 2n=68 to 2n=76, with a clear predominance of acrocentric chromosomes. The Ag-NORs are located in terminal position in all species analyzed. Three species have single Ag-NORs (Hypostomus albopunctatus (Regan, 1908, H. prope plecostomus (Linnaeus, 1758, and H. prope paulinus (Ihering, 1905 and three have multiple Ag-NORs (H. ancistroides (Ihering, 1911, H. prope iheringi (Regan, 1908, and H. strigaticeps (Regan, 1908. In the process of karyotype evolution of the group, the main type of chromosome rearrangements was possibly centric fissions, which may have been facilitated by the putative tetraploid origin of Hypostomus species. The relationship between the karyotype changes and the evolution in the genus is discussed.

A simple approximation to the bivariate normal distribution with large correlation coefficient

NARCIS (Netherlands)

Albers, Willem/Wim; Kallenberg, W.C.M.

1994-01-01

The bivariate normal distribution function is approximated with emphasis on situations where the correlation coefficient is large. The high accuracy of the approximation is illustrated by numerical examples. Moreover, exact upper and lower bounds are presented as well as asymptotic results on the

Increased basal and pulsatile secretion of FSH and LH in young men with 47,XXY or 46,XX karyotypes

DEFF Research Database (Denmark)

Aksglaede, L.; Jensen, Rikke Bodin Beck; Carlsen, E.

2008-01-01

testicular failure due to supernumerary X chromosomes. DESIGN: Cross-sectional study. METHODS: In this study, 7 untreated patients with primary gonadal insufficiency due to SRY-positive 46,XX (n=4) and 46,XXY karyotypes (n=3) aged 18.8 years and 25 age-matched healthy controls participated. Reproductive...... basal, pulsatile, and total LH and FSH secretion were associated with significantly more LH peaks per 24 h in comparison with healthy controls. Thus, our data indicate that in patients with Klinefelter syndrome and XX male karyotypes the entire hypothalamic-pituitary-gonadal axis has undergone...

Global assessment of predictability of water availability: A bivariate probabilistic Budyko analysis

Science.gov (United States)

Wang, Weiguang; Fu, Jianyu

2018-02-01

Estimating continental water availability is of great importance for water resources management, in terms of maintaining ecosystem integrity and sustaining society development. To more accurately quantify the predictability of water availability, on the basis of univariate probabilistic Budyko framework, a bivariate probabilistic Budyko approach was developed using copula-based joint distribution model for considering the dependence between parameter ω of Wang-Tang's equation and the Normalized Difference Vegetation Index (NDVI), and was applied globally. The results indicate the predictive performance in global water availability is conditional on the climatic condition. In comparison with simple univariate distribution, the bivariate one produces the lower interquartile range under the same global dataset, especially in the regions with higher NDVI values, highlighting the importance of developing the joint distribution by taking into account the dependence structure of parameter ω and NDVI, which can provide more accurate probabilistic evaluation of water availability.

Mixed Phenotype Acute Leukemia with Two Immunophenotypically Distinct B and T Blasts Populations, Double Chromosome and Complex Karyotype: Report of an Unusual Case

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Samah A. Kohla

2015-01-01

Full Text Available Mixed phenotype acute leukemia (MPAL is considered as a rare type of leukemia with an incidence of less than 4% of all acute leukemia based on the most recent 2008 WHO classification. Common subtypes are the B/myeloid and T/myeloid; B/T and trilineage MPAL being extremely rare. We present a case of a male in his 20s, whose peripheral blood smears showed 34% blast cells and bone marrow with 70% blasts. Immunophenotyping by multiparametric flow cytometry showed two populations of blasts, the major one with B-lineage and the minor one with T-lineage. Conventional karyotyping revealed complex karyotype with the presence of double Philadelphia chromosome ( Ph + . BCR/ABL1 rearrangement was confirmed by fluorescent in situ hybridization (FISH analysis. The BCR/ABL1 ES probe on interphase cells indicated pl90 minor m-BCR/ABL fusion in 46% and a second abnormal clone with double Ph + in 16% of the cells analyzed confirmed by reverse transcription-PCR (RT-PCR. The case was diagnosed as MPAL with double Philadelphia chromosome Ph + . The patient was treated with dasatinib, four cycle hyper CVAD/methotrexate cytarabin protocol, and allogeneic transplant. He is still alive in complete hematological, cytogenetic, and molecular remission. Mixed phenotype B/T acute leukemia is an extremely rare disease, particularly those with double Philadelphia chromosomes and clinically presents challenges in diagnosis and treatment.

[Combined G-banded karyotyping and multiplex ligation-dependent probe amplification for the detection of chromosomal abnormalities in fetuses with congenital heart defects].

Science.gov (United States)

Liu, Yang; Xie, Jiansheng; Geng, Qian; Xu, Zhiyong; Wu, Weiqin; Luo, Fuwei; Li, Suli; Wang, Qin; Chen, Wubin; Tan, Hongxi; Zhang, Hu

2017-02-10

To assess the value of G-banded karyotyping in combination with multiplex ligation-dependent probe amplification (MLPA) as a tool for the detection of chromosomal abnormalities in fetuses with congenital heart defects. The combined method was used to analyze 104 fetuses with heart malformations identified by ultrasonography. Abnormal findings were confirmed with chromosomal microarray analysis (CMA). Nineteen (18%) fetuses were found to harbor chromosomal aberrations by G-banded karyotyping and MLPA. For 93 cases, CMA has detected abnormalities in 14 cases including 10 pathogenic copy number variations (CNVs) and 4 CNVs of uncertain significance (VOUS). MLPA was able to detect all of the pathogenic CNVs and 1 VOUS CNV. Combined use of G-banded karyotyping and MLPA is a rapid, low-cost and effective method to detect chromosomal abnormalities in fetuses with various heart malformations.

Evidence of separate karyotype evolutionary pathway in Euglossa orchid bees by cytogenetic analyses

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ANDERSON FERNANDES

2013-09-01

Full Text Available Euglossini are solitary bees considered important pollinators of many orchid species. Information regarding chromosome organization is available for only a small number of species in this group. In the present work, the species Euglossa townsendi and E. carolina were analyzed by cytogenetic techniques to collect information that may aid the understanding of their evolution and chromosomal organization. The chromosome number found was n = 21 for males and 2n = 42 for females in the two species. The distribution and amount of heterochromatin regions differed in the two species analyzed, where they were classified as “high” or “low” heterochromatin content, similarly to what has already been performed in social bee species of the genus Melipona. Banding patterns found in this study suggest that other mechanisms may have occurred in the karyotype evolution of this group, unlike those suggested for social bees and ants. Karyotype evolution of solitary bees appears to have occurred as an event separate from other hymenopterans and did not involve chromosome fissions and heterochromatin amplification.

Evidence of separate karyotype evolutionary pathway in Euglossa orchid bees by cytogenetic analyses.

Science.gov (United States)

Fernandes, Anderson; Werneck, Hugo A; Pompolo, Silvia G; Lopes, Denilce M

2013-09-01

Euglossini are solitary bees considered important pollinators of many orchid species. Information regarding chromosome organization is available for only a small number of species in this group. In the present work, the species Euglossa townsendi and E. carolina were analyzed by cytogenetic techniques to collect information that may aid the understanding of their evolution and chromosomal organization. The chromosome number found was n = 21 for males and 2n = 42 for females in the two species. The distribution and amount of heterochromatin regions differed in the two species analyzed, where they were classified as “high” or “low” heterochromatin content, similarly to what has already been performed in social bee species of the genus Melipona. Banding patterns found in this study suggest that other mechanisms may have occurred in the karyotype evolution of this group, unlike those suggested for social bees and ants. Karyotype evolution of solitary bees appears to have occurred as an event separate from other hymenopterans and did not involve chromosome fissions and heterochromatin amplification.

On minimum divergence adaptation of discrete bivariate distributions to given marginals

Czech Academy of Sciences Publication Activity Database

Vajda, Igor; van der Meulen, E. C.

2005-01-01

Roč. 51, č. 1 (2005), s. 313-320 ISSN 0018-9448 R&D Projects: GA ČR GA201/02/1391; GA MŠk 1M0572 Institutional research plan: CEZ:AV0Z10750506 Keywords : approximation of contingency tables * bivariate discrete distributions * minimization of divergences Subject RIV: BD - Theory of Information Impact factor: 2.183, year: 2005

The ancestral chromosomes of Dromiciops gliroides (Microbiotheridae), and its bearings on the karyotypic evolution of American marsupials.

Science.gov (United States)

Suárez-Villota, Elkin Y; Haro, Ronie E; Vargas, Rodrigo A; Gallardo, Milton H

2016-01-01

The low-numbered 14-chromosome karyotype of marsupials has falsified the fusion hypothesis claiming ancestrality from a 22-chromosome karyotype. Since the 14-chromosome condition of the relict Dromiciops gliroides is reminecent of ancestrality, its interstitial traces of past putative fusions and heterochromatin banding patterns were studied and added to available marsupials' cytogenetic data. Fluorescent in situ hybridization (FISH) and self-genomic in situ hybridization (self-GISH) were used to detect telomeric and repetitive sequences, respectively. These were complemented with C-, fluorescent banding, and centromere immunodetection over mitotic spreads. The presence of interstitial telomeric sequences (ITS) and diploid numbers were reconstructed and mapped onto the marsupial phylogenetic tree. No interstitial, fluorescent signals, but clearly stained telomeric regions were detected by FISH and self-GISH. Heterochromatin distribution was sparse in the telomeric/subtelomeric regions of large submetacentric chromosomes. Large AT-rich blocks were detected in the long arm of four submetacentrics and CG-rich block in the telomeric regions of all chromosomes. The ancestral reconstructions both ITS presence and diploid numbers suggested that ITS are unrelated to fusion events. Although the lack of interstitial signals in D. gliroides' karyotype does not prove absence of past fusions, our data suggests its non-rearranged plesiomorphic condition.

A bivariate space-time downscaler under space and time misalignment.

Science.gov (United States)

Berrocal, Veronica J; Gelfand, Alan E; Holland, David M

2010-12-01

Ozone and particulate matter PM(2.5) are co-pollutants that have long been associated with increased public health risks. Information on concentration levels for both pollutants come from two sources: monitoring sites and output from complex numerical models that produce concentration surfaces over large spatial regions. In this paper, we offer a fully-model based approach for fusing these two sources of information for the pair of co-pollutants which is computationally feasible over large spatial regions and long periods of time. Due to the association between concentration levels of the two environmental contaminants, it is expected that information regarding one will help to improve prediction of the other. Misalignment is an obvious issue since the monitoring networks for the two contaminants only partly intersect and because the collection rate for PM(2.5) is typically less frequent than that for ozone.Extending previous work in Berrocal et al. (2009), we introduce a bivariate downscaler that provides a flexible class of bivariate space-time assimilation models. We discuss computational issues for model fitting and analyze a dataset for ozone and PM(2.5) for the ozone season during year 2002. We show a modest improvement in predictive performance, not surprising in a setting where we can anticipate only a small gain.

Genetic variation and differentiation of Gekko gecko from different populations based on mitochondrial cytochrome b gene sequences and karyotypes.

Science.gov (United States)

Qin, Xin-Min; Li, Hui-Min; Zeng, Zhen-Hua; Zeng, De-Long; Guan, Qing-Xin

2012-06-01

Black-spotted and red-spotted tokay geckos are distributed in different regions and have significant differences in morphological appearance, but have been regarded as the same species, Gekko gecko, in taxonomy. To determine whether black-spotted and red-spotted tokay geckos are genetically differentiated, we sequenced the entire mitochondrial cytochrome b gene (1147 bp) from 110 individuals of Gekko gecko collected in 11 areas including Guangxi China, Yunnan China, Vietnam, and Laos. In addition, we performed karyotypic analyses of black-spotted tokay geckos from Guangxi China and red-spotted tokay geckos from Laos. These phylogenetic analyses showed that black-spotted and red-spotted tokay geckos are divided into two branches in molecular phylogenetic trees. The average genetic distances are as follows: 0.12-0.47% among six haplotypes in the black-spotted tokay gecko group, 0.12-1.66% among five haplotypes in the red-spotted tokay gecko group, and 8.76-9.18% between the black-spotted and red-spotted tokay geckos, respectively. The karyotypic analyses showed that the karyotype formula is 2n = 38 = 8m + 2sm + 2st + 26t in red-spotted tokay geckos from Laos compared with 2n = 38 = 8m + 2sm + 28t in black-spotted tokay geckos from Guangxi China. The differences in these two kinds of karyotypes were detected on the 15th chromosome. The clear differences in genetic levels between black-spotted and red-spotted tokay geckos suggest a significant level of genetic differentiation between the two.

Unadjusted Bivariate Two-Group Comparisons: When Simpler is Better.

Science.gov (United States)

Vetter, Thomas R; Mascha, Edward J

2018-01-01

Hypothesis testing involves posing both a null hypothesis and an alternative hypothesis. This basic statistical tutorial discusses the appropriate use, including their so-called assumptions, of the common unadjusted bivariate tests for hypothesis testing and thus comparing study sample data for a difference or association. The appropriate choice of a statistical test is predicated on the type of data being analyzed and compared. The unpaired or independent samples t test is used to test the null hypothesis that the 2 population means are equal, thereby accepting the alternative hypothesis that the 2 population means are not equal. The unpaired t test is intended for comparing dependent continuous (interval or ratio) data from 2 study groups. A common mistake is to apply several unpaired t tests when comparing data from 3 or more study groups. In this situation, an analysis of variance with post hoc (posttest) intragroup comparisons should instead be applied. Another common mistake is to apply a series of unpaired t tests when comparing sequentially collected data from 2 study groups. In this situation, a repeated-measures analysis of variance, with tests for group-by-time interaction, and post hoc comparisons, as appropriate, should instead be applied in analyzing data from sequential collection points. The paired t test is used to assess the difference in the means of 2 study groups when the sample observations have been obtained in pairs, often before and after an intervention in each study subject. The Pearson chi-square test is widely used to test the null hypothesis that 2 unpaired categorical variables, each with 2 or more nominal levels (values), are independent of each other. When the null hypothesis is rejected, 1 concludes that there is a probable association between the 2 unpaired categorical variables. When comparing 2 groups on an ordinal or nonnormally distributed continuous outcome variable, the 2-sample t test is usually not appropriate. The

Evidence for bivariate linkage of obesity and HDL-C levels in the Framingham Heart Study.

Science.gov (United States)

Arya, Rector; Lehman, Donna; Hunt, Kelly J; Schneider, Jennifer; Almasy, Laura; Blangero, John; Stern, Michael P; Duggirala, Ravindranath

2003-12-31

Epidemiological studies have indicated that obesity and low high-density lipoprotein (HDL) levels are strong cardiovascular risk factors, and that these traits are inversely correlated. Despite the belief that these traits are correlated in part due to pleiotropy, knowledge on specific genes commonly affecting obesity and dyslipidemia is very limited. To address this issue, we first conducted univariate multipoint linkage analysis for body mass index (BMI) and HDL-C to identify loci influencing variation in these phenotypes using Framingham Heart Study data relating to 1702 subjects distributed across 330 pedigrees. Subsequently, we performed bivariate multipoint linkage analysis to detect common loci influencing covariation between these two traits. We scanned the genome and identified a major locus near marker D6S1009 influencing variation in BMI (LOD = 3.9) using the program SOLAR. We also identified a major locus for HDL-C near marker D2S1334 on chromosome 2 (LOD = 3.5) and another region near marker D6S1009 on chromosome 6 with suggestive evidence for linkage (LOD = 2.7). Since these two phenotypes have been independently mapped to the same region on chromosome 6q, we used the bivariate multipoint linkage approach using SOLAR. The bivariate linkage analysis of BMI and HDL-C implicated the genetic region near marker D6S1009 as harboring a major gene commonly influencing these phenotypes (bivariate LOD = 6.2; LODeq = 5.5) and appears to improve power to map the correlated traits to a region, precisely. We found substantial evidence for a quantitative trait locus with pleiotropic effects, which appears to influence both BMI and HDL-C phenotypes in the Framingham data.

The bivariate probit model of uncomplicated control of tumor: a heuristic exposition of the methodology

International Nuclear Information System (INIS)

Herbert, Donald

1997-01-01

Purpose: To describe the concept, models, and methods for the construction of estimates of joint probability of uncomplicated control of tumors in radiation oncology. Interpolations using this model can lead to the identification of more efficient treatment regimens for an individual patient. The requirement to find the treatment regimen that will maximize the joint probability of uncomplicated control of tumors suggests a new class of evolutionary experimental designs--Response Surface Methods--for clinical trials in radiation oncology. Methods and Materials: The software developed by Lesaffre and Molenberghs is used to construct bivariate probit models of the joint probability of uncomplicated control of cancer of the oropharynx from a set of 45 patients for each of whom the presence/absence of recurrent tumor (the binary event E-bar 1 /E 1 ) and the presence/absence of necrosis (the binary event E 2 /E-bar 2 ) of the normal tissues of the target volume is recorded, together with the treatment variables dose, time, and fractionation. Results: The bivariate probit model can be used to select a treatment regime that will give a specified probability, say P(S) = 0.60, of uncomplicated control of tumor by interpolation within a set of treatment regimes with known outcomes of recurrence and necrosis. The bivariate probit model can be used to guide a sequence of clinical trials to find the maximum probability of uncomplicated control of tumor for patients in a given prognostic stratum using Response Surface methods by extrapolation from an initial set of treatment regimens. Conclusions: The design of treatments for individual patients and the design of clinical trials might be improved by use of a bivariate probit model and Response Surface Methods

Multidirectional cross-species painting illuminates the history of karyotypic evolution in Perissodactyla

OpenAIRE

Trifonov, V. A.; Stanyon, R.; Nesterenko, A. I.; Fu, B. Y.; Perelman, P. L.; O' Brien, P.C. M.; Stone, G.; Rubtsova, N. V.; Houck, M. L.; Robinson, T. J.; Ferguson Smith, M. A.; Dobigny, Gauthier; Graphodatsky, A. S.; Yang, F. T.

2008-01-01

The order Perissodactyla, the group of odd-toed ungulates, includes three extant families: Equidae, Tapiridae, and Rhinocerotidae. The extremely rapid karyotypic diversification in perissodactyls has so far prevented the establishment of genome-wide homology maps between these three families by traditional cytogenetic approaches. Here we report the first genome-wide comparative chromosome maps of African rhinoceroses, four tapir species, four equine species, and humans. These maps were establ...

Technical note: Towards a continuous classification of climate using bivariate colour mapping

NARCIS (Netherlands)

Teuling, A.J.

2011-01-01

Climate is often defined in terms of discrete classes. Here I use bivariate colour mapping to show that the global distribution of K¨oppen-Geiger climate classes can largely be reproduced by combining the simple means of two key states of the climate system 5 (i.e., air temperature and relative

Intraspecific karyotypic polymorphism is highly concordant with allozyme variation in Lysimachia mauritiana (Primulaceae: Myrsinoideae) in Taiwan: implications for the colonization history and dispersal patterns of coastal plants

Science.gov (United States)

Kono, Yoshiko; Chung, Kuo-Fang; Chen, Chih-Hui; Hoshi, Yoshikazu; Setoguchi, Hiroaki; Chou, Chang-Hung; Oginuma, Kazuo; Peng, Ching-I

2012-01-01

Background and Aims Investigating intraspecific karyotypic and genetic variations jointly can provide unique insights into how historical, ecological and cytogenetic factors influence microevolution. A coastal herb, Lysimachia mauritiana, exhibits extensive karyotypic polymorphism and displays a complex cytogeographic pattern across the Ryukyus. To explore whether a similar degree of chromosomal variation exists south of the Ryukyus, and in an attempt to ascertain the mechanisms that may have generated the patterns, comprehensive sampling was conducted in Taiwan. Methods Karyotypes were analysed at mitotic metaphase for 550 individuals from 42 populations throughout Taiwan Proper and its adjacent islands. In addition, genetic variation was estimated using 12 allozymes (21 loci) of 314 individuals sampled from 12 localities. Key Results Four chromosome numbers and eight cytotypes, including four endemic cytotypes, were detected. Cytotype distributions were highly structured geographically, with single cytotypes present in most populations and four major cytotypes dominating the north, east and south of Taiwan and the Penghu Archipelago. Allozyme variation was very low and F-statistics indicated an extremely high level of population differentiation, implying limited gene flow among populations. Cluster analysis of allozyme variation uncovered four geographic groups, each corresponding perfectly to the four dominant cytotypes. The geographic structure of cytotype distribution and allozyme variation probably resulted from severe genetic drift triggered by genetic bottlenecks, suggesting that Taiwanese populations were likely to be derived from four independent founder events. In the few localities with multiple cytotypes, cytogeographic patterns and inferences of chromosomal evolution revealed a trend of northward dispersal, consistent with the course of the Kuroshio Current that has been influential in shaping the coastal biota of the region. Conclusions The data

Karyotype and genome size analyses in species of Helichrysum (Asteraceae

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Narjes Azizi

2014-09-01

Full Text Available Karyotype studies were performed in 18 populations of eight Helichrysum species in Iran. Those species showed chromosome numbers of 2n = 2x = 14; 2n = 4x = 24, 28 and 32; 2n = 6x = 36; 2n = 7x = 42; 2n = 8x = 48; 2n = 9x = 54; and 2n = 10x = 60. The chromosome numbers of H. davisianum, H. globiferum, H. leucocephalum and H. oocephalum are reported here for the first time. New ploidy levels are reported for H. oligocephalum (2n = 4x = 24 and H. plicatum (2n = 4x = 32. The chromosomes were metacentric and submetacentric. An ANOVA among H. globiferum and H. leucocephalum populations showed significant differences for the coefficient of variation for chromosome size, total form percentage and the asymmetry indices, indicating that changes in the chromosome structure of Helichrysum species occurred during their diversification. Significant positive correlations among the species and populations studied, in terms of the total chromosome length, lengths of the short arms and lengths of the long arms, indicate that these karyotypic features change simultaneously during speciation events. The genome sizes of Helichrysum species are reported here for first time. The 2C DNA content ranged from 8.13 pg (in H. rubicundum to 18.4 pg (in H. leucocephalum and H. davisianum. We found that C-value correlated significantly with ploidy level, total chromosome length, lengths of the long arms and lengths of the short arms (p<0.05, indicating that changes in chromosome structure are accompanied by changes in DNA content.

Karyotypic Evolution in Malagasy Flying Foxes (Pteropodidae, Chiroptera) and Their Hipposiderid Relatives as Determined by Comparative Chromosome Painting.

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Richards, Leigh R; Rambau, Ramugondo V; Goodman, Steven M; Taylor, Peter J; Schoeman, M Corrie; Yang, Fengtang; Lamb, Jennifer M

2016-01-01

Pteropodidae and Hipposideridae are 2 of the 9 chiropteran families that occur on Madagascar. Despite major advancements in the systematic study of the island's bat fauna, few karyotypic data exist for endemic species. We utilized G- and C-banding in combination with chromosome painting with Myotismyotis probes to establish a genome-wide homology among Malagasy species belonging to the families Pteropodidae (Pteropus rufus 2n = 38; Rousettus madagascariensis, 2n = 36), Hipposideridae (Hipposideros commersoni s.s., 2n = 52), and a single South African representative of the Rhinolophidae (Rhinolophus clivosus, 2n = 58). Painting probes of M. myotis detected 26, 28, 28, and 29 regions of homology in R. madagascariensis, P. rufus, H. commersoni s.s, and R. clivosus, respectively. Translocations, pericentric inversions, and heterochromatin additions were responsible for karyotypic differences amongst the Malagasy pteropodids. Comparative chromosome painting revealed a novel pericentric inversion on P. rufus chromosome 4. Chromosomal characters suggest a close evolutionary relationship between Rousettus and Pteropus. H. commersoni s.s. shared several chromosomal characters with extralimital congeners but did not exhibit 2 chromosomal synapomorphies proposed for Hipposideridae. This study provides further insight into the ancestral karyotypes of pteropodid and hipposiderid bats and corroborates certain molecular phylogenetic hypotheses. © 2016 S. Karger AG, Basel.

A method of moments to estimate bivariate survival functions: the copula approach

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Silvia Angela Osmetti

2013-05-01

Full Text Available In this paper we discuss the problem on parametric and non parametric estimation of the distributions generated by the Marshall-Olkin copula. This copula comes from the Marshall-Olkin bivariate exponential distribution used in reliability analysis. We generalize this model by the copula and different marginal distributions to construct several bivariate survival functions. The cumulative distribution functions are not absolutely continuous and they unknown parameters are often not be obtained in explicit form. In order to estimate the parameters we propose an easy procedure based on the moments. This method consist in two steps: in the first step we estimate only the parameters of marginal distributions and in the second step we estimate only the copula parameter. This procedure can be used to estimate the parameters of complex survival functions in which it is difficult to find an explicit expression of the mixed moments. Moreover it is preferred to the maximum likelihood one for its simplex mathematic form; in particular for distributions whose maximum likelihood parameters estimators can not be obtained in explicit form.

Bivariate functional data clustering: grouping streams based on a varying coefficient model of the stream water and air temperature relationship

Science.gov (United States)

H. Li; X. Deng; Andy Dolloff; E. P. Smith

2015-01-01

A novel clustering method for bivariate functional data is proposed to group streams based on their water–air temperature relationship. A distance measure is developed for bivariate curves by using a time-varying coefficient model and a weighting scheme. This distance is also adjusted by spatial correlation of streams via the variogram. Therefore, the proposed...

Karyotype description of two Neotropical Psittacidae species: the endangered Hyacinth Macaw, Anodorhynchus hyacinthinus, and the Hawk-headed Parrot, Deroptyus accipitrinus (Psittaciformes: Aves, and its significance for conservation plans

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Vitor de Oliveira Lunardi

2003-01-01

Full Text Available Neotropical parrots are among the most threatened groups of birds in the world, and many species are facing extinction in a near future. At the same time, the taxonomic position of many species remains unclear. Karyotype analysis has been used to elucidate the phylogenetic status of many bird groups, also providing important information for both in situ and ex situ conservation plans. The objective of the present study was to describe for the first time the karyotypes of the endangered Hyacinth Macaw, Anodorhynchus hyacinthinus, and of the Hawk-headed Parrot, Deroptyus accipitrinus. A diploid number of 2n = 70 and a karyotype similar to the main pattern previously found for the genera Ara, Cyanopsitta, Aratinga, Propyrrhura, Pionites, Pionopsitta, Nandayus, and Guaruba were found for both species. These karyotype descriptions can be a starting point for the genetic monitoring of these two declining species.

Rapid aneuploidy testing (knowing less) versus traditional karyotyping (knowing more) for advanced maternal age: what would be missed, who should decide?

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Leung, W C; Lau, E T; Lau, W L; Tang, Rebecca; Wong, Shell Fean; Lau, T K; Tse, K T; Wong, S F; To, W K; Ng, Lucy K L; Lao, T T; Tang, Mary H Y

2008-02-01

The application of rapid aneuploidy testing as a stand-alone approach in prenatal diagnosis is much debated. The major criticism of this targeted approach is that it will not detect other chromosomal abnormalities that will be picked up by traditional karyotyping. This study aimed to study the nature of such chromosomal abnormalities and whether parents would choose to terminate affected pregnancies. Retrospective study on a cytogenetic database. Eight public hospitals in Hong Kong. The karyotype results of 19 517 amniotic fluid cultures performed for advanced maternal age (>or=35 years) from 1997 to 2002 were classified according to whether they were detectable by rapid aneuploidy testing. The outcomes of pregnancies with abnormal karyotypes were reviewed from patient records. In all, 333 (1.7%) amniotic fluid cultures yielded abnormal karyotypes; 175 (52.6%) of these were detected by rapid aneuploidy testing, and included trisomy 21 (n=94, 28.2%), trisomy 18 or 13 (n=21, 6.3%), and sex chromosome abnormalities (n=60, 18.0%). The other 158 (47.4%) chromosomal abnormalities were not detectable by rapid aneuploidy testing, of which 63 (18.9%) were regarded to be of potential clinical significance and 95 (28.5%) of no clinical significance. Pregnancy outcomes in 327/333 (98.2%) of these patients were retrieved. In total, 143 (42.9%) of these pregnancies were terminated: 93/94 (98.9%) for trisomy 21, 20/21 (95.2%) for trisomy 18 or 13, 19/60 (31.7%) for sex chromosome abnormalities, and 11/63 (17.5%) for other chromosomal abnormalities with potential clinical significance. There were no terminations in the 95 pregnancies in which karyotyping results were regarded to be of no clinical significance. 'Knowing less' by the rapid aneuploidy stand-alone testing could miss about half of all chromosomal abnormalities detectable by amniocentesis performed for advanced maternal age. Findings from two fifths of the latter were of potential clinical significance, and the parents

Molecular phylogenetic reconstruction and localization of the (TTAGGn telomeric repeats in the chromosomes of Acromyrmex striatus (Roger, 1863 suggests a lower ancestral karyotype for leafcutter ants (Hymenoptera

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Tássia Tatiane Pontes Pereira

2018-01-01

Full Text Available Chromosome counts and karyotype characterization have proved to be important features of a genome. Chromosome changes during the diversification of ants might play an important role, given the diversity and success of Formicidae. Comparative karyotype analyses on ants have enriched and helped ant systematics. Among leafcutter ants, two major chromosome counts have been described, one frequent in Atta Fabricius, 1804 (2n = 22 in all Atta spp. whose karyotype is known and the other frequent in Acromyrmex Mayr, 1865 (2n = 38 in the majority of species whose karyotype is known. The main exception is Acromyrmex striatus (Roger, 1863, which harbors a diploid chromosome set of 22. Here we describe the use of fluorescence in situ hybridization (FISH with telomeric probes with (TTAGG6 repeats to describe the telomere composition of A. striatus and to recover potential interstitial non-telomeric signals that may reflect fusion events during the evolution of leafcutter lineage from 38 to 22 chromosomes. Further, we reconstruct the ancestral chromosome numbers of the leafcutter clade based on a recently proposed molecular phylogenetic hypothesis and phylogenomic tree. Distinct signals have been observed in both extremities on the telomere chromosomes of A. striatus. Non-telomeric signals have not been retrieved in our analysis. It could be supposed that the low-numbered karyotype indeed represents the ancestral chromosome number of leafcutters. The phylogenetic reconstruction also recovered a low chromosome number from the diverse approaches implemented, suggesting that n = 11 is the most likely ancestral karyotype of the leafcutter ants and is a plesiomorphic feature shared between A. striatus and Atta spp.

Molecular phylogenetic reconstruction and localization of the (TTAGG)n telomeric repeats in the chromosomes of Acromyrmex striatus (Roger, 1863) suggests a lower ancestral karyotype for leafcutter ants (Hymenoptera).

Science.gov (United States)

Pereira, Tássia Tatiane Pontes; Dos Reis, Ana Caroline Coelho Corrêa; Cardoso, Danon Clemes; Cristiano, Maykon Passos

2018-01-01

Chromosome counts and karyotype characterization have proved to be important features of a genome. Chromosome changes during the diversification of ants might play an important role, given the diversity and success of Formicidae. Comparative karyotype analyses on ants have enriched and helped ant systematics. Among leafcutter ants, two major chromosome counts have been described, one frequent in Atta Fabricius, 1804 (2n = 22 in all Atta spp. whose karyotype is known) and the other frequent in Acromyrmex Mayr, 1865 (2n = 38 in the majority of species whose karyotype is known). The main exception is Acromyrmex striatus (Roger, 1863), which harbors a diploid chromosome set of 22. Here we describe the use of fluorescence in situ hybridization (FISH) with telomeric probes with (TTAGG) 6 repeats to describe the telomere composition of A. striatus and to recover potential interstitial non-telomeric signals that may reflect fusion events during the evolution of leafcutter lineage from 38 to 22 chromosomes. Further, we reconstruct the ancestral chromosome numbers of the leafcutter clade based on a recently proposed molecular phylogenetic hypothesis and phylogenomic tree. Distinct signals have been observed in both extremities on the telomere chromosomes of A. striatus . Non-telomeric signals have not been retrieved in our analysis. It could be supposed that the low-numbered karyotype indeed represents the ancestral chromosome number of leafcutters. The phylogenetic reconstruction also recovered a low chromosome number from the diverse approaches implemented, suggesting that n = 11 is the most likely ancestral karyotype of the leafcutter ants and is a plesiomorphic feature shared between A. striatus and Atta spp.

Karyotypic evolution of ribosomal sites in buffalo subspecies and their crossbreed

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Tiago Marafiga Degrandi

2014-06-01

Full Text Available Domestic buffaloes are divided into two group based on cytogenetic characteristics and habitats: the "river buffaloes" with 2n = 50 and the "swamp buffaloes", 2n = 48. Nevertheless, their hybrids are viable, fertile and identified by a 2n = 49. In order to have a better characterization of these different cytotypes of buffaloes, and considering that NOR-bearing chromosomes are involved in the rearrangements responsible for the karyotypic differences, we applied silver staining (Ag-NOR and performed fluorescent in situ hybridization (FISH experiments using 18S rDNA as probe. Metaphases were obtained through blood lymphocyte culture of 21 individuals, including river, swamp and hybrid cytotypes. Ag-NOR staining revealed active NORs on six chromosome pairs (3p, 4p, 6, 21, 23, 24 in the river buffaloes, whereas the swamp buffaloes presented only five NOR-bearing pairs (4p, 6, 20, 22, 23. The F1 crossbreed had 11 chromosomes with active NORs, indicating expression of both parental chromosomes. FISH analysis confirmed the numerical divergence identified with Ag-NOR. This result is explained by the loss of the NOR located on chromosome 4p in the river buffalo, which is involved in the tandem fusion with chromosome 9 in this subspecies. A comparison with the ancestral cattle karyotype suggests that the NOR found on the 3p of the river buffalo may have originated from a duplication of ribosomal genes, resulting in the formation of new NOR sites in this subspecies.

Improving the modelling of redshift-space distortions - I. A bivariate Gaussian description for the galaxy pairwise velocity distributions

Science.gov (United States)

Bianchi, Davide; Chiesa, Matteo; Guzzo, Luigi

2015-01-01

As a step towards a more accurate modelling of redshift-space distortions (RSD) in galaxy surveys, we develop a general description of the probability distribution function of galaxy pairwise velocities within the framework of the so-called streaming model. For a given galaxy separation r, such function can be described as a superposition of virtually infinite local distributions. We characterize these in terms of their moments and then consider the specific case in which they are Gaussian functions, each with its own mean μ and dispersion σ. Based on physical considerations, we make the further crucial assumption that these two parameters are in turn distributed according to a bivariate Gaussian, with its own mean and covariance matrix. Tests using numerical simulations explicitly show that with this compact description one can correctly model redshift-space distortions on all scales, fully capturing the overall linear and non-linear dynamics of the galaxy flow at different separations. In particular, we naturally obtain Gaussian/exponential, skewed/unskewed distribution functions, depending on separation as observed in simulations and data. Also, the recently proposed single-Gaussian description of RSD is included in this model as a limiting case, when the bivariate Gaussian is collapsed to a two-dimensional Dirac delta function. We also show how this description naturally allows for the Taylor expansion of 1 + ξS(s) around 1 + ξR(r), which leads to the Kaiser linear formula when truncated to second order, explicating its connection with the moments of the velocity distribution functions. More work is needed, but these results indicate a very promising path to make definitive progress in our programme to improve RSD estimators.

Genomic and karyotypic variation in Drosophila parasitoids (Hymenoptera, Cynipoidea, Figitidae

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Vladimir Gokhman

2011-08-01

Full Text Available Drosophila melanogaster Meigen, 1830 has served as a model insect for over a century. Sequencing of the 11 additional Drosophila Fallen, 1823 species marks substantial progress in comparative genomics of this genus. By comparison, practically nothing is known about the genome size or genome sequences of parasitic wasps of Drosophila. Here, we present the first comparative analysis of genome size and karyotype structures of Drosophila parasitoids of the Leptopilina Förster, 1869 and Ganaspis Förster, 1869 species. The gametic genome size of Ganaspis xanthopoda (Ashmead, 1896 is larger than those of the three Leptopilina species studied. The genome sizes of all parasitic wasps studied here are also larger than those known for all Drosophila species. Surprisingly, genome sizes of these Drosophila parasitoids exceed the average value known for all previously studied Hymenoptera. The haploid chromosome number of both Leptopilina heterotoma (Thomson, 1862 and L. victoriae Nordlander, 1980 is ten. A chromosomal fusion appears to have produced a distinct karyotype for L. boulardi (Barbotin, Carton et Keiner-Pillault, 1979 (n = 9, whose genome size is smaller than that of wasps of the L. heterotoma clade. Like L. boulardi, the haploid chromosome number for G. xanthopoda is also nine. Our studies reveal a positive, but non linear, correlation between the genome size and total chromosome length in Drosophila parasitoids. These Drosophila parasitoids differ widely in their host range, and utilize different infection strategies to overcome host defense. Their comparative genomics, in relation to their exceptionally well-characterized hosts, will prove to be valuable for understanding the molecular basis of the host-parasite arms race and how such mechanisms shape the genetic structures of insect communities.

46 XX karyotype during male fertility evaluation; case series and literature review

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Ahmad Majzoub

2017-01-01

Full Text Available Forty-six XX disorder of sex development is an uncommon medical condition observed at times during the evaluation of a man′s fertility. The following is a case series and literature review of phenotypically normal men diagnosed with this karyotype. Our goal is to comprehend the patients′ clinical presentation as well as their laboratory results aiming to explore options available for their management. A formal literature review through PubMed and MEDLINE databases was performed using "46 XX man" as a word search. A total of 55 patients, including those conveyed in this article were diagnosed with a 46 XX karyotype during their fertility evaluation. The patients′ mean age ± s.d. was 34 ± 10 years and their mean height ± s.d. was 166 ± 6.5 cm. Overall, they presented with hypergonadotropic hypogonadism. Sexual dysfunction, reduced hair distribution, and gynecomastia were reported in 20% (4/20, 25.8% (8/31, and 42% (13/31 of the patients, respectively. The SRY gene was detected in 36 (83.7% and was absent in the remaining seven (16.3% patients. We found that a multidisciplinary approach to management is preferred in 46 XX patients. Screening for remnants of the mullerian ducts and for malignant transformation in dysgenetic gonads is imperative. Hypogonadism should be addressed, while fertility options are in vitro fertilization with donor sperm or adoption.

Chromosome numbers and karyotype evolution in holoparasitic Orobanche (Orobanchaceae) and related genera

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Schneeweiss, G.M.; Palomeque, T.; Colwell, A.E.; Weiss-Schneeweiss, H.

2004-01-01

Chromosome numbers and karyotypes of species of Orobanche, Cistanche, and Diphelypaea (Orobanchaceae) were investigated, and 108 chromosome counts of 53 taxa, 19 counted for the first time, are presented with a thorough compilation of previously published data. Additionally, karyotypes of representatives of these genera, including Orobanche sects. Orobanche and Trionychon, are reported. Cistanche (x = 20) has large meta- to submetacentric chromosomes, while those of Diphelypaea (x = 19) are medium-sized submeta-to acrocentrics. Within three analyzed sections of Orobanche, sects. Myzorrhiza (x = 24) and Trionychon (x = 12) possess medium-sized submeta- to acrocentrics, while sect. Orobanche (x = 19) has small, mostly meta- to submetacentric, chromosomes. Polyploidy is unevenly distributed in Orobanche and restricted to a few lineages, e.g., O. sect. Myzorrhiza or Orobanche gracilis and its relatives (sect. Orobanche). The distribution of basic chromosome numbers supports the groups found by molecular phylogenetic analyses: Cistanche has x = 20, the Orobanche-group (Orobanche sect. Orobanche, Diphelypaea) has x = 19, and the Phelipanche-group (Orobanche sects. Gymnocaulis, Myzorrhiza, Trionychon) has x = 12, 24. A model of chromosome number evolution in Orobanche and related genera is presented: from two ancestral base numbers, xh = 5 and xh = 6, independent polyploidizations led to x = 20 (Cistanche) and (after dysploidization) x = 19 (Orobanche-group) and to x = 12 and x = 24 (Phelipanche-group), respectively.

Bivariate genome-wide association meta-analysis of pediatric musculoskeletal traits reveals pleiotropic effects at the SREBF1/TOM1L2 locus

DEFF Research Database (Denmark)

Medina-Gomez, Carolina; Kemp, John P; Dimou, Niki L

2017-01-01

Bone mineral density is known to be a heritable, polygenic trait whereas genetic variants contributing to lean mass variation remain largely unknown. We estimated the shared SNP heritability and performed a bivariate GWAS meta-analysis of total-body lean mass (TB-LM) and total-body less head bone...... as in human muscle tissue. This is the first bivariate GWAS meta-analysis to demonstrate genetic factors with pleiotropic effects on bone mineral density and lean mass.Bone mineral density and lean skeletal mass are heritable traits. Here, Medina-Gomez and colleagues perform bivariate GWAS analyses of total...

Molecular karyotype and chromosomal localization of genes encoding ß-tubulin, cysteine proteinase, hsp 70 and actin in Trypanosoma rangeli

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CB Toaldo

2001-01-01

Full Text Available The molecular karyotype of nine Trypanosoma rangeli strains was analyzed by contour-clamped homogeneous electric field electrophoresis, followed by the chromosomal localization of ß-tubulin, cysteine proteinase, 70 kDa heat shock protein (hsp 70 and actin genes. The T. rangeli strains were isolated from either insects or mammals from El Salvador, Honduras, Venezuela, Colombia, Panama and southern Brazil. Also, T. cruzi CL-Brener clone was included for comparison. Despite the great similarity observed among strains from Brazil, the molecular karyotype of all T. rangeli strains analyzed revealed extensive chromosome polymorphism. In addition, it was possible to distinguish T. rangeli from T. cruzi by the chromosomal DNA electrophoresis pattern. The localization of ß-tubulin genes revealed differences among T. rangeli strains and confirmed the similarity between the isolates from Brazil. Hybridization assays using probes directed to the cysteine proteinase, hsp 70 and actin genes discriminated T. rangeli from T. cruzi, proving that these genes are useful molecular markers for the differential diagnosis between these two species. Numerical analysis based on the molecular karyotype data revealed a high degree of polymorphism among T. rangeli strains isolated from southern Brazil and strains isolated from Central and the northern South America. The T. cruzi reference strain was not clustered with any T. rangeli strain.

Bio-metric study of pig karyotype; Etude biometrique du caryotype du porc

Energy Technology Data Exchange (ETDEWEB)

Haag, J; Lacourly, N; Nizza, P [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

1969-07-01

This study has a twofold purpose, the former is to determine the swine karyotype as accurately as possible, the latter is to try and develop a method of automatic classification and to show its possibilities and limits. (authors) [French] Cette etude a un double objet: d'une part, de definir de la facon aussi precise que possible le caryotype du porc et d'autre part, de tenter une methode de classification automatique et d'en montrer les possibilites ainsi que les limites. (auteurs)

Computational approach to Thornley's problem by bivariate operational calculus

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Bazhlekova, E.; Dimovski, I.

2012-10-01

Thornley's problem is an initial-boundary value problem with a nonlocal boundary condition for linear onedimensional reaction-diffusion equation, used as a mathematical model of spiral phyllotaxis in botany. Applying a bivariate operational calculus we find explicit representation of the solution, containing two convolution products of special solutions and the arbitrary initial and boundary functions. We use a non-classical convolution with respect to the space variable, extending in this way the classical Duhamel principle. The special solutions involved are represented in the form of fast convergent series. Numerical examples are considered to show the application of the present technique and to analyze the character of the solution.

Comparative Study on the Karyotype of Two Species of Megaulacobothrus Caud., 1921 (Acridoidea

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Dorjsuren Altanchimeg

2013-12-01

Full Text Available The karyotypes of Chorthippus ( Megaulacobothrus aethalinus (Zubovsky, 1899 and Chorthippus ( Megaulacobothrus chinensis Tarbinsky, 1927 were compared by means of the conventional cytogenetic method. The results showed that chromosome numbers of two species were 2n( ♂ =17=16+XO, in which three pairs of autosomal and sex chromosomes were terminal chromosomes, and the other fi ve pairs of autosomal ones were metacentric chromosomes, which are the diagnostic characters of Chorthippus . However, these two species could be identifi ed by the different formulae and the relative length of chromosomes. The chromosome formula of Chorthippus (M. aethalinus is K(2n, ♂ =6m+11t=6L+6M+4S+XO, whereas that of Chorthippus (M. chinensis is K(2n, ♂ =6m+11t=6L+8M+2S+XO. In addition, we found that the location and the relative length of sex chromosomes in the two species were different from each other. Sex chromosome of Chorthippus (M. aethalinus located at fi fth position and its relative length was equal to 8.33%, whereas that of Chorthippus (M. chinensis was at eighth position and its relative length was equal to 5.53%. These results showed that signifi cant different karyotype features exist in the two compared species of Chorthippus .

A new karyotype for the genus Cavia from a southern island of Brazil (Rodentia - Caviidae

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A. Gava

1998-03-01

Full Text Available Intraspecific karyotype variation in mammal species is very common and often caused by centromeric fusion of acrocentric chromosomes. We describe here a new karyotype 2n = 62 (FN = 112 for the genus Cavia from the Moleques do Sul Islands, of the southern coast of Brazil. We analyzed two male and four female karyotypes that had twenty-four biarmed pairs and six pairs of acrocentric chromosomes. The sexual pair consisted of a metacentric X-chromosome and a large acrocentric Y. C-bands were found in the centromeric and pericentromeric regions of almost all chromosomes, except for some small biarmed and acrocentric ones. Nucleolus organizer regions appeared in two biarmed chromosomes, and G-banding patterns were also seen.RESUMO A variação cariotípica nas espécies de mamíferos é bastante comum e geralmente causada pela fusão de cromossomos acrocêntricos. Foi descrito neste trabalho um novo cariótipo, com 2n = 62 e FN = 112, para o gênero Cavia proveniente das ilhas Moleques do Sul, da costa sul do Brasil. Foram analisados os cariótipos de dois machos e quatro fêmeas que possuiam 24 pares de cromossomos com dois braços e seis pares de acrocêntricos. O par sexual era constituído por um cromossomo X metacêntrico grande e um Y acrocêntrico. As bandas C estavam localizadas nas regiões centroméricas e pericentroméricas da maioria dos cromossomos, com exceção de alguns acrocêntricos e os cromossomos de dois braços menores. As regiões organizadoras de nucléolo ocorreram em dois cromossomos com dois braços e o padrão de bandamento G foi também apresentado.

Carbon and oxygen isotopic ratio bi-variate distribution for marble artifacts quarry assignment

International Nuclear Information System (INIS)

Pentia, M.

1995-01-01

Statistical description, by a Gaussian bi-variate probability distribution of 13 C/ 12 C and 18 O/ 16 O isotopic ratios in the ancient marble quarries has been done and the new method for obtaining the confidence level quarry assignment for marble artifacts has been presented. (author) 8 figs., 3 tabs., 4 refs

Analysis of horse genomes provides insight into the diversification and adaptive evolution of karyotype.

Science.gov (United States)

Huang, Jinlong; Zhao, Yiping; Shiraigol, Wunierfu; Li, Bei; Bai, Dongyi; Ye, Weixing; Daidiikhuu, Dorjsuren; Yang, Lihua; Jin, Burenqiqige; Zhao, Qinan; Gao, Yahan; Wu, Jing; Bao, Wuyundalai; Li, Anaer; Zhang, Yuhong; Han, Haige; Bai, Haitang; Bao, Yanqing; Zhao, Lele; Zhai, Zhengxiao; Zhao, Wenjing; Sun, Zikui; Zhang, Yan; Meng, He; Dugarjaviin, Manglai

2014-05-14

Karyotypic diversification is more prominent in Equus species than in other mammals. Here, using next generation sequencing technology, we generated and de novo assembled quality genomes sequences for a male wild horse (Przewalski's horse) and a male domestic horse (Mongolian horse), with about 93-fold and 91-fold coverage, respectively. Portion of Y chromosome from wild horse assemblies (3 M bp) and Mongolian horse (2 M bp) were also sequenced and de novo assembled. We confirmed a Robertsonian translocation event through the wild horse's chromosomes 23 and 24, which contained sequences that were highly homologous with those on the domestic horse's chromosome 5. The four main types of rearrangement, insertion of unknown origin, inserted duplication, inversion, and relocation, are not evenly distributed on all the chromosomes, and some chromosomes, such as the X chromosome, contain more rearrangements than others, and the number of inversions is far less than the number of insertions and relocations in the horse genome. Furthermore, we discovered the percentages of LINE_L1 and LTR_ERV1 are significantly increased in rearrangement regions. The analysis results of the two representative Equus species genomes improved our knowledge of Equus chromosome rearrangement and karyotype evolution.

Karyotype analysis and sex determination in Australian Brush-turkeys (Alectura lathami.

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Madison T Ortega

Full Text Available Sexual differentiation across taxa may be due to genetic sex determination (GSD and/or temperature sex determination (TSD. In many mammals, males are heterogametic (XY; whereas females are homogametic (XX. In most birds, the opposite is the case with females being heterogametic (ZW and males the homogametic sex (ZZ. Many reptile species lack sex chromosomes, and instead, sexual differentiation is influenced by temperature with specific temperatures promoting males or females varying across species possessing this form of sexual differentiation, although TSD has recently been shown to override GSD in Australian central beaded dragons (Pogona vitticeps. There has been speculation that Australian Brush-turkeys (Alectura lathami exhibit TSD alone and/or in combination with GSD. Thus, we sought to determine if this species possesses sex chromosomes. Blood was collected from one sexually mature female and two sexually mature males residing at Sylvan Heights Bird Park (SHBP and shipped for karyotype analysis. Karyotype analysis revealed that contrary to speculation, Australian Brush-turkeys possess the classic avian ZW/ZZ sex chromosomes. It remains a possibility that a biased primary sex ratio of Australian Brush-turkeys might be influenced by maternal condition prior to ovulation that result in her laying predominantly Z- or W-bearing eggs and/or sex-biased mortality due to higher sensitivity of one sex in environmental conditions. A better understanding of how maternal and extrinsic factors might differentially modulate ovulation of Z- or W-bearing eggs and hatching of developing chicks possessing ZW or ZZ sex chromosomes could be essential in conservation strategies used to save endangered members of Megapodiidae.

Karyotypical characteristics of two allopatric African populations of anhydrobiotic Polypedilum Kieffer, 1912 (Diptera, Chironomidae) originating from Nigeria and Malawi.

Science.gov (United States)

Petrova, Ninel A; Cornette, Richard; Shimura, Sachiko; Gusev, Oleg A; Pemba, Dylo; Kikawada, Takahiro; Zhirov, Sergey V; Okuda, Takashi

2015-01-01

The African chironomid Polypedilumvanderplanki Hinton, 1951 is the only chironomid able to withstand almost complete desiccation in an ametabolic state known as anhydrobiosis. The karyotypes of two allopatric populations of this anhydrobiotic chironomid, one from Nigeria and another from Malawi, were described according to the polytene giant chromosomes. The karyotype from the Nigerian population was presented as the reference chromosome map for Polypedilumvanderplanki. Both populations, Nigerian and Malawian, showed the same number of chromosomes (2n=8), but important differences were found in the band sequences of polytene chromosomes, and in the number and the arrangement of active regions between the two populations. Such important differences raise the possibility that the Malawian population could constitute a distinct new species of anhydrobiotic chironomid.

Improving runoff risk estimates: Formulating runoff as a bivariate process using the SCS curve number method

Science.gov (United States)

Shaw, Stephen B.; Walter, M. Todd

2009-03-01

The Soil Conservation Service curve number (SCS-CN) method is widely used to predict storm runoff for hydraulic design purposes, such as sizing culverts and detention basins. As traditionally used, the probability of calculated runoff is equated to the probability of the causative rainfall event, an assumption that fails to account for the influence of variations in soil moisture on runoff generation. We propose a modification to the SCS-CN method that explicitly incorporates rainfall return periods and the frequency of different soil moisture states to quantify storm runoff risks. Soil moisture status is assumed to be correlated to stream base flow. Fundamentally, this approach treats runoff as the outcome of a bivariate process instead of dictating a 1:1 relationship between causative rainfall and resulting runoff volumes. Using data from the Fall Creek watershed in western New York and the headwaters of the French Broad River in the mountains of North Carolina, we show that our modified SCS-CN method improves frequency discharge predictions in medium-sized watersheds in the eastern United States in comparison to the traditional application of the method.

Meta-analysis for diagnostic accuracy studies: a new statistical model using beta-binomial distributions and bivariate copulas.

Science.gov (United States)

Kuss, Oliver; Hoyer, Annika; Solms, Alexander

2014-01-15

There are still challenges when meta-analyzing data from studies on diagnostic accuracy. This is mainly due to the bivariate nature of the response where information on sensitivity and specificity must be summarized while accounting for their correlation within a single trial. In this paper, we propose a new statistical model for the meta-analysis for diagnostic accuracy studies. This model uses beta-binomial distributions for the marginal numbers of true positives and true negatives and links these margins by a bivariate copula distribution. The new model comes with all the features of the current standard model, a bivariate logistic regression model with random effects, but has the additional advantages of a closed likelihood function and a larger flexibility for the correlation structure of sensitivity and specificity. In a simulation study, which compares three copula models and two implementations of the standard model, the Plackett and the Gauss copula do rarely perform worse but frequently better than the standard model. We use an example from a meta-analysis to judge the diagnostic accuracy of telomerase (a urinary tumor marker) for the diagnosis of primary bladder cancer for illustration. Copyright © 2013 John Wiley & Sons, Ltd.

A power study of bivariate LOD score analysis of a complex trait and fear/discomfort with strangers.

Science.gov (United States)

Ji, Fei; Lee, Dayoung; Mendell, Nancy Role

2005-12-30

Complex diseases are often reported along with disease-related traits (DRT). Sometimes investigators consider both disease and DRT phenotypes separately and sometimes they consider individuals as affected if they have either the disease or the DRT, or both. We propose instead to consider the joint distribution of the disease and the DRT and do a linkage analysis assuming a pleiotropic model. We evaluated our results through analysis of the simulated datasets provided by Genetic Analysis Workshop 14. We first conducted univariate linkage analysis of the simulated disease, Kofendrerd Personality Disorder and one of its simulated associated traits, phenotype b (fear/discomfort with strangers). Subsequently, we considered the bivariate phenotype, which combined the information on Kofendrerd Personality Disorder and fear/discomfort with strangers. We developed a program to perform bivariate linkage analysis using an extension to the Elston-Stewart peeling method of likelihood calculation. Using this program we considered the microsatellites within 30 cM of the gene pleiotropic for this simulated disease and DRT. Based on 100 simulations of 300 families we observed excellent power to detect linkage within 10 cM of the disease locus using the DRT and the bivariate trait.

A non-stationary cost-benefit based bivariate extreme flood estimation approach

Science.gov (United States)

Qi, Wei; Liu, Junguo

2018-02-01

Cost-benefit analysis and flood frequency analysis have been integrated into a comprehensive framework to estimate cost effective design values. However, previous cost-benefit based extreme flood estimation is based on stationary assumptions and analyze dependent flood variables separately. A Non-Stationary Cost-Benefit based bivariate design flood estimation (NSCOBE) approach is developed in this study to investigate influence of non-stationarities in both the dependence of flood variables and the marginal distributions on extreme flood estimation. The dependence is modeled utilizing copula functions. Previous design flood selection criteria are not suitable for NSCOBE since they ignore time changing dependence of flood variables. Therefore, a risk calculation approach is proposed based on non-stationarities in both marginal probability distributions and copula functions. A case study with 54-year observed data is utilized to illustrate the application of NSCOBE. Results show NSCOBE can effectively integrate non-stationarities in both copula functions and marginal distributions into cost-benefit based design flood estimation. It is also found that there is a trade-off between maximum probability of exceedance calculated from copula functions and marginal distributions. This study for the first time provides a new approach towards a better understanding of influence of non-stationarities in both copula functions and marginal distributions on extreme flood estimation, and could be beneficial to cost-benefit based non-stationary bivariate design flood estimation across the world.

Chromosome isolation by flow sorting in Aegilops umbellulata and Ae. comosa and their allotetraploid hybrids Ae. biuncialis and Ae. geniculata.

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István Molnár

Full Text Available This study evaluates the potential of flow cytometry for chromosome sorting in two wild diploid wheats Aegilops umbellulata and Ae. comosa and their natural allotetraploid hybrids Ae. biuncialis and Ae. geniculata. Flow karyotypes obtained after the analysis of DAPI-stained chromosomes were characterized and content of chromosome peaks was determined. Peaks of chromosome 1U could be discriminated in flow karyotypes of Ae. umbellulata and Ae. biuncialis and the chromosome could be sorted with purities exceeding 95%. The remaining chromosomes formed composite peaks and could be sorted in groups of two to four. Twenty four wheat SSR markers were tested for their position on chromosomes of Ae. umbellulata and Ae. comosa using PCR on DNA amplified from flow-sorted chromosomes and genomic DNA of wheat-Ae. geniculata addition lines, respectively. Six SSR markers were located on particular Aegilops chromosomes using sorted chromosomes, thus confirming the usefulness of this approach for physical mapping. The SSR markers are suitable for marker assisted selection of wheat-Aegilops introgression lines. The results obtained in this work provide new opportunities for dissecting genomes of wild relatives of wheat with the aim to assist in alien gene transfer and discovery of novel genes for wheat improvement.

HEK293 in cell biology and cancer research: phenotype, karyotype, tumorigenicity, and stress-induced genome-phenotype evolution.

Science.gov (United States)

Stepanenko, A A; Dmitrenko, V V

2015-09-15

293 cell line (widely known as the Human Embryonic Kidney 293 cells) and its derivatives were the most used cells after HeLa in cell biology studies and after CHO in biotechnology as a vehicle for the production of adenoviral vaccines and recombinant proteins, for analysis of the neuronal synapse formation, in electrophysiology and neuropharmacology. Despite the historically long-term productive exploitation, the origin, phenotype, karyotype, and tumorigenicity of 293 cells are still debated. 293 cells were considered the kidney epithelial cells or even fibroblasts. However, 293 cells demonstrate no evident tissue-specific gene expression signature and express the markers of renal progenitor cells, neuronal cells and adrenal gland. This complicates efforts to reveal the authentic cell type/tissue of origin. On the other hand, the potential to propagate the highly neurotropic viruses, inducible synaptogenesis, functionality of the endogenous neuron-specific voltage-gated channels, and response to the diverse agonists implicated in neuronal signaling give credibility to consider 293 cells of neuronal lineage phenotype. The compound phenotype of 293 cells can be due to heterogeneous, unstable karyotype. The mean chromosome number and chromosome aberrations differ between 293 cells and derivatives as well as between 293 cells from the different cell banks/labs. 293 cells are tumorigenic, whereas acute changes of expression of the cancer-associated genes aggravate tumorigenicity by promoting chromosome instability. Importantly, the procedure of a stable empty vector transfection can also impact karyotype and phenotype. The discussed issues caution against misinterpretations and pitfalls during the different experimental manipulations with 293 cells. Copyright © 2015 Elsevier B.V. All rights reserved.

KIT D816V Positive Acute Mast Cell Leukemia Associated with Normal Karyotype Acute Myeloid Leukemia.

Science.gov (United States)

Lopes, Marta; Teixeira, Maria Dos Anjos; Casais, Cláudia; Mesquita, Vanessa; Seabra, Patrícia; Cabral, Renata; Palla-García, José; Lau, Catarina; Rodrigues, João; Jara-Acevedo, Maria; Freitas, Inês; Vizcaíno, Jose Ramón; Coutinho, Jorge; Escribano, Luis; Orfao, Alberto; Lima, Margarida

2018-01-01

Mast cell (MC) leukemia (MCL) is extremely rare. We present a case of MCL diagnosed concomitantly with acute myeloblastic leukemia (AML). A 41-year-old woman presented with asthenia, anorexia, fever, epigastralgia, and diarrhea. She had a maculopapular skin rash, hepatosplenomegaly, retroperitoneal adenopathies, pancytopenia, 6% blast cells (BC) and 20% MC in the peripheral blood, elevated lactate dehydrogenase, cholestasis, hypoalbuminemia, hypogammaglobulinemia, and increased serum tryptase (184  μ g/L). The bone marrow (BM) smears showed 24% myeloblasts, 17% promyelocytes, and 16% abnormal toluidine blue positive MC, and flow cytometry revealed 12% myeloid BC, 34% aberrant promyelocytes, a maturation blockage at the myeloblast/promyelocyte level, and 16% abnormal CD2-CD25+ MC. The BM karyotype was normal, and the KIT D816V mutation was positive in BM cells. The diagnosis of MCL associated with AML was assumed. The patient received corticosteroids, disodium cromoglycate, cladribine, idarubicin and cytosine arabinoside, high-dose cytosine arabinoside, and hematopoietic stem cell transplantation (HSCT). The outcome was favorable, with complete hematological remission two years after diagnosis and one year after HSCT. This case emphasizes the need of an exhaustive laboratory evaluation for the concomitant diagnosis of MCL and AML, and the therapeutic options.

Bivariate return periods of temperature and precipitation explain a large fraction of European crop yields

Science.gov (United States)

Zscheischler, Jakob; Orth, Rene; Seneviratne, Sonia I.

2017-07-01

Crops are vital for human society. Crop yields vary with climate and it is important to understand how climate and crop yields are linked to ensure future food security. Temperature and precipitation are among the key driving factors of crop yield variability. Previous studies have investigated mostly linear relationships between temperature and precipitation and crop yield variability. Other research has highlighted the adverse impacts of climate extremes, such as drought and heat waves, on crop yields. Impacts are, however, often non-linearly related to multivariate climate conditions. Here we derive bivariate return periods of climate conditions as indicators for climate variability along different temperature-precipitation gradients. We show that in Europe, linear models based on bivariate return periods of specific climate conditions explain on average significantly more crop yield variability (42 %) than models relying directly on temperature and precipitation as predictors (36 %). Our results demonstrate that most often crop yields increase along a gradient from hot and dry to cold and wet conditions, with lower yields associated with hot and dry periods. The majority of crops are most sensitive to climate conditions in summer and to maximum temperatures. The use of bivariate return periods allows the integration of non-linear impacts into climate-crop yield analysis. This offers new avenues to study the link between climate and crop yield variability and suggests that they are possibly more strongly related than what is inferred from conventional linear models.

Cytogenetic studies and karyotype nomenclature of three wild canid species: maned wolf (Chrysocyon brachyurus), bat-eared fox (Otocyon megalotis) and fennec fox (Fennecus zerda).

Science.gov (United States)

Pieńkowska-Schelling, A; Schelling, C; Zawada, M; Yang, F; Bugno, M; Ferguson-Smith, M

2008-01-01

We have analysed the chromosomes of three wild and endangered canid species: the maned wolf (Chrysocyon brachyurus), the bat-eared fox (Otocyon megalotis) and the fennec fox (Fennecuszerda) using classical and molecular cytogenetic methods. For the first time detailed and encompassing descriptions of the chromosomes are presented including the chromosomal assignment of nucleolar organizer regions and the 5S rRNA gene cluster. We propose a karyotype nomenclature with ideograms including more than 300 bands per haploid set for each of these three species which will form the basis for further research. In addition, we propose four basic different patterns of karyotype organization in the family Canidae. A comparison of these patterns with the most recent molecular phylogeny of Canidae revealed that the karyotype evolution of a species is not always strongly connected with its phylogenetic position. Our findings underline the need and justification for basic cytogenetic work in rare and exotic species. (c) 2008 S. Karger AG, Basel.

Analysis of input variables of an artificial neural network using bivariate correlation and canonical correlation

Energy Technology Data Exchange (ETDEWEB)

Costa, Valter Magalhaes; Pereira, Iraci Martinez, E-mail: valter.costa@usp.b [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

2011-07-01

The monitoring of variables and diagnosis of sensor fault in nuclear power plants or processes industries is very important because a previous diagnosis allows the correction of the fault and, like this, to prevent the production stopped, improving operator's security and it's not provoking economics losses. The objective of this work is to build a set, using bivariate correlation and canonical correlation, which will be the set of input variables of an artificial neural network to monitor the greater number of variables. This methodology was applied to the IEA-R1 Research Reactor at IPEN. Initially, for the input set of neural network we selected the variables: nuclear power, primary circuit flow rate, control/safety rod position and difference in pressure in the core of the reactor, because almost whole of monitoring variables have relation with the variables early described or its effect can be result of the interaction of two or more. The nuclear power is related to the increasing and decreasing of temperatures as well as the amount radiation due fission of the uranium; the rods are controls of power and influence in the amount of radiation and increasing and decreasing of temperatures; the primary circuit flow rate has the function of energy transport by removing the nucleus heat. An artificial neural network was trained and the results were satisfactory since the IEA-R1 Data Acquisition System reactor monitors 64 variables and, with a set of 9 input variables resulting from the correlation analysis, it was possible to monitor 51 variables. (author)

Analysis of input variables of an artificial neural network using bivariate correlation and canonical correlation

International Nuclear Information System (INIS)

Costa, Valter Magalhaes; Pereira, Iraci Martinez

2011-01-01

The monitoring of variables and diagnosis of sensor fault in nuclear power plants or processes industries is very important because a previous diagnosis allows the correction of the fault and, like this, to prevent the production stopped, improving operator's security and it's not provoking economics losses. The objective of this work is to build a set, using bivariate correlation and canonical correlation, which will be the set of input variables of an artificial neural network to monitor the greater number of variables. This methodology was applied to the IEA-R1 Research Reactor at IPEN. Initially, for the input set of neural network we selected the variables: nuclear power, primary circuit flow rate, control/safety rod position and difference in pressure in the core of the reactor, because almost whole of monitoring variables have relation with the variables early described or its effect can be result of the interaction of two or more. The nuclear power is related to the increasing and decreasing of temperatures as well as the amount radiation due fission of the uranium; the rods are controls of power and influence in the amount of radiation and increasing and decreasing of temperatures; the primary circuit flow rate has the function of energy transport by removing the nucleus heat. An artificial neural network was trained and the results were satisfactory since the IEA-R1 Data Acquisition System reactor monitors 64 variables and, with a set of 9 input variables resulting from the correlation analysis, it was possible to monitor 51 variables. (author)

Karyotype analysis of Lilium longiflorum and Lilium rubellum by chromosome banding and fluorescence in situ hybridisation

NARCIS (Netherlands)

Lim, K.B.; Wennekes, J.; Jong, de J.H.S.G.M.; Jacobsen, E.; Tuyl, van J.M.

2001-01-01

Detailed karyotypes of Lilium longiflorum and L. rubellum were constructed on the basis of chromosome arm lengths, C-banding, AgNO3 staining, and PI-DAPI banding, together with fluorescence in situ hybridisation (FISH) with the 5S and 45S rDNA sequences as probes. The C-banding patterns that were

Karyotypes of three species of molossid bats (Molossidae, Chiroptera) from India and western Africa

Czech Academy of Sciences Publication Activity Database

Sreepada, K. S.; Koubínová, D.; Konečný, Adam; Koubek, Petr; Ráb, Petr; Rábová, Marie; Zima, Jan

2008-01-01

Roč. 57, č. 4 (2008), s. 347-357 ISSN 0139-7893 R&D Projects: GA AV ČR IAA6093403; GA MŠk LC06073 Institutional research plan: CEZ:AV0Z60930519; CEZ:AV0Z50450515 Keywords : bats * karyotype evolution * chromosome banding Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.522, year: 2008 http://www.ivb.cz/folia/57/4/347-357_MS1427.pdf

A new karyotype of Calomyscus from the Khorasan Province, Iran

OpenAIRE

Esmaeeli Somayeh; Darvish Jamshid; Haddad Farhang; Ghasemzadeh Fereshteh

2008-01-01

Abstract We report a new karyotype of Calomyscus from two localities of the Khorasan Province (Aghdarband, 36° 11’ 3”N, 60° 44’ 6” E and Khajemorad, 36° 8’ 5” N, 59° 41’ 58” E). Chromosomes were examined by conventional staining and C-banding techniques. The diploid chromosome number (2n) and the fundamental autosomal arm number (FNa) were 44 and 60 respectively. The autosomal set consisted of 12 pairs of telocentrics, 5 pairs of acrocent...

Regression analysis for bivariate gap time with missing first gap time data.

Science.gov (United States)

Huang, Chia-Hui; Chen, Yi-Hau

2017-01-01

We consider ordered bivariate gap time while data on the first gap time are unobservable. This study is motivated by the HIV infection and AIDS study, where the initial HIV contracting time is unavailable, but the diagnosis times for HIV and AIDS are available. We are interested in studying the risk factors for the gap time between initial HIV contraction and HIV diagnosis, and gap time between HIV and AIDS diagnoses. Besides, the association between the two gap times is also of interest. Accordingly, in the data analysis we are faced with two-fold complexity, namely data on the first gap time is completely missing, and the second gap time is subject to induced informative censoring due to dependence between the two gap times. We propose a modeling framework for regression analysis of bivariate gap time under the complexity of the data. The estimating equations for the covariate effects on, as well as the association between, the two gap times are derived through maximum likelihood and suitable counting processes. Large sample properties of the resulting estimators are developed by martingale theory. Simulations are performed to examine the performance of the proposed analysis procedure. An application of data from the HIV and AIDS study mentioned above is reported for illustration.

The Mugil curema species complex (Pisces, Mugilidae): a new karyotype for the Pacific white mullet mitochondrial lineage.

Science.gov (United States)

Nirchio, Mauro; Oliveira, Claudio; Siccha-Ramirez, Zoila R; de Sene, Viviani F; Sola, Luciana; Milana, Valentina; Rossi, Anna Rita

2017-01-01

Recent molecular phylogenetic analyses have shown that the Mugil curema Valenciennes, 1836 species complex includes M. incilis Hancock, 1830, M. thoburni (Jordan & Starks, 1896) and at least four " M. curema " mitochondrial lineages, considered as cryptic species. The cytogenetic data on some representatives of the species complex have shown a high cytogenetic diversity. This research reports the results of cytogenetic and molecular analyses of white mullet collected in Ecuador. The analyzed specimens were molecularly assigned to the Mugil sp. O, the putative cryptic species present in the Pacific Ocean and showed a 2n = 46 karyotype, which is composed of 2 metacentric and 44 subtelocentric/acrocentric chromosomes. This karyotype is different from the one described for M. incilis (2n = 48) and from those of the two western Atlantic lineages Mugil curema (2n = 28), and Mugil margaritae (2n = 24). Data suggest the need for a morphological analysis to assign a species name to this Pacific lineage.

The Mugil curema species complex (Pisces, Mugilidae: a new karyotype for the Pacific white mullet mitochondrial lineage

Directory of Open Access Journals (Sweden)

Mauro Nirchio

2017-04-01

Full Text Available Recent molecular phylogenetic analyses have shown that the Mugil curema Valenciennes, 1836 species complex includes M. incilis Hancock, 1830, M. thoburni (Jordan & Starks, 1896 and at least four “M. curema” mitochondrial lineages, considered as cryptic species. The cytogenetic data on some representatives of the species complex have shown a high cytogenetic diversity. This research reports the results of cytogenetic and molecular analyses of white mullet collected in Ecuador. The analyzed specimens were molecularly assigned to the Mugil sp. O, the putative cryptic species present in the Pacific Ocean and showed a 2n = 46 karyotype, which is composed of 2 metacentric and 44 subtelocentric/acrocentric chromosomes. This karyotype is different from the one described for M. incilis (2n = 48 and from those of the two western Atlantic lineages Mugil curema (2n = 28, and Mugil margaritae (2n = 24. Data suggest the need for a morphological analysis to assign a species name to this Pacific lineage.

A COMPARISON OF SOME ROBUST BIVARIATE CONTROL CHARTS FOR INDIVIDUAL OBSERVATIONS

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Moustafa Omar Ahmed Abu - Shawiesh

2014-06-01

Full Text Available This paper proposed and considered some bivariate control charts to monitor individual observations from a statistical process control. Usual control charts which use mean and variance-covariance estimators are sensitive to outliers. We consider the following robust alternatives to the classical Hoteling's T2: T2MedMAD, T2MCD, T2MVE a simulation study has been conducted to compare the performance of these control charts. Two real life data are analyzed to illustrate the application of these robust alternatives.

A comparison between multivariate and bivariate analysis used in marketing research

Directory of Open Access Journals (Sweden)

Constantin, C.

2012-01-01

Full Text Available This paper is about an instrumental research conducted in order to compare the information given by two multivariate data analysis in comparison with the usual bivariate analysis. The outcomes of the research reveal that sometimes the multivariate methods use more information from a certain variable, but sometimes they use only a part of the information considered the most important for certain associations. For this reason, a researcher should use both categories of data analysis in order to obtain entirely useful information.

Karyotype Diversity and Evolutionary Trends in Armored Catfish Species of the Genus Harttia (Siluriformes: Loricariidae).

Science.gov (United States)

Blanco, Daniel Rodrigues; Vicari, Marcelo Ricardo; Lui, Roberto Laridondo; Traldi, Josiane Baccarin; Bueno, Vanessa; Martinez, Juliana de Fátima; Brandão, Heleno; Oyakawa, Osvaldo Takeshi; Moreira Filho, Orlando

2017-04-01

Most species of the genus Harttia inhabits the headwaters of small tributaries, but some species are restricted to the main channel of some rivers. This feature, combined with limited dispersal ability, leads to the formation of small isolated populations with reduced gene flow. Currently, there are 23 taxonomically defined and recognized species, and 17 of these are found in Brazil, distributed in several hydrographic basins. Despite this diversity, few chromosomal data for the species belonging to this genus are found in the literature. Thus, this study analyzed, by classical and molecular cytogenetics methodologies, the chromosomal diversity of this genus, to discuss the processes that are involved in the evolution and karyotype differentiation of the species of the group. Seven species of Harttia were analyzed: H. kronei, H. longipinna, H. gracilis, H. punctata, H. loricariformis, H. torrenticola, and H. carvalhoi. The chromosomal diversity found in these species includes different diploid and fundamental numbers, distinct distribution of several repetitive sequences, the presence of supernumerary chromosomes in H. longipinna and multiple sex chromosome systems of the type XX/XY 1 Y 2 in H. carvalhoi and X 1 X 1 X 2 X 2 /X 1 X 2 Y in H. punctata. Lastly, our data highlight the genus Harttia as an excellent model for evolutionary studies.

Sorting cancer karyotypes using double-cut-and-joins, duplications and deletions.

Science.gov (United States)

Zeira, Ron; Shamir, Ron

2018-05-03

Problems of genome rearrangement are central in both evolution and cancer research. Most genome rearrangement models assume that the genome contains a single copy of each gene and the only changes in the genome are structural, i.e., reordering of segments. In contrast, tumor genomes also undergo numerical changes such as deletions and duplications, and thus the number of copies of genes varies. Dealing with unequal gene content is a very challenging task, addressed by few algorithms to date. More realistic models are needed to help trace genome evolution during tumorigenesis. Here we present a model for the evolution of genomes with multiple gene copies using the operation types double-cut-and-joins, duplications and deletions. The events supported by the model are reversals, translocations, tandem duplications, segmental deletions, and chromosomal amplifications and deletions, covering most types of structural and numerical changes observed in tumor samples. Our goal is to find a series of operations of minimum length that transform one karyotype into the other. We show that the problem is NP-hard and give an integer linear programming formulation that solves the problem exactly under some mild assumptions. We test our method on simulated genomes and on ovarian cancer genomes. Our study advances the state of the art in two ways: It allows a broader set of operations than extant models, thus being more realistic, and it is the first study attempting to reconstruct the full sequence of structural and numerical events during cancer evolution. Code and data are available in https://github.com/Shamir-Lab/Sorting-Cancer-Karyotypes. ronzeira@post.tau.ac.il, rshamir@tau.ac.il. Supplementary data are available at Bioinformatics online.

Karyotype evolution in Phalaris (Poaceae): The role of reductional dysploidy, polyploidy and chromosome alteration in a wide-spread and diverse genus.

Science.gov (United States)

Winterfeld, Grit; Becher, Hannes; Voshell, Stephanie; Hilu, Khidir; Röser, Martin

2018-01-01

Karyotype characteristics can provide valuable information on genome evolution and speciation, in particular in taxa with varying basic chromosome numbers and ploidy levels. Due to its worldwide distribution, remarkable variability in morphological traits and the fact that ploidy change plays a key role in its evolution, the canary grass genus Phalaris (Poaceae) is an excellent study system to investigate the role of chromosomal changes in species diversification and expansion. Phalaris comprises diploid species with two basic chromosome numbers of x = 6 and 7 as well as polyploids based on x = 7. To identify distinct karyotype structures and to trace chromosome evolution within the genus, we apply fluorescence in situ hybridisation (FISH) of 5S and 45S rDNA probes in four diploid and four tetraploid Phalaris species of both basic numbers. The data agree with a dysploid reduction from x = 7 to x = 6 as the result of reciprocal translocations between three chromosomes of an ancestor with a diploid chromosome complement of 2n = 14. We recognize three different genomes in the genus: (1) the exclusively Mediterranean genome A based on x = 6, (2) the cosmopolitan genome B based on x = 7 and (3) a genome C based on x = 7 and with a distribution in the Mediterranean and the Middle East. Both auto- and allopolyploidy of genomes B and C are suggested for the formation of tetraploids. The chromosomal divergence observed in Phalaris can be explained by the occurrence of dysploidy, the emergence of three different genomes, and the chromosome rearrangements accompanied by karyotype change and polyploidization. Mapping the recognized karyotypes on the existing phylogenetic tree suggests that genomes A and C are restricted to sections Phalaris and Bulbophalaris, respectively, while genome B occurs across all taxa with x = 7.

Karyotype evolution in Phalaris (Poaceae: The role of reductional dysploidy, polyploidy and chromosome alteration in a wide-spread and diverse genus.

Directory of Open Access Journals (Sweden)

Grit Winterfeld

Full Text Available Karyotype characteristics can provide valuable information on genome evolution and speciation, in particular in taxa with varying basic chromosome numbers and ploidy levels. Due to its worldwide distribution, remarkable variability in morphological traits and the fact that ploidy change plays a key role in its evolution, the canary grass genus Phalaris (Poaceae is an excellent study system to investigate the role of chromosomal changes in species diversification and expansion. Phalaris comprises diploid species with two basic chromosome numbers of x = 6 and 7 as well as polyploids based on x = 7. To identify distinct karyotype structures and to trace chromosome evolution within the genus, we apply fluorescence in situ hybridisation (FISH of 5S and 45S rDNA probes in four diploid and four tetraploid Phalaris species of both basic numbers. The data agree with a dysploid reduction from x = 7 to x = 6 as the result of reciprocal translocations between three chromosomes of an ancestor with a diploid chromosome complement of 2n = 14. We recognize three different genomes in the genus: (1 the exclusively Mediterranean genome A based on x = 6, (2 the cosmopolitan genome B based on x = 7 and (3 a genome C based on x = 7 and with a distribution in the Mediterranean and the Middle East. Both auto- and allopolyploidy of genomes B and C are suggested for the formation of tetraploids. The chromosomal divergence observed in Phalaris can be explained by the occurrence of dysploidy, the emergence of three different genomes, and the chromosome rearrangements accompanied by karyotype change and polyploidization. Mapping the recognized karyotypes on the existing phylogenetic tree suggests that genomes A and C are restricted to sections Phalaris and Bulbophalaris, respectively, while genome B occurs across all taxa with x = 7.

Karyotype-specific ear and hearing problems in young adults with turner syndrome and the effect of oxandrolone treatment

NARCIS (Netherlands)

Verver, E.J.; Freriks, K.; Sas, T.C.J.; Huygen, P.L.M.; Pennings, R.J.E.; Smeets, D.F.C.M.; Hermus, A.R.M.M.; Menke, L.A.; Wit, J.M.; Otten, B.J.; Velden, J.A.M. van der; Keizer-Schrama, S.M.; Topsakal, V.; Admiraal, R.J.C.; Timmers, H.J.L.M.; Kunst, H.P.M.

2014-01-01

OBJECTIVE: To evaluate karyotype-specific ear and hearing problems in young-adult patients with Turner syndrome (TS) and assess the effects of previous treatment with oxandrolone (Ox). STUDY DESIGN: Double-blind follow-up study. SETTING: University hospital. PATIENTS: Sixty-five TS patients (mean

Karyotype description of possible new species of the Hypostomus ancistroides complex (Teleostei: Loricariidae and other Hypostominae - doi: 10.4025/actascibiolsci.v34i2.9318

Directory of Open Access Journals (Sweden)

Horácio Ferreira Júlio Júnior

2012-03-01

Full Text Available Cytogenetic analyses were performed in four species of the Hypostominae subfamily, three from Hypostomus (Hypostomini genus and Rhinelepis aspera (Rhinelepini. Three populations of Hypostomus ancistroides were analyzed, which had 2n=68 chromosomes, but presented different karyotype formulas. Hypostomus regani and H. strigaticeps, both from Ivaí river, showed 2n=72 chromosomes with two distinct cytotypes. In turn, R. aspera of the upper Paraná river basin presented 2n=54 chromosome. Multiple Nucleolar Organizer Regions (NORs have been evidenced by silver nitrate staining in species of Hypostomus and single NOR in R. aspera. The observed variation in the chromosome number and the marked variability in karyotype formulas and NORs reveal a certain amount of karyotype variation in the genus Hypostomus suggesting the probable existence of cryptic species with independent chromosome traits. Therefore, our data can be of great value in discriminating species and understanding their chromosomal evolution.

Identification of Proteins Related to Epigenetic Regulation in the Malignant Transformation of Aberrant Karyotypic Human Embryonic Stem Cells by Quantitative Proteomics

Science.gov (United States)

Sun, Yi; Yang, Yixuan; Zeng, Sicong; Tan, Yueqiu; Lu, Guangxiu; Lin, Ge

2014-01-01

Previous reports have demonstrated that human embryonic stem cells (hESCs) tend to develop genomic alterations and progress to a malignant state during long-term in vitro culture. This raises concerns of the clinical safety in using cultured hESCs. However, transformed hESCs might serve as an excellent model to determine the process of embryonic stem cell transition. In this study, ITRAQ-based tandem mass spectrometry was used to quantify normal and aberrant karyotypic hESCs proteins from simple to more complex karyotypic abnormalities. We identified and quantified 2583 proteins, and found that the expression levels of 316 proteins that represented at least 23 functional molecular groups were significantly different in both normal and abnormal hESCs. Dysregulated protein expression in epigenetic regulation was further verified in six pairs of hESC lines in early and late passage. In summary, this study is the first large-scale quantitative proteomic analysis of the malignant transformation of aberrant karyotypic hESCs. The data generated should serve as a useful reference of stem cell-derived tumor progression. Increased expression of both HDAC2 and CTNNB1 are detected as early as the pre-neoplastic stage, and might serve as prognostic markers in the malignant transformation of hESCs. PMID:24465727

Clonal karyotypic abnormalities in colorectal adenomas: clues to the early genetic events in the adenoma-carcinoma sequence

DEFF Research Database (Denmark)

Bomme, L; Bardi, G; Pandis, N

1994-01-01

and together with other numerical changes in another. A +7 was also present in one case with structural aberrations. Other recurrent numerical aberrations were -14 and -18, both found in 2 adenomas with structural karyotypic changes; in addition, one chromosome 14 was lost in one of the tumors with only...

A non-parametric conditional bivariate reference region with an application to height/weight measurements on normal girls

DEFF Research Database (Denmark)

Petersen, Jørgen Holm

2009-01-01

A conceptually simple two-dimensional conditional reference curve is described. The curve gives a decision basis for determining whether a bivariate response from an individual is "normal" or "abnormal" when taking into account that a third (conditioning) variable may influence the bivariate...... response. The reference curve is not only characterized analytically but also by geometric properties that are easily communicated to medical doctors - the users of such curves. The reference curve estimator is completely non-parametric, so no distributional assumptions are needed about the two......-dimensional response. An example that will serve to motivate and illustrate the reference is the study of the height/weight distribution of 7-8-year-old Danish school girls born in 1930, 1950, or 1970....

Bivariate return periods of temperature and precipitation explain a large fraction of European crop yields

Directory of Open Access Journals (Sweden)

J. Zscheischler

2017-07-01

Full Text Available Crops are vital for human society. Crop yields vary with climate and it is important to understand how climate and crop yields are linked to ensure future food security. Temperature and precipitation are among the key driving factors of crop yield variability. Previous studies have investigated mostly linear relationships between temperature and precipitation and crop yield variability. Other research has highlighted the adverse impacts of climate extremes, such as drought and heat waves, on crop yields. Impacts are, however, often non-linearly related to multivariate climate conditions. Here we derive bivariate return periods of climate conditions as indicators for climate variability along different temperature–precipitation gradients. We show that in Europe, linear models based on bivariate return periods of specific climate conditions explain on average significantly more crop yield variability (42 % than models relying directly on temperature and precipitation as predictors (36 %. Our results demonstrate that most often crop yields increase along a gradient from hot and dry to cold and wet conditions, with lower yields associated with hot and dry periods. The majority of crops are most sensitive to climate conditions in summer and to maximum temperatures. The use of bivariate return periods allows the integration of non-linear impacts into climate–crop yield analysis. This offers new avenues to study the link between climate and crop yield variability and suggests that they are possibly more strongly related than what is inferred from conventional linear models.

Analysis of horse genomes provides insight into the diversification and adaptive evolution of karyotype

OpenAIRE

Huang, J. L.; Zhao, Y. P.; Shiraigol, W.; Li, B.; Bai, D. Y.; Ye, W. X.; Daidiikhuu, D.; Yang, L. H.; Jin, Brqqg; Zhao, Q. A.; Gao, Y. H.; Wu, J.; Bao, Wydl; Li, A. A.; Zhang, Y. H. Percival

2014-01-01

Karyotypic diversification is more prominent in Equus species than in other mammals. Here, using next generation sequencing technology, we generated and de novo assembled quality genomes sequences for a male wild horse (Przewalski's horse) and a male domestic horse (Mongolian horse), with about 93-fold and 91-fold coverage, respectively. Portion of Y chromosome from wild horse assemblies (3 M bp) and Mongolian horse (2 M bp) were also sequenced and de novo assembled. We confirmed a Robertsoni...

Karyotype supporting Mugil curema Valenciennes, 1836 and Mugil gaimardianus Desmarest, 1831 (Mugilidae: Teleostei as two valid nominal species

Directory of Open Access Journals (Sweden)

Mauro Nirchio

2003-03-01

Full Text Available In this study, we present the karyotypic features of two taxa, curema and gaimardianus (genus Mugil, supposed to be synonyms by some authors. Their cytogenetic differences are conspicuous and unambiguous, providing evidence that Mugil curema and Mugil gaimardanus are two valid nominal species.

Individualized choice in prenatal diagnosis : the impact of karyotyping and standalone rapid aneuploidy detection on quality of life

NARCIS (Netherlands)

Boormans, E. M. A.; Birnie, E.; Oepkes, D.; Boekkooi, P. F.; Bonsel, G. J.; van Lith, J. M. M.

2010-01-01

Objective To assess the reasons and perceptions of women who are offered a choice between karyotyping and standalone rapid aneuploidy detection (RAD) and to compare the impact of both tests on anxiety and health-related quality of life Methods In this prospective comparative study, women undergoing

Variation of morphology, karyotype and protein band pattern of adenium (Adenium obesum varieties

Directory of Open Access Journals (Sweden)

PRABANG SETYONO

2009-07-01

Full Text Available Hastuti D, Suranto, Setyono P. 2009. Variation of morphology, karyotype and protein band pattern of adenium (Adenium obesum varieties. Nusantara Bioscience 1: 78-83. The aim of this research to find out the Adenium obesum variation from six varieties, namely: obesum, cery, red lucas, red fanta , white bigben and harry potter based on morphology, karyotype, as well as protein banding pattern. The chromosome preparation was made using semi-permanent squash method from the tip of root plant; while protein banding pattern was made using SDS-PAGE method. Qualitative data included shape and color of the leave and flower described from each variety. Data were presented in morphometry and analyzed using ANOVA and then followed by DMRT with 5% of confidence levels, indicated significance difference. Protein banding pattern, the root, stem, leave and all organs were analyzed using Hierarchical Cluster Analysis method with Average Linkage (between Groups using SPSS 10.0. The result of research shows that the six A. obesum varieties have morphological character with no variation of light green to dark green leave, not hairy, smooth leave bone, meanwhile for light red to dark red flower crown color although some of them are white and the same funnel color, yellow. All varieties of A. obesum have same number of chromosome, 2n = 22 and shows the difference ranging from 2.56 to 5.13 um. In the banding pattern formed qualitatively, there is variation among the six varieties.

Karyotypes and Distribution of Tandem Repeat Sequences in Brassica nigra Determined by Fluorescence in situ Hybridization

Czech Academy of Sciences Publication Activity Database

Wang, G.; He, Q.; Macas, Jiří; Novák, Petr; Neumann, Pavel; Meng, D.; Zhao, H.; Guo, N.; Han, S.; Zong, M.; Jin, W.; Liu, F.

2017-01-01

Roč. 152, č. 3 (2017), s. 158-165 ISSN 1424-8581 R&D Projects: GA ČR GBP501/12/G090 Institutional support: RVO:60077344 Keywords : asymmetric somatic hybridization * Fluorescence in situ hybridization * Karyotype * (Peri) centromere Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Genetics and heredity (medical genetics to be 3) Impact factor: 1.354, year: 2016

Comparison of the karyotypes ofPsathyrostachys juncea andP. huashanica (Poaceae) studied by banding techniques

DEFF Research Database (Denmark)

Linde-Laursen, Ib; Bothmer, R. von

1986-01-01

. The patterns of both taxa are polymorphic, supporting that both taxa are outbreeders. The karyotypic characters suggest that P. juncea is more closely related to P. fragilis than either is to P. huashanica. N-banding stains weakly. Silver nitrate staining demonstrates that nucleolus organizers of both species...... have different nucleolus forming capacities. The presence of micronucleoli suggests that both species have an extra unidentified chromosome with nucleolus forming capacity....

Karyotype study of the South American fruit fly, Anastrepha fraterculus (Wied.) in Argentina

International Nuclear Information System (INIS)

Lifschitz, E.; Manso, F.; Basso, A.

1999-01-01

The most frequent karyotype of Anastrepha fraterculus in Argentina is described here on the basis of mitotic metaphase morphology. It was named ''fraterculus Arg 1''. The diploid number is 2n=10+XX/XY and in males it comprises five homomorphic pairs and one heteomorphic pair, the latter being the sexual pair. Samples from different populations were cytologically analyzed, and ''fraterculus Arg 1'' is present in all of them at a high frequency (about 60%). A typical C band pattern of the X chromosome was found only in the Montecarlo (Misiones province) population. (author)

Karyotype Reorganization in the Hokou Gecko (Gekko hokouensis, Gekkonidae): The Process of Microchromosome Disappearance in Gekkota.

Science.gov (United States)

Srikulnath, Kornsorn; Uno, Yoshinobu; Nishida, Chizuko; Ota, Hidetoshi; Matsuda, Yoichi

2015-01-01

The Hokou gecko (Gekko hokouensis: Gekkonidae, Gekkota, Squamata) has the chromosome number 2n = 38, with no microchromosomes. For molecular cytogenetic characterization of the gekkotan karyotype, we constructed a cytogenetic map for G. hokouensis, which retains the ancestral karyotype of Gekkota, with 86 functional genes, and compared it with cytogenetic maps for four Toxicofera species that have many microchromosomes (Elaphe quadrivirgata, Varanus salvator macromaculatus, Leiolepis reevesii rubritaeniata, and Anolis carolinensis) and that for a lacertid species (Lacerta agilis) with only one pair of autosomal microchromosomes. Ten pairs of G. hokouensis chromosomes [GHO1, 2, 3, Z(4), 6, 7, 8, 13, 14, and 15] showed highly conserved linkage homology with macrochromosomes and/or macrochromosome arms of the four Toxicofera species and corresponded to eight L. agilis macrochromosomes (LAG). However, GHO5, GHO9, GHO10, GHO11, and LAG6 were composed of chromosome segments that have a homology with Toxicofera microchromosomes, and no homology was found in the chromosomes between G. hokouensis and L. agilis. These results suggest that repeated fusions of microchromosomes may have occurred independently in each lineage of Gekkota and Lacertidae, leading to the disappearance of microchromosomes and appearance of small-sized macrochromosomes.

Recurrent major depression and right hippocampal volume: A bivariate linkage and association study.

Science.gov (United States)

Mathias, Samuel R; Knowles, Emma E M; Kent, Jack W; McKay, D Reese; Curran, Joanne E; de Almeida, Marcio A A; Dyer, Thomas D; Göring, Harald H H; Olvera, Rene L; Duggirala, Ravi; Fox, Peter T; Almasy, Laura; Blangero, John; Glahn, David C

2016-01-01

Previous work has shown that the hippocampus is smaller in the brains of individuals suffering from major depressive disorder (MDD) than those of healthy controls. Moreover, right hippocampal volume specifically has been found to predict the probability of subsequent depressive episodes. This study explored the utility of right hippocampal volume as an endophenotype of recurrent MDD (rMDD). We observed a significant genetic correlation between the two traits in a large sample of Mexican American individuals from extended pedigrees (ρg = -0.34, p = 0.013). A bivariate linkage scan revealed a significant pleiotropic quantitative trait locus on chromosome 18p11.31-32 (LOD = 3.61). Bivariate association analysis conducted under the linkage peak revealed a variant (rs574972) within an intron of the gene SMCHD1 meeting the corrected significance level (χ(2) = 19.0, p = 7.4 × 10(-5)). Univariate association analyses of each phenotype separately revealed that the same variant was significant for right hippocampal volume alone, and also revealed a suggestively significant variant (rs12455524) within the gene DLGAP1 for rMDD alone. The results implicate right-hemisphere hippocampal volume as a possible endophenotype of rMDD, and in so doing highlight a potential gene of interest for rMDD risk. © 2015 Wiley Periodicals, Inc.

Comparison of Six Methods for the Detection of Causality in a Bivariate Time Series

Czech Academy of Sciences Publication Activity Database

Krakovská, A.; Jakubík, J.; Chvosteková, M.; Coufal, David; Jajcay, Nikola; Paluš, Milan

2018-01-01

Roč. 97, č. 4 (2018), č. článku 042207. ISSN 2470-0045 R&D Projects: GA MZd(CZ) NV15-33250A Institutional support: RVO:67985807 Keywords : comparative study * causality detection * bivariate models * Granger causality * transfer entropy * convergent cross mappings Impact factor: 2.366, year: 2016 https://journals.aps.org/pre/abstract/10.1103/PhysRevE.97.042207

Bivariate- distribution for transition matrix elements in Breit-Wigner to Gaussian domains of interacting particle systems.

Science.gov (United States)

Kota, V K B; Chavda, N D; Sahu, R

2006-04-01

Interacting many-particle systems with a mean-field one-body part plus a chaos generating random two-body interaction having strength lambda exhibit Poisson to Gaussian orthogonal ensemble and Breit-Wigner (BW) to Gaussian transitions in level fluctuations and strength functions with transition points marked by lambda = lambda c and lambda = lambda F, respectively; lambda F > lambda c. For these systems a theory for the matrix elements of one-body transition operators is available, as valid in the Gaussian domain, with lambda > lambda F, in terms of orbital occupation numbers, level densities, and an integral involving a bivariate Gaussian in the initial and final energies. Here we show that, using a bivariate-t distribution, the theory extends below from the Gaussian regime to the BW regime up to lambda = lambda c. This is well tested in numerical calculations for 6 spinless fermions in 12 single-particle states.

Analysis of horse genomes provides insight into the diversification and adaptive evolution of karyotype

OpenAIRE

Huang, Jinlong; Zhao, Yiping; Shiraigol, Wunierfu; Li, Bei; Bai, Dongyi; Ye, Weixing; Daidiikhuu, Dorjsuren; Yang, Lihua; Jin, Burenqiqige; Zhao, Qinan; Gao, Yahan; Wu, Jing; Bao, Wuyundalai; Li, Anaer; Zhang, Yuhong

2014-01-01

Karyotypic diversification is more prominent in Equus species than in other mammals. Here, using next generation sequencing technology, we generated and de novo assembled quality genomes sequences for a male wild horse (Przewalski's horse) and a male domestic horse (Mongolian horse), with about 93-fold and 91-fold coverage, respectively. Portion of Y chromosome from wild horse assemblies (3 M bp) and Mongolian horse (2 M bp) were also sequenced and de novo assembled. We confirmed a Robertsoni...

On the construction of bivariate exponential distributions with an arbitrary correlation coefficient

DEFF Research Database (Denmark)

Bladt, Mogens; Nielsen, Bo Friis

In this paper we use a concept of multivariate phase-type distributions to define a class of bivariate exponential distributions. This class has the following three appealing properties. Firstly, we may construct a pair of exponentially distributed random variables with any feasible correlation...... coefficient (also negative). Secondly, the class satisfies that any linear combination (projection) of the marginal random variables is a phase {type distributions, The latter property is potentially important for the development hypothesis testing in linear models. Thirdly, it is very easy to simulate...

A dynamic bivariate Poisson model for analysing and forecasting match results in the English Premier League

NARCIS (Netherlands)

Koopman, S.J.; Lit, R.

2015-01-01

Summary: We develop a statistical model for the analysis and forecasting of football match results which assumes a bivariate Poisson distribution with intensity coefficients that change stochastically over time. The dynamic model is a novelty in the statistical time series analysis of match results

Karyotypes and fish detection of 5s and 45s rdna loci in chinese medicinal plant atractylodes lancea subsp. luotianensis: cytological evidence for the new taxonomic unit

International Nuclear Information System (INIS)

Duan, Y.S.; Zhu, B.; Li, Z.Y.

2015-01-01

Atractylodes lancea (Thunb.) DC. in the Asteraceae family produces the atractylodes rhizome which is widely used as a traditional medicine in China. The subspecies A. lancea (Thunb.) DC subsp. Luotianensis distributed in mountainous Luotian and Yingshan regions in Hubei Province presented distinct morphology and superior medicinal quality. This study firstly reported the chromosome karyotype of this subspecies and the detection of 5S and 45S rDNA loci by fluorescent in situ hybridization. The karyotype was 2n=24=12m+12sm (2SAT). A single locus of 5S rDNA and two loci of 45S rDNA loci were identified and separated on different chromosomes. Its one pair of the satellited chromosomes rather than two pairs in other Atractylodes species yet still with 2n=24 occurred likely after its occupation of this geographic location. The evidence of karyotype differentiation of this subspecies native to the area is useful for elucidating the genome structure and identifying chromosomes. (author)

Bivariate pointing movements on large touch screens: investigating the validity of a refined Fitts' Law.

Science.gov (United States)

Bützler, Jennifer; Vetter, Sebastian; Jochems, Nicole; Schlick, Christopher M

2012-01-01

On the basis of three empirical studies Fitts' Law was refined for bivariate pointing tasks on large touch screens. In the first study different target width parameters were investigated. The second study considered the effect of the motion angle. Based on the results of the two studies a refined model for movement time in human-computer interaction was formulated. A third study, which is described here in detail, concerns the validation of the refined model. For the validation study 20 subjects had to execute a bivariate pointing task on a large touch screen. In the experimental task 250 rectangular target objects were displayed at a randomly chosen position on the screen covering a broad range of ID values (ID= [1.01; 4.88]). Compared to existing refinements of Fitts' Law, the new model shows highest predictive validity. A promising field of application of the model is the ergonomic design and evaluation of project management software. By using the refined model, software designers can calculate a priori the appropriate angular position and the size of buttons, menus or icons.

Selection effects in the bivariate brightness distribution for spiral galaxies

International Nuclear Information System (INIS)

Phillipps, S.; Disney, M.

1986-01-01

The joint distribution of total luminosity and characteristic surface brightness (the bivariate brightness distribution) is investigated for a complete sample of spiral galaxies in the Virgo cluster. The influence of selection and physical limits of various kinds on the apparent distribution are detailed. While the distribution of surface brightness for bright galaxies may be genuinely fairly narrow, faint galaxies exist right across the (quite small) range of accessible surface brightnesses so no statement can be made about the true extent of the distribution. The lack of high surface brightness bright galaxies in the Virgo sample relative to an overall RC2 sample (mostly field galaxies) supports the contention that the star-formation rate is reduced in the inner region of the cluster for environmental reasons. (author)

Can the bivariate Hurst exponent be higher than an average of the separate Hurst exponents?

Czech Academy of Sciences Publication Activity Database

Krištoufek, Ladislav

2015-01-01

Roč. 431, č. 1 (2015), s. 124-127 ISSN 0378-4371 R&D Projects: GA ČR(CZ) GP14-11402P Institutional support: RVO:67985556 Keywords : Correlations * Power- law cross-correlations * Bivariate Hurst exponent * Spectrum coherence Subject RIV: AH - Economics Impact factor: 1.785, year: 2015 http://library.utia.cas.cz/separaty/2015/E/kristoufek-0452314.pdf

Comparing Johnson’s SBB, Weibull and Logit-Logistic bivariate distributions for modeling tree diameters and heights using copulas

Energy Technology Data Exchange (ETDEWEB)

Cardil Forradellas, A.; Molina Terrén, D.M.; Oliveres, J.; Castellnou, M.

2016-07-01

Aim of study: In this study we compare the accuracy of three bivariate distributions: Johnson’s SBB, Weibull-2P and LL-2P functions for characterizing the joint distribution of tree diameters and heights. Area of study: North-West of Spain. Material and methods: Diameter and height measurements of 128 plots of pure and even-aged Tasmanian blue gum (Eucalyptus globulus Labill.) stands located in the North-west of Spain were considered in the present study. The SBB bivariate distribution was obtained from SB marginal distributions using a Normal Copula based on a four-parameter logistic transformation. The Plackett Copula was used to obtain the bivariate models from the Weibull and Logit-logistic univariate marginal distributions. The negative logarithm of the maximum likelihood function was used to compare the results and the Wilcoxon signed-rank test was used to compare the related samples of these logarithms calculated for each sample plot and each distribution. Main results: The best results were obtained by using the Plackett copula and the best marginal distribution was the Logit-logistic. Research highlights: The copulas used in this study have shown a good performance for modeling the joint distribution of tree diameters and heights. They could be easily extended for modelling multivariate distributions involving other tree variables, such as tree volume or biomass. (Author)

A comparison of bivariate, multivariate random-effects, and Poisson correlated gamma-frailty models to meta-analyze individual patient data of ordinal scale diagnostic tests.

Science.gov (United States)

Simoneau, Gabrielle; Levis, Brooke; Cuijpers, Pim; Ioannidis, John P A; Patten, Scott B; Shrier, Ian; Bombardier, Charles H; de Lima Osório, Flavia; Fann, Jesse R; Gjerdingen, Dwenda; Lamers, Femke; Lotrakul, Manote; Löwe, Bernd; Shaaban, Juwita; Stafford, Lesley; van Weert, Henk C P M; Whooley, Mary A; Wittkampf, Karin A; Yeung, Albert S; Thombs, Brett D; Benedetti, Andrea

2017-11-01

Individual patient data (IPD) meta-analyses are increasingly common in the literature. In the context of estimating the diagnostic accuracy of ordinal or semi-continuous scale tests, sensitivity and specificity are often reported for a given threshold or a small set of thresholds, and a meta-analysis is conducted via a bivariate approach to account for their correlation. When IPD are available, sensitivity and specificity can be pooled for every possible threshold. Our objective was to compare the bivariate approach, which can be applied separately at every threshold, to two multivariate methods: the ordinal multivariate random-effects model and the Poisson correlated gamma-frailty model. Our comparison was empirical, using IPD from 13 studies that evaluated the diagnostic accuracy of the 9-item Patient Health Questionnaire depression screening tool, and included simulations. The empirical comparison showed that the implementation of the two multivariate methods is more laborious in terms of computational time and sensitivity to user-supplied values compared to the bivariate approach. Simulations showed that ignoring the within-study correlation of sensitivity and specificity across thresholds did not worsen inferences with the bivariate approach compared to the Poisson model. The ordinal approach was not suitable for simulations because the model was highly sensitive to user-supplied starting values. We tentatively recommend the bivariate approach rather than more complex multivariate methods for IPD diagnostic accuracy meta-analyses of ordinal scale tests, although the limited type of diagnostic data considered in the simulation study restricts the generalization of our findings. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Achondroplasia with 47, XXY karyotype: a case report of the neonatal diagnosis of an extremely unusual association.

Science.gov (United States)

Ros-Pérez, Purificación; Regidor, Francisco J; Colino, Esmeralda; Martínez-Payo, Cristina; Barroso, Eva; Heath, Karen E

2012-06-29

The association of achondroplasia and Klinefelter syndrome is extremely rare. To date, five cases have been previously reported, all of them diagnosed beyond the postnatal period, and only one was molecularly characterized. We describe the first case of this unusual association diagnosed in the neonatal period, the clinical findings and the molecular studies undertaken. The boy was born at term with clinical and radiological features indicating the diagnosis of achondroplasia or hypochondroplasia combined with the prenatal karyotype of Klinefelter syndrome (47,XXY). Neonatal FGFR3 mutation screening showed that the newborn was heterozygous for the classic achondroplasia G340R mutation. Microsatellite marker analysis showed that the sex chromosome aneuploidy had arisen from a non-disjunction error in paternal meiosis I, with a recombination event in the pseudoautosomal region 1 (PAR1). Specific mutation analysis is appropriate to confirm the clinical diagnosis of achondroplasia for appropriate diagnosis, prognosis, and genetic counseling, especially when the karyotype does not explain the abnormal prenatal sonographic findings. In the present case, a recombination event was observed in the PAR1 region, although recombinational events in paternally derived Klinefelter syndrome cases are much rarer than expected.

Achondroplasia with 47, xxy karyotype: a case report of the neonatal diagnosis of an extremely unusual association

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Ros-Pérez Purificación

2012-06-01

Full Text Available Abstract Background The association of achondroplasia and Klinefelter syndrome is extremely rare. To date, five cases have been previously reported, all of them diagnosed beyond the postnatal period, and only one was molecularly characterized. We describe the first case of this unusual association diagnosed in the neonatal period, the clinical findings and the molecular studies undertaken. Case presentation The boy was born at term with clinical and radiological features indicating the diagnosis of achondroplasia or hypochondroplasia combined with the prenatal karyotype of Klinefelter syndrome (47,XXY. Neonatal FGFR3 mutation screening showed that the newborn was heterozygous for the classic achondroplasia G340R mutation. Microsatellite marker analysis showed that the sex chromosome aneuploidy had arisen from a non-disjunction error in paternal meiosis I, with a recombination event in the pseudoautosomal region 1 (PAR1. Conclusion Specific mutation analysis is appropriate to confirm the clinical diagnosis of achondroplasia for appropriate diagnosis, prognosis, and genetic counseling, especially when the karyotype does not explain the abnormal prenatal sonographic findings. In the present case, a recombination event was observed in the PAR1 region, although recombinational events in paternally derived Klinefelter syndrome cases are much rarer than expected.

Mitotic karyotype of the tropical freshwater crayfish Procambarus (Austrocambarus llamasi (Decapoda: Cambaridae

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Jeane R Indy

2010-06-01

Full Text Available In Mexico, the biology of Procambarus has been more studied than the biology of other Cambarids because of its diversity and potential use in aquaculture. We determined the karyotype of the Mexican tropical freshwater crayfish Procambarus (Austrocambarus llamasi from 189 metaphase spreads from gill tissues of 17 adults. They had 98-120 chromosomes (mode 2n=120 chromosomes. There are 60 pairs of monoarm, telocentric chromosomes. Sex chromosomes were not detected and we propose that the P. llamasi karyotype can be used to distinguish this species from other Mexican crayfish. Additionally, we suggest using karyological data in aquaculture and conservation biology. Rev. Biol. Trop. 58 (2: 655-662. Epub 2010 June 02.El género Procambarus ha recibido mayor atención en los estudios de los principios fundamentales de su biología debido a su diversidad en el territorio mexicano y potencial uso en acuicultura. El cariotipo típico del acocil tropical mexicano Procambarus (Austrocambarus llamasi, se estudió mediante 189 dispersiones cromosómicas en metafase del tejido branquial de 17 adultos tratados con la técnica citológica de inmersión. Encontramos un amplio número de cromosomas, que variaron entre 98-120 elementos cromosómicos, con número modal diploide de 2n=120 elementos cromosómicos. El cariotipo del acocil tropical esta constituido por 60 pares de cromosomas monorrámeos, todos los centrómero están en la región telocéntrica de los cromosomas. En las metafases mitóticas de hembras y machos no fueron identificados cromosomas sexuales. Sugerimos considerar la estructura cromosómica del cariotipo como una herramienta citotaxonómica así como el empleo de datos cariológicos para propósitos de acuicultura y conservación del acocil tropical.

Karyotype rearrangements and telomere analysis in Myzus persicae (Hemiptera, Aphididae) strains collected on Lavandula sp. plants

Science.gov (United States)

Mandrioli, Mauro; Zanasi, Federica; Manicardi, Gian Carlo

2014-01-01

Abstract Karyotype analysis of nine strains of the peach-potato aphid Myzus persicae (Sulzer, 1776), collected on Lavandula sp. plants, evidenced showed that five of them had a standard 2n = 12 karyotype, one possessed a fragmentation of the X chromosome occurring at the telomere opposite to the NOR-bearing one and three strains had a chromosome number 2n = 11 due to a non-reciprocal translocation of an autosome A3 onto an A1 chromosome. Interestingly, the terminal portion of the autosome A1 involved in the translocation was the same in all the three strains, as evidenced by FISH with the histone cluster as a probe. The study of telomeres in the Myzus persicae strain with the X fission evidenced that telomerase synthesised de novo telomeres at the breakpoints resulting in the stabilization of the chromosomal fragments. Lastly, despite the presence of a conserved telomerase, aphid genome is devoid of genes coding for shelterin, a complex of proteins involved in telomere functioning frequently reported as conserved in eukaryotes. The absence of this complex, also confirmed in the genome of other arthropods, suggests that the shift in the sequence of the telomeric repeats has been accompanied by other changes in the telomere components in arthropods in respect to other metazoans. PMID:25610541

Karyotype Reorganization in the Hokou Gecko (Gekko hokouensis, Gekkonidae: The Process of Microchromosome Disappearance in Gekkota.

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Kornsorn Srikulnath

Full Text Available The Hokou gecko (Gekko hokouensis: Gekkonidae, Gekkota, Squamata has the chromosome number 2n = 38, with no microchromosomes. For molecular cytogenetic characterization of the gekkotan karyotype, we constructed a cytogenetic map for G. hokouensis, which retains the ancestral karyotype of Gekkota, with 86 functional genes, and compared it with cytogenetic maps for four Toxicofera species that have many microchromosomes (Elaphe quadrivirgata, Varanus salvator macromaculatus, Leiolepis reevesii rubritaeniata, and Anolis carolinensis and that for a lacertid species (Lacerta agilis with only one pair of autosomal microchromosomes. Ten pairs of G. hokouensis chromosomes [GHO1, 2, 3, Z(4, 6, 7, 8, 13, 14, and 15] showed highly conserved linkage homology with macrochromosomes and/or macrochromosome arms of the four Toxicofera species and corresponded to eight L. agilis macrochromosomes (LAG. However, GHO5, GHO9, GHO10, GHO11, and LAG6 were composed of chromosome segments that have a homology with Toxicofera microchromosomes, and no homology was found in the chromosomes between G. hokouensis and L. agilis. These results suggest that repeated fusions of microchromosomes may have occurred independently in each lineage of Gekkota and Lacertidae, leading to the disappearance of microchromosomes and appearance of small-sized macrochromosomes.

The relationship of initial embryo crown--rump length to pregnancy outcome and abortus karyotype based on new growth curves for the 2-31 mm embryo.

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Dickey, R P; Gasser, R F; Olar, T T; Curole, D N; Taylor, S N; Matulich, E M; West, J D; Tsien, F

1994-02-01

The objective of this study was to determine if measurement of initial crown--rump length (CRL) is helpful in predicting low birth weight, newborn length, spontaneous abortions, or abortus karyotype. We measured CRL prospectively in 837 consecutive singleton pregnancies at the time a heart rate was first detectable with transvaginal ultrasonography and compared these measurements to normal values for the 10th through 90th centiles determined from 227 transvaginal ultrasound measurements in in-vitro fertilization and gamete intra-Fallopian transfer pregnancies with known ovulation dates. The relationship of initial CRL to birth weight and length and to abortion and abortus karyotype was analysed after all pregnancies had delivered. Initial CRL measured after the 28th post-ovulation day was predictive of subsequent abortion, but not of low birth weight or length. The abortion rate was 3.3% [95% confidence interval (CI) 1.5%, 5.1%] when initial CRL > or = 50th centile, compared to 19.4% (95% CI 15.4%, 23.4%) when aborti. These results indicate that initial CRL measured after the 28th post-ovulation day may help to identify pregnancies at increased risk of abortion due to abnormal karyotypes.

Application of bivariate mapping for hydrological classification and analysis of temporal change and scale effects in Switzerland

NARCIS (Netherlands)

Speich, Matthias J.R.; Bernhard, Luzi; Teuling, Ryan; Zappa, Massimiliano

2015-01-01

Hydrological classification schemes are important tools for assessing the impacts of a changing climate on the hydrology of a region. In this paper, we present bivariate mapping as a simple means of classifying hydrological data for a quantitative and qualitative assessment of temporal change.

Karyotyping and in situ chromosomal localization of rDNA sites in black cumin Bunium persicum (Boiss B. Fedtsch,1915 (Apiaceae

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R. K. Chahota

2011-11-01

Full Text Available The fluorescent in situ hybridization (FISH technique has been applied to somatic chromosomes in the medicinally important species, Bunium persicum, to elucidate its karyotypes. The bicolour FISH technique involving 18S-5.8S-26S and 5S ribosomal RNA genes as probes was used to assign physical localization and measurement of rDNA sites on homologous pairs of chromosomes. The two 18S-5.8S-26S rRNA gene sites were at the terminal regions of the short arms of the chromosomes 1 and 2 involving NOR region of chromosome 1. The 5S rDNA sites were found on subtelomeric region of the long arm of the chromosome number 5 and at interstitial regions of the short arm of chromosome 7. Based on direct visual analysis of chromosome length, morphology and position of FISH signals, a pioneer attempt has been made to construct metaphase karyotype in B. persicum, an endangered medicinal plant of North Western Himalayas.

Genome Size Diversity in Lilium (Liliaceae Is Correlated with Karyotype and Environmental Traits

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Yun-peng Du

2017-07-01

Full Text Available Genome size (GS diversity is of fundamental biological importance. The occurrence of giant genomes in angiosperms is restricted to just a few lineages in the analyzed genome size of plant species so far. It is still an open question whether GS diversity is shaped by neutral or natural selection. The genus Lilium, with giant genomes, is phylogenetically and horticulturally important and is distributed throughout the northern hemisphere. GS diversity in Lilium and the underlying evolutionary mechanisms are poorly understood. We performed a comprehensive study involving phylogenetically independent analysis on 71 species to explore the diversity and evolution of GS and its correlation with karyological and environmental traits within Lilium (including Nomocharis. The strong phylogenetic signal detected for GS in the genus provides evidence consistent with that the repetitive DNA may be the primary contributors to the GS diversity, while the significant positive relationships detected between GS and the haploid chromosome length (HCL provide insights into patterns of genome evolution. The relationships between GS and karyotypes indicate that ancestral karyotypes of Lilium are likely to have exhibited small genomes, low diversity in centromeric index (CVCI values and relatively high relative variation in chromosome length (CVCL values. Significant relationships identified between GS and annual temperature and between GS and annual precipitation suggest that adaptation to habitat strongly influences GS diversity. We conclude that GS in Lilium is shaped by both neutral (genetic drift and adaptive evolution. These findings will have important consequences for understanding the evolution of giant plant genomes, and exploring the role of repetitive DNA fraction and chromosome changes in a plant group with large genomes and conservation of chromosome number.

The Evaluation of Bivariate Mixed Models in Meta-analyses of Diagnostic Accuracy Studies with SAS, Stata and R.

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Vogelgesang, Felicitas; Schlattmann, Peter; Dewey, Marc

2018-05-01

Meta-analyses require a thoroughly planned procedure to obtain unbiased overall estimates. From a statistical point of view not only model selection but also model implementation in the software affects the results. The present simulation study investigates the accuracy of different implementations of general and generalized bivariate mixed models in SAS (using proc mixed, proc glimmix and proc nlmixed), Stata (using gllamm, xtmelogit and midas) and R (using reitsma from package mada and glmer from package lme4). Both models incorporate the relationship between sensitivity and specificity - the two outcomes of interest in meta-analyses of diagnostic accuracy studies - utilizing random effects. Model performance is compared in nine meta-analytic scenarios reflecting the combination of three sizes for meta-analyses (89, 30 and 10 studies) with three pairs of sensitivity/specificity values (97%/87%; 85%/75%; 90%/93%). The evaluation of accuracy in terms of bias, standard error and mean squared error reveals that all implementations of the generalized bivariate model calculate sensitivity and specificity estimates with deviations less than two percentage points. proc mixed which together with reitsma implements the general bivariate mixed model proposed by Reitsma rather shows convergence problems. The random effect parameters are in general underestimated. This study shows that flexibility and simplicity of model specification together with convergence robustness should influence implementation recommendations, as the accuracy in terms of bias was acceptable in all implementations using the generalized approach. Schattauer GmbH.

Differentiation of sex chromosomes and karyotypic evolution in the eye-lid geckos (Squamata: Gekkota: Eublepharidae), a group with different modes of sex determination.

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Pokorná, Martina; Rábová, Marie; Ráb, Petr; Ferguson-Smith, Malcolm A; Rens, Willem; Kratochvíl, Lukáš

2010-11-01

The eyelid geckos (family Eublepharidae) include both species with temperature-dependent sex determination and species where genotypic sex determination (GSD) was suggested based on the observation of equal sex ratios at several incubation temperatures. In this study, we present data on karyotypes and chromosomal characteristics in 12 species (Aeluroscalabotes felinus, Coleonyx brevis, Coleonyx elegans, Coleonyx variegatus, Eublepharis angramainyu, Eublepharis macularius, Goniurosaurus araneus, Goniurosaurus lichtenfelderi, Goniurosaurus luii, Goniurosaurus splendens, Hemitheconyx caudicinctus, and Holodactylus africanus) covering all genera of the family, and search for the presence of heteromorphic sex chromosomes. Phylogenetic mapping of chromosomal changes showed a long evolutionary stasis of karyotypes with all acrocentric chromosomes followed by numerous chromosomal rearrangements in the ancestors of two lineages. We have found heteromorphic sex chromosomes in only one species, which suggests that sex chromosomes in most GSD species of the eyelid geckos are not morphologically differentiated. The sexual difference in karyotype was detected only in C. elegans which has a multiple sex chromosome system (X(1)X(2)Y). The metacentric Y chromosome evolved most likely via centric fusion of two acrocentric chromosomes involving loss of interstitial telomeric sequences. We conclude that the eyelid geckos exhibit diversity in sex determination ranging from the absence of any sexual differences to heteromorphic sex chromosomes, which makes them an interesting system for exploring the evolutionary origin of sexually dimorphic genomes.

Larva of Glyptotendipes (Glyptotendipes) glaucus (Meigen 1818) (Chironomidae, Diptera)-morphology by Scanning Electron Microscope (SEM), karyotype, and biology in laboratory conditions.

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Kownacki, Andrzej; Woznicka, Olga; Szarek-Gwiazda, Ewa; Michailova, Paraskeva

2016-09-21

Larvae belonging to the family Chironomidae are difficult to identify. The aim of the present study was to describe the larval morphology of G. (G.) glaucus with the aid of a Scanning Electron Microscope (SEM), the karyotype and biology based on materials obtained from laboratory culture. Describing the morphology of larvae, special attention was paid to rarely or never described structures like the maxilla (lacinia and maxillary palp), the long plate situated below the ventromental plate, and plate X situated between lacinia and mentum. The use of SEM allowed also to obtain better images of labrum and ventromental plate. Morphological features of this species have been supplemented by karyotype and biology of larvae in laboratory conditions. Under controlled experimental conditions we found non-synchronous development of G. (G.) glaucus larvae hatched from one egg mass reflected in different lengths of larvae and emerged imagoes.

Dynamic karyotype evolution and unique sex determination systems in Leptidea wood white butterflies

Czech Academy of Sciences Publication Activity Database

Šíchová, Jindra; Voleníková, A.; Dincă, A.; Nguyen, Petr; Vila, R.; Sahara, K.; Marec, František

2015-01-01

Roč. 15, č. 1 (2015), article number 89 ISSN 1471-2148 R&D Projects: GA AV ČR IAA600960925; GA ČR(CZ) GP14-35819P; GA ČR(CZ) GA14-22765S Grant - others:GA JU(CZ) 063/2012/P; Spanish Ministerio de Economia y Competitividad(ES) CGL2013-48277-P; GA JU(CZ) 052/2013/P; 7th European Community Framework Programme(CZ) 625997; JSPS(JP) 23380030 Institutional support: RVO:60077344 Keywords : Lepidoptera * wood white butteflies * karyotype variability Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.406, year: 2015 http://www.biomedcentral.com/content/pdf/s12862-015-0375-4.pdf

Bivariate Genomic Footprinting Detects Changes in Transcription Factor Activity

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Songjoon Baek

2017-05-01

Full Text Available In response to activating signals, transcription factors (TFs bind DNA and regulate gene expression. TF binding can be measured by protection of the bound sequence from DNase digestion (i.e., footprint. Here, we report that 80% of TF binding motifs do not show a measurable footprint, partly because of a variable cleavage pattern within the motif sequence. To more faithfully portray the effect of TFs on chromatin, we developed an algorithm that captures two TF-dependent effects on chromatin accessibility: footprinting and motif-flanking accessibility. The algorithm, termed bivariate genomic footprinting (BaGFoot, efficiently detects TF activity. BaGFoot is robust to different accessibility assays (DNase-seq, ATAC-seq, all examined peak-calling programs, and a variety of cut bias correction approaches. BaGFoot reliably predicts TF binding and provides valuable information regarding the TFs affecting chromatin accessibility in various biological systems and following various biological events, including in cases where an absolute footprint cannot be determined.

Chromosome Mapping of Repetitive Sequences in Rachycentron canadum (Perciformes: Rachycentridae: Implications for Karyotypic Evolution and Perspectives for Biotechnological Uses

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Uedson Pereira Jacobina

2011-01-01

Full Text Available The cobia, Rachycentron canadum, a species of marine fish, has been increasingly used in aquaculture worldwide. It is the only member of the family Rachycentridae (Perciformes showing wide geographic distribution and phylogenetic patterns still not fully understood. In this study, the species was cytogenetically analyzed by different methodologies, including Ag-NOR and chromomycin A3 (CMA3/DAPI staining, C-banding, early replication banding (RGB, and in situ fluorescent hybridization with probes for 18S and 5S ribosomal genes and for telomeric sequences (TTAGGGn. The results obtained allow a detailed chromosomal characterization of the Atlantic population. The chromosome diversification found in the karyotype of the cobia is apparently related to pericentric inversions, the main mechanism associated to the karyotypic evolution of Perciformes. The differential heterochromatin replication patterns found were in part associated to functional genes. Despite maintaining conservative chromosomal characteristics in relation to the basal pattern established for Perciformes, some chromosome pairs in the analyzed population exhibit markers that may be important for cytotaxonomic, population, and biodiversity studies as well as for monitoring the species in question.

[Karyotypic comparison of five species of Lutzomyia (diptera: psychodidae) of the series townsendi and the verrucarum group in Colombia].

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Escovar, Jesús; Ferro, Cristina; Cárdenas, Estrella; Bello, Felio

2002-12-01

Cytogenetic characteristics were established for five native species of phlebotomine sand flies (Lutzomyia, series townsendi, verrucarum group): Lutzomyia longiflocosa, Lutzomyia townsendi, Lutzomyia spinicrassa, Lutzomyia torvida and Lutzomyia youngi. Karyotypes and chromosomal morphometry were compared. Using the squash technique, brain tissues from late 4th instar larvae provided the necessary mitotic chromosomes. Chromosomal measurements were made on the following chromosomal characteristics: short arm, long arm, arm ratio, total length, relative length, centromeric index and relative length average of chromosomes. Chromosomes were classified according to their morphometry and position of the centromere. The taxonomic distance was calculated, and the relationships among the species displayed in a phenogram. All five species possessed four pairs of chromosomes as diploid number (2N = 8). None of the karyotypes indicated presence of heteromorphic chromosomes. Statistical analysis of the morphometric data showed highly significant differences among the chromosomes pairs of the five species. However, the total length of the genome was very similar, with the exception of L. youngi. In conclusion, these closely related species were distinguishable at cytological level.

Recidivous offence in sadistic homosexual pedophile with karyotype 48, XXXY after testicular pulpectomy. A case report.

Science.gov (United States)

Lachman, M; Brzek, A; Mellan, J; Hampl, R; Starka, L; Motlik, K

1991-01-01

The case of recidivous sexual offender with genetically caused mental retardation and primary hypogonadism (Klinefelter's syndrome with karyotype 48, XXXY) is described. He was examined after sadistic abuse of a boy aged 13 that he had committed 19 years after performed testicular pulpectomy. Plasmatic level of testosterone was found 4x higher than mean level in men after orchidectomy. Histological examination of residual scrotal tissues proved that the source of androgens were hyperplastic nodules of extratesticular Leydig cells.

Agnathia-holoprosencephaly associated with a 46,XY,-21,+t(21q;21q) karyotype

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Niedermeyer, K.K.; McCorquodale, M.M.; Burton, B.K. [Univ. of Illinois, Chicago, IL (United States)

1994-09-01

We report an unusual case of agnathia-holoprosencephaly associated with Down syndrome due to a 21/21 translocation. The patient presented prenatally at 21 wks gestation. A fetal ultrasound revealed multiple CNS anomalies including hydrocephalus, compressed cerebellum, absent septum pellucidum and possible cranial meningocele or encephalocele. High resolution ultrasound & fetal karyotype were recommended. The patient refused & elected to have a pregnancy termination. Chromosomal analysis performed on products of conception revealed a 46,XY,-21,+t(21q;21q) karyotype. Fluorescence in situ hybridization was performed and confirmed the 21/21 translocation chromosome. An autopsy revealed agnathia and multiple CNS anomalies including absence of the septum pellucidum, absence of the corpus callosum, arhinencephaly, an occiptal meningoencephalocele, dilation of the lateral ventricles, and extensive dysgenesis & heterotopias of the central cerebrum & mid-brain. Additional abnormalities included a persistent left superior vena cava, atrial & ventricular septal defects, irregular length of the fingers with absence of the middle phalanges of the right 2nd and 5th & left 5th digits and bilateral simian creases. Agnathia can be an isolated abnormality but often is associated with holoprosencephaly and/or situs inversus. The majority of familial case of agnathis-holoprosencephaly was caused by an inherited unbalanced translocation resulting in duplication of 6p and monosomy of 18p. Our patient had a translocation form of trisomy 21 but did not have a phenotype consistent with Down syndrome. Trisomy 21 has not been previously reported in other cases of agnathia-holoprosencephaly. Whether the chromosomal abnormality caused the phenotypic abnormalities or if it is a coincidental finding cannot be determined.

Evidence of genetic differentiation and karyotype evolution of the sedges Cyperus ligularis L. and C. odoratus L. (Cyperaceae

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Geyner Alves dos Santos Cruz

2018-01-01

Full Text Available ABSTRACT The taxonomy of Cyperaceae is complex, with genera like Cyperus harboring species complexes. We analyzed the genetic similarity between Cyperus ligularis L. and C. odoratus L. based on DNA fingerprinting and cytogenetics. Significative genetic differentiation (G ST = 0.363 and low gene flow (N m = 0.877 indicated a clear genetic distinction between the two species. Moreover, the clustering analysis showed two distinct genetic groups, suggesting a lack of evidence for hybridization. The phenogram revealed two different lineages, and although all individuals of C. odoratus were collected from plots close to each other, they possessed greater genetic diversity than that observed among individuals of C. ligularis, which were sampled over a wider geographic range. Variation in chromosome number within the two species exhibited the opposite pattern, indicating greater karyotype stability in C. odoratus with 2n = 72 and 2n = 76, while the diploid number for C. ligularis varied from 2n = 66 to 88. The lower genetic variation in C. ligularis may be a result of the founder effect associated with seed dispersion and clonal reproduction. Field observations and analysis of reproductive biology should enrich the understanding of the genetic structure of the investigated populations and their role in successional processes.

Powerful bivariate genome-wide association analyses suggest the SOX6 gene influencing both obesity and osteoporosis phenotypes in males.

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Yao-Zhong Liu

2009-08-01

Full Text Available Current genome-wide association studies (GWAS are normally implemented in a univariate framework and analyze different phenotypes in isolation. This univariate approach ignores the potential genetic correlation between important disease traits. Hence this approach is difficult to detect pleiotropic genes, which may exist for obesity and osteoporosis, two common diseases of major public health importance that are closely correlated genetically.To identify such pleiotropic genes and the key mechanistic links between the two diseases, we here performed the first bivariate GWAS of obesity and osteoporosis. We searched for genes underlying co-variation of the obesity phenotype, body mass index (BMI, with the osteoporosis risk phenotype, hip bone mineral density (BMD, scanning approximately 380,000 SNPs in 1,000 unrelated homogeneous Caucasians, including 499 males and 501 females. We identified in the male subjects two SNPs in intron 1 of the SOX6 (SRY-box 6 gene, rs297325 and rs4756846, which were bivariately associated with both BMI and hip BMD, achieving p values of 6.82x10(-7 and 1.47x10(-6, respectively. The two SNPs ranked at the top in significance for bivariate association with BMI and hip BMD in the male subjects among all the approximately 380,000 SNPs examined genome-wide. The two SNPs were replicated in a Framingham Heart Study (FHS cohort containing 3,355 Caucasians (1,370 males and 1,985 females from 975 families. In the FHS male subjects, the two SNPs achieved p values of 0.03 and 0.02, respectively, for bivariate association with BMI and femoral neck BMD. Interestingly, SOX6 was previously found to be essential to both cartilage formation/chondrogenesis and obesity-related insulin resistance, suggesting the gene's dual role in both bone and fat.Our findings, together with the prior biological evidence, suggest the SOX6 gene's importance in co-regulation of obesity and osteoporosis.

Powerful Bivariate Genome-Wide Association Analyses Suggest the SOX6 Gene Influencing Both Obesity and Osteoporosis Phenotypes in Males

Science.gov (United States)

Liu, Yao-Zhong; Pei, Yu-Fang; Liu, Jian-Feng; Yang, Fang; Guo, Yan; Zhang, Lei; Liu, Xiao-Gang; Yan, Han; Wang, Liang; Zhang, Yin-Ping; Levy, Shawn; Recker, Robert R.; Deng, Hong-Wen

2009-01-01

Background Current genome-wide association studies (GWAS) are normally implemented in a univariate framework and analyze different phenotypes in isolation. This univariate approach ignores the potential genetic correlation between important disease traits. Hence this approach is difficult to detect pleiotropic genes, which may exist for obesity and osteoporosis, two common diseases of major public health importance that are closely correlated genetically. Principal Findings To identify such pleiotropic genes and the key mechanistic links between the two diseases, we here performed the first bivariate GWAS of obesity and osteoporosis. We searched for genes underlying co-variation of the obesity phenotype, body mass index (BMI), with the osteoporosis risk phenotype, hip bone mineral density (BMD), scanning ∼380,000 SNPs in 1,000 unrelated homogeneous Caucasians, including 499 males and 501 females. We identified in the male subjects two SNPs in intron 1 of the SOX6 (SRY-box 6) gene, rs297325 and rs4756846, which were bivariately associated with both BMI and hip BMD, achieving p values of 6.82×10−7 and 1.47×10−6, respectively. The two SNPs ranked at the top in significance for bivariate association with BMI and hip BMD in the male subjects among all the ∼380,000 SNPs examined genome-wide. The two SNPs were replicated in a Framingham Heart Study (FHS) cohort containing 3,355 Caucasians (1,370 males and 1,985 females) from 975 families. In the FHS male subjects, the two SNPs achieved p values of 0.03 and 0.02, respectively, for bivariate association with BMI and femoral neck BMD. Interestingly, SOX6 was previously found to be essential to both cartilage formation/chondrogenesis and obesity-related insulin resistance, suggesting the gene's dual role in both bone and fat. Conclusions Our findings, together with the prior biological evidence, suggest the SOX6 gene's importance in co-regulation of obesity and osteoporosis. PMID:19714249

SNPMClust: Bivariate Gaussian Genotype Clustering and Calling for Illumina Microarrays

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Stephen W. Erickson

2016-07-01

Full Text Available SNPMClust is an R package for genotype clustering and calling with Illumina microarrays. It was originally developed for studies using the GoldenGate custom genotyping platform but can be used with other Illumina platforms, including Infinium BeadChip. The algorithm first rescales the fluorescent signal intensity data, adds empirically derived pseudo-data to minor allele genotype clusters, then uses the package mclust for bivariate Gaussian model fitting. We compared the accuracy and sensitivity of SNPMClust to that of GenCall, Illumina's proprietary algorithm, on a data set of 94 whole-genome amplified buccal (cheek swab DNA samples. These samples were genotyped on a custom panel which included 1064 SNPs for which the true genotype was known with high confidence. SNPMClust produced uniformly lower false call rates over a wide range of overall call rates.

Women’s Attitudes towards the Option to Choose between Karyotyping and Rapid Targeted Testing during Pregnancy

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Angelique J. A. Kooper

2013-01-01

Full Text Available Objectives. Pregnant women, referred because of an increased risk of fetal Down syndrome, who underwent an invasive prenatal procedure were offered a choice between karyotyping and rapid targeted testing. This study aims to assess women’s attitudes and experiences towards what option to choose. Methods. A retrospective multicentre survey (2008–2010 was conducted among 1370 women. General questions were asked about decision making issues, followed by personal questions about their experiences in choice making, test preference, influence of others, and possible regrets. Results. In total, 90.1% of the respondents (N=825 indicated that pregnant women are able to choose, although 33.1% stated that the choice can best be made by a professional. 18.4% indicated that making a choice places a burden on women. In 96.4%, respondents preferred to have the option to choose again in case of a next pregnancy, whereas 2.7% preferred the choice to be made by a professional. Regret was indicated by 1.2%. Decision making was influenced by others in 64.9%. A slightly higher preference for karyotyping was indicated by 52.7% of the respondents. Conclusions. Positive attitudes and experiences were expressed towards the option to choose. Respondents took decisions freely, although sometimes influenced by a partner or a professional, to follow their individual perspectives.

Evidence of Chromosomal Instability in Prostate Cancer Determined by Spectral Karyotyping (SKY and Interphase FISH Analysis

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Ben Beheshti

2001-01-01

Full Text Available The way in which cytogenetic aberrations develop in prostate cancer (Cap is poorly understood. Spectral karyotype (SKY analysis of Cap cell lines has shown that they have unstable karyotypes and also have features associated with chromosomal instability (CIN. To accurately determine the incidence of de novo structural and numerical aberrations in vitro in Cap, we performed SKY analysis of three independent clones derived from one representative cell line, DU145. The frequent generation of new chromosomal rearrangements and a wide variation in the number of structural aberrations within two to five passages suggested that this cell line exhibited some of the features associated with a CIN phenotype. To study numerical cell-to-cell variation, chromosome 8 aneusomy was assessed in the LNCaP, DU145, and PC-3 cell lines and a patient cohort of 15 Cap primary tumors by interphase fluorescence in situ hybridization (FISH. This analysis showed that a high frequency of numerical alteration affecting chromosome 8 was present in both in vitro and in Cap tissues. In comparison to normal controls, the patient cohort had a statistically significant (P<.05, greater frequency of cells with one and three centromere 8 copies. These data suggest that a CIN-like process may be contributing towards the generation of de novo numerical and structural chromosome abnormalities in Cap.

Molecular structures of centromeric heterochromatin and karyotypic evolution in the Siamese crocodile (Crocodylus siamensis) (Crocodylidae, Crocodylia).

Science.gov (United States)

Kawagoshi, Taiki; Nishida, Chizuko; Ota, Hidetoshi; Kumazawa, Yoshinori; Endo, Hideki; Matsuda, Yoichi

2008-01-01

Crocodilians have several unique karyotypic features, such as small diploid chromosome numbers (30-42) and the absence of dot-shaped microchromosomes. Of the extant crocodilian species, the Siamese crocodile (Crocodylus siamensis) has no more than 2n = 30, comprising mostly bi-armed chromosomes with large centromeric heterochromatin blocks. To investigate the molecular structures of C-heterochromatin and genomic compartmentalization in the karyotype, characterized by the disappearance of tiny microchromosomes and reduced chromosome number, we performed molecular cloning of centromeric repetitive sequences and chromosome mapping of the 18S-28S rDNA and telomeric (TTAGGG)( n ) sequences. The centromeric heterochromatin was composed mainly of two repetitive sequence families whose characteristics were quite different. Two types of GC-rich CSI-HindIII family sequences, the 305 bp CSI-HindIII-S (G+C content, 61.3%) and 424 bp CSI-HindIII-M (63.1%), were localized to the intensely PI-stained centric regions of all chromosomes, except for chromosome 2 with PI-negative heterochromatin. The 94 bp CSI-DraI (G+C content, 48.9%) was tandem-arrayed satellite DNA and localized to chromosome 2 and four pairs of small-sized chromosomes. The chromosomal size-dependent genomic compartmentalization that is supposedly unique to the Archosauromorpha was probably lost in the crocodilian lineage with the disappearance of microchromosomes followed by the homogenization of centromeric repetitive sequences between chromosomes, except for chromosome 2.

Bivariate Rainfall and Runoff Analysis Using Shannon Entropy Theory

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Rahimi, A.; Zhang, L.

2012-12-01

Rainfall-Runoff analysis is the key component for many hydrological and hydraulic designs in which the dependence of rainfall and runoff needs to be studied. It is known that the convenient bivariate distribution are often unable to model the rainfall-runoff variables due to that they either have constraints on the range of the dependence or fixed form for the marginal distributions. Thus, this paper presents an approach to derive the entropy-based joint rainfall-runoff distribution using Shannon entropy theory. The distribution derived can model the full range of dependence and allow different specified marginals. The modeling and estimation can be proceeded as: (i) univariate analysis of marginal distributions which includes two steps, (a) using the nonparametric statistics approach to detect modes and underlying probability density, and (b) fitting the appropriate parametric probability density functions; (ii) define the constraints based on the univariate analysis and the dependence structure; (iii) derive and validate the entropy-based joint distribution. As to validate the method, the rainfall-runoff data are collected from the small agricultural experimental watersheds located in semi-arid region near Riesel (Waco), Texas, maintained by the USDA. The results of unviariate analysis show that the rainfall variables follow the gamma distribution, whereas the runoff variables have mixed structure and follow the mixed-gamma distribution. With this information, the entropy-based joint distribution is derived using the first moments, the first moments of logarithm transformed rainfall and runoff, and the covariance between rainfall and runoff. The results of entropy-based joint distribution indicate: (1) the joint distribution derived successfully preserves the dependence between rainfall and runoff, and (2) the K-S goodness of fit statistical tests confirm the marginal distributions re-derived reveal the underlying univariate probability densities which further

Karyotype of Ophiopogon reversus (Convallariaceae from Taiwan and the Southern Ryukyus

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Tetsuo Denda

2006-06-01

Full Text Available Karyotypes of Ophiopogon reversus (Convallariaceae collected from four localities in Taiwan and one locality on Yonaguni-jima Island in the southern Ryukyus of Japan were reported for the first time. Those of O. jaburan collected from three major islands (Amami-oshima, Tokuno-shima and Okinawa-jima of the central Ryukyus were also investigated for comparison. All plants of O. reversus and O. jaburan investigated were diploid (2n = 36 based on the basic chromosome number of x = 18. Among 36 chromosomes of O. reversus, one pair of short chromosomes with submedian centromeres had secondary constrictions at the proximal region of the long arms. Based on this character, O. reversus is cytologically distinguishable from O. jaburan, in which one pair of short metacentric chromosomes had secondary constrictions at the proximal region of the short arms.

Karyotype divergence and spreading of 5S rDNA sequences between genomes of two species: darter and emerald gobies ( Ctenogobius , Gobiidae).

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Lima-Filho, P A; Bertollo, L A C; Cioffi, M B; Costa, G W W F; Molina, W F

2014-01-01

Karyotype analyses of the cryptobenthic marine species Ctenogobius boleosoma and C. smaragdus were performed by means of classical and molecular cytogenetics, including physical mapping of the multigene 18S and 5S rDNA families. C. boleosoma has 2n = 44 chromosomes (2 submetacentrics + 42 acrocentrics; FN = 46) with a single chromosome pair each carrying 18S and 5S ribosomal sites; whereas C. smaragdus has 2n = 48 chromosomes (2 submetacentrics + 46 acrocentrics; FN = 50), also with a single pair bearing 18S rDNA, but an extensive increase in the number of GC-rich 5S rDNA sites in 21 chromosome pairs. The highly divergent karyotypes among Ctenogobius species contrast with observations in several other marine fish groups, demonstrating an accelerated rate of chromosomal evolution mediated by both chromosomal rearrangements and the extensive dispersion of 5S rDNA sequences in the genome. © 2014 S. Karger AG, Basel.

Fluorescence in situ hybridization karyotyping reveals the presence of two distinct genomes in the taxon Aegilops tauschii

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Zhao, Laibin; Ning, Shunzong; Yi, Yingjin; Zhang, Lianquan; Yuan, Zhongwei; Wang, Jirui; Zheng, Youliang; Hao, Ming; Liu, Dengcai

2018-01-01

Background Aegilops tauschii is the donor of the bread wheat D genome. Based on spike morphology, the taxon has conventionally been subdivided into ssp. tauschii and ssp. strangulata. The present study was intended to address the poor match between this whole plant morphology-based subdivision and genetic relationships inferred from genotyping by fluorescence in situ hybridization karyotyping a set of 31 Ae. tauschii accessions. Results The distribution of sites hybridizing to the two probes ...

T-cell acute lymphoblastic leukemia associated with complex karyotype and SET-NUP214 rearrangement: a case study and review of the literature.

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Lee, Sang-Guk; Park, Tae Sung; Cho, Sun Young; Lim, Gayoung; Park, Gwang Jin; Oh, Seung Hwan; Cho, Eun Hae; Chong, So Young; Huh, Ji Young

2011-01-01

SET-NUP214 rearrangements have been rarely reported in T-cell acute lymphoblastic leukemia (T-ALL), acute undifferentiated leukemia, and acute myeloid leukemia, and most documented cases have been associated with normal karyotypes in conventional cytogenetic analyses. Here, we describe a novel case of T-ALL associated with a mediastinal mass and a SET-NUP214 rearrangement, which was masked by a complex karyotype at the time of initial diagnosis. Using multiplex reverse transcriptase-polymerase chain reaction analysis, we detected a cryptic SET-NUP214 rearrangement in our patient. As only 11 cases (including the present study) of T-ALL with SET-NUP214 rearrangement have been reported, the clinical features and treatment outcomes have not been fully determined. Further studies are necessary to evaluate the incidence of SET-NUP214 rearrangement in T-ALL patients and the treatment responses as well as prognosis of these patients.

Acrania/encephalocele sequence (exencephaly) associated with 92,XXXX karyotype: early prenatal diagnosis at 9(+5) weeks by 3D transvaginal ultrasound and coelocentesis.

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Tonni, Gabriele; Ventura, Alessandro; Bonasoni, Maria Paola

2009-09-01

A 27-year-old pregnant woman was diagnosed by 3D transvaginal ultrasound as carrying a fetus of 9(+5) weeks gestation affected by acrania/encephalocele (exencephaly) sequence. A 2D transvaginal ultrasound-guided aspiration of 5 mL of extra-coelomic fluid was performed under cervical block before uterine suction. Conventional cytogenetic analysis demonstrated a 92,XXXX karyotype. Transvaginal 2D ultrasound-guided coelocentesis for rapid karyotyping can be proposed to women who are near to miscarriage or in cases where a prenatal ultrasound diagnosis of congenital anomaly is performed at an early stage of development. Genetic analysis can be performed using traditional cytogenetic analysis or can be aided by fluorescence in situ hybridization (FISH). Coelocentesis may become an integral part of first trimester armamentarium and may be clinically useful in the understanding of the pathogenesis of early prenatally diagnosed congenital anomalies.

Major prognostic value of complex karyotype in addition to TP53 and IGHV mutational status in first-line chronic lymphocytic leukemia.

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Le Bris, Yannick; Struski, Stéphanie; Guièze, Romain; Rouvellat, Caroline; Prade, Naïs; Troussard, Xavier; Tournilhac, Olivier; Béné, Marie C; Delabesse, Eric; Ysebaert, Loïc

2017-12-01

Chronic lymphocytic leukemia (CLL) is a lymphoproliferative disorder of remarkable heterogeneity as demonstrated by cytogenetics and molecular analyses. Complex karyotype (CK), TP53 deletions and/or mutations (TP53 disruption), IGVH mutational status, and, more recently, recurrent somatic mutations have been identified as prognostic markers in CLL. On a cohort of 110 patients with CLL treated with first-line fludarabin, cyclophosphamide, and rituximab treatment compared with 33 untreated (watch and wait) patients with CLL, we report more frequent complex karyotypes (34 vs 15%; P = .05), unmutated IGHV (70 vs 21%; P < .0001), ATM deletion (25 vs 6%, P = .02), and NOTCH mutation (3 vs 17%, P = .04). Among treated patients, 39 relapsed during the follow-up period. These patients were characterized before treatment by a higher incidence of trisomy 12 (38 vs 11%, P < .001) and TP53 disruption (31 vs 4%, P = .0002). A significantly shorter 5-year overall survival was found for treated patients with CK (72.4 vs 85.8%; P = .007), unmutated IGHV (70 vs 100%; P = .04), or TP53 disruption (55.7 vs 82.7%; P < .0001). Three risk groups were defined based on the status of TP53 disruption or unmutated IGVH, which differed significantly in terms of 5-year overall survival. Moreover, the presence of CK impacted pejoratively 5-year overall survival and progression-free survival in all these 3 groups. Conventional karyotyping therefore appears to be of value, CK being an additional factor, undetectable in classical FISH, in patients with CLL at the stage when therapy becomes required. Copyright © 2016 John Wiley & Sons, Ltd.

Historical and future drought in Bangladesh using copula-based bivariate regional frequency analysis

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Mortuza, Md Rubayet; Moges, Edom; Demissie, Yonas; Li, Hong-Yi

2018-02-01

The study aims at regional and probabilistic evaluation of bivariate drought characteristics to assess both the past and future drought duration and severity in Bangladesh. The procedures involve applying (1) standardized precipitation index to identify drought duration and severity, (2) regional frequency analysis to determine the appropriate marginal distributions for both duration and severity, (3) copula model to estimate the joint probability distribution of drought duration and severity, and (4) precipitation projections from multiple climate models to assess future drought trends. Since drought duration and severity in Bangladesh are often strongly correlated and do not follow same marginal distributions, the joint and conditional return periods of droughts are characterized using the copula-based joint distribution. The country is divided into three homogeneous regions using Fuzzy clustering and multivariate discordancy and homogeneity measures. For given severity and duration values, the joint return periods for a drought to exceed both values are on average 45% larger, while to exceed either value are 40% less than the return periods from the univariate frequency analysis, which treats drought duration and severity independently. These suggest that compared to the bivariate drought frequency analysis, the standard univariate frequency analysis under/overestimate the frequency and severity of droughts depending on how their duration and severity are related. Overall, more frequent and severe droughts are observed in the west side of the country. Future drought trend based on four climate models and two scenarios showed the possibility of less frequent drought in the future (2020-2100) than in the past (1961-2010).

Karyotype of cryopreserved bone marrow cells

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M.L.L.F. Chauffaille

2003-07-01

Full Text Available The analysis of chromosomal abnormalities is important for the study of hematological neoplastic disorders since it facilitates classification of the disease. The ability to perform chromosome analysis of cryopreserved malignant marrow or peripheral blast cells is important for retrospective studies. In the present study, we compared the karyotype of fresh bone marrow cells (20 metaphases to that of cells stored with a simplified cryopreservation method, evaluated the effect of the use of granulocyte-macrophage colony-stimulating factor (GM-CSF as an in vitro mitotic index stimulator, and compared the cell viability and chromosome morphology of fresh and cryopreserved cells whenever possible (sufficient metaphases for analysis. Twenty-five bone marrow samples from 24 patients with hematological disorders such as acute myeloid leukemia, acute lymphoblastic leukemia, myelodysplastic syndrome, chronic myeloid leukemia, megaloblastic anemia and lymphoma (8, 3, 3, 8, 1, and 1 patients, respectively were selected at diagnosis, at relapse or during routine follow-up and one sample was obtained from a bone marrow donor after informed consent. Average cell viability before and after freezing was 98.8 and 78.5%, respectively (P < 0.05. Cytogenetic analysis was successful in 76% of fresh cell cultures, as opposed to 52% of cryopreserved samples (P < 0.05. GM-CSF had no proliferative effect before or after freezing. The morphological aspects of the chromosomes in fresh and cryopreserved cells were subjectively the same. The present study shows that cytogenetic analysis of cryopreserved bone marrow cells can be a reliable alternative when fresh cell analysis cannot be done, notwithstanding the reduced viability and lower percent of successful analysis that are associated with freezing.

Karyotype of cryopreserved bone marrow cells.

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Chauffaille, M L L F; Pinheiro, R F; Stefano, J T; Kerbauy, J

2003-07-01

The analysis of chromosomal abnormalities is important for the study of hematological neoplastic disorders since it facilitates classification of the disease. The ability to perform chromosome analysis of cryopreserved malignant marrow or peripheral blast cells is important for retrospective studies. In the present study, we compared the karyotype of fresh bone marrow cells (20 metaphases) to that of cells stored with a simplified cryopreservation method, evaluated the effect of the use of granulocyte-macrophage colony-stimulating factor (GM-CSF) as an in vitro mitotic index stimulator, and compared the cell viability and chromosome morphology of fresh and cryopreserved cells whenever possible (sufficient metaphases for analysis). Twenty-five bone marrow samples from 24 patients with hematological disorders such as acute myeloid leukemia, acute lymphoblastic leukemia, myelodysplastic syndrome, chronic myeloid leukemia, megaloblastic anemia and lymphoma (8, 3, 3, 8, 1, and 1 patients, respectively) were selected at diagnosis, at relapse or during routine follow-up and one sample was obtained from a bone marrow donor after informed consent. Average cell viability before and after freezing was 98.8 and 78.5%, respectively (P < 0.05). Cytogenetic analysis was successful in 76% of fresh cell cultures, as opposed to 52% of cryopreserved samples (P < 0.05). GM-CSF had no proliferative effect before or after freezing. The morphological aspects of the chromosomes in fresh and cryopreserved cells were subjectively the same. The present study shows that cytogenetic analysis of cryopreserved bone marrow cells can be a reliable alternative when fresh cell analysis cannot be done, notwithstanding the reduced viability and lower percent of successful analysis that are associated with freezing.

Collective estimation of multiple bivariate density functions with application to angular-sampling-based protein loop modeling

KAUST Repository

Maadooliat, Mehdi

2015-10-21

This paper develops a method for simultaneous estimation of density functions for a collection of populations of protein backbone angle pairs using a data-driven, shared basis that is constructed by bivariate spline functions defined on a triangulation of the bivariate domain. The circular nature of angular data is taken into account by imposing appropriate smoothness constraints across boundaries of the triangles. Maximum penalized likelihood is used to fit the model and an alternating blockwise Newton-type algorithm is developed for computation. A simulation study shows that the collective estimation approach is statistically more efficient than estimating the densities individually. The proposed method was used to estimate neighbor-dependent distributions of protein backbone dihedral angles (i.e., Ramachandran distributions). The estimated distributions were applied to protein loop modeling, one of the most challenging open problems in protein structure prediction, by feeding them into an angular-sampling-based loop structure prediction framework. Our estimated distributions compared favorably to the Ramachandran distributions estimated by fitting a hierarchical Dirichlet process model; and in particular, our distributions showed significant improvements on the hard cases where existing methods do not work well.

Cost-offsets of prescription drug expenditures: data analysis via a copula-based bivariate dynamic hurdle model.

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Deb, Partha; Trivedi, Pravin K; Zimmer, David M

2014-10-01

In this paper, we estimate a copula-based bivariate dynamic hurdle model of prescription drug and nondrug expenditures to test the cost-offset hypothesis, which posits that increased expenditures on prescription drugs are offset by reductions in other nondrug expenditures. We apply the proposed methodology to data from the Medical Expenditure Panel Survey, which have the following features: (i) the observed bivariate outcomes are a mixture of zeros and continuously measured positives; (ii) both the zero and positive outcomes show state dependence and inter-temporal interdependence; and (iii) the zeros and the positives display contemporaneous association. The point mass at zero is accommodated using a hurdle or a two-part approach. The copula-based approach to generating joint distributions is appealing because the contemporaneous association involves asymmetric dependence. The paper studies samples categorized by four health conditions: arthritis, diabetes, heart disease, and mental illness. There is evidence of greater than dollar-for-dollar cost-offsets of expenditures on prescribed drugs for relatively low levels of spending on drugs and less than dollar-for-dollar cost-offsets at higher levels of drug expenditures. Copyright © 2013 John Wiley & Sons, Ltd.

Collective estimation of multiple bivariate density functions with application to angular-sampling-based protein loop modeling

KAUST Repository

Maadooliat, Mehdi; Zhou, Lan; Najibi, Seyed Morteza; Gao, Xin; Huang, Jianhua Z.

2015-01-01

This paper develops a method for simultaneous estimation of density functions for a collection of populations of protein backbone angle pairs using a data-driven, shared basis that is constructed by bivariate spline functions defined on a triangulation of the bivariate domain. The circular nature of angular data is taken into account by imposing appropriate smoothness constraints across boundaries of the triangles. Maximum penalized likelihood is used to fit the model and an alternating blockwise Newton-type algorithm is developed for computation. A simulation study shows that the collective estimation approach is statistically more efficient than estimating the densities individually. The proposed method was used to estimate neighbor-dependent distributions of protein backbone dihedral angles (i.e., Ramachandran distributions). The estimated distributions were applied to protein loop modeling, one of the most challenging open problems in protein structure prediction, by feeding them into an angular-sampling-based loop structure prediction framework. Our estimated distributions compared favorably to the Ramachandran distributions estimated by fitting a hierarchical Dirichlet process model; and in particular, our distributions showed significant improvements on the hard cases where existing methods do not work well.

Efficient estimation of semiparametric copula models for bivariate survival data

KAUST Repository

Cheng, Guang

2014-01-01

A semiparametric copula model for bivariate survival data is characterized by a parametric copula model of dependence and nonparametric models of two marginal survival functions. Efficient estimation for the semiparametric copula model has been recently studied for the complete data case. When the survival data are censored, semiparametric efficient estimation has only been considered for some specific copula models such as the Gaussian copulas. In this paper, we obtain the semiparametric efficiency bound and efficient estimation for general semiparametric copula models for possibly censored data. We construct an approximate maximum likelihood estimator by approximating the log baseline hazard functions with spline functions. We show that our estimates of the copula dependence parameter and the survival functions are asymptotically normal and efficient. Simple consistent covariance estimators are also provided. Numerical results are used to illustrate the finite sample performance of the proposed estimators. © 2013 Elsevier Inc.

Identification of the linkage group of the Z sex chromosomes of the sand lizard (Lacerta agilis, Lacertidae) and elucidation of karyotype evolution in lacertid lizards.

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Srikulnath, Kornsorn; Matsubara, Kazumi; Uno, Yoshinobu; Nishida, Chizuko; Olsson, Mats; Matsuda, Yoichi

2014-12-01

The sand lizard (Lacerta agilis, Lacertidae) has a chromosome number of 2n = 38, with 17 pairs of acrocentric chromosomes, one pair of microchromosomes, a large acrocentric Z chromosome, and a micro-W chromosome. To investigate the process of karyotype evolution in L. agilis, we performed chromosome banding and fluorescent in situ hybridization for gene mapping and constructed a cytogenetic map with 86 functional genes. Chromosome banding revealed that the Z chromosome is the fifth largest chromosome. The cytogenetic map revealed homology of the L. agilis Z chromosome with chicken chromosomes 6 and 9. Comparison of the L. agilis cytogenetic map with those of four Toxicofera species with many microchromosomes (Elaphe quadrivirgata, Varanus salvator macromaculatus, Leiolepis reevesii rubritaeniata, and Anolis carolinensis) showed highly conserved linkage homology of L. agilis chromosomes (LAG) 1, 2, 3, 4, 5(Z), 7, 8, 9, and 10 with macrochromosomes and/or macrochromosome segments of the four Toxicofera species. Most of the genes located on the microchromosomes of Toxicofera were localized to LAG6, small acrocentric chromosomes (LAG11-18), and a microchromosome (LAG19) in L. agilis. These results suggest that the L. agilis karyotype resulted from frequent fusions of microchromosomes, which occurred in the ancestral karyotype of Toxicofera and led to the disappearance of microchromosomes and the appearance of many small macrochromosomes.

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

Science.gov (United States)

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

2016-05-01

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

First cytogenetic analysis of Ichthyoelephas humeralis (Günther, 1860 by conventional and molecular methods with comments on the karyotypic evolution in Prochilodontidae

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Mauro Nirchio Tursellino

2016-11-01

Full Text Available We used conventional cytogenetic techniques (Giemsa, C-banding, Ag-NOR, and fluorescent in situ hybridization (FISH with 5S and 18S rDNA probes to investigate the karyotype and cytogenetic characteristics of Ichthyoelephas humeralis (Günther, 1860 from Ecuador. The specimens studied have a karyotype with 2n=54 biarmed chromosomes (32 M + 22 SM and C-positive heterochromatin located on the centromeric, pericentromeric, interstitial, and terminal regions of some chromosomes. The nucleolus organizer regions occurred terminally on the long arm of chromosome pair 2. FISH confirmed the presence of only one 18S rDNA cluster with nonsyntenic localization with the 5S rDNA. Cytogenetic data allow us to refute the earlier morphological hypothesis of a sister relationship between Semaprochilodus Fowler, 1941 and Ichthyoelephas Posada Arango, 1909 and support the molecular proposal that Ichthyoelephas is a sister group to the monophyletic clade containing Prochilodus Agassiz, 1829 and Semaprochilodus.

A bivariate measurement error model for semicontinuous and continuous variables: Application to nutritional epidemiology.

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Kipnis, Victor; Freedman, Laurence S; Carroll, Raymond J; Midthune, Douglas

2016-03-01

Semicontinuous data in the form of a mixture of a large portion of zero values and continuously distributed positive values frequently arise in many areas of biostatistics. This article is motivated by the analysis of relationships between disease outcomes and intakes of episodically consumed dietary components. An important aspect of studies in nutritional epidemiology is that true diet is unobservable and commonly evaluated by food frequency questionnaires with substantial measurement error. Following the regression calibration approach for measurement error correction, unknown individual intakes in the risk model are replaced by their conditional expectations given mismeasured intakes and other model covariates. Those regression calibration predictors are estimated using short-term unbiased reference measurements in a calibration substudy. Since dietary intakes are often "energy-adjusted," e.g., by using ratios of the intake of interest to total energy intake, the correct estimation of the regression calibration predictor for each energy-adjusted episodically consumed dietary component requires modeling short-term reference measurements of the component (a semicontinuous variable), and energy (a continuous variable) simultaneously in a bivariate model. In this article, we develop such a bivariate model, together with its application to regression calibration. We illustrate the new methodology using data from the NIH-AARP Diet and Health Study (Schatzkin et al., 2001, American Journal of Epidemiology 154, 1119-1125), and also evaluate its performance in a simulation study. © 2015, The International Biometric Society.

Karyotype, chromosomal characteristics of multiple rDNA clusters and intragenomic variability of ribosomal ITS2 in Caryophyllaeides fennica (Cestoda)

Czech Academy of Sciences Publication Activity Database

Orosová, Martina; Kraľová-Hromadová, I.; Bazsalovicsová, E.; Špakulová, M.

2010-01-01

Roč. 59, č. 3 (2010), s. 351-357 ISSN 1383-5769 R&D Projects: GA ČR GA524/08/0885; GA MŠk LC522 Institutional research plan: CEZ:AV0Z60220518 Keywords : Tapeworm cytogenetic * Karyotype * Heterochromatin * Fluorescent in situ hybridization * Nucleolar organizer region * Divergent ITS copies Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 2.259, year: 2010

Asexual Reproduction Does Not Apparently Increase the Rate of Chromosomal Evolution: Karyotype Stability in Diploid and Triploid Clonal Hybrid Fish (Cobitis, Cypriniformes, Teleostei).

Science.gov (United States)

Majtánová, Zuzana; Choleva, Lukáš; Symonová, Radka; Ráb, Petr; Kotusz, Jan; Pekárik, Ladislav; Janko, Karel

2016-01-01

Interspecific hybridization, polyploidization and transitions from sexuality to asexuality considerably affect organismal genomes. Especially the last mentioned process has been assumed to play a significant role in the initiation of chromosomal rearrangements, causing increased rates of karyotype evolution. We used cytogenetic analysis and molecular dating of cladogenetic events to compare the rate of changes of chromosome morphology and karyotype in asexually and sexually reproducing counterparts in European spined loach fish (Cobitis). We studied metaphases of three sexually reproducing species and their diploid and polyploid hybrid clones of different age of origin. The material includes artificial F1 hybrid strains, representatives of lineage originated in Holocene epoch, and also individuals of an oldest known age to date (roughly 0.37 MYA). Thereafter we applied GISH technique as a marker to differentiate parental chromosomal sets in hybrids. Although the sexual species accumulated remarkable chromosomal rearrangements after their speciation, we observed no differences in chromosome numbers and/or morphology among karyotypes of asexual hybrids. These hybrids possess chromosome sets originating from respective parental species with no cytogenetically detectable recombinations, suggesting their integrity even in a long term. The switch to asexual reproduction thus did not provoke any significant acceleration of the rate of chromosomal evolution in Cobitis. Asexual animals described in other case studies reproduce ameiotically, while Cobitis hybrids described here produce eggs likely through modified meiosis. Therefore, our findings indicate that the effect of asexuality on the rate of chromosomal change may be context-dependent rather than universal and related to particular type of asexual reproduction.

Asexual Reproduction Does Not Apparently Increase the Rate of Chromosomal Evolution: Karyotype Stability in Diploid and Triploid Clonal Hybrid Fish (Cobitis, Cypriniformes, Teleostei.

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Zuzana Majtánová

Full Text Available Interspecific hybridization, polyploidization and transitions from sexuality to asexuality considerably affect organismal genomes. Especially the last mentioned process has been assumed to play a significant role in the initiation of chromosomal rearrangements, causing increased rates of karyotype evolution. We used cytogenetic analysis and molecular dating of cladogenetic events to compare the rate of changes of chromosome morphology and karyotype in asexually and sexually reproducing counterparts in European spined loach fish (Cobitis. We studied metaphases of three sexually reproducing species and their diploid and polyploid hybrid clones of different age of origin. The material includes artificial F1 hybrid strains, representatives of lineage originated in Holocene epoch, and also individuals of an oldest known age to date (roughly 0.37 MYA. Thereafter we applied GISH technique as a marker to differentiate parental chromosomal sets in hybrids. Although the sexual species accumulated remarkable chromosomal rearrangements after their speciation, we observed no differences in chromosome numbers and/or morphology among karyotypes of asexual hybrids. These hybrids possess chromosome sets originating from respective parental species with no cytogenetically detectable recombinations, suggesting their integrity even in a long term. The switch to asexual reproduction thus did not provoke any significant acceleration of the rate of chromosomal evolution in Cobitis. Asexual animals described in other case studies reproduce ameiotically, while Cobitis hybrids described here produce eggs likely through modified meiosis. Therefore, our findings indicate that the effect of asexuality on the rate of chromosomal change may be context-dependent rather than universal and related to particular type of asexual reproduction.

Interclonal variations in the molecular karyotype of Trypanosoma cruzi: chromosome rearrangements in a single cell-derived clone of the G strain.

Science.gov (United States)

Lima, Fabio Mitsuo; Souza, Renata Torres; Santori, Fábio Rinaldo; Santos, Michele Fernandes; Cortez, Danielle Rodrigues; Barros, Roberto Moraes; Cano, Maria Isabel; Valadares, Helder Magno Silva; Macedo, Andréa Mara; Mortara, Renato Arruda; da Silveira, José Franco

2013-01-01

Trypanosoma cruzi comprises a pool of populations which are genetically diverse in terms of DNA content, growth and infectivity. Inter- and intra-strain karyotype heterogeneities have been reported, suggesting that chromosomal rearrangements occurred during the evolution of this parasite. Clone D11 is a single-cell-derived clone of the T. cruzi G strain selected by the minimal dilution method and by infecting Vero cells with metacyclic trypomastigotes. Here we report that the karyotype of clone D11 differs from that of the G strain in both number and size of chromosomal bands. Large chromosomal rearrangement was observed in the chromosomes carrying the tubulin loci. However, most of the chromosome length polymorphisms were of small amplitude, and the absence of one band in clone D11 in relation to its reference position in the G strain could be correlated to the presence of a novel band migrating above or below this position. Despite the presence of chromosomal polymorphism, large syntenic groups were conserved between the isolates. The appearance of new chromosomal bands in clone D11 could be explained by chromosome fusion followed by a chromosome break or interchromosomal exchange of large DNA segments. Our results also suggest that telomeric regions are involved in this process. The variant represented by clone D11 could have been induced by the stress of the cloning procedure or could, as has been suggested for Leishmania infantum, have emerged from a multiclonal, mosaic parasite population submitted to frequent DNA amplification/deletion events, leading to a 'mosaic' structure with different individuals having differently sized versions of the same chromosomes. If this is the case, the variant represented by clone D11 would be better adapted to survive the stress induced by cloning, which includes intracellular development in the mammalian cell. Karyotype polymorphism could be part of the T. cruzi arsenal for responding to environmental pressure.

Cytotaxonomy of Eurypyga helias (Gruiformes, Eurypygidae): First Karyotypic Description and Phylogenetic Proximity with Rynochetidae

Science.gov (United States)

dos Santos, Michelly da Silva; Tagliarini, Marcella Mergulhão; O´Brien, Patricia C. M.; Ferguson-Smith, Malcolm A.; de Oliveira, Edivaldo H. C.

2015-01-01

The sunbittern (Eurypyga helias) is a South American Gruiformes, the only member of Family Eurypigidae. In most phylogenetic proposals, it is placed in a more distant position than other families of the so-called “core Gruiformes”. Different studies based on molecular, morphological and biogeographical data suggest that the Eurypigidae is closely related to the kagu (Rhynochetos jubatus), the only species in Rynochetidae, another family not included in the core Gruiformes. Here, the karyotype of the sunbittern is described for the first time, by classical and molecular cytogenetics, using whole chromosome probes derived from Gallus gallus and Leucopternis albicollis. We found a diploid number of 80, with only one pair of biarmed autosomal macrochromosomes, similar to that observed in the kagu. Chromosome painting revealed that most syntenies found in the avian putative ancestral karyotype (PAK) were conserved in the sunbittern. However, PAK1, PAK2, and PAK5 corresponded to two chromosome pairs each. Probes derived from L. albicollis confirm that fissions in PAK1 and PAK2 were centric, whereas in PAK5 the fission is interstitial. In addition, there is fusion of segments homologous to PAK2q and PAK5. From a phylogenetic point of view, comparisons of our results with two other Gruiformes belonging to family Rallidae suggest that the PAK5q fission might be a synapomorphy for Gruiformes. Fissions in PAK1 and PAK2 are found only in Eurypigidae, and might also occur in Rynochetidae, in view of the similar chromosomal morphology between the sunbittern and the kagu. This suggests a close phylogenetic relationship between Eurypigidae and Rynochetidae, whose common ancestor was separated by the Gondwana vicariancy in South America and New Caledonia, respectively. PMID:26624624

Double trisomy (XXX+21 karyotype) in a six-year-old girl with down phenotype.

Science.gov (United States)

Vergara-Mendez, Laura Daniela; Talero-Gutiérrez, Claudia; Velez-Van-Meerbeke, Alberto

2018-03-01

We describe a case of a six-year-old girl who presents multiple dysmorphic features characteristic of Down's syndrome. She has a significant general developmental delay, with a score that correspond to 32 months of developmental age. This delay is especially in language, with a very scant vocabulary. She communicates with some hand sign words or pointing, although her auditory responses in hearing test were normal. Two previous karyotype studies showed 47, XXX, +21 anomalies. This double trisomy is a rare condition described in isolated cases in the literature and none of these refers to the developmental aspects of these children (Balwan et al. 2008; Li et al. 2004; Park et al. 1995; Day et al. 1963).

The Turner syndrome in patient with 45X/47XXX mosaic karyotype--case report.

Science.gov (United States)

Maciejewska-Jeske, Marzena; Czyzyk, Adam; Meczekalski, Blazej

2015-07-01

Turner syndrome (TS) is a gonadal dysgenesis related to partial or total lack of one of the X chromosomes. It this report we describe a young patient presenting some somatic features of TS, who underwent spontaneous puberty and was eumenoorheic up to the age of 23. Using fluorescent in situ hybridization (FISH) mosaic karyotype (45X[131]/47XXX[9]) of TS and triple X syndrome was found. She presented uncommon for TS somatic hemihypotrophy and underwent growth hormone and surgical therapy. The patient was diagnosed with premature ovarian failure when she was 23, with absent follicular reserve. Clinical features of this case and a few published cases will be reviewed briefly.

Quasi-bivariate variational mode decomposition as a tool of scale analysis in wall-bounded turbulence

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Wang, Wenkang; Pan, Chong; Wang, Jinjun

2018-01-01

The identification and separation of multi-scale coherent structures is a critical task for the study of scale interaction in wall-bounded turbulence. Here, we propose a quasi-bivariate variational mode decomposition (QB-VMD) method to extract structures with various scales from instantaneous two-dimensional (2D) velocity field which has only one primary dimension. This method is developed from the one-dimensional VMD algorithm proposed by Dragomiretskiy and Zosso (IEEE Trans Signal Process 62:531-544, 2014) to cope with a quasi-2D scenario. It poses the feature of length-scale bandwidth constraint along the decomposed dimension, together with the central frequency re-balancing along the non-decomposed dimension. The feasibility of this method is tested on both a synthetic flow field and a turbulent boundary layer at moderate Reynolds number (Re_{τ } = 3458) measured by 2D particle image velocimetry (PIV). Some other popular scale separation tools, including pseudo-bi-dimensional empirical mode decomposition (PB-EMD), bi-dimensional EMD (B-EMD) and proper orthogonal decomposition (POD), are also tested for comparison. Among all these methods, QB-VMD shows advantages in both scale characterization and energy recovery. More importantly, the mode mixing problem, which degrades the performance of EMD-based methods, is avoided or minimized in QB-VMD. Finally, QB-VMD analysis of the wall-parallel plane in the log layer (at y/δ = 0.12) of the studied turbulent boundary layer shows the coexistence of large- or very large-scale motions (LSMs or VLSMs) and inner-scaled structures, which can be fully decomposed in both physical and spectral domains.

The prognostic value of monosomal karyotype (MK) in higher-risk patients with myelodysplastic syndromes treated with 5-Azacitidine. A retrospective analysis of the Hellenic (Greek) MDS Study Group.

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Papageorgiou, Sotirios G; Vasilatou, Diamantina; Kontos, Christos K; Kotsianidis, Ioannis; Symeonidis, Argiris; Galanopoulos, Athanasios G; Hatzimichael, Eleftheria; Megalakaki, Aekaterini; Poulakidas, Elias; Diamantopoulos, Panagiotis; Vassilakopoulos, Theodoros; Zikos, Panagiotis; Papadaki, Helen; Mparmparousi, Despoina; Bouronikou, Eleni; Panayiotidis, Panayiotis; Viniou, Nora-Athina; Pappa, Vassiliki

2018-04-16

In this study, we investigated the incidence and prognostic impact of monosomal karyotype (MK) in 405 higher-risk MDS patients treated with 5-AZA. The MK was present in 66 out of 405 (16.3%) patients, most of whom had complex karyotype (CK). MK was strongly associated with CK and the cytogenetic risk defined according to IPSS-R, as well as with high-risk disease, according to IPSS (P=0.029), IPSS-R (PMDS treated with 5-AZA. Furthermore, we showed that in MDS with high or very-high IPSS-R risk score, MK can further distinguish patients with worse outcome. This article is protected by copyright. All rights reserved. © 2018 Wiley Periodicals, Inc.

An integrated user-friendly ArcMAP tool for bivariate statistical modeling in geoscience applications

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Jebur, M. N.; Pradhan, B.; Shafri, H. Z. M.; Yusof, Z.; Tehrany, M. S.

2014-10-01

Modeling and classification difficulties are fundamental issues in natural hazard assessment. A geographic information system (GIS) is a domain that requires users to use various tools to perform different types of spatial modeling. Bivariate statistical analysis (BSA) assists in hazard modeling. To perform this analysis, several calculations are required and the user has to transfer data from one format to another. Most researchers perform these calculations manually by using Microsoft Excel or other programs. This process is time consuming and carries a degree of uncertainty. The lack of proper tools to implement BSA in a GIS environment prompted this study. In this paper, a user-friendly tool, BSM (bivariate statistical modeler), for BSA technique is proposed. Three popular BSA techniques such as frequency ratio, weights-of-evidence, and evidential belief function models are applied in the newly proposed ArcMAP tool. This tool is programmed in Python and is created by a simple graphical user interface, which facilitates the improvement of model performance. The proposed tool implements BSA automatically, thus allowing numerous variables to be examined. To validate the capability and accuracy of this program, a pilot test area in Malaysia is selected and all three models are tested by using the proposed program. Area under curve is used to measure the success rate and prediction rate. Results demonstrate that the proposed program executes BSA with reasonable accuracy. The proposed BSA tool can be used in numerous applications, such as natural hazard, mineral potential, hydrological, and other engineering and environmental applications.

An integrated user-friendly ArcMAP tool for bivariate statistical modelling in geoscience applications

Science.gov (United States)

Jebur, M. N.; Pradhan, B.; Shafri, H. Z. M.; Yusoff, Z. M.; Tehrany, M. S.

2015-03-01

Modelling and classification difficulties are fundamental issues in natural hazard assessment. A geographic information system (GIS) is a domain that requires users to use various tools to perform different types of spatial modelling. Bivariate statistical analysis (BSA) assists in hazard modelling. To perform this analysis, several calculations are required and the user has to transfer data from one format to another. Most researchers perform these calculations manually by using Microsoft Excel or other programs. This process is time-consuming and carries a degree of uncertainty. The lack of proper tools to implement BSA in a GIS environment prompted this study. In this paper, a user-friendly tool, bivariate statistical modeler (BSM), for BSA technique is proposed. Three popular BSA techniques, such as frequency ratio, weight-of-evidence (WoE), and evidential belief function (EBF) models, are applied in the newly proposed ArcMAP tool. This tool is programmed in Python and created by a simple graphical user interface (GUI), which facilitates the improvement of model performance. The proposed tool implements BSA automatically, thus allowing numerous variables to be examined. To validate the capability and accuracy of this program, a pilot test area in Malaysia is selected and all three models are tested by using the proposed program. Area under curve (AUC) is used to measure the success rate and prediction rate. Results demonstrate that the proposed program executes BSA with reasonable accuracy. The proposed BSA tool can be used in numerous applications, such as natural hazard, mineral potential, hydrological, and other engineering and environmental applications.

Differentiation of sex chromosomes and karyotypic evolution in the eye-lid geckos (Squamata: Gekkota: Eublepharidae), a group with different modes of sex determination

Czech Academy of Sciences Publication Activity Database

Pokorná, M.; Rábová, Marie; Ráb, Petr; Kratochvíl, L.

2010-01-01

Roč. 18, č. 6 (2010), s. 748-748 ISSN 0967-3849. [19th International Colloquium on animal cytogenetics and gene mapping. 06.06.-09.06.2010, Krakow] Institutional research plan: CEZ:AV0Z50450515 Keywords : sex chromosomes * karyotypic evolution * eye-lid geckos Subject RIV: EB - Genetics ; Molecular Biology

Chromosomal study of lettuce and its allied species (Lactuca spp., Asteraceae) by means of karyotype analysis and fluorescence in situ hybridization.

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Matoba, Hideyuki; Mizutani, Takayuki; Nagano, Katsuya; Hoshi, Yoshikazu; Uchiyama, Hiroshi

2007-12-01

In this study, in addition to the karyotype analysis, the chromosomal distributions of 5 S and 18 S rDNAs, and the Arabidopsis-type (T3AG3) telomeric sequences were detected by means of fluorescence in situ hybridization (FISH) to promote the information of chromosomal organization and evolution in the cultivated lettuce and its wild relatives, L. sativa, L. serriola, L. saligna and L. virosa. The karyotype analysis revealed the dissimilarity between L. virosa and the remaining species. In all four Lactuca species studied, one 5 S rDNA and two 18 S rDNA loci were detected. The simultaneous FISH of 5 S and 18 S rDNAs revealed that both rDNA loci of L. sativa, L. serriola and L. saligna were identical, however, that of L. virosa was different from the other species. These analyses indicate the closer relationships between L. sativa/L. serriola and L. saligna rather than L. virosa. Arabidopsis-type telomeric sequences were detected at both ends of their chromatids of all chromosomes not in the other regions. This observation suggests the lack of telomere-mediated chromosomal rearrangements among the Lactuca chromosomes.

Using bivariate latent basis growth curve analysis to better understand treatment outcome in youth with anorexia nervosa.

Science.gov (United States)

Byrne, Catherine E; Wonderlich, Joseph A; Curby, Timothy; Fischer, Sarah; Lock, James; Le Grange, Daniel

2018-04-25

This study explored the relation between eating-related obsessionality and weight restoration utilizing bivariate latent basis growth curve modelling. Eating-related obsessionality is a moderator of treatment outcome for adolescents with anorexia nervosa (AN). This study examined the degree to which the rate of change in eating-related obsessionality was associated with the rate of change in weight over time in family-based treatment (FBT) and individual therapy for AN. Data were drawn from a 2-site randomized controlled trial that compared FBT and adolescent focused therapy for AN. Bivariate latent basis growth curves were used to examine the differences of the relations between trajectories of body weight and symptoms associated with eating and weight obsessionality. In the FBT group, the slope of eating-related obsessionality scores and the slope of weight were significantly (negatively) correlated. This finding indicates that a decrease in overall eating-relating obsessionality is significantly associated with an increase in weight for individuals who received FBT. However, there was no relation between change in obsessionality scores and change in weight in the adolescent focused therapy group. Results suggest that FBT has a specific impact on both weight gain and obsessive compulsive behaviour that is distinct from individual therapy. Copyright © 2018 John Wiley & Sons, Ltd and Eating Disorders Association.

Fissions, fusions, and translocations shaped the karyotype and multiple sex chromosome constitution of the northeast-Asian wood white butterfly, Leptidea amurensis

Czech Academy of Sciences Publication Activity Database

Šíchová, Jindra; Ohno, M.; Dincă, V.; Watanabe, M.; Sahara, K.; Marec, František

2016-01-01

Roč. 118, č. 3 (2016), s. 457-471 ISSN 0024-4066 R&D Projects: GA ČR(CZ) GA14-22765S Grant - others:GA JU(CZ) 052/2013/P Institutional support: RVO:60077344 Keywords : karyotype evolution * meiotic pairing * multiple sex chromosomes Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.288, year: 2016 http://onlinelibrary.wiley.com/doi/10.1111/bij.12756/full

An efficient algorithm for generating random number pairs drawn from a bivariate normal distribution

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Campbell, C. W.

1983-01-01

An efficient algorithm for generating random number pairs from a bivariate normal distribution was developed. Any desired value of the two means, two standard deviations, and correlation coefficient can be selected. Theoretically the technique is exact and in practice its accuracy is limited only by the quality of the uniform distribution random number generator, inaccuracies in computer function evaluation, and arithmetic. A FORTRAN routine was written to check the algorithm and good accuracy was obtained. Some small errors in the correlation coefficient were observed to vary in a surprisingly regular manner. A simple model was developed which explained the qualities aspects of the errors.

Bivariate Cointegration Analysis of Energy-Economy Interactions in Iran

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Ismail Oladimeji Soile

2015-12-01

Full Text Available Fixing the prices of energy products below their opportunity cost for welfare and redistribution purposes is common with governments of many oil producing developing countries. This has often resulted in huge energy consumption in developing countries and the question that emerge is whether this increased energy consumption results in higher economic activities. Available statistics show that Iran’s economy growth shrunk for the first time in two decades from 2011 amidst the introduction of pricing reform in 2010 and 2014 suggesting a relationship between energy use and economic growth. Accordingly, the study examined the causality and the likelihood of a long term relationship between energy and economic growth in Iran. Unlike previous studies which have focused on the effects and effectiveness of the reform, the paper investigates the rationale for the reform. The study applied a bivariate cointegration time series econometric approach. The results reveals a one-way causality running from economic growth to energy with no feedback with evidence of long run connection. The implication of this is that energy conservation policy is not inimical to economic growth. This evidence lend further support for the ongoing subsidy reforms in Iran as a measure to check excessive and inefficient use of energy.

Influence of Flow Velocity on Tsunami Loss Estimation

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Jie Song

2017-11-01

Full Text Available Inundation depth is commonly used as an intensity measure in tsunami fragility analysis. However, inundation depth cannot be taken as the sole representation of tsunami impact on structures, especially when structural damage is caused by hydrodynamic and debris impact forces that are mainly determined by flow velocity. To reflect the influence of flow velocity in addition to inundation depth in tsunami risk assessment, a tsunami loss estimation method that adopts both inundation depth and flow velocity (i.e., bivariate intensity measures in evaluating tsunami damage is developed. To consider a wide range of possible tsunami inundation scenarios, Monte Carlo-based tsunami simulations are performed using stochastic earthquake slip distributions derived from a spectral synthesis method and probabilistic scaling relationships of earthquake source parameters. By focusing on Sendai (plain coast and Onagawa (ria coast in the Miyagi Prefecture of Japan in a case study, the stochastic tsunami loss is evaluated by total economic loss and its spatial distribution at different scales. The results indicate that tsunami loss prediction is highly sensitive to modelling resolution and inclusion of flow velocity for buildings located less than 1 km from the sea for Sendai and Onagawa of Miyagi Prefecture.

Transformation of Sordaria macrospora to hygromycin B resistance: characterization of transformants by electrophoretic karyotyping and tetrad analysis.

Science.gov (United States)

Walz, M; Kück, U

1995-12-01

The ascomycete Sordaria macrospora was transformed using different plasmid molecules containing the bacterial hygromycin B resistance gene (hph) under the control of different expression signals. The highest transformation frequency was obtained with vector pMW1. On this plasmid molecule, expression of the hph gene is directed by the upstream region of the isopenicillin N synthetase gene (pcbC) from the deuteromycete Acremonium chrysogenum. Southern analysis suggests that the vector copies are integrated as tandem repeats into the S. macrospora chromosomes and that duplicated sequences are most probably not inactivated by methylation during meiosis. Furthermore, the hygromycin B resistance (hygR) is not correlated with the number of integrated vector molecules. Electrophoretic karyotyping was used to further characterize S. macrospora transformants. Five chromosomal bands were separated by pulsed-field gel electrophoresis (PFGE) representing seven chromosomes with a total genome size of 39.5Mb. Hybridization analysis revealed ectopic integration of vector DNA into different chromosomes. In a few transformants, major rearrangements were detected. Transformants were sexually propagated to analyze the fate of the heterologous vector DNA. Although the hygR phenotype is stably maintained during mitosis, about a third of all lines tested showed loss of the resistance marker gene after meiosis. However, as was concluded from electrophoretic karyotyping, the resistant spores showed a Mendelian segregation of the integrated vector molecules in at least three consecutive generations. Our data indicate that heterologous marker genes can be used for transformation tagging, or the molecular mapping of chromosomal loci in S. macrospora.

Growth and ovarian function in girls with 48,XXXX karyotype--patient report and review of the literature.

Science.gov (United States)

Rooman, Raoul P A; Van Driessche, Karen; Du Caju, Marc V L

2002-01-01

The loss of an X chromosome results in short stature and often in primary ovarian failure, but the effect of extra X chromosomes is less clear, especially in 48,XXXX women. We report a girl with a 48,XXXX karyotype with tall stature (181.8 cm), primary ovarian failure and low DHEAS levels. A review of the literature shows that, apart from an intellectual deficit, the phenotype is very heterogeneous. The few data that are available in the literature indicate that tall stature and primary ovarian failure are not essential characteristics of the 48,XXXX phenotype.

Somatic mutations of isocitrate dehydrogenases 1 and 2 are prognostic and follow-up markers in patients with acute myeloid leukaemia with normal karyotype

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Virijevic Marijana

2016-12-01

Full Text Available Mutations in the isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2 genes are frequent molecular lesions in acute myeloid leukaemia with normal karyotype (AML-NK. The effects of IDH mutations on clinical features and treatment outcome in AML-NK have been widely investigated, but only a few studies monitored these mutations during follow-up.

Genetic correlations between body condition scores and fertility in dairy cattle using bivariate random regression models.

Science.gov (United States)

De Haas, Y; Janss, L L G; Kadarmideen, H N

2007-10-01

Genetic correlations between body condition score (BCS) and fertility traits in dairy cattle were estimated using bivariate random regression models. BCS was recorded by the Swiss Holstein Association on 22,075 lactating heifers (primiparous cows) from 856 sires. Fertility data during first lactation were extracted for 40,736 cows. The fertility traits were days to first service (DFS), days between first and last insemination (DFLI), calving interval (CI), number of services per conception (NSPC) and conception rate to first insemination (CRFI). A bivariate model was used to estimate genetic correlations between BCS as a longitudinal trait by random regression components, and daughter's fertility at the sire level as a single lactation measurement. Heritability of BCS was 0.17, and heritabilities for fertility traits were low (0.01-0.08). Genetic correlations between BCS and fertility over the lactation varied from: -0.45 to -0.14 for DFS; -0.75 to 0.03 for DFLI; from -0.59 to -0.02 for CI; from -0.47 to 0.33 for NSPC and from 0.08 to 0.82 for CRFI. These results show (genetic) interactions between fat reserves and reproduction along the lactation trajectory of modern dairy cows, which can be useful in genetic selection as well as in management. Maximum genetic gain in fertility from indirect selection on BCS should be based on measurements taken in mid lactation when the genetic variance for BCS is largest, and the genetic correlations between BCS and fertility is strongest.

Karyotype differentiation in 19 species of river loach fishes (Nemacheilidae, Teleostei): extensive variability associated with rDNA and heterochromatin distribution and its phylogenetic and ecological interpretation

Czech Academy of Sciences Publication Activity Database

Sember, Alexandr; Bohlen, Jörg; Šlechtová, Vendula; Altmanová, M.; Symonová, Radka; Ráb, Petr

2015-01-01

Roč. 15, č. 251 (2015) ISSN 1471-2148 R&D Projects: GA ČR GA206/08/0637 Institutional support: RVO:67985904 Keywords : fish cytotaxonomy * karyotype variability vs. 2n uniformity * FISH Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.406, year: 2015

A bivariate contaminated binormal model for robust fitting of proper ROC curves to a pair of correlated, possibly degenerate, ROC datasets.

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Zhai, Xuetong; Chakraborty, Dev P

2017-06-01

The objective was to design and implement a bivariate extension to the contaminated binormal model (CBM) to fit paired receiver operating characteristic (ROC) datasets-possibly degenerate-with proper ROC curves. Paired datasets yield two correlated ratings per case. Degenerate datasets have no interior operating points and proper ROC curves do not inappropriately cross the chance diagonal. The existing method, developed more than three decades ago utilizes a bivariate extension to the binormal model, implemented in CORROC2 software, which yields improper ROC curves and cannot fit degenerate datasets. CBM can fit proper ROC curves to unpaired (i.e., yielding one rating per case) and degenerate datasets, and there is a clear scientific need to extend it to handle paired datasets. In CBM, nondiseased cases are modeled by a probability density function (pdf) consisting of a unit variance peak centered at zero. Diseased cases are modeled with a mixture distribution whose pdf consists of two unit variance peaks, one centered at positive μ with integrated probability α, the mixing fraction parameter, corresponding to the fraction of diseased cases where the disease was visible to the radiologist, and one centered at zero, with integrated probability (1-α), corresponding to disease that was not visible. It is shown that: (a) for nondiseased cases the bivariate extension is a unit variances bivariate normal distribution centered at (0,0) with a specified correlation ρ 1 ; (b) for diseased cases the bivariate extension is a mixture distribution with four peaks, corresponding to disease not visible in either condition, disease visible in only one condition, contributing two peaks, and disease visible in both conditions. An expression for the likelihood function is derived. A maximum likelihood estimation (MLE) algorithm, CORCBM, was implemented in the R programming language that yields parameter estimates and the covariance matrix of the parameters, and other statistics

Classification of Knee Joint Vibration Signals Using Bivariate Feature Distribution Estimation and Maximal Posterior Probability Decision Criterion

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Fang Zheng

2013-04-01

Full Text Available Analysis of knee joint vibration or vibroarthrographic (VAG signals using signal processing and machine learning algorithms possesses high potential for the noninvasive detection of articular cartilage degeneration, which may reduce unnecessary exploratory surgery. Feature representation of knee joint VAG signals helps characterize the pathological condition of degenerative articular cartilages in the knee. This paper used the kernel-based probability density estimation method to model the distributions of the VAG signals recorded from healthy subjects and patients with knee joint disorders. The estimated densities of the VAG signals showed explicit distributions of the normal and abnormal signal groups, along with the corresponding contours in the bivariate feature space. The signal classifications were performed by using the Fisher’s linear discriminant analysis, support vector machine with polynomial kernels, and the maximal posterior probability decision criterion. The maximal posterior probability decision criterion was able to provide the total classification accuracy of 86.67% and the area (Az of 0.9096 under the receiver operating characteristics curve, which were superior to the results obtained by either the Fisher’s linear discriminant analysis (accuracy: 81.33%, Az: 0.8564 or the support vector machine with polynomial kernels (accuracy: 81.33%, Az: 0.8533. Such results demonstrated the merits of the bivariate feature distribution estimation and the superiority of the maximal posterior probability decision criterion for analysis of knee joint VAG signals.

A bivariate Chebyshev spectral collocation quasilinearization method for nonlinear evolution parabolic equations.

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Motsa, S S; Magagula, V M; Sibanda, P

2014-01-01

This paper presents a new method for solving higher order nonlinear evolution partial differential equations (NPDEs). The method combines quasilinearisation, the Chebyshev spectral collocation method, and bivariate Lagrange interpolation. In this paper, we use the method to solve several nonlinear evolution equations, such as the modified KdV-Burgers equation, highly nonlinear modified KdV equation, Fisher's equation, Burgers-Fisher equation, Burgers-Huxley equation, and the Fitzhugh-Nagumo equation. The results are compared with known exact analytical solutions from literature to confirm accuracy, convergence, and effectiveness of the method. There is congruence between the numerical results and the exact solutions to a high order of accuracy. Tables were generated to present the order of accuracy of the method; convergence graphs to verify convergence of the method and error graphs are presented to show the excellent agreement between the results from this study and the known results from literature.

A Bivariate Chebyshev Spectral Collocation Quasilinearization Method for Nonlinear Evolution Parabolic Equations

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S. S. Motsa

2014-01-01

Full Text Available This paper presents a new method for solving higher order nonlinear evolution partial differential equations (NPDEs. The method combines quasilinearisation, the Chebyshev spectral collocation method, and bivariate Lagrange interpolation. In this paper, we use the method to solve several nonlinear evolution equations, such as the modified KdV-Burgers equation, highly nonlinear modified KdV equation, Fisher's equation, Burgers-Fisher equation, Burgers-Huxley equation, and the Fitzhugh-Nagumo equation. The results are compared with known exact analytical solutions from literature to confirm accuracy, convergence, and effectiveness of the method. There is congruence between the numerical results and the exact solutions to a high order of accuracy. Tables were generated to present the order of accuracy of the method; convergence graphs to verify convergence of the method and error graphs are presented to show the excellent agreement between the results from this study and the known results from literature.

An assessment on the use of bivariate, multivariate and soft computing techniques for collapse susceptibility in GIS environ

Science.gov (United States)

Yilmaz, Işik; Marschalko, Marian; Bednarik, Martin

2013-04-01

The paper presented herein compares and discusses the use of bivariate, multivariate and soft computing techniques for collapse susceptibility modelling. Conditional probability (CP), logistic regression (LR) and artificial neural networks (ANN) models representing the bivariate, multivariate and soft computing techniques were used in GIS based collapse susceptibility mapping in an area from Sivas basin (Turkey). Collapse-related factors, directly or indirectly related to the causes of collapse occurrence, such as distance from faults, slope angle and aspect, topographical elevation, distance from drainage, topographic wetness index (TWI), stream power index (SPI), Normalized Difference Vegetation Index (NDVI) by means of vegetation cover, distance from roads and settlements were used in the collapse susceptibility analyses. In the last stage of the analyses, collapse susceptibility maps were produced from the models, and they were then compared by means of their validations. However, Area Under Curve (AUC) values obtained from all three models showed that the map obtained from soft computing (ANN) model looks like more accurate than the other models, accuracies of all three models can be evaluated relatively similar. The results also showed that the conditional probability is an essential method in preparation of collapse susceptibility map and highly compatible with GIS operating features.

Optical Coherence Tomography Noise Reduction Using Anisotropic Local Bivariate Gaussian Mixture Prior in 3D Complex Wavelet Domain.

Science.gov (United States)

Rabbani, Hossein; Sonka, Milan; Abramoff, Michael D

2013-01-01

In this paper, MMSE estimator is employed for noise-free 3D OCT data recovery in 3D complex wavelet domain. Since the proposed distribution for noise-free data plays a key role in the performance of MMSE estimator, a priori distribution for the pdf of noise-free 3D complex wavelet coefficients is proposed which is able to model the main statistical properties of wavelets. We model the coefficients with a mixture of two bivariate Gaussian pdfs with local parameters which are able to capture the heavy-tailed property and inter- and intrascale dependencies of coefficients. In addition, based on the special structure of OCT images, we use an anisotropic windowing procedure for local parameters estimation that results in visual quality improvement. On this base, several OCT despeckling algorithms are obtained based on using Gaussian/two-sided Rayleigh noise distribution and homomorphic/nonhomomorphic model. In order to evaluate the performance of the proposed algorithm, we use 156 selected ROIs from 650 × 512 × 128 OCT dataset in the presence of wet AMD pathology. Our simulations show that the best MMSE estimator using local bivariate mixture prior is for the nonhomomorphic model in the presence of Gaussian noise which results in an improvement of 7.8 ± 1.7 in CNR.

Optical Coherence Tomography Noise Reduction Using Anisotropic Local Bivariate Gaussian Mixture Prior in 3D Complex Wavelet Domain

Directory of Open Access Journals (Sweden)

Hossein Rabbani

2013-01-01

Full Text Available In this paper, MMSE estimator is employed for noise-free 3D OCT data recovery in 3D complex wavelet domain. Since the proposed distribution for noise-free data plays a key role in the performance of MMSE estimator, a priori distribution for the pdf of noise-free 3D complex wavelet coefficients is proposed which is able to model the main statistical properties of wavelets. We model the coefficients with a mixture of two bivariate Gaussian pdfs with local parameters which are able to capture the heavy-tailed property and inter- and intrascale dependencies of coefficients. In addition, based on the special structure of OCT images, we use an anisotropic windowing procedure for local parameters estimation that results in visual quality improvement. On this base, several OCT despeckling algorithms are obtained based on using Gaussian/two-sided Rayleigh noise distribution and homomorphic/nonhomomorphic model. In order to evaluate the performance of the proposed algorithm, we use 156 selected ROIs from 650 × 512 × 128 OCT dataset in the presence of wet AMD pathology. Our simulations show that the best MMSE estimator using local bivariate mixture prior is for the nonhomomorphic model in the presence of Gaussian noise which results in an improvement of 7.8 ± 1.7 in CNR.

Fragment length analysis screening for detection of CEBPA mutations in intermediate-risk karyotype acute myeloid leukemia.

Science.gov (United States)

Fuster, Oscar; Barragán, Eva; Bolufer, Pascual; Such, Esperanza; Valencia, Ana; Ibáñez, Mariam; Dolz, Sandra; de Juan, Inmaculada; Jiménez, Antonio; Gómez, Maria Teresa; Buño, Ismael; Martínez, Joaquín; Cervera, José; Montesinos, Pau; Moscardó, Federico; Sanz, Miguel Ángel

2012-01-01

During last years, molecular markers have been increased as prognostic factors routinely screened in acute myeloid leukemia (AML). Recently, an increasing interest has been reported in introducing to clinical practice screening for mutations in the CCAAT/enhancer-binding protein α (CEBPA) gene in AML, as it seems to be a good prognostic factor. However, there is no reliable established method for assessing CEBPA mutations during the diagnostic work-up of AMLs. We describe here a straightforward and reliable fragment analysis method based in PCR capillary electrophoresis (PCR-CE) for screening of CEBPA mutations; moreover, we present the results obtained in 151 intermediate-risk karyotype AML patients (aged 16-80 years). The method gave a specificity of 100% and sensitivity of 93% with a lower detection limit of 1-5% for CEBPA mutations. The series found 19 mutations and four polymorphisms in 12 patients, seven of whom (58%) presented two mutations. The overall frequency of CEBPA mutations in AML was 8% (n = 12). CEBPA mutations showed no coincidence with FLT3-ITD or NPM1 mutations. CEBPA mutation predicted better disease-free survival in the group of patients without FLT3-ITD, NPM, or both genes mutated (HR 3.6, IC 95%; 1.0-13.2, p = 0.05) and better overall survival in patients younger than 65 of this group without molecular markers (HR 4.0, IC 95%; 1.0-17.4, p = 0.05). In conclusion, the fragment analysis method based in PCR-CE is a rapid, specific, and sensitive method for CEBPA mutation screening and our results confirm that CEBPA mutations can identify a subgroup of patients with favorable prognosis in AML with intermediate-risk karyotype.

Which global stock indices trigger stronger contagion risk in the Vietnamese stock market? Evidence using a bivariate analysis

OpenAIRE

Wang Kuan-Min; Lai Hung-Cheng

2013-01-01

This paper extends recent investigations into risk contagion effects on stock markets to the Vietnamese stock market. Daily data spanning October 9, 2006 to May 3, 2012 are sourced to empirically validate the contagion effects between stock markets in Vietnam, and China, Japan, Singapore, and the US. To facilitate the validation of contagion effects with market-related coefficients, this paper constructs a bivariate EGARCH model of dynamic conditional correlation coefficients. Using the...

Análise do cariótipo de Apuleia leiocarpa (Vog. Macbr. Analysis of Apuleia leiocarpa (Vog. Macbr. karyotype

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Neiva Maria Frizon Auler

1999-03-01

Full Text Available Estudos citogenéticos da Apuleia leiocarpa foram realizados com o objetivo de determinar e montar o cariótipo da espécie. As sementes utilizadas foram coletadas na localidade de Cerrito, município de Santa Maria - RS. A pesquisa foi conduzida no Laboratório de Citogenética Vegetal e Biotecnologia do Departamento de Biologia da Universidade federal de Santa Maria - RS, nos anos de 1996 - 1997. Em metáfases de mitose foi encontrada uma variação no número de cromossomos de 20 a 28, sugerindo ser a Apuleia leiocarpa uma leguminosa com capacidade de polissomatia. O número de cromossomos da espécie é 2n = 2x = 26, distribuídos na fórmula cariotípica 20m + 4 sm + 2 t.Cytogenetic studies of Apuleia leiocarpa were carried out in order to determine and arrange the species karyotype. Seeds were collected in Cerrito, Santa Maria - RS. The research was developed at the Laboratory of Vegetal Cytogenetics and Biotechnology of the Biology Department at the Federal University of Santa Maria - RS, during 1996 and 1997. A variation in the number of chromosomes from 20 to 28 was found in metaphases of mitosis. Such variation suggests that Apuleia leiocarpa is a leguminous with polysomy capacity. The chromosomal number of the species is 2n = 2x = 26, distributed in the karyotypic formula 20m + 4 sm + 2 t.

Age-related variability of some characters of karyotype instability in the mouse line CC57W/Mv

International Nuclear Information System (INIS)

Glazko, T.T.; Safonova, N.A.; Kovaleva, O.A.; Stolina, M.P.; Solomko, A.P.; Malyuta, S.S.; Glazko, V.I.; AN Ukrainskoj SSR, Kiev

1995-01-01

The investigations of relations between cytogenetical variability in cells of bone marrow of the mouse line CC57W/Mv and factors of age and radioactivity pollution (the specific vivarium in the 30-km Chernobyl zone) were carried out. The karyotype instability on some characters were similarly between young mice in the Chernobyl zone and old mice under control conditions. The old Chernobyl mice differentiated from old control ones by a low frequency of some cytogenetic anomalies and higher values of the mitotic index. The contribution of the intensity of cell division into observed variabilities of cytogenetic character between different mouse groups was discussed

Two-Stage Urethroplasty with Buccal Mucosa for Penoscrotal Hypospadias Reconstruction in a Male with a 46,XX Karyotype.

Science.gov (United States)

D'hulst, Pieter; Darras, Jochen; Joniau, Steven; Mattelaer, Pieter; Winne, Linsey; Ponette, Diederik

2017-09-01

We present a case regarding a 32-year old African male with penoscrotal hypospadias, left cryptorchidism and a left inguinal hernia. There were moderate masculinization characteristics. He underwent a Lichtenstein hernia repair with perioperative biopsies of the left inguinal testis and epididymis. Microscopic examination showed a Sertoli-only left testis with Leydig-cell hyperplasia and the left epididymis consisted of ovarian tissue with corpora albicantia and maturing follicles. Endocrinological evaluation showed a sex-determining region Y (SRY) negative 46,XX karyotype. We successfully performed a two-stage urethroplasty with buccal mucosa graft to reconstruct his penoscrotal hypospadias.

Applying Emax model and bivariate thin plate splines to assess drug interactions.

Science.gov (United States)

Kong, Maiying; Lee, J Jack

2010-01-01

We review the semiparametric approach previously proposed by Kong and Lee and extend it to a case in which the dose-effect curves follow the Emax model instead of the median effect equation. When the maximum effects for the investigated drugs are different, we provide a procedure to obtain the additive effect based on the Loewe additivity model. Then, we apply a bivariate thin plate spline approach to estimate the effect beyond additivity along with its 95 per cent point-wise confidence interval as well as its 95 per cent simultaneous confidence interval for any combination dose. Thus, synergy, additivity, and antagonism can be identified. The advantages of the method are that it provides an overall assessment of the combination effect on the entire two-dimensional dose space spanned by the experimental doses, and it enables us to identify complex patterns of drug interaction in combination studies. In addition, this approach is robust to outliers. To illustrate this procedure, we analyzed data from two case studies.

A new record of Chironomus (Chironomus) acidophilus Keyl (Diptera, Chironomidae) from the Uzon volcanic caldera (Kronotsky Reserve, Kamchatka Peninsula, Russia), its karyotype, ecology and biology.

Science.gov (United States)

Orel, Oksana V; Lobkova, Ludmila E; Zhirov, Sergey V; Petrova, Ninel A

2015-07-03

Morphology, cytology, ecology and biology of Holarctic Chironomus (Chironomus) acidophilus Keyl, 1960 (Diptera, Chironomidae) was examined from material collected in the geothermal Vosmerka Lake (pH=2.0-2.5). An illustrated redescription of C. acidophilus is given on the basis of adult males reared from field-collected pupae, and of simultaneously collected larvae. Additional larvae belonging to the pseudothummi-complex were identified as C. acidophilus on the basis of their karyotype. The karyotype of C. acidophilus (2n=8) and detailed mapping of the 4 chromosome arms A, E, D and F are provided. The population of C. acidophilus from Kamchatka was found to be karyologically monomorphic. Information on distribution and ecology of C. acidophilus from Vosmerka Lake (total mineralization 1583.5 mg/l) is also given. Chironomus acidophilus is the only species of aquatic insects recorded in this lake. Lack of competition and a richness of food resources contribute to the high abundance (35161 ind./m2) and biomass (11.342 g/m2) of the larvae of C. acidophilus in Vosmerka Lake.

Asymptotics of bivariate generating functions with algebraic singularities

Science.gov (United States)

Greenwood, Torin

Flajolet and Odlyzko (1990) derived asymptotic formulae the coefficients of a class of uni- variate generating functions with algebraic singularities. Gao and Richmond (1992) and Hwang (1996, 1998) extended these results to classes of multivariate generating functions, in both cases by reducing to the univariate case. Pemantle and Wilson (2013) outlined new multivariate ana- lytic techniques and used them to analyze the coefficients of rational generating functions. After overviewing these methods, we use them to find asymptotic formulae for the coefficients of a broad class of bivariate generating functions with algebraic singularities. Beginning with the Cauchy integral formula, we explicity deform the contour of integration so that it hugs a set of critical points. The asymptotic contribution to the integral comes from analyzing the integrand near these points, leading to explicit asymptotic formulae. Next, we use this formula to analyze an example from current research. In the following chapter, we apply multivariate analytic techniques to quan- tum walks. Bressler and Pemantle (2007) found a (d + 1)-dimensional rational generating function whose coefficients described the amplitude of a particle at a position in the integer lattice after n steps. Here, the minimal critical points form a curve on the (d + 1)-dimensional unit torus. We find asymptotic formulae for the amplitude of a particle in a given position, normalized by the number of steps n, as n approaches infinity. Each critical point contributes to the asymptotics for a specific normalized position. Using Groebner bases in Maple again, we compute the explicit locations of peak amplitudes. In a scaling window of size the square root of n near the peaks, each amplitude is asymptotic to an Airy function.

The use of bivariate spatial modeling of questionnaire and parasitology data to predict the distribution of Schistosoma haematobium in Coastal Kenya.

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Hugh J W Sturrock

Full Text Available Questionnaires of reported blood in urine (BIU distributed through the existing school system provide a rapid and reliable method to classify schools according to the prevalence of Schistosoma haematobium, thereby helping in the targeting of schistosomiasis control. However, not all schools return questionnaires and it is unclear whether treatment is warranted in such schools. This study investigates the use of bivariate spatial modelling of available and multiple data sources to predict the prevalence of S. haematobium at every school along the Kenyan coast.Data from a questionnaire survey conducted by the Kenya Ministry of Education in Coast Province in 2009 were combined with available parasitological and environmental data in a Bayesian bivariate spatial model. This modeled the relationship between BIU data and environmental covariates, as well as the relationship between BIU and S. haematobium infection prevalence, to predict S. haematobium infection prevalence at all schools in the study region. Validation procedures were implemented to assess the predictive accuracy of endemicity classification.The prevalence of BIU was negatively correlated with distance to nearest river and there was considerable residual spatial correlation at small (~15 km spatial scales. There was a predictable relationship between the prevalence of reported BIU and S. haematobium infection. The final model exhibited excellent sensitivity (0.94 but moderate specificity (0.69 in identifying low (<10% prevalence schools, and had poor performance in differentiating between moderate and high prevalence schools (sensitivity 0.5, specificity 1.Schistosomiasis is highly focal and there is a need to target treatment on a school-by-school basis. The use of bivariate spatial modelling can supplement questionnaire data to identify schools requiring mass treatment, but is unable to distinguish between moderate and high prevalence schools.

Epileptic seizure prediction based on a bivariate spectral power methodology.

Science.gov (United States)

Bandarabadi, Mojtaba; Teixeira, Cesar A; Direito, Bruno; Dourado, Antonio

2012-01-01

The spectral power of 5 frequently considered frequency bands (Alpha, Beta, Gamma, Theta and Delta) for 6 EEG channels is computed and then all the possible pairwise combinations among the 30 features set, are used to create a 435 dimensional feature space. Two new feature selection methods are introduced to choose the best candidate features among those and to reduce the dimensionality of this feature space. The selected features are then fed to Support Vector Machines (SVMs) that classify the cerebral state in preictal and non-preictal classes. The outputs of the SVM are regularized using a method that accounts for the classification dynamics of the preictal class, also known as "Firing Power" method. The results obtained using our feature selection approaches are compared with the ones obtained using minimum Redundancy Maximum Relevance (mRMR) feature selection method. The results in a group of 12 patients of the EPILEPSIAE database, containing 46 seizures and 787 hours multichannel recording for out-of-sample data, indicate the efficiency of the bivariate approach as well as the two new feature selection methods. The best results presented sensitivity of 76.09% (35 of 46 seizures predicted) and a false prediction rate of 0.15(-1).

Maintenance of syntenic groups between Cathartidae and Gallus gallus indicates symplesiomorphic karyotypes in new world vultures

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Marcella M. Tagliarini

2011-01-01

Full Text Available Similarities between New World and Old World vultures have been interpreted to reflect a close relationship and to suggest the inclusion of both in Accipitridae (Falconiformes. However, deeper analyses indicated that the placement of the New World vultures (cathartids in this Order is uncertain. Chromosome analysis has shown that cathartids retained a karyotype similar to the putative avian ancestor. In order to verify the occurrence of intrachromosomal rearrangements in cathartids, we hybridized whole chromosome probes of two species (Gallus gallus and Leucopternis albicollis onto metaphases of Cathartes aura. The results showed that not only were the syntenic groups conserved between Gallus and C. aura, but probably also the general gene order, suggesting that New World vultures share chromosomal symplesiomorphies with most bird lineages.

Obtaining DDF Curves of Extreme Rainfall Data Using Bivariate Copula and Frequency Analysis

DEFF Research Database (Denmark)

Sadri, Sara; Madsen, Henrik; Mikkelsen, Peter Steen

2009-01-01

, situated near Copenhagen in Denmark. For rainfall extracted using method 2, the marginal distribution of depth was found to fit the Generalized Pareto distribution while duration was found to fit the Gamma distribution, using the method of L-moments. The volume was fit with a generalized Pareto...... with duration for a given return period and name them DDF (depth-duration-frequency) curves. The copula approach does not assume the rainfall variables are independent or jointly normally distributed. Rainfall series are extracted in three ways: (1) by maximum mean intensity; (2) by depth and duration...... distribution and the duration was fit with a Pearson type III distribution for rainfall extracted using method 3. The Clayton copula was found to be appropriate for bivariate analysis of rainfall depth and duration for both methods 2 and 3. DDF curves derived using the Clayton copula for depth and duration...

A Basic Bivariate Structure of Personality Attributes Evident Across Nine Languages.

Science.gov (United States)

Saucier, Gerard; Thalmayer, Amber Gayle; Payne, Doris L; Carlson, Robert; Sanogo, Lamine; Ole-Kotikash, Leonard; Church, A Timothy; Katigbak, Marcia S; Somer, Oya; Szarota, Piotr; Szirmák, Zsofia; Zhou, Xinyue

2014-02-01

Here, two studies seek to characterize a parsimonious common-denominator personality structure with optimal cross-cultural replicability. Personality differences are observed in all human populations and cultures, but lexicons for personality attributes contain so many distinctions that parsimony is lacking. Models stipulating the most important attributes have been formulated by experts or by empirical studies drawing on experience in a very limited range of cultures. Factor analyses of personality lexicons of nine languages of diverse provenance (Chinese, Korean, Filipino, Turkish, Greek, Polish, Hungarian, Maasai, and Senoufo) were examined, and their common structure was compared to that of several prominent models in psychology. A parsimonious bivariate model showed evidence of substantial convergence and ubiquity across cultures. Analyses involving key markers of these dimensions in English indicate that they are broad dimensions involving the overlapping content of the interpersonal circumplex, models of communion and agency, and morality/warmth and competence. These "Big Two" dimensions-Social Self-Regulation and Dynamism-provide a common-denominator model involving the two most crucial axes of personality variation, ubiquitous across cultures. The Big Two might serve as an umbrella model serving to link diverse theoretical models and associated research literatures. © 2013 Wiley Periodicals, Inc.

Karyotype characterization of Trigona fulviventris Guérin, 1835 (Hymenoptera, Meliponini by C banding and fluorochrome staining: report of a new chromosome number in the genus

Directory of Open Access Journals (Sweden)

Domingues Alayne Magalhães Trindade

2005-01-01

Full Text Available Although many species of the genus Trigona have been taxonomically described, cytogenetic studies of these species are still rare. The aim of the present study was to obtain cytogenetic data by conventional staining, C banding and fluorochrome staining for the karyotype characterization of the species Trigona fulviventris. Cytogenetic analysis revealed that this species possesses a diploid chromosome number of 2n = 32, different from most other species of this genus studied so far. This variation was probably due to the centric fusion in a higher numbered ancestral karyotype, this fusion producing the large metacentric chromosome pair and the lower chromosome number observed in Trigona fulviventris. Heterochromatin was detected in the pericentromeric region of the first chromosome pair and in one of the arms of the remaining pairs. Base-specific fluorochrome staining with 4'-6-diamidino-2-phenylindole (DAPI showed that the heterochromatin was rich in AT base pairs (DAPI+ except for pair 13, which was chromomycin A3 (CMA3 positive indicating an excess of GC base pairs. Our data also suggests that there was variation in heterochromatin base composition.

[CpG-oligodeoxynucleotide stimulation improves the success for karyotypic analysis of chronic lymphocytic leukemia cells].

Science.gov (United States)

Liu, Qiong; Xu, Wei; Qiu, Hai-rong; Wang, Rong; Yu, Hui; Fan, Lei; Miao, Kou-rong; Li, Jian-yong

2009-09-01

To explore the effect of CpG-oligodeoxynucleotides (ODN) in chromosome study of chronic lymphocytic leukemia (CLL). Blood or bone marrow cells of 70 CLL patients were cultured for 72 h with PHA, CpG-ODN and CpG-ODN combined with IL-2, respectively. Routine karyotype analysis with R banding technique and interphase fluorescence in situ hybridization (FISH) were performed. The metaphase number>or=20 was considered as successful stimulation, which in PHA, CpG-ODN and CpG-ODN combined IL-2 groups were 90.0%, 68.6% and 68.6%, respectively, and the detection rates of chromosome aberrations were 3.2%, 43.6% and 43.6%, respectively. The aberrations rates detected by interphase FISH with a panel of probes was 64.3%. CpG-ODN DSP30 can effectively raise the detection rate of chromosome aberrations in CLL patients.

Bivariate Drought Analysis Using Streamflow Reconstruction with Tree Ring Indices in the Sacramento Basin, California, USA

Directory of Open Access Journals (Sweden)

Jaewon Kwak

2016-03-01

Full Text Available Long-term streamflow data are vital for analysis of hydrological droughts. Using an artificial neural network (ANN model and nine tree-ring indices, this study reconstructed the annual streamflow of the Sacramento River for the period from 1560 to 1871. Using the reconstructed streamflow data, the copula method was used for bivariate drought analysis, deriving a hydrological drought return period plot for the Sacramento River basin. Results showed strong correlation among drought characteristics, and the drought with a 20-year return period (17.2 million acre-feet (MAF per year in the Sacramento River basin could be considered a critical level of drought for water shortages.

Optical Coherence Tomography Noise Reduction Using Anisotropic Local Bivariate Gaussian Mixture Prior in 3D Complex Wavelet Domain

OpenAIRE

Rabbani, Hossein; Sonka, Milan; Abramoff, Michael D.

2013-01-01

In this paper, MMSE estimator is employed for noise-free 3D OCT data recovery in 3D complex wavelet domain. Since the proposed distribution for noise-free data plays a key role in the performance of MMSE estimator, a priori distribution for the pdf of noise-free 3D complex wavelet coefficients is proposed which is able to model the main statistical properties of wavelets. We model the coefficients with a mixture of two bivariate Gaussian pdfs with local parameters which are able to capture th...

Aquaculture in artificially developed wetlands in urban areas: an application of the bivariate relationship between soil and surface water in landscape ecology.

Science.gov (United States)

Paul, Abhijit

2011-01-01

Wetlands show a strong bivariate relationship between soil and surface water. Artificially developed wetlands help to build landscape ecology and make built environments sustainable. The bheries, wetlands of eastern Calcutta (India), utilize the city sewage to develop urban aquaculture that supports the local fish industries and opens a new frontier in sustainable environmental planning research.

Bivariate empirical mode decomposition for ECG-based biometric identification with emotional data.

Science.gov (United States)

Ferdinando, Hany; Seppanen, Tapio; Alasaarela, Esko

2017-07-01

Emotions modulate ECG signals such that they might affect ECG-based biometric identification in real life application. It motivated in finding good feature extraction methods where the emotional state of the subjects has minimum impacts. This paper evaluates feature extraction based on bivariate empirical mode decomposition (BEMD) for biometric identification when emotion is considered. Using the ECG signal from the Mahnob-HCI database for affect recognition, the features were statistical distributions of dominant frequency after applying BEMD analysis to ECG signals. The achieved accuracy was 99.5% with high consistency using kNN classifier in 10-fold cross validation to identify 26 subjects when the emotional states of the subjects were ignored. When the emotional states of the subject were considered, the proposed method also delivered high accuracy, around 99.4%. We concluded that the proposed method offers emotion-independent features for ECG-based biometric identification. The proposed method needs more evaluation related to testing with other classifier and variation in ECG signals, e.g. normal ECG vs. ECG with arrhythmias, ECG from various ages, and ECG from other affective databases.

A bivariate optimal replacement policy for a multistate repairable system

International Nuclear Information System (INIS)

Zhang Yuanlin; Yam, Richard C.M.; Zuo, Ming J.

2007-01-01

In this paper, a deteriorating simple repairable system with k+1 states, including k failure states and one working state, is studied. It is assumed that the system after repair is not 'as good as new' and the deterioration of the system is stochastic. We consider a bivariate replacement policy, denoted by (T,N), in which the system is replaced when its working age has reached T or the number of failures it has experienced has reached N, whichever occurs first. The objective is to determine the optimal replacement policy (T,N)* such that the long-run expected profit per unit time is maximized. The explicit expression of the long-run expected profit per unit time is derived and the corresponding optimal replacement policy can be determined analytically or numerically. We prove that the optimal policy (T,N)* is better than the optimal policy N* for a multistate simple repairable system. We also show that a general monotone process model for a multistate simple repairable system is equivalent to a geometric process model for a two-state simple repairable system in the sense that they have the same structure for the long-run expected profit (or cost) per unit time and the same optimal policy. Finally, a numerical example is given to illustrate the theoretical results

Karyotype analysis of a male exhibiting Meckel's diverticulum and aural atresia

Energy Technology Data Exchange (ETDEWEB)

Frizzell, B.; Hicks, M.F. (David Lipscomb Univ., Nashville, TN (United States))

Patau's Syndrome is caused by inheritance of an extra chromosome 13. It is characterized primarily by severe mental retardation, cleft palate, and retarded growth. Most fetuses expressing Patau's Syndrome spontaneously abort, and those that are born usually die before one year. Both Meckel's diverticulum and aural atresia are defects found in patients with Patau's at levels higher than those in the general population. An otherwise asymptomatic male expressing only Meckel's diverticulum and aural atresia has a female sibling whose son expressed Patau's syndrome. Twenty percent of patients with Patau's show a translocation of part of chromosome 13 to another D chromosome. If a translocation were the cause of the expression of Patau's in this family, it is possible that the normal male inherited a balanced translocation and the Patau's male received an unbalanced translocation. A karyotype analysis of the non-Patau's male was done to determine if such a translocation were present.

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

Czech Academy of Sciences Publication Activity Database

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

2011-01-01

Roč. 139, č. 3 (2011), s. 281-289 ISSN 0016-6707 R&D Projects: GA ČR GA522/09/1940 Grant - others:AV ČR(CZ) KJB501410901; Grant Agency of the University of South Bohemia(CZ) 137/2010/P Institutional research plan: CEZ:AV0Z50070508 Keywords : Diuraphis noxia * karyotype * genome size Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.148, year: 2011

A study on karyotype of the pileated gibbon, Hylobates pileatus (Primates, Hylobatidae, by conventional staining

Directory of Open Access Journals (Sweden)

Alongkoad Tanomtong

2008-07-01

Full Text Available Cytogenetics of the pileated gibbon (Hylobates pileatus at Nakhon Ratchasima Zoo, Thailand, was studied. Bloodsamples were taken from two female and two male gibbons. After lymphocyte culture, the mitotic chromosome preparationwas done by hypotonic-fixation-air-drying method and conventional Giemsa’s staining. The results show that diploid chromosomenumber was 44 (2n=2x=44, and the fundamental number (NF were 88 chromosomes in both female and male.The autosomes consist of 12 large metacentric, 6 medium metacentric, 2 medium submetacentric, 2 medium acrocentric, 12small metacentric and 8 small submetacentric chromosomes. In addition, the chromosome 15 showed clearly observablesatellite chromosomes. The X chromosome was a medium submetacentric chromosome and the Y chromosome was a tinyacrocentric chromosome. The karyotype formula for the pileated gibbon is as follows:2n (44 = Lm12+Mm6+Msm2+Ma2+Sm12+Ssm8+sex-chromosomes

A Bivariate Mixture Model for Natural Antibody Levels to Human Papillomavirus Types 16 and 18: Baseline Estimates for Monitoring the Herd Effects of Immunization.

Directory of Open Access Journals (Sweden)

Margaretha A Vink

Full Text Available Post-vaccine monitoring programs for human papillomavirus (HPV have been introduced in many countries, but HPV serology is still an underutilized tool, partly owing to the weak antibody response to HPV infection. Changes in antibody levels among non-vaccinated individuals could be employed to monitor herd effects of immunization against HPV vaccine types 16 and 18, but inference requires an appropriate statistical model. The authors developed a four-component bivariate mixture model for jointly estimating vaccine-type seroprevalence from correlated antibody responses against HPV16 and -18 infections. This model takes account of the correlation between HPV16 and -18 antibody concentrations within subjects, caused e.g. by heterogeneity in exposure level and immune response. The model was fitted to HPV16 and -18 antibody concentrations as measured by a multiplex immunoassay in a large serological survey (3,875 females carried out in the Netherlands in 2006/2007, before the introduction of mass immunization. Parameters were estimated by Bayesian analysis. We used the deviance information criterion for model selection; performance of the preferred model was assessed through simulation. Our analysis uncovered elevated antibody concentrations in doubly as compared to singly seropositive individuals, and a strong clustering of HPV16 and -18 seropositivity, particularly around the age of sexual debut. The bivariate model resulted in a more reliable classification of singly and doubly seropositive individuals than achieved by a combination of two univariate models, and suggested a higher pre-vaccine HPV16 seroprevalence than previously estimated. The bivariate mixture model provides valuable baseline estimates of vaccine-type seroprevalence and may prove useful in seroepidemiologic assessment of the herd effects of HPV vaccination.

Karyotype Stability and Unbiased Fractionation in the Paleo-Allotetraploid Cucurbita Genomes.

Science.gov (United States)

Sun, Honghe; Wu, Shan; Zhang, Guoyu; Jiao, Chen; Guo, Shaogui; Ren, Yi; Zhang, Jie; Zhang, Haiying; Gong, Guoyi; Jia, Zhangcai; Zhang, Fan; Tian, Jiaxing; Lucas, William J; Doyle, Jeff J; Li, Haizhen; Fei, Zhangjun; Xu, Yong

2017-10-09

The Cucurbita genus contains several economically important species in the Cucurbitaceae family. Here, we report high-quality genome sequences of C. maxima and C. moschata and provide evidence supporting an allotetraploidization event in Cucurbita. We are able to partition the genome into two homoeologous subgenomes based on different genetic distances to melon, cucumber, and watermelon in the Benincaseae tribe. We estimate that the two diploid progenitors successively diverged from Benincaseae around 31 and 26 million years ago (Mya), respectively, and the allotetraploidization happened at some point between 26 Mya and 3 Mya, the estimated date when C. maxima and C. moschata diverged. The subgenomes have largely maintained the chromosome structures of their diploid progenitors. Such long-term karyotype stability after polyploidization has not been commonly observed in plant polyploids. The two subgenomes have retained similar numbers of genes, and neither subgenome is globally dominant in gene expression. Allele-specific expression analysis in the C. maxima × C. moschata interspecific F 1 hybrid and their two parents indicates the predominance of trans-regulatory effects underlying expression divergence of the parents, and detects transgressive gene expression changes in the hybrid correlated with heterosis in important agronomic traits. Our study provides insights into polyploid genome evolution and valuable resources for genetic improvement of cucurbit crops. Copyright © 2017 The Author. Published by Elsevier Inc. All rights reserved.

Chromosome reshuffling in birds of prey: the karyotype of the world's largest eagle (Harpy eagle, Harpia harpyja) compared to that of the chicken (Gallus gallus).

Science.gov (United States)

de Oliveira, Edivaldo H C; Habermann, Felix A; Lacerda, Oneida; Sbalqueiro, Ives J; Wienberg, Johannes; Müller, Stefan

2005-11-01

Like various other diurnal birds of prey, the world's largest eagle, the Harpy (Harpia harpyja), presents an atypical bird karyotype with 2n=58 chromosomes. There is little knowledge about the dramatic changes in the genomic reorganization of these species compared to other birds. Since recently, the chicken provides a "default map" for various birds including the first genomic DNA sequence of a bird species. Obviously, the gross division of the chicken genome into relatively gene-poor macrochromosomes and predominantly gene-rich microchromosomes has been conserved for more than 150 million years in most bird species. Here, we present classical features of the Harpy eagle karyotype but also chromosomal homologies between H. harpyja and the chicken by chromosome painting and comparison to the chicken genome map. We used two different sets of painting probes: (1) chicken chromosomes were divided into three size categories: (a) macrochromosomes 1-5 and Z, (b) medium-sized chromosomes 6-10, and (c) 19 microchromosomes; (2) combinatorially labeled chicken chromosome paints 1-6 and Z. Both probe sets were visualized on H. harpyja chromosomes by multicolor fluorescence in situ hybridization (FISH). Our data show how the organization into micro- and macrochromosomes has been lost in the Harpy eagle, seemingly without any preference or constraints.

Development and progression of karyotypic variability in melanoma K1735 following X-irradiation

International Nuclear Information System (INIS)

Wolman, S.R.; McMorrow, L.E.; Fidler, I.J.; Talmadge, J.E.

1985-01-01

Chromosomal aberrations are often assumed to be deleterious to cells. However, the authors have found that many metastases are populated by cells with chromosomal recombinants induced by radiation of the original tumor population. The tumor, K-1735-M2, was already capable of metastasis so that the recombinant chromosomes were not necessary for this property of the tumor. Stable recombinants, like other aberrant forms, could be disadvantageous or, alternatively, could confer selective advantage to some tumor cells. The authors investigated these possibilities by irradiating the parental tumor line and examining the formation and persistence of chromosomal markers in cell culture and in s.c. tumors. The karyotype of the K-1735-M2 parental tumor is composed entirely of telocentric chromosomes, and recombinant forms are relatively easy to recognize. Unstable forms of chromosome damage were lost rapidly. The frequency of stable recombinants after two weeks in culture was higher than that in tumors growing in primary inoculation sites. In contrast, secondary (spontaneous metastatic) foci showed a far greater frequency of chromosomal markers, suggesting a positive association between markers and acquisition of properties benefiting growth and metastasis

Karyotype and male pre-reductional meiosis of the sharpshooter Tapajosa rubromarginata (Hemiptera: Cicadellidae

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Graciela R de Bigliardo

2011-03-01

Full Text Available Cicadellidae in one of the best represented families in the Neotropical Region, and the tribe Proconiini comprises most of the xylem-feeding insects, including the majority of the known vectors of xylem-born phytopathogenic organisms. The cytogenetics of the Proconiini remains largely unexplored. We studied males of Tapajosa rubromarginata (Signoret collected at El Manantial (Tucumán, Argentina on native spontaneous vegetation where Sorghum halepense predominates. Conventional cytogenetic techniques were used in order to describe the karyotype and male meiosis of this sharpshooter. T. rubromarginata has a male karyological formula of 2n=21 and a sex chromosome system XO:XX (♂:♀. The chromosomes do not have a primary constriction, being holokinetic and the meiosis is pre-reductional, showing similar behavior both for autosomes and sex chromosomes during anaphase I. For this stage, chromosomes are parallel to the acromatic spindle with kinetic activities in the telomeres. They segregate reductionally in the anaphase I, and towards the equator during the second division of the meiosis. This is the first contribution to cytogenetic aspects on proconines sharpshooters, particularly on this economic relevant Auchenorrhyncha species. Rev. Biol. Trop. 59 (1: 309-314. Epub 2011 March 01.

Bivariate frequency analysis of rainfall intensity and duration for urban stormwater infrastructure design

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Jun, Changhyun; Qin, Xiaosheng; Gan, Thian Yew; Tung, Yeou-Koung; De Michele, Carlo

2017-10-01

This study presents a storm-event based bivariate frequency analysis approach to determine design rainfalls in which, the number, intensity and duration of actual rainstorm events were considered. To derive more realistic design storms, the occurrence probability of an individual rainstorm event was determined from the joint distribution of storm intensity and duration through a copula model. Hourly rainfall data were used at three climate stations respectively located in Singapore, South Korea and Canada. It was found that the proposed approach could give a more realistic description of rainfall characteristics of rainstorm events and design rainfalls. As results, the design rainfall quantities from actual rainstorm events at the three studied sites are consistently lower than those obtained from the conventional rainfall depth-duration-frequency (DDF) method, especially for short-duration storms (such as 1-h). It results from occurrence probabilities of each rainstorm event and a different angle for rainfall frequency analysis, and could offer an alternative way of describing extreme rainfall properties and potentially help improve the hydrologic design of stormwater management facilities in urban areas.

GnRH-dependent precocious puberty manifested at the age of 14 months in a girl with 47,XXX karyotype.

Science.gov (United States)

Skordis, Nicos; Ferrari, Eleana; Antoniadou, Aria; Phylactou, Leonidas A; Fanis, Pavlos; Neocleous, Vassos

2017-07-01

This case report describes a 47,XXX girl who presented very early, at the age of 14 months, with signs of sexual precocity (breast and pubic hair development, menarche) and was finally diagnosed with GnRH dependent precocious puberty with no evidence of underlying central nervous system pathology. Molecular testing did not identify any genetic defect in any of the genes tested (KISS1, KISS1R, DLK1 and the intronless MKRN3). Though previous studies have shown a link between karyotype 47,XXX and precocious puberty, this is the youngest patient reported so far. Treatment with GnRH analog was commenced and proved to be effective, indicating a successful suppression of the hypothalamic-pituitary-ovarian axis.

THE BIVARIATE SIZE-LUMINOSITY RELATIONS FOR LYMAN BREAK GALAXIES AT z {approx} 4-5

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Huang, Kuang-Han; Su, Jian [Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 (United States); Ferguson, Henry C. [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States); Ravindranath, Swara, E-mail: kuanghan@pha.jhu.edu [The Inter-University Center for Astronomy and Astrophysics, Pune University Campus, Pune 411007, Maharashtra (India)

2013-03-01

We study the bivariate size-luminosity distribution of Lyman break galaxies (LBGs) selected at redshifts around 4 and 5 in GOODS and the HUDF fields. We model the size-luminosity distribution as a combination of log-normal distribution (in size) and Schechter function (in luminosity), therefore it enables a more detailed study of the selection effects. We perform extensive simulations to quantify the dropout-selection completenesses and measurement biases and uncertainties in two-dimensional size and magnitude bins, and transform the theoretical size-luminosity distribution to the expected distribution for the observed data. Using maximum-likelihood estimator, we find that the Schechter function parameters for B {sub 435}-dropouts and are consistent with the values in the literature, but the size distributions are wider than expected from the angular momentum distribution of the underlying dark matter halos. The slope of the size-luminosity (RL) relation is similar to those found for local disk galaxies, but considerably shallower than local early-type galaxies.

THE BIVARIATE SIZE-LUMINOSITY RELATIONS FOR LYMAN BREAK GALAXIES AT z ∼ 4-5

International Nuclear Information System (INIS)

Huang, Kuang-Han; Su, Jian; Ferguson, Henry C.; Ravindranath, Swara

2013-01-01

We study the bivariate size-luminosity distribution of Lyman break galaxies (LBGs) selected at redshifts around 4 and 5 in GOODS and the HUDF fields. We model the size-luminosity distribution as a combination of log-normal distribution (in size) and Schechter function (in luminosity), therefore it enables a more detailed study of the selection effects. We perform extensive simulations to quantify the dropout-selection completenesses and measurement biases and uncertainties in two-dimensional size and magnitude bins, and transform the theoretical size-luminosity distribution to the expected distribution for the observed data. Using maximum-likelihood estimator, we find that the Schechter function parameters for B 435 -dropouts and are consistent with the values in the literature, but the size distributions are wider than expected from the angular momentum distribution of the underlying dark matter halos. The slope of the size-luminosity (RL) relation is similar to those found for local disk galaxies, but considerably shallower than local early-type galaxies.

Bivariate Gaussian bridges: directional factorization of diffusion in Brownian bridge models.

Science.gov (United States)

Kranstauber, Bart; Safi, Kamran; Bartumeus, Frederic

2014-01-01

In recent years high resolution animal tracking data has become the standard in movement ecology. The Brownian Bridge Movement Model (BBMM) is a widely adopted approach to describe animal space use from such high resolution tracks. One of the underlying assumptions of the BBMM is isotropic diffusive motion between consecutive locations, i.e. invariant with respect to the direction. Here we propose to relax this often unrealistic assumption by separating the Brownian motion variance into two directional components, one parallel and one orthogonal to the direction of the motion. Our new model, the Bivariate Gaussian bridge (BGB), tracks movement heterogeneity across time. Using the BGB and identifying directed and non-directed movement within a trajectory resulted in more accurate utilisation distributions compared to dynamic Brownian bridges, especially for trajectories with a non-isotropic diffusion, such as directed movement or Lévy like movements. We evaluated our model with simulated trajectories and observed tracks, demonstrating that the improvement of our model scales with the directional correlation of a correlated random walk. We find that many of the animal trajectories do not adhere to the assumptions of the BBMM. The proposed model improves accuracy when describing the space use both in simulated correlated random walks as well as observed animal tracks. Our novel approach is implemented and available within the "move" package for R.

Contributory fault and level of personal injury to drivers involved in head-on collisions: Application of copula-based bivariate ordinal models.

Science.gov (United States)

Wali, Behram; Khattak, Asad J; Xu, Jingjing

2018-01-01

The main objective of this study is to simultaneously investigate the degree of injury severity sustained by drivers involved in head-on collisions with respect to fault status designation. This is complicated to answer due to many issues, one of which is the potential presence of correlation between injury outcomes of drivers involved in the same head-on collision. To address this concern, we present seemingly unrelated bivariate ordered response models by analyzing the joint injury severity probability distribution of at-fault and not-at-fault drivers. Moreover, the assumption of bivariate normality of residuals and the linear form of stochastic dependence implied by such models may be unduly restrictive. To test this, Archimedean copula structures and normal mixture marginals are integrated into the joint estimation framework, which can characterize complex forms of stochastic dependencies and non-normality in residual terms. The models are estimated using 2013 Virginia police reported two-vehicle head-on collision data, where exactly one driver is at-fault. The results suggest that both at-fault and not-at-fault drivers sustained serious/fatal injuries in 8% of crashes, whereas, in 4% of the cases, the not-at-fault driver sustained a serious/fatal injury with no injury to the at-fault driver at all. Furthermore, if the at-fault driver is fatigued, apparently asleep, or has been drinking the not-at-fault driver is more likely to sustain a severe/fatal injury, controlling for other factors and potential correlations between the injury outcomes. While not-at-fault vehicle speed affects injury severity of at-fault driver, the effect is smaller than the effect of at-fault vehicle speed on at-fault injury outcome. Contrarily, and importantly, the effect of at-fault vehicle speed on injury severity of not-at-fault driver is almost equal to the effect of not-at-fault vehicle speed on injury outcome of not-at-fault driver. Compared to traditional ordered probability

Immunostimulation by cytosine-phosphate-guanine oligodeoxynucleotides in combination with IL-2 can improve the success rate of karyotype analysis in chronic lymphocytic leukaemia.

Science.gov (United States)

Lin, Xiaolan; Chen, Jiadi; Huang, Huifang

2016-07-01

To assess whether immunostimulatory cytosine-phosphate-guanine oligodeoxynucleotides (CpG-ODN) combined with interleukin-2 (IL-2) improves the number of mitotic metaphases and the detection rate of chromosomal abnormalities in chronic lymphocytic leukaemia (CLL). Bone marrow specimens were collected from 36 patients with CLL. CLL cells were cultured with CpG-ODN type DSP30 plus IL-2 for 72 h, following which R-banding analysis was conducted. Conventional culture without the immunostimulant served as the control group. The incidence of genetic abnormalities was measured by fluorescence in situ hybridisation (FISH) using a panel of five specific probes: D13S25 (13q14.3), RB1 (13q14), P53 (17p13), ATM (11q22.3) and CSP12 (trisomy 12, +12). In the control group, chromosome analysis achieved a success rate of only 22.2, and 11.1% of abnormal karyotypes were detected. After immunostimulation with DSP30 plus IL-2, chromosome analysis achieved a success rate of up to 91.6, and 41.6% of abnormal karyotypes were detected. FISH analysis detected 77.7% of abnormalities. FISH combined with CpG-ODN DSP30 plus IL-2 improved the detection rate of chromosomal abnormalities in CLL to 83.3%. CpG-ODN DSP30 combined with IL-2 is effective in improving the detection rate of chromosomal abnormalities in CLL cells. This combination with FISH analysis is conducive to increasing the detection rate of genetic abnormalities in CLL.

Karyotypic variation in Rhinophylla pumilio Peters, 1865 and comparative analysis with representatives of two subfamilies of Phyllostomidae (Chiroptera

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A Gomes

2012-05-01

Full Text Available The family Phyllostomidae belongs to the most abundant and diverse group of bats in the Neotropics with more morphological traits variation at the family level than any other group within mammals. In this work, we present data of chromosome banding (G, C and Ag-NOR and Fluorescence In Situ Hybridization (FISH for representatives of Rhinophylla pumilio Peters, 1865 collected in four states of Brazil (Amazonas, Bahia, Mato Grosso and Pará. Two karyomorphs were found in this species: 2n=34, FN=64 in populations from western Pará and Mato Grosso states and 2n=34, FN=62 from Amazonas, Bahia, and northeastern Pará and Marajó Island (northern. Difference in the Fundamental Number is determined by variation in the size of the Nucleolar Organizer Region (NOR accompanied with heterochromatin on chromosomes of pair 16 or, alternatively, a pericentric inversion. The C-banding technique detected constitutive heterochromatin in the centromeric regions of all chromosomes and on the distal part of the long arm of pair 15 of specimens from all localities. FISH with a DNA telomeric probe did not show any interstitial sequence, and an 18S rDNA probe and silver staining revealed the presence of NOR in the long arm of the pair 15, associated with heterochromatin, and in the short arm of the pair 16 for all specimens. The intra-specific analysis using chromosome banding did not show any significant difference between the samples. The comparative analyses using G-banding have shown that nearly all chromosomes of R. pumilio were conserved in the chromosome complements of Glossophaga soricina Pallas, 1766, Phyllostomus hastatus Pallas, 1767, Phyllostomus discolor Wagner, 1843 and Mimon crenulatum Geoffroy, 1801, with a single chromosomal pair unique to R. pumilio (pair 15. However, two chromosomes of M. crenulatum are polymorphic for two independent pericentric inversions. The karyotype with 2n=34, NF=62 is probably the ancestral one for the other karyotypes

Chromosomal rearrangements and gene flow over time in an inter-specific hybrid zone of the Sorex araneus group.

Science.gov (United States)

Yannic, G; Basset, P; Hausser, J

2009-06-01

Most hybrid zones have existed for hundreds or thousands of years but have generally been observed for only a short time period. Studies extending over periods long enough to track evolutionary changes in the zones or assess the ultimate outcome of hybridization are scarce. Here, we describe the evolution over time of the level of genetic isolation between two karyotypically different species of shrews (Sorex araneus and Sorex antinorii) at a hybrid zone located in the Swiss Alps. We first evaluated hybrid zone movement by contrasting patterns of gene flow and changes in cline parameters (centre and width) using 24 microsatellite loci, between two periods separated by 10 years apart. Additionally, we tested the role of chromosomal rearrangements on gene flow by analysing microsatellite loci located on both rearranged and common chromosomes to both species. We did not detect any movement of the hybrid zone during the period analysed, suggesting that the zone is a typical tension zone. However, the gene flow was significantly lower among the rearranged than the common chromosomes for the second period, whereas the difference was only marginally significant for the first period. This further supports the role of chromosomal rearrangements on gene flow between these taxa.

Unbiased ascertainment of a patient with a 47,XY, +pseudic (15)t(15;15)(q13;q13) karyotype by amniocentesis

Energy Technology Data Exchange (ETDEWEB)

Spector, E.; Prochazka, G.; Hamilton, S. [Univ. of Colorado School of Medicine, Denver (United States)] [and others

1994-09-01

A 47,XY,+mar male karyotype was found in all metaphases on an amniocentesis from a 36-year-old woman (G1,P0). The marker was G group size. Chromosome studies on the parents were normal. C-banding, NOR staining and FISH demonstrated that the marker was dicentric, bisatellited, derived from No. 15 and contained 2 copies of the chromosomal region flanked by the Prader-Willi/Angelman A and B probes. The final karyotype was: 47,XY,+pseudic(15)t(15;15)(q13;q13), making the fetus tetrasomic for the genes in the duplicated region. DNA marker studies for No. 15 (performed in the laboratory of Dr. David Ledbetter) revealed that the fetus had inherited on No. 15 from each parent and that the marker was derived from both maternal No. 15 chromosomes. The parents chose to continue the pregnancy. The baby was born at 38 weeks gestation, was mildly edematous and had Apgar scores of 4, 7, and 8 at 1, 5, and 10 min, respectively. The marker was confirmed to be present in placenta and the baby`s blood. Examination at 6 weeks showed appropriate growth and development. Data from published cases predict that this baby will be mentally retarded and may have seizures because he is tetrasomic for 15pter-q13, but will not have Prader-Willi or Angelman syndromes since he has biparental inheritance of his normal No. 15s. However, the published cases may represent a biased sample as most were identified in mentally retarded individuals, not by prenatal diagnosis. This infant`s development will continue to be followed closely.

Karyotype, heterochromatin distribution and meiosis of Zabrotes subfasciatus (Bohemann) (Coleoptera: Chrysomelidae, Bruchinae)

International Nuclear Information System (INIS)

Correa, Ronan X.; Santos, Igor S.; Silva, Janisete G.; Costa, Marco A.; Pompolo, Silvia G.

2008-01-01

Zabrotes subfasciatus (Boh.) has been extensively studied in its agronomic and biochemical aspects due to its importance as a damaging insect to leguminous grains during storage. The few cytogenetic studies published on this species yielded conflicting results. In this study, the karyotype was analyzed in order to accurately describe the chromosome C-banding patterns and meiosis. The brain ganglion at the pre pupa and the adult and pupal testes were analyzed. All individuals had 26 chromosomes in both brain ganglion and spermatogonic mitotic metaphases. These chromosomes were classified as follows: the 12 th pair and the Y chromosome were telocentric; the X chromosome was acrocentric; the 4 th and 5 th pairs were sub metacentric; and the remaining pairs were all metacentric. One of the members of the 5 th pair presented a secondary constriction. All chromosomes presented pericentromeric heterochromatin. The large arms of the pairs 5, 9 and X presented heterochromatin. The X chromosome showed to be heteropyknotic throughout the prophase of the fi rst meiotic division. The sub phases of prophase I were atypical and meiosis II was rarely identified. Testes of all males showed a few cells; the bivalents were rod-like shaped in metaphase I. Karyological formulae were 2n = 24 + XX in females and 2n = 24 + XYp and either n = 12 + X or n = 12 + Y in males. (author)

Clonal proliferation and karyotypic features of cells in bone marrow after irradiation

International Nuclear Information System (INIS)

Kohno, S.; Ishihara, T.

1979-01-01

Single stem cells in which chromosome abnormalities are induced by radiation may multiply to form the chromosomally abnormal clones of cells that may replace most of the cells in regenerating hematopoietic tissues after irradiation. It is only a limited number of karyotypes out of a variety of the cells with radiation-induced chromosome abnormalities that can persist as proliferative clones. Such clones in the bone marrows of irradiated rats were found to have aneusomic chromosome constitutions with trisomy or monosomy. This finding is contradictory to the general beliefs that the chromosomally abnormal clones surviving after irradiation would have the chromosome constitutions comparable to a normal diploid set making such clone cells selectively neutral, and that autosomally monosomic cells would not be able to compete against the cells in normal somatic tissues. The proliferation of aneusomic cells in hematopoietic tissues is a phenomenon observable in various blood disorders such as leukemia. The fact that almost all of the aneuploid clones observed possessed various chromosomal rearrangements in addition to their numerical changes appears to indicate that the chromosomal imbalance in original clones may predispose their chromosomes to non-disjunction. The process of the leukemic development of cells may require two steps: the leukemic transformation of cells and the proliferation of such transformed cells up to the manifestation of the disease. (Yamashita, S.)

Karyotype, heterochromatin distribution and meiosis of Zabrotes subfasciatus (Bohemann) (Coleoptera: Chrysomelidae, Bruchinae)

Energy Technology Data Exchange (ETDEWEB)

Correa, Ronan X.; Santos, Igor S.; Silva, Janisete G.; Costa, Marco A. [Universidade Estadual de Santa Cruz, Ilheus, BA (Brazil). Dept. de Ciencias Biologicas; Pompolo, Silvia G. [Universidade Federal de Vicosa, MG (Brazil). Dept. de Biologia Geral

2008-09-15

Zabrotes subfasciatus (Boh.) has been extensively studied in its agronomic and biochemical aspects due to its importance as a damaging insect to leguminous grains during storage. The few cytogenetic studies published on this species yielded conflicting results. In this study, the karyotype was analyzed in order to accurately describe the chromosome C-banding patterns and meiosis. The brain ganglion at the pre pupa and the adult and pupal testes were analyzed. All individuals had 26 chromosomes in both brain ganglion and spermatogonic mitotic metaphases. These chromosomes were classified as follows: the 12{sup th} pair and the Y chromosome were telocentric; the X chromosome was acrocentric; the 4{sup th} and 5{sup th} pairs were sub metacentric; and the remaining pairs were all metacentric. One of the members of the 5{sup th} pair presented a secondary constriction. All chromosomes presented pericentromeric heterochromatin. The large arms of the pairs 5, 9 and X presented heterochromatin. The X chromosome showed to be heteropyknotic throughout the prophase of the fi rst meiotic division. The sub phases of prophase I were atypical and meiosis II was rarely identified. Testes of all males showed a few cells; the bivalents were rod-like shaped in metaphase I. Karyological formulae were 2n = 24 + XX in females and 2n = 24 + XYp and either n = 12 + X or n = 12 + Y in males. (author)

Pleomorphic adenoma cells vary in their susceptibility to SV40 transformation depending on the initial karyotype.

Science.gov (United States)

Kazmierczak, B; Thode, B; Bartnitzke, S; Bullerdiek, J; Schloot, W

1992-07-01

Chromosomal aberrations involving 8q12 or 12q13-15 characterize two cytogenetic subgroups of salivary gland pleomorphic adenomas. As the tumors of the two groups differ in their clinical and histologic characteristics, we decided to determine their susceptibility to SV40 transformation. We transfected cell cultures from 13 adenomas with aberrations involving 8q12 and from seven adenomas with involvement of 12q13-15 using an SV40 plasmid coding for the early region of the viral genome. Whereas all cultures with aberrations of 12q13-15 showed transformed foci, only 4 of the 13 cultures with 8q12 abnormalities showed foci of transformed cells. We also observed a much higher immortalization rate in the first group (3/7 vs. 1/13). All successfully transformed tumor cell cultures showed a relatively stable karyotype in the pre-crisis stage and a high mitotic index, were T-antigen positive, and had an extended life span in vitro.

IDF relationships using bivariate copula for storm events in Peninsular Malaysia

Science.gov (United States)

Ariff, N. M.; Jemain, A. A.; Ibrahim, K.; Wan Zin, W. Z.

2012-11-01

SummaryIntensity-duration-frequency (IDF) curves are used in many hydrologic designs for the purpose of water managements and flood preventions. The IDF curves available in Malaysia are those obtained from univariate analysis approach which only considers the intensity of rainfalls at fixed time intervals. As several rainfall variables are correlated with each other such as intensity and duration, this paper aims to derive IDF points for storm events in Peninsular Malaysia by means of bivariate frequency analysis. This is achieved through utilizing the relationship between storm intensities and durations using the copula method. Four types of copulas; namely the Ali-Mikhail-Haq (AMH), Frank, Gaussian and Farlie-Gumbel-Morgenstern (FGM) copulas are considered because the correlation between storm intensity, I, and duration, D, are negative and these copulas are appropriate when the relationship between the variables are negative. The correlations are attained by means of Kendall's τ estimation. The analysis was performed on twenty rainfall stations with hourly data across Peninsular Malaysia. Using Akaike's Information Criteria (AIC) for testing goodness-of-fit, both Frank and Gaussian copulas are found to be suitable to represent the relationship between I and D. The IDF points found by the copula method are compared to the IDF curves yielded based on the typical IDF empirical formula of the univariate approach. This study indicates that storm intensities obtained from both methods are in agreement with each other for any given storm duration and for various return periods.

GIS-based bivariate statistical techniques for groundwater potential analysis (an example of Iran)

Science.gov (United States)

Haghizadeh, Ali; Moghaddam, Davoud Davoudi; Pourghasemi, Hamid Reza

2017-12-01

Groundwater potential analysis prepares better comprehension of hydrological settings of different regions. This study shows the potency of two GIS-based data driven bivariate techniques namely statistical index (SI) and Dempster-Shafer theory (DST) to analyze groundwater potential in Broujerd region of Iran. The research was done using 11 groundwater conditioning factors and 496 spring positions. Based on the ground water potential maps (GPMs) of SI and DST methods, 24.22% and 23.74% of the study area is covered by poor zone of groundwater potential, and 43.93% and 36.3% of Broujerd region is covered by good and very good potential zones, respectively. The validation of outcomes displayed that area under the curve (AUC) of SI and DST techniques are 81.23% and 79.41%, respectively, which shows SI method has slightly a better performance than the DST technique. Therefore, SI and DST methods are advantageous to analyze groundwater capacity and scrutinize the complicated relation between groundwater occurrence and groundwater conditioning factors, which permits investigation of both systemic and stochastic uncertainty. Finally, it can be realized that these techniques are very beneficial for groundwater potential analyzing and can be practical for water-resource management experts.

SRY mutation analysis by next generation (deep sequencing in a cohort of chromosomal Disorders of Sex Development (DSD patients with a mosaic karyotype

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Hersmus Remko

2012-11-01

Full Text Available Abstract Background The presence of the Y-chromosome or Y chromosome-derived material is seen in 4-60% of Turner syndrome patients (Chromosomal Disorders of Sex Development (DSD. DSD patients with specific Y-chromosomal material in their karyotype, the GonadoBlastoma on the Y-chromosome (GBY region, have an increased risk of developing type II germ cell tumors/cancer (GCC, most likely related to TSPY. The Sex determining Region on the Y gene (SRY is located on the short arm of the Y-chromosome and is the crucial switch that initiates testis determination and subsequent male development. Mutations in this gene are responsible for sex reversal in approximately 10-15% of 46,XY pure gonadal dysgenesis (46,XY DSD cases. The majority of the mutations described are located in the central HMG domain, which is involved in the binding and bending of the DNA and harbors two nuclear localization signals. SRY mutations have also been found in a small number of patients with a 45,X/46,XY karyotype and might play a role in the maldevelopment of the gonads. Methods To thoroughly investigate the presence of possible SRY gene mutations in mosaic DSD patients, we performed next generation (deep sequencing on the genomic DNA of fourteen independent patients (twelve 45,X/46,XY, one 45,X/46,XX/46,XY, and one 46,XX/46,XY. Results and conclusions The results demonstrate that aberrations in SRY are rare in mosaic DSD patients and therefore do not play a significant role in the etiology of the disease.

A new karyotype of Calomyscus from the Khorasan Province, Iran

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Esmaeeli Somayeh

2008-07-01

Full Text Available Abstract We report a new karyotype of Calomyscus from two localities of the Khorasan Province (Aghdarband, 36° 11’ 3”N, 60° 44’ 6” E and Khajemorad, 36° 8’ 5” N, 59° 41’ 58” E. Chromosomes were examined by conventional staining and C-banding techniques. The diploid chromosome number (2n and the fundamental autosomal arm number (FNa were 44 and 60 respectively. The autosomal set consisted of 12 pairs of telocentrics, 5 pairs of acrocentrics and 4 pairs of sub-metacentrics. Both heterosomes were small telocentrics. Riassunto Un nuovo cariotipo del genere Calomyscus dalla provincia di Khorasan, Iran. Si descrive un nuovo cariotipo appartenente al genere Calomyscus, scoperto in due località della provincia di Khorasan (Aghdarband, 36° 11’ 3”N, 60° 44’ 6” E e Khajemorad, 36° 8’ 5” N, 59° 41’ 58” E. I cromosomi sono stati analizzati con le tecniche standard di colorazione e bandeggio. Il numero diploide di cromosomi (2n e il numero fondamentale di bracci autosomici sono risultati pari a 44 e 60 rispettivamente. Il set di cromosomi autosomici è composto da 12 paia di telocentrici, 5 di acrocentrici e 4 di sub-metacentrici. Entrambi i cromosomi sessuali si presentano come piccoli telocentrici.

Patients with 47, XXX karyotype who experienced premature ovarian failure (POF): two case reports.

Science.gov (United States)

Sugawara, Nobuo; Maeda, Machiko; Manome, Tomomi; Nagai, Rie; Araki, Yasuhisa

2013-10-01

Pubertal onset and sexual development are usually normal in 47, XXX individuals; however, we report two cases of premature ovarian failure (POF) in infertile women with trisomy X. Chromosome analysis was conducted with G-banding and fluorescence in situ hybridization using X- and Y-bearing probe. Hormonal administration was primarily Kaufmann's treatment or long-term estradiol treatment, followed by withdrawal bleeding from estrogen and progesterone. Two patients with trisomy X, aged 31 (patient 1) and 27 years (patient 2), were diagnosed with POF due to hypergonadotropic hypogonadism. Their ovaries were small. Patient 1 had a FSH level of 44.6 mIU/ml and patient 2 had a FSH level of 74.6 mIU/ml. In patient 1, with Kaufmann's treatment, the FSH decreased to 13.5 mIU/ml; however, follicle growth did not occur following HMG stimulation. In patient 2, FSH did not decrease despite Kaufmann's treatment; therefore, she was given a GnRH agonist and her FSH level decreased to 7.1 mIU/ml. However, her ovaries never responded to HMG stimulation. We report on two patients with a 47, XXX karyotype who became infertile due to POF. We recommend that when a patient is diagnosed with trisomy X, the possibility of POF must be strongly considered.

The Role of Wealth and Health in Insurance Choice: Bivariate Probit Analysis in China

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Yiding Yue

2014-01-01

Full Text Available This paper captures the correlation between the choices of health insurance and pension insurance using the bivariate probit model and then studies the effect of wealth and health on insurance choice. Our empirical evidence shows that people who participate in a health care program are more likely to participate in a pension plan at the same time, while wealth and health have different effects on the choices of the health care program and the pension program. Generally, the higher an individual’s wealth level is, the more likelihood he will participate in a health care program; but wealth has no effect on the participation of pension. Health status has opposite effects on choices of health care programs and pension plans; the poorer an individual’s health is, the more likely he is to participate in health care programs, while the better health he enjoys, the more likely he is to participate in pension plans. When the investigation scope narrows down to commercial insurance, there is only a significant effect of health status on commercial health insurance. The commercial insurance choice and the insurance choice of the agricultural population are more complicated.

Incidence and significance of FLT3-ITD and NPM1 mutations in patients with normal karyotype acute myeloid leukaemia.

LENUS (Irish Health Repository)

Haslam, K

2012-02-01

BACKGROUND: Acute myeloid leukaemia (AML) is a heterogeneous clonal disorder of haematopoietic progenitor cells. Approximately half of all adult AML patients have a normal karyotype (NK-AML) and an intermediate risk prognosis. AIMS: To determine the incidence and prognostic significance of NPM1 and FLT3-ITD mutations in a population of patients with NK-AML. METHODS: FLT3-ITD and NPM1 mutation status was retrospectively sought in presentation samples from 44 NK-AML patients. RESULTS: FLT3-ITD and NPM1 mutations were detected in 45.5 and 54.5% of patients, respectively, allowing stratification according to genotype. CONCLUSIONS: FLT3-ITD and NPM1 mutation status can be defined in NK-AML. Prospective screening for these mutations is advocated in all NK-AML patients, as the genotype is of clinical importance when considering treatment options including stem cell transplantation.

Spatio-temporal structure of turbulent Reynolds stress zonal flow drive in 3D magnetic configuration

International Nuclear Information System (INIS)

Schmid, B; Ramisch, M; Manz, P; Stroth, U

2017-01-01

The poloidal dependence of the zonal flow drive and the underlying Reynolds stress structure are studied at the stellarator experiment TJ-K by means of a poloidal Langmuir-probe array. This gives the unique possibility to study the locality of the Reynolds stress in a complex toroidal magnetic geometry. It is found that the Reynolds stress is not homogeneously distributed along the flux surface but has a strong poloidal asymmetry where it is concentrated on the outboard side with a maximum above the midplane. The average tilt of the turbulent structures is thereby reflected in the anisotropy of the bivariant velocity distribution. Using a conditional averaging technique the temporal dynamics reveal that the zonal flow drive is also maximal in this particular region. The results suggest an influence of the magnetic field line curvature, which controls the underlying plasma turbulence. The findings are a basis for further comparison with turbulence simulations in 3D geometry and demonstrate the need for a global characterisation of plasma turbulence. (paper)

REGRES: A FORTRAN-77 program to calculate nonparametric and ``structural'' parametric solutions to bivariate regression equations

Science.gov (United States)

Rock, N. M. S.; Duffy, T. R.

REGRES allows a range of regression equations to be calculated for paired sets of data values in which both variables are subject to error (i.e. neither is the "independent" variable). Nonparametric regressions, based on medians of all possible pairwise slopes and intercepts, are treated in detail. Estimated slopes and intercepts are output, along with confidence limits, Spearman and Kendall rank correlation coefficients. Outliers can be rejected with user-determined stringency. Parametric regressions can be calculated for any value of λ (the ratio of the variances of the random errors for y and x)—including: (1) major axis ( λ = 1); (2) reduced major axis ( λ = variance of y/variance of x); (3) Y on Xλ = infinity; or (4) X on Y ( λ = 0) solutions. Pearson linear correlation coefficients also are output. REGRES provides an alternative to conventional isochron assessment techniques where bivariate normal errors cannot be assumed, or weighting methods are inappropriate.

DNA characterization and karyotypic evolution in the bee genus Melipona (Hymenoptera, Meliponini).

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Rocha, Marla Piumbini; Pompolo, Silvia Das Graças; Dergam, Jorge Abdala; Fernandes, Anderson; Campos, Lucio Antonio De Oliveira

2002-01-01

We analyzed patterns of heterochromatic bands in the Neotropical stingless bee genus Melipona (Hymenoptera, Meliponini). Group I species (Melipona bicolor bicolor, Melipona quadrifasciata, Melipona asilvae, Melipona marginata, Melipona subnitida) were characterized by low heterochromatic content. Group II species (Melipona capixaba, Melipona compressipes, Melipona crinita, Melipona seminigra fuscopilosa e Melipona scutellaris) had high heterochromatic content. All species had 2n = 18 and n = 9. In species of Group I heterochromatin was pericentromeric and located on the short arm of acrocentric chromosomes, while in Group II species heterochromatin was distributed along most of the chromosome length. The most effective sequential staining was quinacrine mustard (QM)/distamycin (DA)/chromomycin A3(CMA3)/4-6-diamidino-2-phenylindole (DAPI). Heterochromatic and euchromatic bands varied extensively within Group I. In Group II species euchromatin was restricted to the chromosome tips and it was uniformly GC+. Patterns of restriction enzymes (EcoRI, DraI, HindIII) showed that heterochromatin was heterogeneous. In all species the first pair of homologues was of unequal size and showed heteromorphism of a GC+ pericentromeric heterochromatin. In M. asilvae (Group I) this pair bore NOR and in M. compressipes (Group II) it hybridized with a rDNA FISH probe. As for Group I species the second pair was AT+ in M. subnitida and neutral for AT and GC in the remaining species of this group. Outgroup comparison indicates that high levels of heterochromatin represent a derived condition within Melipona. The pattern of karyotypic evolution sets Melipona in an isolated position within the Meliponini.

Is the diversification of Mediterranean Basin plant lineages coupled to karyotypic changes?

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Escudero, M; Balao, F; Martín-Bravo, S; Valente, L; Valcárcel, V

2018-01-01

The Mediterranean Basin region, home to 25,000 plant species, is included in the worldwide list of hotspots of biodiversity. Despite the indisputably important role of chromosome transitions in plant evolution and diversification, no reference study to date has dealt with the possible relationship between chromosome evolution and lineage diversification in the Mediterranean Basin. Here we study patterns of diversification, patterns of chromosome number transition (either polyploidy or dysploidy) and the relationship between the two for 14 Mediterranean Basin angiosperm lineages using previously published phylogenies. We found a mixed pattern, with half of the lineages displaying a change in chromosome transition rates after the onset of the Mediterranean climate (six increases, one decrease) and the other half (six) experiencing constant rates of chromosome transitions through time. We have also found a heterogeneous pattern regarding diversification rates, with lineages exhibiting moderate (five phylogenies) or low (six) initial diversification rates that either increased (six) or declined (five) through time. Our results reveal no clear link between diversification rates and chromosome number transition rates. By promoting the formation of new habitats and driving the extinction of many species, the Mediterranean onset and the posterior Quaternary climatic oscillations could have been key for the establishment of new chromosomal variants in some plant phylogenies but not in others. While the biodiversity of the Mediterranean Basin may be partly influenced by the chromosomal diversity of its lineages, this study concludes that lineage diversification in the region is largely decoupled from karyotypic evolution. © 2017 German Botanical Society and The Royal Botanical Society of the Netherlands.

Familial ring (18) mosaicism in a 23-year-old young adult with 46,XY,r(18) (::p11→q21::)/46,XY karyotype, intellectual disability, motor retardation and single maxillary incisor and in his phenotypically normal mother, karyotype 47,XX,+r(18)(::p11→q21::)/46,XX.

Science.gov (United States)

Balci, Sevim; Tümer, Celal; Karaca, Ciğdem; Bartsch, Oliver

2011-05-01

We report on a 23-year-old man with craniofacial findings of the holoprosencephaly spectrum disorder (microcephaly, hypotelorism, depressed nasal bridge, single median maxillary central incisor), fusion of C2-C3 vertebrae, intellectual disability, and severe sleep apnea. Chromosome analysis of blood lymphocytes showed 75% ring (18) cells and 25% normal cells, karyotype mos 46,XY,r(18)(::p11→q21::)[75]/46,XY[25]. His mother was phenotypically normal except for a double ureter and bifid renal pelvis as in his son. She had a supernumerary ring (18) in 10% of blood lymphocytes, karyotype mos 47,XX,+r(18)(::p11→q21::)[10]/46,XX[90]. Familial ring (18) is a rare cytogenetic abnormality. This is the first report of a mother with a supernumerary ring (18) and a son with ring (18) mosaicism. Interestingly, the son showed a true mosaicism (mixoploidy) of ring (18) and normal cells. The mother's 46,XX cells could be easily explained by mitotic instability and ring loss during cell division. However, the coexistence of ring (18) and normal cells in the son is unusual. Possibly, during early postzygotic divisions of a 47,XY,+r(18) zygote, two (possibly subsequent) genetic events could have occurred, one when one normal chromosome 18 was lost (resulting in a cell line with ring 18), and one when the ring 18 was lost (resulting in a cell line without ring, "escape to normal"). Alternatively, the zygote of the son could have been 46,XY,r(18), and postzygotic loss of the ring 18 could have resulted in monosomy 18 cells followed by duplication of chromosome 18 in these cells (a rare mechanism for cell survival previously described as "compensatory" isodisomy). Copyright © 2011 Wiley-Liss, Inc.

A Hybrid Forecasting Model Based on Bivariate Division and a Backpropagation Artificial Neural Network Optimized by Chaos Particle Swarm Optimization for Day-Ahead Electricity Price

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Zhilong Wang

2014-01-01

Full Text Available In the electricity market, the electricity price plays an inevitable role. Nevertheless, accurate price forecasting, a vital factor affecting both government regulatory agencies and public power companies, remains a huge challenge and a critical problem. Determining how to address the accurate forecasting problem becomes an even more significant task in an era in which electricity is increasingly important. Based on the chaos particle swarm optimization (CPSO, the backpropagation artificial neural network (BPANN, and the idea of bivariate division, this paper proposes a bivariate division BPANN (BD-BPANN method and the CPSO-BD-BPANN method for forecasting electricity price. The former method creatively transforms the electricity demand and price to be a new variable, named DV, which is calculated using the division principle, to forecast the day-ahead electricity by multiplying the forecasted values of the DVs and forecasted values of the demand. Next, to improve the accuracy of BD-BPANN, chaos particle swarm optimization and BD-BPANN are synthesized to form a novel model, CPSO-BD-BPANN. In this study, CPSO is utilized to optimize the initial parameters of BD-BPANN to make its output more stable than the original model. Finally, two forecasting strategies are proposed regarding different situations.

Single nucleotide polymorphism array karyotyping: a diagnostic and prognostic tool in myelodysplastic syndromes with unsuccessful conventional cytogenetic testing.

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Arenillas, Leonor; Mallo, Mar; Ramos, Fernando; Guinta, Kathryn; Barragán, Eva; Lumbreras, Eva; Larráyoz, María-José; De Paz, Raquel; Tormo, Mar; Abáigar, María; Pedro, Carme; Cervera, José; Such, Esperanza; José Calasanz, María; Díez-Campelo, María; Sanz, Guillermo F; Hernández, Jesús María; Luño, Elisa; Saumell, Sílvia; Maciejewski, Jaroslaw; Florensa, Lourdes; Solé, Francesc

2013-12-01

Cytogenetic aberrations identified by metaphase cytogenetics (MC) have diagnostic, prognostic, and therapeutic implications in myelodysplastic syndromes (MDS). However, in some MDS patients MC study is unsuccesful. Single nucleotide polymorphism array (SNP-A) based karyotyping could be helpful in these cases. We performed SNP-A in 62 samples from bone marrow or peripheral blood of primary MDS with an unsuccessful MC study. SNP-A analysis enabled the detection of aberrations in 31 (50%) patients. We used the copy number alteration information to apply the International Prognostic Scoring System (IPSS) and we observed differences in survival between the low/intermediate-1 and intermediate-2/high risk patients. We also saw differences in survival between very low/low/intermediate and the high/very high patients when we applied the revised IPSS (IPSS-R). In conclusion, SNP-A can be used successfully in PB samples and the identification of CNA by SNP-A improve the diagnostic and prognostic evaluation of this group of MDS patients. Copyright © 2013 Wiley Periodicals, Inc.

Second case of chronic granulocytic leukemia with karyotypic evolution at acute crisis, occurring in so-called Nishiyama district

Energy Technology Data Exchange (ETDEWEB)

Yao, E; Tomonaga, Yu; Nishino, K; Matsunaga, M; Sadamori, N [Nagasaki Univ. (Japan). School of Medicine

1978-09-01

The whole process of a second case of chronic granulocytic leukemia in Nishiyama district where a very small amount of radiation existed for a long time was reported together with data measured by a human counter and the results of chromosomal analysis. No significantly high K or /sup 137/Cs values were measured by a human counter immediately after the onset. Chromosomal division aberration and chromosomal aberration, which seemed to be induced by radiation, also were not observed. However, granulocytic leukemia was diagnosed after chromosomal analysis of peripheral blood revealed Ph/sup 1/ chromosomes, white cell count increased, juvenile cells appeared, and basophil cells increased. Clinical features of typical chronic granulocytic leukemia in the exposed were observed during the chronic stage (7 years). In the acute stage, abnormal clones were discovered in all 16 chromosomes analyzed. Much karyotypic evolution identical to that in persons directly exposed to the A-bomb was also observed.

A Bivariate Generalized Linear Item Response Theory Modeling Framework to the Analysis of Responses and Response Times.

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Molenaar, Dylan; Tuerlinckx, Francis; van der Maas, Han L J

2015-01-01

A generalized linear modeling framework to the analysis of responses and response times is outlined. In this framework, referred to as bivariate generalized linear item response theory (B-GLIRT), separate generalized linear measurement models are specified for the responses and the response times that are subsequently linked by cross-relations. The cross-relations can take various forms. Here, we focus on cross-relations with a linear or interaction term for ability tests, and cross-relations with a curvilinear term for personality tests. In addition, we discuss how popular existing models from the psychometric literature are special cases in the B-GLIRT framework depending on restrictions in the cross-relation. This allows us to compare existing models conceptually and empirically. We discuss various extensions of the traditional models motivated by practical problems. We also illustrate the applicability of our approach using various real data examples, including data on personality and cognitive ability.

Inference for the Bivariate and Multivariate Hidden Truncated Pareto(type II) and Pareto(type IV) Distribution and Some Measures of Divergence Related to Incompatibility of Probability Distribution

Science.gov (United States)

Ghosh, Indranil

2011-01-01

Consider a discrete bivariate random variable (X, Y) with possible values x[subscript 1], x[subscript 2],..., x[subscript I] for X and y[subscript 1], y[subscript 2],..., y[subscript J] for Y. Further suppose that the corresponding families of conditional distributions, for X given values of Y and of Y for given values of X are available. We…

X-ray effects on karyotype of Drosophila pseudo obscure. Pilot experience

International Nuclear Information System (INIS)

Salceda, V. M.

2009-10-01

Four groups of 100 males of Drosophila pseudo obscure carriers of genetic sequence Tree Line were treated with X-rays, through the use of a X-ray equipment Phillips MCN321; with absorbed individual doses of 28.2 Gy, 37.6 Gy, 47.6 Gy and 56.4 Gy, once irradiated these were crossed individually with two or three virgin females of the same constitution and the descendant emergency was took a larva of each crossing in order to detect the radiation effect on karyotype Tree Line of these organisms, chromosomal aberrations fundamentally, as well as on masculine sterility. Our observations gave as result for smaller dose, in a total of 61 analyzed larva, the obtaining of seven translocations equivalent to 11.5% as well as an inversion of 1.6%; with the following dose (58 analyzed larva) were obtained four translocations equal to 6.9%, two corresponding inversions to 3.4%, a mosaic and a deletion equivalent to 1.7%; with the dose of 47.6 Gy four translocations were induced 6.8% and deletion corresponding to 1.1%, again two respective inversions to 3.4% and a mosaic 1.7% in 59 analyzed larvas, meantime with the dose of 56.4 Gy appeared two translocations only equal to 3.7% in a sample of 54 individuals. The effect about masculine sterility was equal that the witness of 12% and for two following doses and finally of 41 and 46% respectively for the remaining doses. Comparisons with another authors gave similar values in the total cases. In accordance with our main objective, it is suggested to increase the sample size and to repeat the experiments using different genetic sequences as well as the possibility to use different radiation sources like gamma radiation and this way to utilize this system like a biological dosemeter. (Author)

Mixed gonadal dysgenesis with Turner`s phenotype and mosaic karyotype

Energy Technology Data Exchange (ETDEWEB)

Tarim, O.; Lieber, E. [Maimonides Medical Center, Brooklyn, NY (United States)]|[Interfaith Medical Center, Brooklyn, NY (United States)

1994-09-01

A 14 8/12-year-old white female patient was evaluated for short stature and amenorrhea. The past and family history were unremarkable. The physical examination revealed a short girl (131.4 cm; height age: 9) with a weight of 39.5kg (weight age: 11-6/12). The blood pressure was in the normal range in all four extremities and the peripheral pulses were positive. She had stigmata of Turner`s syndrome including short neck and slight webbing, cubitus valgus, and shield chest. There was no heart murmur. The only pubertal sign was pubic hair of Tanner stage II. The chromosome study showed a mosaic pattern. A total of 67 cultured lymphocytes from peripheral blood were analyzed which revealed 13 cells with 45,XO; 14 with 46,XY,r(Y); 39 with 46,XY. The patient had a normal vagina and hypoplastic uterus by sonogram. The diagnosis of mixed gonadal dysgenesis was confirmed by exploratory laparotomy and bilateral gonadectomy. The histologic examination of the gonads showed a testicle on the left and a streak ovary on right. The karyotype of the testicular tissue revealed 45,XO in 32 out of 40 and 46,XY in the remaining 8 cells. Pre-operative hormonal evaluation showed elevated gonadotropin levels of FSH 73.5 and LH 12.5 mIU/ml, low estradiol level of 5 pg/ml, normal testosterone level of 18 and DHEA-S of 181 mcg/dl, and normal thyroid function test with T4 of 6 mcg/dl and TSH of 4.2 mIU/ml. Her bone age was 12 years. The patient was also found to have subnormal growth hormone (GH) secretion by overnight GH study (1.55 ng/ml), clonidine stimulation test (7.3ng/ml), and insulin stimulation test (9.2 ng/ml). She responded well to human synthetic GH treatment with a growth velocity of 11.5 cm in two years. Replacement of sex hormones will be initiated after the completion of growth.

Bone marrow immunophenotyping by flow cytometry in refractory cytopenia of childhood

NARCIS (Netherlands)

A.M. Aalbers (Anna Maartje); M.M. van den Heuvel-Eibrink (Marry); I. Baumann (Irith); M.N. Dworzak (Michael); H. Hasle (Henrik); F. Locatelli (Franco); B. de Moerloose (Barbara); M. Schmugge; E. Mejstříková (Ester); M. Nováková (Michaela); M. Zecca (Marco); C.M. Zwaan (Christian Michel); J.G. te Marvelde (Jeroen); A.W. Langerak (Anton); J.J.M. van Dongen (Jacques); R. Pieters (Rob); C.M. Niemeyer (Charlotte); V.H.J. van der Velden (Vincent)

2015-01-01

textabstractRefractory cytopenia of childhood is the most common type of childhood myelodysplastic syndrome. Because the majority of children with refractory cytopenia have a normal karyotype and a hypocellular bone marrow, differentiating refractory cytopenia from the immune-mediated bone marrow

Chromosomal Rearrangements in Post-Chernobyl Papillary Thyroid Carcinomas: Evaluation by Spectral Karyotyping and Automated Interphase FISH

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Ludwig Hieber

2011-01-01

Full Text Available Structural genomic rearrangements are frequent findings in human cancers. Therefore, papillary thyroid carcinomas (PTCs were investigated for chromosomal aberrations and rearrangements of the RET proto-oncogene. For this purpose, primary cultures from 23 PTC have been established and metaphase preparations were analysed by spectral karyotyping (SKY. In addition, interphase cell preparations of the same cases were investigated by fluorescence in situ hybridisation (FISH for the presence of RET/PTC rearrangements using RET-specific DNA probes. SKY analysis of PTC revealed structural aberrations of chromosome 11 and several numerical aberrations with frequent loss of chromosomes 20, 21, and 22. FISH analysis for RET/PTC rearrangements showed prevalence of this rearrangement in 72% (16 out of 22 of cases. However, only subpopulations of tumour cells exhibited this rearrangement indicating genetic heterogeneity. The comparison of visual and automated scoring of FISH signals revealed concordant results in 19 out of 22 cases (87% indicating reliable scoring results using the optimised scoring parameter for RET/PTC with the automated Metafer4 system. It can be concluded from this study that genomic rearrangements are frequent in PTC and therefore important events in thyroid carcinogenesis.

Description of the karyotype of Rhagomys rufescens Thomas, 1886 (Rodentia, Sigmodontinae from Southern Brazil Atlantic forest

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André Filipe Testoni

2010-01-01

Full Text Available Rhagomys rufescens (Rodentia: Sigmodontinae is an endemic species of the Atlantic forest from Southern and Southeastern Brazil. Some authors consider Rhagomys as part of the tribe Thomasomyini; but its phylogenetic relationships remain unclear. Chromosomal studies on eight specimens of Rhagomys rufescens revealed a diploid number of 2n = 36 and a number of autosome arms FN = 50. GTG, CBG and Ag-NOR banding and CMA3/DAPI staining were performed on metaphase chromosomes. Eight biarmed and nine acrocentric pairs were found in the karyotype of this species. The X and Y chromosomes were both acrocentric. Most of the autosomes and the sex chromosomes showed positive C-bands in the pericentromeric region. The X chromosome showed an additional heterochromatic block in the proximal region of the long arm. Nucleolus organizer regions (NORs were located in the pericentromeric region of three biarmed autosomes (pairs 4, 6 and 8 and in the telomeric region of the short arm of three acrocentrics (pairs 10, 12 and 17. CMA3/DAPI staining produced fluorescent signals in many autosomes, especially in pairs 4, 6, and 8. This study presents cytogenetic data of Rhagomys rufescens for the first time.

CARIOTIPO DEL TITÍ GRIS (Saguinus leucopus MEDIANTE BANDAS R-REPLICATIVAS KARYOTYPE OF TITÍ GREY (Saguinus leucopus THROUGH R-REPLICATIVE BANDS

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Susana Posada Céspedes

2012-06-01

dispersers. Morphologically characterized by small size, brown fur and silver back. It is organized in family groups formed by the couple and their offspring, with a dominant female, which is the only breeding. Due mainly to anthropogenic factors, is listed as endangered species by IUCN and is registered in Appendix I of CITES. Although studies have been conducted on the basic biology of S. leucopus, there are few reports on the cytogenetic evaluation and none on banded karyotype R - Replicative. In this research was performed the karyotype and ideogram with replicating R-bands by incorporating 5'-bromo-2'-deoxyuridine (BrdU in peripheral blood stimulated with phytohemaglutinine of S. leucopus. The results showed a karyotype 2n = 46, with a fundamental number (NF of 76. Chromosomes are organized into five groups according to their shape and size. Group A, is made up of three pairs of large submetacentric chromosomes; group B for 5 pairs of chromosomes metacentric or submetacentric average size; group C for 6 acrocentric pairs; and group D by 8 pairs subtelocentric and sexual pair XX/XY. The "X" chromosome is medium submetacentric, and the "Y" is metacentric and the smallest genome. Finally, we propose an R-banded ideogram based Replicative mitosis stage III replication.

Semiparametric bivariate zero-inflated Poisson models with application to studies of abundance for multiple species

Science.gov (United States)

Arab, Ali; Holan, Scott H.; Wikle, Christopher K.; Wildhaber, Mark L.

2012-01-01

Ecological studies involving counts of abundance, presence–absence or occupancy rates often produce data having a substantial proportion of zeros. Furthermore, these types of processes are typically multivariate and only adequately described by complex nonlinear relationships involving externally measured covariates. Ignoring these aspects of the data and implementing standard approaches can lead to models that fail to provide adequate scientific understanding of the underlying ecological processes, possibly resulting in a loss of inferential power. One method of dealing with data having excess zeros is to consider the class of univariate zero-inflated generalized linear models. However, this class of models fails to address the multivariate and nonlinear aspects associated with the data usually encountered in practice. Therefore, we propose a semiparametric bivariate zero-inflated Poisson model that takes into account both of these data attributes. The general modeling framework is hierarchical Bayes and is suitable for a broad range of applications. We demonstrate the effectiveness of our model through a motivating example on modeling catch per unit area for multiple species using data from the Missouri River Benthic Fishes Study, implemented by the United States Geological Survey.

A new numerical investigation of some thermo-physical properties on unsteady MHD non-Darcian flow past an impulsively started vertical surface

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Motsa Sandile Sydney

2015-01-01

Full Text Available The behaviour of unsteady non-Darcian magnetohydrodynamic fluid flow past an impulsively started vertical porous surface is investigated. The effect of thermophoresis due to migration of colloidal particles in response to a macroscopic temperature gradient is taken into account. It is assumed that both dynamic viscosity and thermal conductivity are linear functions of temperature. The governing equations are non-dimensionalized by using suitable similarity transformation which can unravel the behaviour of the flow at short time and long time periods. A novel iteration scheme, called bivariate spectral local linearization method is developed for solving the corresponding systems of highly non-linear partial differential equations. The results of the numerical solutions obtained are presented graphically and analyzed for the effects of the various important parameters entering into the problem on velocity, temperature, and concentration field within the boundary layer.

Modeling both of the number of pausibacillary and multibacillary leprosy patients by using bivariate poisson regression

Science.gov (United States)

Winahju, W. S.; Mukarromah, A.; Putri, S.

2015-03-01

Leprosy is a chronic infectious disease caused by bacteria of leprosy (Mycobacterium leprae). Leprosy has become an important thing in Indonesia because its morbidity is quite high. Based on WHO data in 2014, in 2012 Indonesia has the highest number of new leprosy patients after India and Brazil with a contribution of 18.994 people (8.7% of the world). This number makes Indonesia automatically placed as the country with the highest number of leprosy morbidity of ASEAN countries. The province that most contributes to the number of leprosy patients in Indonesia is East Java. There are two kind of leprosy. They consist of pausibacillary and multibacillary. The morbidity of multibacillary leprosy is higher than pausibacillary leprosy. This paper will discuss modeling both of the number of multibacillary and pausibacillary leprosy patients as responses variables. These responses are count variables, so modeling will be conducted by using bivariate poisson regression method. Unit experiment used is in East Java, and predictors involved are: environment, demography, and poverty. The model uses data in 2012, and the result indicates that all predictors influence significantly.

Effectiveness of enforcement levels of speed limit and drink driving laws and associated factors – Exploratory empirical analysis using a bivariate ordered probit model

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Behram Wali

2017-06-01

Full Text Available The contemporary traffic safety research comprises little information on quantifying the simultaneous association between drink driving and speeding among fatally injured drivers. Potential correlation between driver's drink driving and speeding behavior poses a substantial methodological concern which needs investigation. This study therefore focused on investigating the simultaneous impact of socioeconomic factors, fatalities, vehicle ownership, health services and highway agency road safety policies on enforcement levels of speed limit and drink driving laws. The effectiveness of enforcement levels of speed limit and drink driving laws has been investigated through development of bivariate ordered probit model using data extricated from WHO's global status report on road safety in 2013. The consistent and intuitive parameter estimates along with statistically significant correlation between response outcomes validates the statistical supremacy of bivariate ordered probit model. The results revealed that fatalities per thousand registered vehicles, hospital beds per hundred thousand population and road safety policies are associated with a likely medium or high effectiveness of enforcement levels of speed limit and drink driving laws, respectively. Also, the model encapsulates the effect of several other agency related variables and socio-economic status on the response outcomes. Marginal effects are reported for analyzing the impact of such factors on intermediate categories of response outcomes. The results of this study are expected to provide necessary insights to elemental enforcement programs. Also, marginal effects of explanatory variables may provide useful directions for formulating effective policy countermeasures for overcoming driver's speeding and drink driving behavior.

Karyotype description of Pomacea patula catemacensis (Caenogastropoda, Ampullariidae), with an assessment of the taxonomic status of Pomacea patula.

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Diupotex-Chong, María Esther; Cazzaniga, Néstor J; Hernández-Santoyo, Alejandra; Betancourt-Rule, José Miguel

2004-12-01

Mitotic chromosomes of the freshwater snail Pomacea patula catemacensis (Baker 1922) were analyzed on gill tissue of specimens from the type locality (Lake Catemaco, Mexico). The diploid number of chromosomes is 2n = 26, including nine metacentric and four submetacentric pairs; therefore, the fundamental number is FN = 52, No sex chromosomes could be identified. The same chromosome number and morphology were already reported for P. flagellata, i.e., the other species of the genus living in Mexico. The basic haploid number for family Ampullariidae was reported to be n = 14 in the literature; so, its reduction to n = 13 is probably an apomorphy of the Mexican Pomacea snails. Lanistes bolteni, from Egypt, also shows n = 13, but its karyotype is much more asymmetrical, and seems to have evolved independently from P. flagellata and P. patula catemacensis. The nominotypical subspecies, P. patula patula (Reeve 1856), is a poorly known taxon, whose original locality is unknown. A taxonomical account is presented here, and a Mexican origin postulated as the most parsimonious hypothesis.

Anomalias e prognóstico fetal associados à translucência nucal aumentada e cariótipo anormal Fetal abnormalities and prognosis associated with increased nuchal translucency and abnormal karyotype

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Fátima Aparecida Targino Saldanha

2009-01-01

Full Text Available OBJETIVO: Descrever a frequência de anomalias cromossômicas em fetos com translucência nucal (TN aumentada, e a frequência de malformações estruturais, a evolução e o resultado da gestação nos fetos com TN aumentada e cariótipo anormal. MÉTODOS: Estudo retrospectivo envolvendo 246 casos com medida da TN acima do percentil 95º para a idade gestacional, com cariótipo fetal conhecido ou avaliação clínica das crianças no período pós-natal. Os casos foram acompanhados no setor de Medicina Fetal do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo. RESULTADOS: O resultado do cariótipo fetal esteve alterado em 14,2% dos casos. O acompanhamento dessas gestações revelou anormalidade estruturais em 80,8% dos fetos, sendo as anormalidades cardíacas as mais comuns (61,5%. Resultados gestacionais adversos, como abortamento, óbitos intraútero e neonatal ocorreram em 76,5% dos fetos. CONCLUSÃO: Translucência nucal aumentada, entre 11 - 13 semanas e 6 dias, é importante marcador de anomalias cromossômicas fetais e malformações estruturais fetais, principalmente cardíacas. Diante deste achado, há aumento do risco de abortamento, óbito intrauterino e neonatal para estas gestações.OBJECTIVES: This study aimed to evaluate the incidence of chromosomal abnormalities in fetuses with increased nuchal translucency (NT measurement. Incidence of structural abnormalities and pregnancy outcome was also described in fetuses with increased NT and abnormal karyotype. METHODS: This was a retrospective study involving 246 fetuses with increased NT and known karyotype followed at the Fetal Medicine Unit, Hospital das Clínicas, São Paulo University Medical School. RESULTS: Fetal karyotype was abnormal in 14.2% of the cases. Ultrasound anomaly scan and specialized echocardiographic studies in these cases showed fetal structural abnormalities in 80.8% and cardiac defects were found in 61.5% of the fetuses. Pregnancy

Bivariate spatial analysis of temperature and precipitation from general circulation models and observation proxies

KAUST Repository

Philbin, R.

2015-05-22

This study validates the near-surface temperature and precipitation output from decadal runs of eight atmospheric ocean general circulation models (AOGCMs) against observational proxy data from the National Centers for Environmental Prediction/National Center for Atmospheric Research (NCEP/NCAR) reanalysis temperatures and Global Precipitation Climatology Project (GPCP) precipitation data. We model the joint distribution of these two fields with a parsimonious bivariate Matérn spatial covariance model, accounting for the two fields\\' spatial cross-correlation as well as their own smoothnesses. We fit output from each AOGCM (30-year seasonal averages from 1981 to 2010) to a statistical model on each of 21 land regions. Both variance and smoothness values agree for both fields over all latitude bands except southern mid-latitudes. Our results imply that temperature fields have smaller smoothness coefficients than precipitation fields, while both have decreasing smoothness coefficients with increasing latitude. Models predict fields with smaller smoothness coefficients than observational proxy data for the tropics. The estimated spatial cross-correlations of these two fields, however, are quite different for most GCMs in mid-latitudes. Model correlation estimates agree well with those for observational proxy data for Australia, at high northern latitudes across North America, Europe and Asia, as well as across the Sahara, India, and Southeast Asia, but elsewhere, little consistent agreement exists.

Bivariate spatial analysis of temperature and precipitation from general circulation models and observation proxies

KAUST Repository

Philbin, R.; Jun, M.

2015-01-01

This study validates the near-surface temperature and precipitation output from decadal runs of eight atmospheric ocean general circulation models (AOGCMs) against observational proxy data from the National Centers for Environmental Prediction/National Center for Atmospheric Research (NCEP/NCAR) reanalysis temperatures and Global Precipitation Climatology Project (GPCP) precipitation data. We model the joint distribution of these two fields with a parsimonious bivariate Matérn spatial covariance model, accounting for the two fields' spatial cross-correlation as well as their own smoothnesses. We fit output from each AOGCM (30-year seasonal averages from 1981 to 2010) to a statistical model on each of 21 land regions. Both variance and smoothness values agree for both fields over all latitude bands except southern mid-latitudes. Our results imply that temperature fields have smaller smoothness coefficients than precipitation fields, while both have decreasing smoothness coefficients with increasing latitude. Models predict fields with smaller smoothness coefficients than observational proxy data for the tropics. The estimated spatial cross-correlations of these two fields, however, are quite different for most GCMs in mid-latitudes. Model correlation estimates agree well with those for observational proxy data for Australia, at high northern latitudes across North America, Europe and Asia, as well as across the Sahara, India, and Southeast Asia, but elsewhere, little consistent agreement exists.

Changes in karyotype in domestic animals discovered on the farms in Vojvodina and their influence on reproduction

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Košarčić Slavica

2006-01-01

Full Text Available New directions in animal husbandry demand raising of animal kinds that are adjusted to intensive way of breeding. In order to accomplish these demands, beside known methods in selection, Cytogenetic control of existing genotypes is needed that has been carried through ten year examination on pig, cattle and stud farms in Vojvodina. Chromosome aberration of numeric polyploidy and aneuploidy but also structural translocation, deletion, duplication, inversion, ring, break and other segregations were discovered. Numeric and structural changes on animal karyotype influenced on reproduction disturbance, phenotype expression, as well as selection program and stability of genofond. Different aspects of reproductive disturbance were noted like for example: small litter, embryo mortality, frequent repeated breeding, abortion, stillbirth and mummified embryo, offspring with anomalities, different kinds of sterility, Analyses of the results obtained from monitoring the herd book and making genealogy show on existence of chromosomepathy on our farms. The aim of this work is to inform scientists and experts with the fact that these changes are spreading, especially through among the breeding animals. Therefore genetic control and timely exclusion of chromosome aberration is necessary.

New insights into the karyotype evolution of the free-living flatworm Macrostomum lignano (Platyhelminthes, Turbellaria).

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Zadesenets, Kira S; Schärer, Lukas; Rubtsov, Nikolay B

2017-07-20

The free-living flatworm Macrostomum lignano is a model organism for evolutionary and developmental biology studies. Recently, an unusual karyotypic diversity was revealed in this species. Specifically, worms are either 'normal' 2n = 8, or they are aneuploid with one or two additional large chromosome(s) (i.e. 2n = 9 or 2n = 10, respectively). Aneuploid worms did not show visible behavioral or morphological abnormalities and were successful in reproduction. In this study, we generated microdissected DNA probes from chromosome 1 (further called MLI1), chromosome 2 (MLI2), and a pair of similar-sized smaller chromosomes (MLI3, MLI4). FISH using these probes revealed that MLI1 consists of contiguous regions homologous to MLI2-MLI4, suggesting that MLI1 arose due to the whole genome duplication and subsequent fusion of one full chromosome set into one large metacentric chromosome. Therefore, one presumably full haploid genome was packed into MLI1, leading to hidden tetraploidy in the M. lignano genome. The study of Macrostomum sp. 8 - a sibling species of M. lignano - revealed that it usually has one additional pair of large chromosomes (2n = 10) showing a high homology to MLI1, thus suggesting hidden hexaploidy in its genome. Possible evolutionary scenarios for the emergence of the M. lignano and Macrostomum sp. 8 genomes are discussed.

Telomere-Centromere-Driven Genomic Instability Contributes to Karyotype Evolution in a Mouse Model of Melanoma

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Amanda Gonçalves dos Santos Silva

2010-01-01

Full Text Available Aneuploidy and chromosomal instability (CIN are hallmarks of most solid tumors. These alterations may result from inaccurate chromosomal segregation during mitosis, which can occur through several mechanisms including defective telomere metabolism, centrosome amplification, dysfunctional centromeres, and/or defective spindle checkpoint control. In this work, we used an in vitro murine melanoma model that uses a cellular adhesion blockade as a transforming factor to characterize telomeric and centromeric alterations that accompany melanocyte transformation. To study the timing of the occurrence of telomere shortening in this transformation model, we analyzed the profile of telomere length by quantitative fluorescent in situ hybridization and found that telomere length significantly decreased as additional rounds of cell adhesion blockages were performed. Together with it, an increase in telomere-free ends and complex karyotypic aberrations were also found, which include Robertsonian fusions in 100% of metaphases of the metastatic melanoma cells. These findings are in agreement with the idea that telomere length abnormalities seem to be one of the earliest genetic alterations acquired in the multistep process of malignant transformation and that telomere abnormalities result in telomere aggregation, breakage-bridge-fusion cycles, and CIN. Another remarkable feature of this model is the abundance of centromeric instability manifested as centromere fragments and centromeric fusions. Taken together, our results illustrate for this melanoma model CIN with a structural signature of centromere breakage and telomeric loss.

Which global stock indices trigger stronger contagion risk in the Vietnamese stock market? Evidence using a bivariate analysis

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Wang Kuan-Min

2013-01-01

Full Text Available This paper extends recent investigations into risk contagion effects on stock markets to the Vietnamese stock market. Daily data spanning October 9, 2006 to May 3, 2012 are sourced to empirically validate the contagion effects between stock markets in Vietnam, and China, Japan, Singapore, and the US. To facilitate the validation of contagion effects with market-related coefficients, this paper constructs a bivariate EGARCH model of dynamic conditional correlation coefficients. Using the correlation contagion test and Dungey et al.’s (2005 contagion test, we find contagion effects between the Vietnamese and four other stock markets, namely Japan, Singapore, China, and the US. Second, we show that the Japanese stock market causes stronger contagion risk in the Vietnamese stock market compared to the stock markets of China, Singapore, and the US. Finally, we show that the Chinese and US stock markets cause weaker contagion effects in the Vietnamese stock market because of stronger interdependence effects between the former two markets.

Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles

KAUST Repository

Maadooliat, Mehdi; Gao, Xin; Huang, Jianhua Z.

2012-01-01

Despite considerable progress in the past decades, protein structure prediction remains one of the major unsolved problems in computational biology. Angular-sampling-based methods have been extensively studied recently due to their ability to capture the continuous conformational space of protein structures. The literature has focused on using a variety of parametric models of the sequential dependencies between angle pairs along the protein chains. In this article, we present a thorough review of angular-sampling-based methods by assessing three main questions: What is the best distribution type to model the protein angles? What is a reasonable number of components in a mixture model that should be considered to accurately parameterize the joint distribution of the angles? and What is the order of the local sequence-structure dependency that should be considered by a prediction method? We assess the model fits for different methods using bivariate lag-distributions of the dihedral/planar angles. Moreover, the main information across the lags can be extracted using a technique called Lag singular value decomposition (LagSVD), which considers the joint distribution of the dihedral/planar angles over different lags using a nonparametric approach and monitors the behavior of the lag-distribution of the angles using singular value decomposition. As a result, we developed graphical tools and numerical measurements to compare and evaluate the performance of different model fits. Furthermore, we developed a web-tool (http://www.stat.tamu. edu/~madoliat/LagSVD) that can be used to produce informative animations. © The Author 2012. Published by Oxford University Press.

Assessing protein conformational sampling methods based on bivariate lag-distributions of backbone angles

KAUST Repository

Maadooliat, Mehdi

2012-08-27

Despite considerable progress in the past decades, protein structure prediction remains one of the major unsolved problems in computational biology. Angular-sampling-based methods have been extensively studied recently due to their ability to capture the continuous conformational space of protein structures. The literature has focused on using a variety of parametric models of the sequential dependencies between angle pairs along the protein chains. In this article, we present a thorough review of angular-sampling-based methods by assessing three main questions: What is the best distribution type to model the protein angles? What is a reasonable number of components in a mixture model that should be considered to accurately parameterize the joint distribution of the angles? and What is the order of the local sequence-structure dependency that should be considered by a prediction method? We assess the model fits for different methods using bivariate lag-distributions of the dihedral/planar angles. Moreover, the main information across the lags can be extracted using a technique called Lag singular value decomposition (LagSVD), which considers the joint distribution of the dihedral/planar angles over different lags using a nonparametric approach and monitors the behavior of the lag-distribution of the angles using singular value decomposition. As a result, we developed graphical tools and numerical measurements to compare and evaluate the performance of different model fits. Furthermore, we developed a web-tool (http://www.stat.tamu. edu/~madoliat/LagSVD) that can be used to produce informative animations. © The Author 2012. Published by Oxford University Press.

A view on coupled cluster perturbation theory using a bivariational Lagrangian formulation.

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Kristensen, Kasper; Eriksen, Janus J; Matthews, Devin A; Olsen, Jeppe; Jørgensen, Poul

2016-02-14

We consider two distinct coupled cluster (CC) perturbation series that both expand the difference between the energies of the CCSD (CC with single and double excitations) and CCSDT (CC with single, double, and triple excitations) models in orders of the Møller-Plesset fluctuation potential. We initially introduce the E-CCSD(T-n) series, in which the CCSD amplitude equations are satisfied at the expansion point, and compare it to the recently developed CCSD(T-n) series [J. J. Eriksen et al., J. Chem. Phys. 140, 064108 (2014)], in which not only the CCSD amplitude, but also the CCSD multiplier equations are satisfied at the expansion point. The computational scaling is similar for the two series, and both are term-wise size extensive with a formal convergence towards the CCSDT target energy. However, the two series are different, and the CCSD(T-n) series is found to exhibit a more rapid convergence up through the series, which we trace back to the fact that more information at the expansion point is utilized than for the E-CCSD(T-n) series. The present analysis can be generalized to any perturbation expansion representing the difference between a parent CC model and a higher-level target CC model. In general, we demonstrate that, whenever the parent parameters depend upon the perturbation operator, a perturbation expansion of the CC energy (where only parent amplitudes are used) differs from a perturbation expansion of the CC Lagrangian (where both parent amplitudes and parent multipliers are used). For the latter case, the bivariational Lagrangian formulation becomes more than a convenient mathematical tool, since it facilitates a different and faster convergent perturbation series than the simpler energy-based expansion.

Evolution of association between renal and liver functions while awaiting heart transplant: An application using a bivariate multiphase nonlinear mixed effects model.

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Rajeswaran, Jeevanantham; Blackstone, Eugene H; Barnard, John

2018-07-01

In many longitudinal follow-up studies, we observe more than one longitudinal outcome. Impaired renal and liver functions are indicators of poor clinical outcomes for patients who are on mechanical circulatory support and awaiting heart transplant. Hence, monitoring organ functions while waiting for heart transplant is an integral part of patient management. Longitudinal measurements of bilirubin can be used as a marker for liver function and glomerular filtration rate for renal function. We derive an approximation to evolution of association between these two organ functions using a bivariate nonlinear mixed effects model for continuous longitudinal measurements, where the two submodels are linked by a common distribution of time-dependent latent variables and a common distribution of measurement errors.

Karyotype Variability and Inter-Population Genomic Differences in Freshwater Ostracods (Crustacea Showing Geographical Parthenogenesis

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Radka Symonová

2018-03-01

Full Text Available Transitions from sexual to asexual reproduction are often associated with polyploidy and increased chromosomal plasticity in asexuals. We investigated chromosomes in the freshwater ostracod species Eucypris virens (Jurine, 1820, where sexual, asexual and mixed populations can be found. Our initial karyotyping of multiple populations from Europe and North Africa, both sexual and asexual, revealed a striking variability in chromosome numbers. This would suggest that chromosomal changes are likely to be accelerated in asexuals because the constraints of meiosis are removed. Hence, we employed comparative genomic hybridization (CGH within and among sexual and asexual populations to get insights into E. virens genome arrangements. CGH disclosed substantial genomic imbalances among the populations analyzed, and three patterns of genome arrangement between these populations: 1. Only putative ribosomal DNA (rDNA-bearing regions were conserved in the two populations compared indicating a high sequence divergence between these populations. This pattern is comparable with our findings at the interspecies level of comparison; 2. Chromosomal regions were shared by both populations to a varying extent with a distinct copy number variation in pericentromeric and presumable rDNA-bearing regions. This indicates a different rate of evolution in repetitive sequences; 3. A mosaic pattern of distribution of genomic material that can be explained as non-reciprocal genetic introgression and evidence of a hybrid origin of these individuals. We show an overall increased chromosomal dynamics in E. virens that is complementary with available phylogenetic and population genetic data reporting highly differentiated diploid sexual and asexual lineages with a wide variety of genetic backgrounds.

The unique karyotype of Henochilus wheatlandii, a critically endangered fish living in a fast-developing region in Minas Gerais State, Brazil.

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Priscilla C Silva

Full Text Available Henochilus wheatlandii, the only species of this genus, is critically endangered and was considered extinct for over a century. The rediscovery of this fish in 1996 made it possible to study its phylogenetic relationships with other species in the subfamily Bryconinae. The aim of this study was to characterise the karyotype of H. wheatlandii. Standard staining, C-positive heterochromatin and nucleolar organiser region (NOR banding, chromomycin A(3 staining, and fluorescent in situ hybridisation (FISH using 5S rDNA and 18S rDNA probes were conducted on nineteen specimens collected in the Santo Antonio River, a sub-basin of the Doce River in Ferros municipality, Minas Gerais State, Brazil. Henochilus wheatlandii shared the same diploid number and chromosome morphology as other species of Bryconinae. However, its heterochromatin distribution patterns, NOR localisation, and FISH patterns revealed a cytogenetic profile unique among Neotropical Bryconinae, emphasizing the evolutionary uniqueness of this threatened species.

B chromosomes are more frequent in mammals with acrocentric karyotypes: support for the theory of centromeric drive.

Science.gov (United States)

Palestis, Brian G; Burt, Austin; Jones, R Neil; Trivers, Robert

2004-02-07

The chromosomes of mammals tend to be either mostly acrocentric (having one long arm) or mostly bi-armed, with few species having intermediate karyotypes. The theory of centromeric drive suggests that this observation reflects a bias during female meiosis, favouring either more centromeres or fewer, and that the direction of this bias changes frequently over evolutionary time. B chromosomes are selfish genetic elements found in some individuals within some species. B chromosomes are often harmful, but persist because they drive (i.e. they are transmitted more frequently than expected). We predicted that species with mainly acrocentric chromosomes would be more likely to harbour B chromosomes than those with mainly bi-armed chromosomes, because female meiosis would favour more centromeres over fewer in species with one-armed chromosomes. Our results show that B chromosomes are indeed more common in species with acrocentric chromosomes, across all mammals, among rodents, among non-rodents and in a test of independent taxonomic contrasts. These results provide independent evidence supporting the theory of centromeric drive and also help to explain the distribution of selfish DNA across species. In addition, we demonstrate an association between the shape of the B chromosomes and the shape of the typical ('A') chromosomes.

Generation and multiplication of plantlets from callus derived from Haplopappus gracilus (Nutt.) Gray and their karyotype analysis

Science.gov (United States)

Kann, R. P.; O'Connor, S. A.; Levine, H. G.; Krikorian, A. D.

1991-01-01

Unopened flower heads of Haplopappus gracilis (2n = 4) provided primary explants for callus production and subsequent induction of organized growth. Callus was initiated from small (3-5 mm in length) floral buds with benzylaminopurine (BAP) (44.4 micromoles; 10 mg/l) and naphthalene acetic acid (NAA) (0.54 micromole; 0.1 mg/l). Lowering the BAP level to 4.44 micromoles (1 mg/l) but maintaining the NAA level, gave rise to organized but highly compressed shoot growing points from an otherwise undifferentiated callus mass. Shoots selected from such cultures were maintainable and could be proliferated by growing 1-1.5-cm stem tip cuttings on Murashige and Skoog basal medium (solidified with agar) containing 0.444 micromole (0.1 mg/l) BAP and 0.054 micromole (0.01 mg/l) NAA. The stem tip multiplication rates obtainable by these means permit reliable strategies for shoot multiplication or production of rooted plantlets. Prolonged subculture and maintenance of shoots on growth regulator-free medium leads to in vitro flowering and greatly reduces rooting capacity. Karyotype analysis of chromosomes from root tip cells at metaphase and chromosome measurements show that karyologically uniform plantlets (based on chromosome number and morphology) can be obtained.

Assessing characteristics related to the use of seatbelts and cell phones by drivers: application of a bivariate probit model.

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Russo, Brendan J; Kay, Jonathan J; Savolainen, Peter T; Gates, Timothy J

2014-06-01

The effects of cell phone use and safety belt use have been an important focus of research related to driver safety. Cell phone use has been shown to be a significant source of driver distraction contributing to substantial degradations in driver performance, while safety belts have been demonstrated to play a vital role in mitigating injuries to crash-involved occupants. This study examines the prevalence of cell phone use and safety belt non-use among the driving population through direct observation surveys. A bivariate probit model is developed to simultaneously examine the factors that affect cell phone and safety belt use among motor vehicle drivers. The results show that several factors may influence drivers' decision to use cell phones and safety belts, and that these decisions are correlated. Understanding the factors that affect both cell phone use and safety belt non-use is essential to targeting policy and programs that reduce such behavior. Copyright © 2014 Elsevier Ltd. All rights reserved.

Cloud-In-Cell modeling of shocked particle-laden flows at a ``SPARSE'' cost

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Taverniers, Soren; Jacobs, Gustaaf; Sen, Oishik; Udaykumar, H. S.

2017-11-01

A common tool for enabling process-scale simulations of shocked particle-laden flows is Eulerian-Lagrangian Particle-Source-In-Cell (PSIC) modeling where each particle is traced in its Lagrangian frame and treated as a mathematical point. Its dynamics are governed by Stokes drag corrected for high Reynolds and Mach numbers. The computational burden is often reduced further through a ``Cloud-In-Cell'' (CIC) approach which amalgamates groups of physical particles into computational ``macro-particles''. CIC does not account for subgrid particle fluctuations, leading to erroneous predictions of cloud dynamics. A Subgrid Particle-Averaged Reynolds-Stress Equivalent (SPARSE) model is proposed that incorporates subgrid interphase velocity and temperature perturbations. A bivariate Gaussian source distribution, whose covariance captures the cloud's deformation to first order, accounts for the particles' momentum and energy influence on the carrier gas. SPARSE is validated by conducting tests on the interaction of a particle cloud with the accelerated flow behind a shock. The cloud's average dynamics and its deformation over time predicted with SPARSE converge to their counterparts computed with reference PSIC models as the number of Gaussians is increased from 1 to 16. This work was supported by AFOSR Grant No. FA9550-16-1-0008.

Using bivariate signal analysis to characterize the epileptic focus: the benefit of surrogates.

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Andrzejak, R G; Chicharro, D; Lehnertz, K; Mormann, F

2011-04-01

The disease epilepsy is related to hypersynchronous activity of networks of neurons. While acute epileptic seizures are the most extreme manifestation of this hypersynchronous activity, an elevated level of interdependence of neuronal dynamics is thought to persist also during the seizure-free interval. In multichannel recordings from brain areas involved in the epileptic process, this interdependence can be reflected in an increased linear cross correlation but also in signal properties of higher order. Bivariate time series analysis comprises a variety of approaches, each with different degrees of sensitivity and specificity for interdependencies reflected in lower- or higher-order properties of pairs of simultaneously recorded signals. Here we investigate which approach is best suited to detect putatively elevated interdependence levels in signals recorded from brain areas involved in the epileptic process. For this purpose, we use the linear cross correlation that is sensitive to lower-order signatures of interdependence, a nonlinear interdependence measure that integrates both lower- and higher-order properties, and a surrogate-corrected nonlinear interdependence measure that aims to specifically characterize higher-order properties. We analyze intracranial electroencephalographic recordings of the seizure-free interval from 29 patients with an epileptic focus located in the medial temporal lobe. Our results show that all three approaches detect higher levels of interdependence for signals recorded from the brain hemisphere containing the epileptic focus as compared to signals recorded from the opposite hemisphere. For the linear cross correlation, however, these differences are not significant. For the nonlinear interdependence measure, results are significant but only of moderate accuracy with regard to the discriminative power for the focal and nonfocal hemispheres. The highest significance and accuracy is obtained for the surrogate-corrected nonlinear

不同颜色肉质萝卜核型分析研究%Karyotype Analysis of Radish(Raphanus sativus L.)with Different Freshy Colors

Institute of Scientific and Technical Information of China (English)

许江; 许冬梅; 姚启伦; 陈发波

2011-01-01

Thirty two radish(Raphanus sativus L. ) accessions with different flesh colors were used to analyze the karyotypes and the red pigment content for the first time. It showed that the red accessions with red flesh had a high red pigment content as high as 16. 21% on the average (ranging from 3. 4%o~28. 8%o) , and there existed significant differences in the red pigment content between accessions. With the same number of chromosomes (2n = 2x=18) the karyotype formulae of the red radish with red flesh,green radish with red flesh,white radish with red flesh, and white radish were 14m + 4sm, 16 tn + 2 sm,as well as 18m,and belonged to 2A,Lb,La,and 1 A, respectively. As all the accessions without satellites presented almost exclusively m and sm chromosomes,some changes in chromosome size and structure occurred but no great changes in chromosome morphology were obseved. Ranking of radish accessions based on the chromosomal a-symmetry index was in turn: the red radish with red flesh,green radish with red flesh,red radish with white flesh,and white radish. With respect to the karyotype evolution,the white flesh radish could be considered more ancestral than the red flesh accessions. In additon,it was deduced that the latter might be a variant of the former.%以红皮红心、绿皮红心、红皮白心和白皮白心4种不同肉质颜色的32份萝卜品种为材料,室内检测红色肉质萝卜的色素含量及镜检观测不同颜色肉质萝卜的核型.结果表明,供试红色肉质萝卜色素含量变幅为3.4‰～28.8％,基因型间存在显著差异.不同颜色肉质萝卜品种的染色体数目均为2n=2x=18,且未见随体,红皮红心萝卜核型公式为2n=2x=14m+4 sm,属于2A型,核不对称系数为59.28％；绿皮红心萝卜核型公式为2n=2 x=16m+2 sm,属于1B型；红皮白心萝卜核型公式为2 n=2 x=18 m,属于1A型；白皮白心萝卜核型公式为2 n=2x=16m+2sm,属于1A型.从核型进化看,红色肉质萝卜比白色肉质萝卜进化程度高,红色肉质萝卜可能是由白色肉质萝卜演化而来,据此推测,红色肉质萝卜可能是白色肉质萝卜的变种.

Karyotypes, constitutive heterochromatin, and genomic DNA values in the blowfly genera Chrysomya, Lucilia, and Protophormia (Diptera: Calliphoridae).

Science.gov (United States)

Ullerich, Fritz-Helmut; Schöttke, Michael

2006-06-01

The karyotypes and C-banding patterns of Chrysomya species C. marginalis, C. phaonis, C. pinguis, C. saffranea, C. megacephala (New Guinean strain), Lucilia sericata, and Protophormia terraenovae are described. All species are amphogenic and have similar chromosome complements (2n = 12), including an XY-XX sex-chromosome pair varying in size and morphology between species. Additionally, the C-banding pattern of the monogenic species Chrysomya albiceps is presented. The DNA contents of these and of further species Chrysomya rufifacies, Chrysomya varipes, and Chrysomya putoria were assessed on mitotic metaphases by Feulgen cytophotometry. The average 2C DNA value of the male genomes ranged from 1.04 pg in C. varipes to 2.31 pg in C. pinguis. The DNA content of metaphase X chromosomes varied from 0.013 pg (= 1.23% of the total genome) in C. varipes to 0.277 pg (12.20%) in L. sericata; that of Y chromosomes ranged from 0.003 pg (0.27%) in C. varipes to 0.104 pg (5.59%) in L. sericata. In most species, the corresponding 5 large chromosome pairs showed similar relative DNA contents. The data suggest that the interspecific DNA differences in most species are mainly due to quantitative variation of (repetitive) sequences lying outside the centromeric heterochromatin blocks of the large chromosomes. The results are also discussed with regard to phylogenetic relationships of some species.

New Colors for Histology: Optimized Bivariate Color Maps Increase Perceptual Contrast in Histological Images.

Science.gov (United States)

Kather, Jakob Nikolas; Weis, Cleo-Aron; Marx, Alexander; Schuster, Alexander K; Schad, Lothar R; Zöllner, Frank Gerrit

2015-01-01

Accurate evaluation of immunostained histological images is required for reproducible research in many different areas and forms the basis of many clinical decisions. The quality and efficiency of histopathological evaluation is limited by the information content of a histological image, which is primarily encoded as perceivable contrast differences between objects in the image. However, the colors of chromogen and counterstain used for histological samples are not always optimally distinguishable, even under optimal conditions. In this study, we present a method to extract the bivariate color map inherent in a given histological image and to retrospectively optimize this color map. We use a novel, unsupervised approach based on color deconvolution and principal component analysis to show that the commonly used blue and brown color hues in Hematoxylin-3,3'-Diaminobenzidine (DAB) images are poorly suited for human observers. We then demonstrate that it is possible to construct improved color maps according to objective criteria and that these color maps can be used to digitally re-stain histological images. To validate whether this procedure improves distinguishability of objects and background in histological images, we re-stain phantom images and N = 596 large histological images of immunostained samples of human solid tumors. We show that perceptual contrast is improved by a factor of 2.56 in phantom images and up to a factor of 2.17 in sets of histological tumor images. Thus, we provide an objective and reliable approach to measure object distinguishability in a given histological image and to maximize visual information available to a human observer. This method could easily be incorporated in digital pathology image viewing systems to improve accuracy and efficiency in research and diagnostics.

Bivariate quadratic method in quantifying the differential capacitance and energy capacity of supercapacitors under high current operation

Science.gov (United States)

Goh, Chin-Teng; Cruden, Andrew

2014-11-01

Capacitance and resistance are the fundamental electrical parameters used to evaluate the electrical characteristics of a supercapacitor, namely the dynamic voltage response, energy capacity, state of charge and health condition. In the British Standards EN62391 and EN62576, the constant capacitance method can be further improved with a differential capacitance that more accurately describes the dynamic voltage response of supercapacitors. This paper presents a novel bivariate quadratic based method to model the dynamic voltage response of supercapacitors under high current charge-discharge cycling, and to enable the derivation of the differential capacitance and energy capacity directly from terminal measurements, i.e. voltage and current, rather than from multiple pulsed-current or excitation signal tests across different bias levels. The estimation results the author achieves are in close agreement with experimental measurements, within a relative error of 0.2%, at various high current levels (25-200 A), more accurate than the constant capacitance method (4-7%). The archival value of this paper is the introduction of an improved quantification method for the electrical characteristics of supercapacitors, and the disclosure of the distinct properties of supercapacitors: the nonlinear capacitance-voltage characteristic, capacitance variation between charging and discharging, and distribution of energy capacity across the operating voltage window.

Chromosomal studies of five species of the marine fishes from the Paranaguá Bay and the karyotypic diversity in the marine teleostei of the Brazilian coast

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Roger Raupp Cipriano

2008-04-01

Full Text Available In this study, five species of marine fishes from the Paranaguá Bay in the Brazilian coast were evaluated. Eucinostomus argenteus and Diapterus rhombeus (Gerreidae presented 48 chromosomes, all of which more acrocentric (FN = 48; Strongylura timucu and S. marina (Belonidae also presented 48 chromosomes, but with a higher karyotypic complexity than the Gerreidae, 10M+2SM+36A (FN = 60 and 4M+44A (FN = 52, respectively. The fifth species, Mugil curema (Mugilidae, different than the others, presented only 28 chromosomes 20M+4ST+4A (FN = 48. The species presented diversity in the karyotypic macro-structure, which should be relevant for the cytotaxonomy and the evolution of this group of the vertebrate.Nas últimas décadas tem ocorrido no Brasil um incremento de estudos cariotípicos em peixes marinhos. Atualmente são conhecidos os cariótipos de 118 espécies, distribuídas em 43 famílias e 80 gêneros. Foram estudadas cinco espécies de peixes marinhos do complexo estuarino da Baía de Paranaguá na costa brasileira. Eucinostomus argenteus e Diapterus rhombeus (Gerreidae, apresentaram 48 cromossomos todos acrocêntricos (NF = 48; Strongylura timucu e S. marina (Belonidae apresentaram 48 cromossomos, porém com complexidade cariotípica maior do que apresentada pelos gerreídeos, 10M+2SM+36A (NF = 60 e 4M+44A (NF = 52, respectivamente. A quinta espécie, Mugil curema (Mugilidae, ao contrário das outras quatro espécies aqui analisadas, apresentou apenas 28 cromossomos 20M+4ST+4A (NF = 48. Apesar da tendência em se verificar um cariótipo constituído por 48 cromossomos em teleósteos marinhos, as espécies aqui analisadas apresentam uma diversidade para a macroestrutura cariotípica a ser considerada para a citotaxonomia e evolução desse grupo de vertebrados.

Spreading of heterochromatin and karyotype differentiation in two Tropidacris Scudder, 1869 species (Orthoptera, Romaleidae)

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Rocha, Marília de França; Pine, Mariana Bozina; Oliveira, Elizabeth Felipe Alves dos Santos; Loreto, Vilma; Gallo, Raquel Bozini; da Silva, Carlos Roberto Maximiano; de Domenico, Fernando Campos; da Rosa, Renata

2015-01-01

Abstract Tropidacris Scudder, 1869 is a genus widely distributed throughout the Neotropical region where speciation was probably promoted by forest reduction during the glacial and interglacial periods. There are no cytogenetic studies of Tropidacris, and information allowing inference or confirmation of the evolutionary events involved in speciation within the group is insufficient. In this paper, we used cytogenetic markers in two species, Tropidacris collaris (Stoll, 1813) and Tropidacris cristata grandis (Thunberg, 1824), collected in different Brazilian biomes. Both species exhibited 2n=24,XX for females and 2n=23,X0 for males. All chromosomes were acrocentric. There were some differences in the karyotype macrostructure, e.g. in the chromosome size. A wide interspecific variation in the chromosome banding (C-banding and CMA3/DAPI staining) indicated strong differences in the distribution of repetitive DNA sequences. Specifically, Tropidacris cristata grandis had a higher number of bands in relation to Tropidacris collaris. FISH with 18S rDNA revealed two markings coinciding with the NORs in both species. However, two analyzed samples of Tropidacris collaris revealed a heterozygous condition for the rDNA site of S10 pair. In Tropidacris collaris, the histone H3 genes were distributed on three chromosome pairs, whereas in Tropidacris cristata grandis, these genes were observed on 14 autosomes and on the X chromosome, always in terminal regions. Our results demonstrate that, although the chromosome number and morphology are conserved in the genus, Tropidacris cristata grandis substantially differs from Tropidacris collaris in terms of the distribution of repetitive sequences. The devastation and fragmentation of the Brazilian rainforest may have led to isolation between these species, and the spreading of these repetitive sequences could contribute to speciation within the genus. PMID:26312132

Spreading of heterochromatin and karyotype differentiation in two Tropidacris Scudder, 1869 species (Orthoptera, Romaleidae

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Marília de França Rocha

2015-07-01

Full Text Available Tropidacris Scudder, 1869 is a genus widely distributed throughout the Neotropical region where speciation was probably promoted by forest reduction during the glacial and interglacial periods. There are no cytogenetic studies of Tropidacris, and information allowing inference or confirmation of the evolutionary events involved in speciation within the group is insufficient. In this paper, we used cytogenetic markers in two species, T. collaris (Stoll, 1813 and T. cristata grandis (Thunberg, 1824, collected in different Brazilian biomes. Both species exhibited 2n=24,XX for females and 2n=23,X0 for males. All chromosomes were acrocentric. There were some differences in the karyotype macrostructure, e.g. in the chromosome size. A wide interspecific variation in the chromosome banding (C-banding and CMA3/DAPI staining indicated strong differences in the distribution of repetitive DNA sequences. Specifically, T. cristata grandis had a higher number of bands in relation to T. collaris. FISH with 18S rDNA revealed two markings coinciding with the NORs in both species. However, two analyzed samples of T. collaris revealed a heterozygous condition for the rDNA site of S10 pair. In T. collaris, the histone H3 genes were distributed on three chromosome pairs, whereas in T. cristata grandis, these genes were observed on 14 autosomes and on the X chromosome, always in terminal regions. Our results demonstrate that, although the chromosome number and morphology are conserved in the genus, T. cristata grandis substantially differs from T. collaris in terms of the distribution of repetitive sequences. The devastation and fragmentation of the Brazilian rainforest may have led to isolation between these species, and the spreading of these repetitive sequences could contribute to speciation within the genus.

Comparative physical mapping of 18S rDNA in the karyotypes of six leafcutter ant species of the genera Atta and Acromyrmex (Formicidae: Myrmicinae).

Science.gov (United States)

Teixeira, Gisele Amaro; Barros, Luísa Antônia Campos; de Aguiar, Hilton Jeferson Alves Cardoso; das Graças Pompolo, Silvia

2017-10-01

Leafcutter ants of the Atta and Acromyrmex genera are important plagues in different cultures. Cytogenetic data on chromosome number, morphology, and chromosomal banding pattern are only available for 17 species of leafcutter ants. Molecular cytogenetic data for the detection of ribosomal genes by the FISH technique are scarce, and only 15 Neotropical ant species have been studied. This study aimed to physically map the 18S ribosomal RNA genes (rDNA) of six leafcutter ants belonging to the genera Atta and Acromyrmex using FISH. The results were compared with data on the fluorochrome CMA 3 currently available for these species. All analyzed species presented the 18S rDNA on one pair of chromosomes. In Acromyrmex subterraneus molestans and Ac. aspersus, FISH signals were observed in the terminal region of the short arm of the largest subtelocentric pair, while in Atta bisphaerica, A. laevigata, and A. sexdens, FISH signals were observed in the interstitial region of the long arm of the fourth metacentric pair. In Acromyrmex striatus, 18S rDNA was located in the interstitial region of the second metacentric pair. The karyotypic formula for Ac. aspersus was 2n = 38 (8m + 10sm + 16st + 4a), representing the first report in this species. The observed 18S rDNA regions in A. laevigata, A. sexdens, A. bisphaerica, Ac. aspersus, and Ac. subterraneus molestans corresponded to the CMA 3 + bands, while in Ac. striatus, several GC-rich bands and one pair of 18S rDNA bands were observed. No differential bands were visible using the DAPI fluorochrome. Karyotype uniformity with previously studied Atta spp. was also observed at the level of molecular cytogenetics using 18S rDNA FISH. A difference in the size of the chromosomal pair carrying the 18S rDNA gene was observed in Ac. striatus (2n = 22) and Atta spp. (2n = 22) highlighting the dissimilarity between these species. The results from the present study contribute to the description of 18S rDNA clusters

Mapping debris flow susceptibility using analytical network process ...

Indian Academy of Sciences (India)

Evangelin Ramani Sujatha

2017-11-23

Nov 23, 2017 ... methods known as the analytical network process (ANP) is used to map the ..... ciated in any prospective way, through feedbacks ..... slide susceptibility by means of multivariate statistical .... and bivariate statistics: A case study in southern Italy;. Nat. ... combination applied to Tevankarai Stream Watershed,.

Evaluating genome-wide DNA methylation changes in mice by Methylation Specific Digital Karyotyping

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Maruoka Shuichiro

2008-12-01

Full Text Available Abstract Background The study of genome-wide DNA methylation changes has become more accessible with the development of various array-based technologies though when studying species other than human the choice of applications are limited and not always within reach. In this study, we adapted and tested the applicability of Methylation Specific Digital Karyotyping (MSDK, a non-array based method, for the prospective analysis of epigenetic changes after perinatal nutritional modifications in a mouse model of allergic airway disease. MSDK is a sequenced based method that allows a comprehensive and unbiased methylation profiling. The method generates 21 base pairs long sequence tags derived from specific locations in the genome. The resulting tag frequencies determine in a quantitative manner the methylation level of the corresponding loci. Results Genomic DNA from whole lung was isolated and subjected to MSDK analysis using the methylation-sensitive enzyme Not I as the mapping enzyme and Nla III as the fragmenting enzyme. In a pair wise comparison of the generated mouse MSDK libraries we identified 158 loci that are significantly differentially methylated (P-value = 0.05 after perinatal dietary changes in our mouse model. Quantitative methylation specific PCR and sequence analysis of bisulfate modified genomic DNA confirmed changes in methylation at specific loci. Differences in genomic MSDK tag counts for a selected set of genes, correlated well with changes in transcription levels as measured by real-time PCR. Furthermore serial analysis of gene expression profiling demonstrated a dramatic difference in expressed transcripts in mice exposed to perinatal nutritional changes. Conclusion The genome-wide methylation survey applied in this study allowed for an unbiased methylation profiling revealing subtle changes in DNA methylation in mice maternally exposed to dietary changes in methyl-donor content. The MSDK method is applicable for mouse models

The return period analysis of natural disasters with statistical modeling of bivariate joint probability distribution.

Science.gov (United States)

Li, Ning; Liu, Xueqin; Xie, Wei; Wu, Jidong; Zhang, Peng

2013-01-01

New features of natural disasters have been observed over the last several years. The factors that influence the disasters' formation mechanisms, regularity of occurrence and main characteristics have been revealed to be more complicated and diverse in nature than previously thought. As the uncertainty involved increases, the variables need to be examined further. This article discusses the importance and the shortage of multivariate analysis of natural disasters and presents a method to estimate the joint probability of the return periods and perform a risk analysis. Severe dust storms from 1990 to 2008 in Inner Mongolia were used as a case study to test this new methodology, as they are normal and recurring climatic phenomena on Earth. Based on the 79 investigated events and according to the dust storm definition with bivariate, the joint probability distribution of severe dust storms was established using the observed data of maximum wind speed and duration. The joint return periods of severe dust storms were calculated, and the relevant risk was analyzed according to the joint probability. The copula function is able to simulate severe dust storm disasters accurately. The joint return periods generated are closer to those observed in reality than the univariate return periods and thus have more value in severe dust storm disaster mitigation, strategy making, program design, and improvement of risk management. This research may prove useful in risk-based decision making. The exploration of multivariate analysis methods can also lay the foundation for further applications in natural disaster risk analysis. © 2012 Society for Risk Analysis.

1 Mapping Debris Flow Susceptibility using Analytical Network ...

Indian Academy of Sciences (India)

54

activities in the past. In this study, one of the less explored heuristic methods known. 10 ...... can be associated in any prospective way, through feedbacks and inter-relationships. 25 ..... means of multivariate statistical techniques. .... susceptibility assessment using GIS and bivariate statistics: a case study in southern. 9. Italy.

Process-Based Ecological River Restoration: Visualizing Three-Dimensional Connectivity and Dynamic Vectors to Recover Lost Linkages

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G. Mathias. Kondolf

2006-12-01

Full Text Available Human impacts to aquatic ecosystems often involve changes in hydrologic connectivity and flow regime. Drawing upon examples in the literature and from our experience, we developed conceptual models and used simple bivariate plots to visualize human impacts and restoration efforts in terms of connectivity and flow dynamics. Human-induced changes in longitudinal, lateral, and vertical connectivity are often accompanied by changes in flow dynamics, but in our experience restoration efforts to date have more often restored connectivity than flow dynamics. Restoration actions have included removing dams to restore fish passage, reconnecting flow through artificially cut-off side channels, setting back or breaching levees, and removing fine sediment deposits that block vertical exchange with the bed, thereby partially restoring hydrologic connectivity, i.e., longitudinal, lateral, or vertical. Restorations have less commonly affected flow dynamics, presumably because of the social and economic importance of water diversions or flood control. Thus, as illustrated in these bivariate plots, the trajectories of ecological restoration are rarely parallel with degradation trajectories because restoration is politically and economically easier along some axes more than others.

New Colors for Histology: Optimized Bivariate Color Maps Increase Perceptual Contrast in Histological Images.

Directory of Open Access Journals (Sweden)

Jakob Nikolas Kather

Full Text Available Accurate evaluation of immunostained histological images is required for reproducible research in many different areas and forms the basis of many clinical decisions. The quality and efficiency of histopathological evaluation is limited by the information content of a histological image, which is primarily encoded as perceivable contrast differences between objects in the image. However, the colors of chromogen and counterstain used for histological samples are not always optimally distinguishable, even under optimal conditions.In this study, we present a method to extract the bivariate color map inherent in a given histological image and to retrospectively optimize this color map. We use a novel, unsupervised approach based on color deconvolution and principal component analysis to show that the commonly used blue and brown color hues in Hematoxylin-3,3'-Diaminobenzidine (DAB images are poorly suited for human observers. We then demonstrate that it is possible to construct improved color maps according to objective criteria and that these color maps can be used to digitally re-stain histological images.To validate whether this procedure improves distinguishability of objects and background in histological images, we re-stain phantom images and N = 596 large histological images of immunostained samples of human solid tumors. We show that perceptual contrast is improved by a factor of 2.56 in phantom images and up to a factor of 2.17 in sets of histological tumor images.Thus, we provide an objective and reliable approach to measure object distinguishability in a given histological image and to maximize visual information available to a human observer. This method could easily be incorporated in digital pathology image viewing systems to improve accuracy and efficiency in research and diagnostics.

Screening for trisomy 21 based on maternal age, nuchal translucency measurement, first trimester biochemistry and quantitative and qualitative assessment of the flow in the DV - the assessment of efficacy.

Science.gov (United States)

Czuba, Bartosz; Zarotyński, Dariusz; Dubiel, Mariusz; Borowski, Dariusz; Węgrzyn, Piotr; Cnota, Wojciech; Reska-Nycz, Małgorzata; Mączka, Marek; Wielgoś, Mirosław; Sodowski, Krzysztof; Serafin, Dawid; Kubaty, Anna; Bręborowicz, Grzegorz H

2017-01-01

The aim of the study was to compare effects of addition of two methods of ductus venosus (DV) flow assessment: qualitative - the assessment of shape of the A-wave (positive or negative), and quantitative - based on the pulsatility index for veins (DVPI) to the basic screening for trisomy 21 at 11 to 13 + 6 weeks of pregnancy. The ultrasound examination was performed in 8230 fetuses in singleton pregnancies at 11- -13 + 6 wks, as a part of a routine screening for chromosomal defects. In DV A-wave was assessed and DVPI was calculated. After the scan blood sample was taken for first trimester biochemistry (BC). Risk for chromosomal defects was calculated and high-risk patients were offered an invasive test for karyotyping. Basic screening with following combination of markers: MA, NT and BC provided lowest detection rate (DR) 87.50% for FPR = 6.94%. After adding qualitative DV A-wave assessment DR increased to 88.75% for FPR = 5.65%. The best DR = 93.75% for FPR = 5.55% was achieved when quantitative DVPI was added. The application of the Receiver Operating Curves curve confirmed validity of the addition of DV flow assessment to the screening model. The highest diagnostic power of the test was achieved when DVPI was added, with the ROC AUC of 0.974. The assessment of DV flow performed at 11-13 + 6 weeks increases DR for trisomy 21 and reduces FPR. The screening model based on the quantitative DV flow analysis (DVPI) gives better results compared to the qualitative flow assessment.

An improved method for bivariate meta-analysis when within-study correlations are unknown.

Science.gov (United States)

Hong, Chuan; D Riley, Richard; Chen, Yong

2018-03-01

Multivariate meta-analysis, which jointly analyzes multiple and possibly correlated outcomes in a single analysis, is becoming increasingly popular in recent years. An attractive feature of the multivariate meta-analysis is its ability to account for the dependence between multiple estimates from the same study. However, standard inference procedures for multivariate meta-analysis require the knowledge of within-study correlations, which are usually unavailable. This limits standard inference approaches in practice. Riley et al proposed a working model and an overall synthesis correlation parameter to account for the marginal correlation between outcomes, where the only data needed are those required for a separate univariate random-effects meta-analysis. As within-study correlations are not required, the Riley method is applicable to a wide variety of evidence synthesis situations. However, the standard variance estimator of the Riley method is not entirely correct under many important settings. As a consequence, the coverage of a function of pooled estimates may not reach the nominal level even when the number of studies in the multivariate meta-analysis is large. In this paper, we improve the Riley method by proposing a robust variance estimator, which is asymptotically correct even when the model is misspecified (ie, when the likelihood function is incorrect). Simulation studies of a bivariate meta-analysis, in a variety of settings, show a function of pooled estimates has improved performance when using the proposed robust variance estimator. In terms of individual pooled estimates themselves, the standard variance estimator and robust variance estimator give similar results to the original method, with appropriate coverage. The proposed robust variance estimator performs well when the number of studies is relatively large. Therefore, we recommend the use of the robust method for meta-analyses with a relatively large number of studies (eg, m≥50). When the

Detection and quantification of live, apoptotic, and necrotic human peripheral lymphocytes by single-laser flow cytometry.

Science.gov (United States)

Liegler, T J; Hyun, W; Yen, T S; Stites, D P

1995-05-01

Regulation of peripheral lymphocyte number involves a poorly understood balance between cell renewal and loss. Disrupting this balance leads to a large number of disease states. Methods which allow qualitative and quantitative measurements of cell viability are increasingly valuable to studies directed at revealing the mechanisms underlying apoptotic and necrotic cell death. Here, we have characterized a method using single-laser flow cytometry that differentiates and quantifies the relative number of live, apoptotic, and late-stage apoptotic and necrotic peripheral lymphocytes. Following in vitro gamma irradiation and staining with acridine orange in combination with ethidium bromide, three distinct populations were seen by bivariate analysis of green versus red fluorescence. The identity of each distinct fluorescent population (whether live, apoptotic, or necrotic) was determined by sorting and examination of cellular morphology by electron microscopy. This flow cytometric method is directly compared with the techniques of trypan blue exclusion and DNA fragmentation to quantify cell death following exposure to various doses of in vitro gamma irradiation and postirradiation incubation times. We extend our findings to illustrate the utility of this method beyond analyzing radiation-induced apoptotic peripheral blood mononuclear cells (PBMC); similar fluorescent patterns are shown for radiation- and corticosteroid-treated murine thymocytes, activated human PBMC, and PBMC from human immunodeficiency virus-infected individuals. Our results demonstrate that dual-parameter flow cytometric analysis of acridine orange-ethidium bromide-stained lymphocytes is overall a superior method with increased sensitivity, greater accuracy, and decreased subjectivity in comparison with the other methods tested. By using standard laser and filter settings commonly available to flow cytometric laboratories, this method allows rapid measurement of a large number of cells from a

Discrete bivariate population balance modelling of heteroaggregation processes.

Science.gov (United States)

Rollié, Sascha; Briesen, Heiko; Sundmacher, Kai

2009-08-15

Heteroaggregation in binary particle mixtures was simulated with a discrete population balance model in terms of two internal coordinates describing the particle properties. The considered particle species are of different size and zeta-potential. Property space is reduced with a semi-heuristic approach to enable an efficient solution. Aggregation rates are based on deterministic models for Brownian motion and stability, under consideration of DLVO interaction potentials. A charge-balance kernel is presented, relating the electrostatic surface potential to the property space by a simple charge balance. Parameter sensitivity with respect to the fractal dimension, aggregate size, hydrodynamic correction, ionic strength and absolute particle concentration was assessed. Results were compared to simulations with the literature kernel based on geometric coverage effects for clusters with heterogeneous surface properties. In both cases electrostatic phenomena, which dominate the aggregation process, show identical trends: impeded cluster-cluster aggregation at low particle mixing ratio (1:1), restabilisation at high mixing ratios (100:1) and formation of complex clusters for intermediate ratios (10:1). The particle mixing ratio controls the surface coverage extent of the larger particle species. Simulation results are compared to experimental flow cytometric data and show very satisfactory agreement.

Abnormal sex chromosome constitution and longitudinal growth: serum levels of insulin-like growth factor (IGF)-I, IGF binding protein-3, luteinizing hormone, and testosterone in 109 males with 47,XXY, 47,XYY, or sex-determining region of the Y chromosome (SRY)-positive 46,XX karyotypes

DEFF Research Database (Denmark)

Aksglaede, L.; Skakkebaek, N.E.; Juul, A.

2008-01-01

CONTEXT: Growth is a highly complex process regulated by the interaction between sex steroids and the GH IGF-axis. However, other factors such as sex chromosome-related genes play independent roles. AIM: The aim of the study was to evaluate the role of abnormal chromosome constitution for longitu......CONTEXT: Growth is a highly complex process regulated by the interaction between sex steroids and the GH IGF-axis. However, other factors such as sex chromosome-related genes play independent roles. AIM: The aim of the study was to evaluate the role of abnormal chromosome constitution...... and sitting height, serum levels of reproductive hormones, IGF-I, and IGFBP-3 were measured. RESULTS: In boys with 47,XXY and 47,XYY karyotypes, growth was accelerated already in childhood, compared with healthy boys. 46,XX-males were significantly shorter than healthy boys but matched the stature of healthy...... and elevated LH levels after puberty, whereas the sex hormone secretion of the 47,XYY boys remained normal. CONCLUSION: We found accelerated growth in early childhood in boys with 47,XXY and 47,XYY karyotypes, whereas 46,XX-males were shorter than controls. These abnormal growth patterns were not reflected...

Reappraisal of Rhamdia branneri Haseman, 1911 and R. voulezi Haseman, 1911 (Siluriformes: Heptapteridae from the rio Iguaçu with notes on their morphometry and karyotype

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Julio Cesar Garavello

Full Text Available ABSTRACT The species Rhamdia branneri Haseman, 1911 and the subspecies Rhamdia branneri voulezi Haseman, 1911 from rio Iguaçu are currently recognized as synonyms of Rhamdia quelen (Quoy & Gaimard, 1824. However, recent karyotype and ecomorphology studies distinguish R. branneri and R. voulezi as different species. Examination of Rhamdia populations from rio Iguaçu, including type specimens, together with other congeners from rio Tibagi, allowed to properly reexamine the situation of these Haseman's taxa and references given to Rhamdia in the Iguaçu. The species R. branneri and R. voulezi have strong serrae with large basis on both margins of the pectoral-fin spine, uncommon in the remaining species of Rhamdia and different from the fine serrate margins of the pectoral spine of R. quelen ; a regular dorsal profile, slightly curved between supraoccipital and dorsal fin; with dorsal dark-brown or light-gray coloration along body, abdomen pale, without profuse small black spots, common in populations of the upper Paraná species and the type-material of R. quelen . Also the following morphometric characters discriminate these species: Rhamdia voulezi , adipose fin elongate; smaller distance between dorsal and adipose fin; smaller length between adipose fin to base of caudal fin and smaller distance from posterior margin of eye to opercular border. Rhamdia branneri , larger distance from dorsal and adipose fins; deeper caudal peduncle; higher trunk depth in the vertical distance through adipose, between pelvic and anal fins; larger scapular bridge; shorter maxillary barbel; shorter external mental barbel; shorter interorbital distance; shorter length of dorsal fin basis and shorter adipose-fin base length. A PCA between the populations of Rhamdia from Iguaçu and a population from rio Tibagi, upper Paraná basin, discriminates the population from Tibagi on basis of dorsal to adipose fin distance, dorsal-fin spine length, maxillary barbel length

Identification of distinct evolutionary units in allopatric populations of Hypostomus cf. wuchereri Günther, 1864 (Siluriformes: Loricariidae: karyotypic evidence

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Jamille de Araújo Bitencourt

Full Text Available Few chromosomal reports are available for the endemic fish fauna from coastal basins in northeastern Brazil, and regional biodiversity remains partially or completely unknown. This is particularly true for Loricariidae, the most diverse family of armored catfishes. In the present work, allopatric populations of Hypostomus cf. wuchereri (Siluriformes: Loricariidae from two basins in Bahia (northeastern Brazil were cytogenetically analyzed. Both populations shared 2n = 76 chromosomes, a karyotype formula of 10m+18sm+48st/a (FN = 104 and single terminal GC-rich NORs on the second metacentric pair. Nevertheless, microstructural differences were detected by C-banding, fluorochrome staining and chromosomal digestion with restriction enzymes (Alu I, Bam HI, Hae III, and Dde I. The population from Una River (Recôncavo Sul basin showed conspicuous heterochromatin blocks and a remarkable heterogeneity of base composition (presence of interspersed AT/GC-rich and exclusively AT- or GC-rich sites, while the population from Mutum river (Contas River basin presented interstitial AT-rich C-bands and terminal GC/AT-rich heterochromatin. Each enzyme yielded a specific band profile per population which allowed us characterizing up to five heterochromatin families in each population. Based on the present data, we infer that these populations have been evolving independently, as favored by their geographic isolation, probably representing cryptic species.

Repetitive DNAs highlight the role of chromosomal fusions in the karyotype evolution of Dascyllus species (Pomacentridae, Perciformes).

Science.gov (United States)

Getlekha, Nuntaporn; Molina, Wagner Franco; de Bello Cioffi, Marcelo; Yano, Cassia Fernanda; Maneechot, Nuntiya; Bertollo, Luiz Antonio Carlos; Supiwong, Weerayuth; Tanomtong, Alongklod

2016-04-01

The Dascyllus genus consists of 11 species spread over vast regions of the Indo-Pacific, showing remarkable reductions in the diploid chromosome numbers (2n). The present study analyzed the karyotypes and other chromosomal characteristics of D. trimaculatus (2n = 48; 2st + 46a; NF = 50), D. carneus (2n = 48; 2st + 46a; NF = 50) and D. aruanus (2n = 30; 18m + 2st + 10a; NF = 50) from the Thailand Gulf (Pacific Ocean) and D. melanurus (2n = 48; 2st + 46a; NF = 50) from the Andaman Sea (Indian Ocean), employing conventional cytogenetic analyses and the chromosomal mapping of repetitive DNAs, using 18S and 5S rDNA, telomeric sequences and (CA)15, (GA)15, and (CAA)10 microsatellites as probes. The C-positive heterochromatin was found in the centromeric regions of most chromosomal pairs and 18S rDNA phenotypes were single in all species. However, in D. aruanus (2n = 30), which harbors nine metacentric pairs; the 5S rDNA sites were located in the centromeric region of the shortest one. The mapping of the telomeric sequences in D. aruanus revealed the presence of interstitial telomeric sites (ITS) in the centromeric region of four metacentric pairs, with one of these pairs also displaying an additional ITS in the long arms. Distinct chromosomal markers confirmed the reduction of the 2n by chromosomal fusions, highlighting the precise characterization of these rearrangements by the cytogenetic mapping of the repetitive DNAs.

Análisis del tamaño del genoma y cariotipo de Agave aktites Gentry (Agavaceae de Sonora, México Genome size and karyotype analysis of Agave aktites Gentry (Agavaceae from Sonora, Mexico

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Guadalupe Palomino

2010-12-01

Full Text Available Se determinó el tamaño del genoma y la estructura del cariotipo de 2 poblaciones silvestres de Agave aktites Gentry de Las Bocas y San Carlos, Sonora, México. El contenido de ADN nuclear en tejido foliar se determinó por citometría de flujo y los cromosomas se observaron en metafase mitótica de meristemos radiculares. Las plantas en ambas poblaciones son diploides (2n= 2x= 60. El contenido promedio 2C de ADN nuclear fue de 8.404 pg; 1Cx= 4 120 millones de pares de nucleótidos. El cariotipo bimodal fue similar en las 2 poblaciones y consistió de 10 cromosomas grandes y 50 pequeños y correspondió a 46m+6st+8t: también mostró un par de cromosomas telocéntricos grandes con constricción secundaria. El cociente de los brazos cromosómicos fue diferente en los pares 7, 8, 14 y 16 del grupo de cromosomas pequeños que presentan diferencias morfológicas entre las 2 poblaciones. Estos rearreglos cromosómicos podrían deberse a intercambios cromosómicos heterocigóticos espontáneos y son evidencia de que los genomas de distintas poblaciones de A. aktites se encuentran en un activo proceso de diferenciación que podría llevar a la especiación. Los análisis son básicos para conocer la diversidad genética intraespecífica de A. aktites y para establecer estrategias de conservación in situ y ex situ para esta especie.Genome size and karyotype structure of 2 wild populations of Agave aktites Gentry from Las Bocas and San Carlos, Sonora, Mexico were determined. Nuclear DNA content of leaf tissue was measured through flow cytometry, and chromosomes were observed in mitotic metaphase of root tips. All individual plants studied in both populations are diploids (2n= 2x= 60. The mean 2C nuclear DNA content was 8.404 pg; 1Cx= 4 120 million of base pairs. All plants of the 2 populations of A. aktites show a bimodal karyotype consisting of 10 large + 50 small chromosomes and corresponded to 46m+6st+8t; they also have a pair of large telocentric

Investigating the relationship between costs and outcomes for English mental health providers: a bi-variate multi-level regression analysis.

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Moran, Valerie; Jacobs, Rowena

2018-06-01

Provider payment systems for mental health care that incentivize cost control and quality improvement have been a policy focus in a number of countries. In England, a new prospective provider payment system is being introduced to mental health that should encourage providers to control costs and improve outcomes. The aim of this research is to investigate the relationship between costs and outcomes to ascertain whether there is a trade-off between controlling costs and improving outcomes. The main data source is the Mental Health Minimum Data Set (MHMDS) for the years 2011/12 and 2012/13. Costs are calculated using NHS reference cost data while outcomes are measured using the Health of the Nation Outcome Scales (HoNOS). We estimate a bivariate multi-level model with costs and outcomes simultaneously. We calculate the correlation and plot the pairwise relationship between residual costs and outcomes at the provider level. After controlling for a range of demographic, need, social, and treatment variables, residual variation in costs and outcomes remains at the provider level. The correlation between residual costs and outcomes is negative, but very small, suggesting that cost-containment efforts by providers should not undermine outcome-improving efforts under the new payment system.

Extensão bivariada do índice de confiabilidade univariado para avaliação da estabilidade fenotípica Bivariate extension of univariate reliability index for evaluating phenotypic stability

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Suzankelly Cunha Arruda de Abreu

2004-10-01

Full Text Available Com o presente trabalho, objetiva-se realizar a derivação teórica da extensão bivariada dos métodos de Annicchiarico (1992 e Annicchiarico et al. (1995 para estudar a estabilidade fenotípica. A partir dos ensaios com genótipos em ambientes e mensurações de duas variáveis, cada genótipo teve seu valor padronizado com relação a cada variável k = 1, 2. Essa padronização foi realizada em função da média do ambiente, da seguinte forma: Wijk = Yijk/×100 ; em que Wijk representa o valor padronizado do genótipo i, no ambiente j para a variável k; representa a média observada do genótipo , no ambiente para a variável k e , a média de todos genótipos para o ambiente e variável k. Com os valores padronizados foram estimados o vetor média e a matriz de variância e covariância de cada genótipo. Foi obtida a derivação teórica da extensão bivariada do índice de risco (Ii de Annicchiarico com sucesso e foi proposto um segundo índice de risco baseado nas probabilidades bivariada (Prb i; os dois índices apresentaram grande concordância nos resultados obtidos em um exemplo ilustrativo com genótipos de melões.The objective of this work was to obtain the theoretical derivation of the bivariate extension to the methods proposed by Annicchiarico (1992 and Annicchiarico et al. (1995 for studing phenotypic stability. Considering assays with genotypes in environments and two variates, every genotype had the response of each variate (k = 1, 2 standardized. This standardization has been made using the environment means as follows: Wijk = Yijk/×100 ; where Wijk represents the ith genotype standard value in the jth environment for the kth variate; represents the observed mean of the ith genotype, in jth environment for the kth variate e the overall genotypes means for jth environment to kth variate. Considering the standardized values, the genotypes mean vector and covariance matrix were estimated. The theoretical derivation of the

Effect of catchment properties and flood generation regime on copula selection for bivariate flood frequency analysis

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Filipova, Valeriya; Lawrence, Deborah; Klempe, Harald

2018-02-01

Applying copula-based bivariate flood frequency analysis is advantageous because the results provide information on both the flood peak and volume. More data are, however, required for such an analysis, and it is often the case that only data series with a limited record length are available. To overcome this issue of limited record length, data regarding climatic and geomorphological properties can be used to complement statistical methods. In this paper, we present a study of 27 catchments located throughout Norway, in which we assess whether catchment properties, flood generation processes and flood regime have an effect on the correlation between flood peak and volume and, in turn, on the selection of copulas. To achieve this, the annual maximum flood events were first classified into events generated primarily by rainfall, snowmelt or a combination of these. The catchments were then classified into flood regime, depending on the predominant flood generation process producing the annual maximum flood events. A contingency table and Fisher's exact test were used to determine the factors that affect the selection of copulas in the study area. The results show that the two-parameter copulas BB1 and BB7 are more commonly selected in catchments with high steepness, high mean annual runoff and rainfall flood regime. These findings suggest that in these types of catchments, the dependence structure between flood peak and volume is more complex and cannot be modeled effectively using a one-parameter copula. The results illustrate that by relating copula types to flood regime and catchment properties, additional information can be supplied for selecting copulas in catchments with limited data.

SV40 T antigen alone drives karyotype instability that precedes neoplastic transformation of human diploid fibroblasts.

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Ray, F A; Peabody, D S; Cooper, J L; Cram, L S; Kraemer, P M

1990-01-01

To define the role of SV40 large T antigen in the transformation and immortalization of human cells, we have constructed a plasmid lacking most of the unique coding sequences of small t antigen as well as the SV40 origin of replication. The promoter for T antigen, which lies within the origin of replication, was deleted and replaced by the Rous sarcoma virus promoter. This minimal construct was co-electroporated into normal human fibroblasts of neonatal origin along with a plasmid containing the neomycin resistance gene (neo). Three G418-resistant, T antigen-positive clones were expanded and compared to three T antigen-positive clones that received the pSV3neo plasmid (capable of expressing large and small T proteins and having two origins of replication). Autonomous replication of plasmid DNA was observed in all three clones that received pSV3neo but not in any of the three origin minus clones. Immediately after clonal expansion, several parameters of neoplastic transformation were assayed. Low percentages of cells in T antigen-positive populations were anchorage independent or capable of forming colonies in 1% fetal bovine serum. The T antigen-positive clones generally exhibited an extended lifespan in culture but rarely became immortalized. Large numbers of dead cells were continually generated in all T antigen-positive, pre-crisis populations. Ninety-nine percent of all T antigen-positive cells had numerical or structural chromosome aberrations. Control cells that received the neo gene did not have an extended life span, did not have noticeable numbers of dead cells, and did not exhibit karyotype instability. We suggest that the role of T antigen protein in the transformation process is to generate genetic hypervariability, leading to various consequences including neoplastic transformation and cell death.

[Chromosome study on chronic lymphocytic leukemia using CpG-oligodeoxynucleotide as immunostimulant agent].

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Wu, Yafang; Xue, Yongquan; Chen, Suning; Yao, Li; Jiang, Hui; Zhang, Jun; Shen, Juan; Pan, Jinlan; Wang, Yong; Bai, Shuxiao

2010-02-01

To investigate whether CpG-oligodeoxynucleotide (CpG-ODN) can improve the detection rate of the karyotypic abnormalities in chronic lymphocytic leukemia (CLL). The bone marrow (BM) or peripheral blood (PB) cells from 57 cases of CLL were collected and cultured with CpG-ODN DSP30+interleukin-2 (IL-2), phytohemagglutinin (PHA), pokeweed (PWM) or IL-2, respectively. Five days later cells were harvested for chromosome preparation. Karyotypic analysis was done using R banding technique. Panel fluorescence in situ hybridization (FISH) was carried out on 19 cases of CLL with normal karyotypes using the following probes: Cen12, D13S25, Rb1, ATM, p53, MYB and IgH. Genomic DNA from 21 cases of them was extracted from BM or PB leukocytes. The immunoglobulin variable heavy chain (IgVH) was amplified by polymerase chain reaction (PCR) and sequenced. CD38 and ZAP70 expressions in the leukemic cells were determined by flow cytometry (FCM). The detection rate of karyotypic abnormalities in the CpG-ODN+IL-2 group (43.85%) was obviously higher than that in the PHA (15.09%), PWM (17.31%) and IL-2 (3.13%) groups (P<0.01). Fifty-two types of karyotypic abnormalities were found. Among them, trisomy12 (+12) or +12 with other abnormalities were the most common, while translocations were the most frequent structural abnormalities including 3 unbalanced and 11 balanced translocations, among them 7 had rearrangements involving 14q32. Thirteen cases showed one or more abnormalities on FISH including trisomy 12 and p53 deletion each in one case, IgH rearrangement and partial deletion each in one case, 13q14.3 deletion in 11 cases of which 5 cases also had Rb1 deletion, 1 case had Rb1 partial deletion. No case with ATM or MYB deletions was found. PCR detected IgVH mutations in 10/21 cases. FCM showed 10/45 cases were CD38 positive, but 35 /45 were CD38 negative, 11/27 cases expressed ZAP70, but 16/27 did not. Among the 26 cases examined for CD38 and ZAP70 expressions simultaneously, 5 cases

Refinement of the karyological aspects of Psidium guineense (Swartz, 1788): a comparison with Psidium guajava (Linnaeus, 1753).

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Marques, Anelise Machado; Tuler, Amélia Carlos; Carvalho, Carlos Roberto; Carrijo, Tatiana Tavares; Ferreira, Marcia Flores da Silva; Clarindo, Wellington Ronildo

2016-01-01

Euploidy plays an important role in the evolution and diversification of Psidium Linnaeus, 1753. However, few data about the nuclear DNA content, chromosome characterization (morphometry and class) and molecular markers have been reported for this genus. In this context, the present study aims to shed light on the genome of Psidium guineense Swartz, 1788, comparing it with Psidium guajava Linnaeus, 1753. Using flow cytometry, the nuclear 2C value of Psidium guineense was 2C = 1.85 picograms (pg), and the karyotype showed 2n = 4x = 44 chromosomes. Thus, Psidium guineense has four chromosome sets, in accordance with the basic chromosome number of Psidium (x = 11). In addition, karyomorphometric analysis revealed morphologically identical chromosome groups in the karyotype of Psidium guineense. The high transferability of microsatellites (98.6%) further corroborates with phylogenetic relationship between Psidium guajava and Psidium guineense. Based on the data regarding nuclear genome size, karyotype morphometry and molecular markers of Psidium guineense and Psidium guajava (2C = 0.95 pg, 2n = 2x = 22 chromosomes), Psidium guineense is a tetraploid species. These data reveal the role of euploidy in the diversification of the genus Psidium.

Ancient tetraploidy and slow molecular evolution in Scaphiophryne: ecological correlates of speciation mode in Malagasy relict amphibians.

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Vences, Miguel; Aprea, Gennaro; Capriglione, Teresa; Andreone, Franco; Odierna, Gaetano

2002-01-01

Karyotypes of three microhylid frog species of the Malagasy relict genus Scaphiophryne were studied: Scaphiophryne gottlebei, S. madagascariensis and S. spinosa. The latter two showed a plesiomorphic ranoid karyotype of 2n = 26. In contrast, tetraploidy was demonstrated in S. gottlebei, which constitutes an exceptional state among Malagasy amphibians. A combination of different banding techniques and of rDNA-FISH provided evidence for allopolyploidy in the species and for a completed subsequent functional and structural diploidization. Phylogenetic analysis of mitochondrial 16S rDNA sequences revealed a significant deceleration of nucleotide substitution rates in Scaphiophryne. The tetraploidy of S. gottlebei probably occurred early in their radiation. Ecological and behavioural patterns of Scaphiophryne probably favoured intraspecific gene flow and hybridization events, thereby leading to slow molecular substitution rates and to allopolyploid chromosome speciation in S. gottlebei.

Contrasting the Chromosomal Organization of Repetitive DNAs in Two Gryllidae Crickets with Highly Divergent Karyotypes.

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Octavio M Palacios-Gimenez

Full Text Available A large percentage of eukaryotic genomes consist of repetitive DNA that plays an important role in the organization, size and evolution. In the case of crickets, chromosomal variability has been found using classical cytogenetics, but almost no information concerning the organization of their repetitive DNAs is available. To better understand the chromosomal organization and diversification of repetitive DNAs in crickets, we studied the chromosomes of two Gryllidae species with highly divergent karyotypes, i.e., 2n(♂ = 29,X0 (Gryllus assimilis and 2n = 9, neo-X1X2Y (Eneoptera surinamensis. The analyses were performed using classical cytogenetic techniques, repetitive DNA mapping and genome-size estimation. Conserved characteristics were observed, such as the occurrence of a small number of clusters of rDNAs and U snDNAs, in contrast to the multiple clusters/dispersal of the H3 histone genes. The positions of U2 snDNA and 18S rDNA are also conserved, being intermingled within the largest autosome. The distribution and base-pair composition of the heterochromatin and repetitive DNA pools of these organisms differed, suggesting reorganization. Although the microsatellite arrays had a similar distribution pattern, being dispersed along entire chromosomes, as has been observed in some grasshopper species, a band-like pattern was also observed in the E. surinamensis chromosomes, putatively due to their amplification and clustering. In addition to these differences, the genome of E. surinamensis is approximately 2.5 times larger than that of G. assimilis, which we hypothesize is due to the amplification of repetitive DNAs. Finally, we discuss the possible involvement of repetitive DNAs in the differentiation of the neo-sex chromosomes of E. surinamensis, as has been reported in other eukaryotic groups. This study provided an opportunity to explore the evolutionary dynamics of repetitive DNAs in two non-model species and will contribute to the

Karyotype of the invasive species Pterois volitans (Scorpaeniformes: Scorpaenidae) from Margarita Island, Venezuela.

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Nirchio, Mauro; Ehemann, Nicolás; Siccha-Ramirez, Raquel; Ron, Ernesto; Pérez, Julio Eduardo; Rossi, Anna Rita; Oliveira, Claudio

2014-12-01

The genus Pterois includes nine valid species, native to the Red Sea and Indian Ocean throughout the Western Pacific. P. volitans and P. miles are native to the Indo-Pacific, and were introduced into Florida waters as a result of aquarium releases, and have been recently recognized as invaders of the Western Atlantic and Caribbean Sea (Costa Rica to Venezuela). Thus far, cytogenetic studies of the genus Pterois only cover basic aspects of three species, including P. volitans from Indo-Pacific Ocean. Considering the lack of more detailed information about cytogenetic characteristics of this invasive species, the objective of the present study was to investigate the basic and molecular cytogenetic characteristics of P. volitans in Venezuela, and compare the results with those from the original distribution area. For this, the karyotypic characteristics of four lionfish caught in Margarita Island, Venezuela, were investigated by examining metaphase chromosomes by Giemsa staining, C-banding, Ag-NOR, and two-colour-Fluorescent in situ hybridization (FISH) for mapping of 18S and 5S ribosomal genes. Comparing the sequences of the 16S gene of the specimens analyzed, with sequences already included in the Genbank, we corroborated that our specimens identified as P. volitans are in fact this species, and hence exclude the possibility of a misidentification of P. miles. The diploid number was 2n = 48 (2m + 10sm + 36a) with FN = 60. Chromosomes uniformly decreased in size, making it difficult to clearly identify the homologues except for the only metacentric pair, and the pairs number two, the largest of the submetacentric series. C-banding revealed only three pairs of chromosomes negative for C-band, whereas all remaining chromosomes presented telomeric and some interstitial C-positive blocks. Only two chromosomes were C-banding positive at the pericentromeric regions. Sequential staining revealed Ag-NOR on the tips of the short arms of chromosome pair number two and the FISH

Karyotype and male pre-reductional meiosis of the sharpshooter Tapajosa rubromarginata (Hemiptera: Cicadellidae

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Graciela R de Bigliardo

2011-03-01

Full Text Available Cicadellidae in one of the best represented families in the Neotropical Region, and the tribe Proconiini comprises most of the xylem-feeding insects, including the majority of the known vectors of xylem-born phytopathogenic organisms. The cytogenetics of the Proconiini remains largely unexplored. We studied males of Tapajosa rubromarginata (Signoret collected at El Manantial (Tucumán, Argentina on native spontaneous vegetation where Sorghum halepense predominates. Conventional cytogenetic techniques were used in order to describe the karyotype and male meiosis of this sharpshooter. T. rubromarginata has a male karyological formula of 2n=21 and a sex chromosome system XO:XX (♂:♀. The chromosomes do not have a primary constriction, being holokinetic and the meiosis is pre-reductional, showing similar behavior both for autosomes and sex chromosomes during anaphase I. For this stage, chromosomes are parallel to the acromatic spindle with kinetic activities in the telomeres. They segregate reductionally in the anaphase I, and towards the equator during the second division of the meiosis. This is the first contribution to cytogenetic aspects on proconines sharpshooters, particularly on this economic relevant Auchenorrhyncha species. Rev. Biol. Trop. 59 (1: 309-314. Epub 2011 March 01.Los Cicadellidae son una de las familias mejor representadas en la región neotropical. La tribu Proconiini incluye a muchos de los insectos que se alimentan de xilema y la mayoría de los vectores de organismos fitopatógenos asociados con dicho tejido de conducción. La citogenética de los Proconiini es prácticamente inexplorada. Por lo tanto, se utilizaron técnicas citogenéticas convencionales para describir el cariotipo y la meiosis en los machos de Tapajosa rubromarginata Signoret. Este cicadélido presenta el complemento cromosómico diploide de 2n=20A+X0 en los machos. Los cromosomas no presentan constricción primaria, son holocinéticos, y la meiosis es

Karyotypic analysis in species of the genus Dasyprocta (Rodentia: Dasyproctidae found in Brazilian Amazon

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ROSEMAR S. L. RAMOS

2003-03-01

Full Text Available A total of 30 animals of the genus Dasyprocta were cytogenetically studied. They belong to the following species: D. prymnolopha (N=20, D. leporina (N=6, D. fuliginosa (N=1 and Dasyprocta sp. (N=3 (Dasyproctidae, Hystricognathi. Cell suspensions were obtained by peripheral blood culture, besides bone marrow and spleen cells, from D. prymnolopha and D. leporina. The diploid number was 64/65 for all samples. The karyotypes showed similarity, and chromosomal polymorphism was not detected by Giemsa conventional staining and G banding. The constitutive heterochromatin distribution at the pericentromeric region of all the chromosomes was similar in all species. D. prymnolopha, D. leporina and Dasyprocta sp. presented variation in the heterochromatical block size at one of the homologues of the A18 pair. D. fuliginosa presented the heterochromatin uniformly distributed in all chromosomes. There was not variation in the NORs pattern in the species studied.Foram estudados citogeneticamente um total de 30 animais das espécies D. prymnolopha (N=20, D. leporina (N=6, D. fuliginosa (N=1 e Dasyprocta sp. (N=3 (Dasyproctidae, Histricognathi. As preparações cromossômicas foram obtidas do cultivo de sangue periférico, além de medula óssea e baço em D. prymnolopha e D. leporina. O número diplóide foi de 64/65 em todos os exemplares. O cariótipo mostrou similaridade, não sendo detectado, através de coloração convencional de giemsa e de banda G, polimorfismo cromossômico em qualquer uma das espécies estudadas. A distribuição da heterocromatina constitutiva na região pericentromérica de todos os cromossomos foi similar nas quatro espécies. D. prymnolopha, D. leporina e Dasyprocta sp. apresentaram variação no tamanho do bloco heterocromático em um dos homólogos do par A18. D. fuliginosa apresentou a heterocromatina uniformemente distribuída em todos os cromossomos. Não houve variação no padrão das RONs entre as esp��cies estudadas.

Bivariate least squares linear regression: Towards a unified analytic formalism. I. Functional models

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Caimmi, R.

2011-08-01

Concerning bivariate least squares linear regression, the classical approach pursued for functional models in earlier attempts ( York, 1966, 1969) is reviewed using a new formalism in terms of deviation (matrix) traces which, for unweighted data, reduce to usual quantities leaving aside an unessential (but dimensional) multiplicative factor. Within the framework of classical error models, the dependent variable relates to the independent variable according to the usual additive model. The classes of linear models considered are regression lines in the general case of correlated errors in X and in Y for weighted data, and in the opposite limiting situations of (i) uncorrelated errors in X and in Y, and (ii) completely correlated errors in X and in Y. The special case of (C) generalized orthogonal regression is considered in detail together with well known subcases, namely: (Y) errors in X negligible (ideally null) with respect to errors in Y; (X) errors in Y negligible (ideally null) with respect to errors in X; (O) genuine orthogonal regression; (R) reduced major-axis regression. In the limit of unweighted data, the results determined for functional models are compared with their counterparts related to extreme structural models i.e. the instrumental scatter is negligible (ideally null) with respect to the intrinsic scatter ( Isobe et al., 1990; Feigelson and Babu, 1992). While regression line slope and intercept estimators for functional and structural models necessarily coincide, the contrary holds for related variance estimators even if the residuals obey a Gaussian distribution, with the exception of Y models. An example of astronomical application is considered, concerning the [O/H]-[Fe/H] empirical relations deduced from five samples related to different stars and/or different methods of oxygen abundance determination. For selected samples and assigned methods, different regression models yield consistent results within the errors (∓ σ) for both

Unstimulated Saliva-Related Caries Risk Factors in Individuals with Cystic Fibrosis: A Cross-Sectional Analysis of Unstimulated Salivary Flow, pH, and Buffering Capacity.

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Alkhateeb, Alaa A; Mancl, Lloyd A; Presland, Richard B; Rothen, Marilynn L; Chi, Donald L

2017-01-01

Salivary flow rate, pH, and buffering capacity are associated with dental caries, but studies from the cystic fibrosis (CF) literature are inconclusive regarding these salivary factors and caries. The aim of this study was to evaluate these factors and their associations with dental caries in individuals with CF. Unstimulated whole saliva was collected from individuals aged 6-20 years at Seattle Children's Hospital CF Clinic, USA (n = 83). Salivary flow rate was measured in milliliters per minute. Salivary pH was assessed using a laboratory pH meter. Buffering capacity was assessed by titration with HCl. The outcome measure was caries prevalence, defined as the number of decayed, missing, or filled primary and permanent tooth surfaces. Spearman's rank correlation coefficient and the t test were used to test for bivariate associations. Multiple variable linear regression models were used to (1) run confounder-adjusted analyses and (2) assess for potential interactions. There was no significant association between salivary flow rate or buffering capacity and caries prevalence. There was a significant negative association between salivary pH and caries prevalence, but this association was no longer significant after adjusting for age. There was no significant interaction between salivary flow rate and buffering capacity or between antibiotic use and the 3 salivary factors. Our results indicate that unstimulated salivary factors are not associated with dental caries prevalence in individuals with CF. Future studies should investigate other potential saliva-related caries risk factors in individuals with CF such as cariogenic bacteria levels, salivary host defense peptide levels, and medication use. © 2016 S. Karger AG, Basel.

Evaluation of Factors Affecting E-Bike Involved Crash and E-Bike License Plate Use in China Using a Bivariate Probit Model

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Yanyong Guo

2017-01-01

Full Text Available The primary objective of this study is to evaluate factors affecting e-bike involved crash and license plate use in China. E-bike crashes data were collected from police database and completed through a telephone interview. Noncrash samples were collected by a questionnaire survey. A bivariate probit (BP model was developed to simultaneously examine the significant factors associated with e-bike involved crash and e-bike license plate and to account for the correlations between them. Marginal effects for contributory factors were calculated to quantify their impacts on the outcomes. The results show that several contributory factors, including gender, age, education level, driver license, car in household, experiences in using e-bike, law compliance, and aggressive driving behaviors, are found to have significant impacts on both e-bike involved crash and license plate use. Moreover, type of e-bike, frequency of using e-bike, impulse behavior, degree of riding experience, and risk perception scale are found to be associated with e-bike involved crash. It is also found that e-bike involved crash and e-bike license plate use are strongly correlated and are negative in direction. The result enhanced our comprehension of the factors related to e-bike involved crash and e-bike license plate use.

Flow-Signature Analysis of Water Consumption in Nonresidential Building Water Networks Using High-Resolution and Medium-Resolution Smart Meter Data: Two Case Studies

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Clifford, Eoghan; Mulligan, Sean; Comer, Joanne; Hannon, Louise

2018-01-01

Real-time monitoring of water consumption activities can be an effective mechanism to achieve efficient water network management. This approach, largely enabled by the advent of smart metering technologies, is gradually being practiced in domestic and industrial contexts. In particular, identifying water consumption habits from flow-signatures, i.e., the specific end-usage patterns, is being investigated as a means for conservation in both the residential and nonresidential context. However, the quality of meter data is bivariate (dependent on number of meters and data temporal resolution) and as a result, planning a smart metering scheme is relatively difficult with no generic design approach available. In this study, a comprehensive medium-resolution to high-resolution smart metering program was implemented at two nonresidential trial sites to evaluate the effect of spatial and temporal data aggregation. It was found that medium-resolution water meter data were capable of exposing regular, continuous, peak use, and diurnal patterns which reflect group wide end-usage characteristics. The high-resolution meter data permitted flow-signature at a personal end-use level. Through this unique opportunity to observe water usage characteristics via flow-signature patterns, newly defined hydraulic-based design coefficients determined from Poisson rectangular pulse were developed to intuitively aid in the process of pattern discovery with implications for automated activity recognition applications. A smart meter classification and siting index was introduced which categorizes meter resolution in terms of their suitable application.

SMPLNORM: A simple model for obtaining the joint probabilities of two flows and the level that depends on them. SMPLNORM: Un modele simple pour obtenir les probabilites conjointes de deux debits et le niveau qui en depend

Energy Technology Data Exchange (ETDEWEB)

Bruneau, P. (Hydro-Quebec, Montreal, PQ (Canada)); Ashkar, F. (Moncton Univ., NB (Canada)); Bobee, B. (Inst. National de la Recherche Scientifique, Saint-Foy, PQ (Canada))

1994-01-01

Most bivariate models assume the same type of marginal distribution, with two parameters, for two variables. The disadvantage of these models for hydrologic flow studies is that it is often difficult to make adjustments for observed flows. A complete example is presented of the application flexibility of the SMPLNORM program, which calculates the joint probability of two variables, Q1 and Q2, with marginal distributions that have three parameters. The program can also provide the probability of nonexceedence of a third variable H, mathematically related to the first two variables. Two applications are discussed, in which Q1 and Q2 are the flows of two rivers controlling the variable H, which is a water level in both cases. Theoretically, this model could also be applied to other types of variables. The proposed model is based on the hypothesis that a Box-Cox type of power transformation could reduce the marginal distributions of Q1 and Q2 to a normal distribution. One of the main conclusions of the study addresses the importance of taking into account the correlation between Q1 and Q2 to obtain a valid estimate of H. 11 refs., 14 figs., 7 tabs.

Karyotype of the invasive species Pterois volitans (Scorpaeniformes: Scorpaenidae from Margarita Island, Venezuela

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Mauro Nirchio

2014-12-01

Full Text Available The genus Pterois includes nine valid species, native to the Red Sea and Indian Ocean throughout the Western Pacific. P. volitans and P. miles are native to the Indo-Pacific, and were introduced into Florida waters as a result of aquarium releases, and have been recently recognized as invaders of the Western Atlantic and Caribbean Sea (Costa Rica to Venezuela. Thus far, cytogenetic studies of the genus Pterois only cover basic aspects of three species, including P. volitans from Indo-Pacific Ocean. Considering the lack of more detailed information about cytogenetic characteristics of this invasive species, the objective of the present study was to investigate the basic and molecular cytogenetic characteristics of P. volitans in Venezuela, and compare the results with those from the original distribution area. For this, the karyotypic characteristics of four lionfish caught in Margarita Island, Venezuela, were investigated by examining metaphase chromosomes by Giemsa staining, C-banding, Ag-NOR, and two-colour-Fluorescent in situ hybridization (FISH for mapping of 18S and 5S ribosomal genes. Comparing the sequences of the 16S gene of the specimens analyzed, with sequences already included in the Genbank, we corroborated that our specimens identified as P. volitans are in fact this species, and hence exclude the possibility of a misidentification of P. miles. The diploid number was 2n=48 (2m+10sm+36a with FN=60. Chromosomes uniformly decreased in size, making it difficult to clearly identify the homologues except for the only metacentric pair, and the pairs number two, the largest of the submetacentric series. C-banding revealed only three pairs of chromosomes negative for C-band, whereas all remaining chromosomes presented telomeric and some interstitial C-positive blocks. Only two chromosomes were C-banding positive at the pericentromeric regions. Sequential staining revealed Ag-NOR on the tips of the short arms of chromosome pair number two and

Should we question early feminizing genitoplasty for patients with congenital adrenal hyperplasia and XX karyotype?

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Binet, A; Lardy, H; Geslin, D; Francois-Fiquet, C; Poli-Merol, M L

2016-03-01

There is a wide difference of opinion between the medical-surgical community and advocacy group regarding Disorders of Sexual Development (DSD) secondary to congenital adrenal hyperplasia (CAH) being ranked in the intersex category. This rupture is even more evident when the issue of genitoplasty is brought up. For physicians it is obvious and unequivocal that a person with CAH and an XX karyotype has a female gender identity, whereas associations tend to rank persons with CAH in the intersex category and advocate holding-off on surgical management. A retrospective case study vs. control group, spanning over 40years, included 21 patients who were treated in 3 different centers. Each patient and their parents were contacted independently and interviewed regarding interpersonal relationships, psychological impact of genitoplasty, gender identity and opinion on optimal care management for this disorder. Three couples controls (parent-child) per CAH patients were used and matched according to age, sex assigned at birth and ethnic origin. Sex assigned at birth seemed to concord with the gender identity perceived by the patients in 85.7% of cases. In fact, 89.7% of patients and 100% of parents felt that feminizing genitoplasty should be performed within the first year of life. There is however a significant difference compared to controls who felt that surgical management should occur later on in life. No difference was highlighted during childhood regarding parents-child relationships or social integration. However, during adolescence, the parents-child relationship tended to be significantly more painful for the CAH group. Integrating their parenting role was significantly harder for patients in the CAH-DSD group. In the population of CAH-DSD patients who had genitoplasty the level of sexual fulfillment was not lower to the one reported by the control group. Female sex assignment seems legitimate according to this study and the development of gender identity in these

Oligo-based High-resolution aCGH Analysis Enhances Routine Cytogenetic Diagnostics in Haematological Malignancies.

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Kjeldsen, Eigil

2015-01-01

The purpose of the present study was to evaluate the detection rate of genomic aberrations in haematological malignancies using oligobased array-CGH (oaCGH) analysis in combination with karyotyping and fluorescence in situ hybridization (FISH) analyses, and its feasibility in a clinical pragmatic approach. The 4x180K Cancer Cytochip array was applied in 96 patients with various haematological malignancies in a prospective setting and in 41 acute myeloid leukemia (AML) patients retrospectively. Combined use of oaCGH analysis and karyotyping improved the overall detection rate in comparison to karyotyping-alone and vice versa. In cases with normal karyotypes oaCGH analysis detected genomic aberrations in 66% (39/60) of cases. In the group of simple karyotypes oaCGH analysis extended karyotypic findings in 39% (12/31) while oaCGH analysis extended the karyotypic findings in 89% (39/44) of cases with complex karyotypes. In 7% (5/75) of cases oaCGH analysis failed in detecting the observed abnormalities by karyotyping. oaCGH analysis is a valuable asset in routine cytogenetics of haematological malignancies. Copyright© 2015, International Institute of Anticancer Research (Dr. John G. Delinasios), All rights reserved.

Fluid intelligence, traits of personality and personality disorders in a cohort of adult KS patients with the classic 47, XXY karyotype.

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Liberato, D; Granato, S; Grimaldi, D; Rossi, F M; Tahani, N; Gianfrilli, D; Anzuini, A; Lenzi, A; Cavaggioni, G; Radicioni, A F

2017-11-01

Klinefelter's syndrome (KS) is associated with specific neurobehavioral features and personality traits. The aim of our study was to investigate fluid intelligence, personality traits and personality disorders (PD) and possible correlations with testosterone in a cohort of adult KS patients. We analyzed 58 adult KS patients with the classic 47, XXY karyotype. The Structured Clinical Interview for axis II disorders was used to assess DSM IV personality disorders. Personality traits were assessed using MMPI-2. Fluid intelligence was tested by using Raven's Standard Progressive Matrices (SPM) Test. Testosterone blood concentration was measured by CMIA. PD prevalence was 31%. Four altered MMPI scales (Social Responsibility, Dominance, Ego Strength and Repression) were found in more than 40% of patients. Overcontrolled hostility and MacAndrew Alcoholism Scale-Revised scales were altered in the PD- group only. Biz-Odd Thinking and Post-Traumatic Stress Disorder scale were associated with the presence of personality disorder. The raw SPM score was 44 ± 10.8 without any significant correlation with testosterone. No significant difference in mean age, SPM raw score and MMPI score was observed between eugonadal, hypogonadal and treated patients. Most KS patients had average fluid intelligence. PD prevalence was higher than in the general population. Testosterone was not correlated with fluid intelligence, personality traits or PD, but a reduction in marital distress was observed in treated patients. This could suggest that testosterone therapy can improve physical symptoms and this effect could also improve relationship abilities and wellness awareness.

Array-based molecular karyotyping in 115 VATER/VACTERL and VATER/VACTERL-like patients identifies disease-causing copy number variations.

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Zhang, Rong; Marsch, Florian; Kause, Franziska; Degenhardt, Franziska; Schmiedeke, Eeberhard; Märzheuser, Stefanie; Hoppe, Bernd; Bachour, Haitham; Boemers, Thomas M; Schäfer, Matthias; Spychalski, Nicole; Neser, Jörg; Leonhardt, Johannes; Kosch, Ferdinand; Ure, Benno; Gómez, Barbara; Lacher, Martin; Deffaa, Oliver J; Palta, Markus; Wittekindt, Boris; Kleine, Katharina; Schmedding, Andrea; Grasshoff-Derr, Sabine; Ven, Amelie van der; Heilmann-Heimbach, Stefanie; Zwink, Nadine; Jenetzky, Ekkehart; Ludwig, Michael; Reutter, Heiko

2017-07-17

The acronym VATER/VACTERL refers to the rare nonrandom association of the following component features (CF): vertebral defects (V), anorectal malformations (A), cardiac defects (C), tracheoesophageal fistula with or without esophageal atresia, renal malformations (R), and limb defects (L). Patients presenting with at least three CFs are diagnosed as having VATER/VACTERL association while patients presenting with only two CFs are diagnosed as having VATER/VACTERL-like phenotypes. Recently, rare causative copy number variations (CNVs) have been identified in patients with VATER/VACTERL association and VATER/VACTERL-like phenotypes. To detect further causative CNVs we performed array based molecular karyotyping in 75 VATER/VACTERL and 40 VATER/VACTERL-like patients. Following the application of stringent filter criteria, we identified 13 microdeletions and seven microduplications in 20 unrelated patients all of which were absent in 1,307 healthy inhouse controls (n microdeletion at 17q12 was confirmed to be de novo. Three microdeletions at 5q23.1, 16q23.3, 22q11.21, and one microduplication at 10q11.21 were all absent in the available parent. Microdeletion of chromosomal region 22q11.21 was previously found in VATER/VACTERL patients rendering it to be causative in our patient. The remaining 15 CNVs were inherited from a healthy parent. In two of 115 patients' causative CNVs were found (2%). The remaining identified rare CNVs represent candidates for further evaluation. Rare inherited CNVs may constitute modifiers of, or contributors to, multifactorial VATER/VACTERL or VATER/VACTERL-like phenotypes. Birth Defects Research 109:1063-1069, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Karyotype characteristics, larval morphology and chromosomal polymorphism peculiarities of Glyptotendipes salinus Michailova, 1983 (Diptera, Chironomidae) from Tambukan Lake, Central Caucasus

Science.gov (United States)

Karmokov, Mukhamed Kh.; Akkizov, Azamat Y.

2016-01-01

Abstract Data on the karyotype characteristics, larval morphology and features of chromosomal polymorphism of a population of Glyptotendipes salinus Michailova, 1983 (Diptera, Chironomidae) from Tambukan Lake (on the northern macroslope of the central Caucasus) are presented. It was found that diagnostic larval characters of Glyptotendipes salinus from Caucasus in general are similar to those described in previous studies, but with some significant differences. By some morphological characteristics Caucasian larvae appeared to be closer to Glyptotendipes barbipes than to ones provided for European larvae of Glyptotendipes salinus by Contreras-Lichtenberg (1999). Obtained morphological data make possible to conclude that Caucasian population of Glyptotendipes salinus can be a markedly diverged population of the species, probably even subspecies. In the Caucasian population 12 banding sequences were found: two in arms A, B, C, E, and G, and one in arms D and F. Eight of these are already known for this species, and four, salA2, salB2, salEX, and salG3, are described for the first time. Genetic distances between all the previously studied populations of Glyptotendipes salinus were measured using Nei criteria (1972). The population of the central Caucasus occupies a distinct position on the dendrogram compared with populations from Altai and Kazakhstan. All the obtained morphological and cytogenetic data can indicate the plausible relative isolation and complexity of the Caucasus from the viewpoint of microevolution. More researches are required in other parts of Caucasus and other geographically distant regions for more specific allegations. PMID:28123679

Karyotype characteristics, larval morphology and chromosomal polymorphism peculiarities of Glyptotendipes salinus Michailova, 1983 (Diptera, Chironomidae from Tambukan Lake, Central Caucasus

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Mukhamed Karmokov

2016-11-01

Full Text Available Data on the karyotype characteristics, larval morphology and features of chromosomal polymorphism of a population of Glyptotendipes salinus Michailova, 1983 (Diptera, Chironomidae from Tambukan Lake (on the northern macroslope of the central Caucasus are presented. It was found that diagnostic larval characters of G. salinus from Caucasus in general are similar to those described in previous studies, but with some significant differences. By some morphological characteristics Caucasian larvae appeared to be closer to G. barbipes than to ones provided for European larvae of G. salinus by Contreras-Lichtenberg (1999. Obtained morphological data make possible to conclude that Caucasian population of G. salinus can be a markedly diverged population of the species, probably even subspecies. In the Caucasian population 12 banding sequences were found: two in arms A, B, C, E, and G, and one in arms D and F. Eight of these are already known for this species, and four, salA2, salB2, salEX, and salG3, are described for the first time. Genetic distances between all the previously studied populations of G. salinus were measured using Nei criteria (1972. The population of the central Caucasus occupies a distinct position on the dendrogram compared with populations from Altai and Kazakhstan. All the obtained morphological and cytogenetic data can indicate the plausible relative isolation and complexity of the Caucasus from the viewpoint of microevolution. More researches are required in other parts of Caucasus and other geographically distant regions for more specific allegations.

Cellular and molecular biology group

International Nuclear Information System (INIS)

Anon.

1976-01-01

Model DNA polymers have been employed to measure physico-chemical effects of X-irradiation and the influence of known base sequences on the transcription by RNA polymerases. These experiments allow quantitative estimates of the fidelity of transcription in the presence of physical and chemical agents. Cells in culture provide the basic system for studying radiation effects on DNA synthesis, organization of DNA in the nucleus, effects of pollutants on genetic information transfer and gene expression, nucleic acid structure, proliferation capacity, histone phosphorylation, and chromatin structure and function. Mathematical models of the immune response have been formulated, and the biochemical properties of the cell surface have been characterized. The use of flow systems to provide rapid karyotype analysis has been established for relatively simple karyotypes, and a series of cell-cycle-dependent, temperature-sensitive mutant mammalian cell lines have been derived and appear useful for cycle progression and mutagenesis studies

identification of hydrogeochemical processes in groundwater using

African Journals Online (AJOL)

PROF EKWUEME

and the hydrochemical data was subjected to multivariate statistical analysis and conventional ... Groundwater flows through geological materials as it moves along ... using various conventional graphical methods and ...... from recharge zone to discharge zone, a bivariate plot of. Ca2+ + .... Handbook of Applied Hydrology,.

Flow patterns in vertical two-phase flow

International Nuclear Information System (INIS)

McQuillan, K.W.; Whalley, P.B.

1985-01-01

This paper is concerned with the flow patterns which occur in upwards gas-liquid two-phase flow in vertical tubes. The basic flow patterns are described and the use of flow patter maps is discussed. The transition between plug flow and churn flow is modelled under the assumption that flooding of the falling liquid film limits the stability of plug flow. The resulting equation is combined with other flow pattern transition equations to produce theoretical flow pattern maps, which are then tested against experimental flow pattern data. Encouraging agreement is obtained

Modelling the vicious circle between obesity and physical activity in children and adolescents using a bivariate probit model with endogenous regressors.

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Yeh, C-Y; Chen, L-J; Ku, P-W; Chen, C-M

2015-01-01

The increasing prevalence of obesity in children and adolescents has become one of the most important public health issues around the world. Lack of physical activity is a risk factor for obesity, while being obese could reduce the likelihood of participating in physical activity. Failing to account for the endogeneity between obesity and physical activity would result in biased estimation. This study investigates the relationship between overweight and physical activity by taking endogeneity into consideration. It develops an endogenous bivariate probit model estimated by the maximum likelihood method. The data included 4008 boys and 4197 girls in the 5th-9th grades in Taiwan in 2007-2008. The relationship between overweight and physical activity is significantly negative in the endogenous model, but insignificant in the comparative exogenous model. This endogenous relationship presents a vicious circle in which lower levels of physical activity lead to overweight, while those who are already overweight engage in less physical activity. The results not only reveal the importance of endogenous treatment, but also demonstrate the robust negative relationship between these two factors. An emphasis should be put on overweight and obese children and adolescents in order to break the vicious circle. Promotion of physical activity by appropriate counselling programmes and peer support could be effective in reducing the prevalence of obesity in children and adolescents.

Effects of gamma irradiation on the karyotype of plutella xylostella l., and the histology of the testis

International Nuclear Information System (INIS)

Noran, A.M.; Nadia, M.T.K.

2002-01-01

The aim of this study is to produce semi-sterile Palatal xylo stella males that can compete with the wild males for the normal females, with the resulting progeny being sterile. Semi-sterile males were produced by exposing male pupae 24 hours before emergence to gamma (Co 60 ) irradiation at a dose of 175 Gy. The chromosome study was done through squashes of the testes with aceto-orsin staining from fourth in star larvae of the irradiated male parent, the F I males resulting from crosses between irradiated parents, from crosses between irradiated males and normal females and vice versa. For the histological study, the irradiated males were crossed with normal females to get the F Is and the resulting progeny then used to subsequently get the F2, F and F4 generations, respectively. Back crosses to the normal males or females for each of these generations were also carried out. Samples of the testes of resulting males from every cross were removed and subjected to the usual processing for preparation of glass slides using haematoxlin and eosin staining. Exposure to 175 Gy was found to be sufficient to cause chromosomal aberrations like short- and long chain formations or a combination of both as well as ring formations in the treated groups. The least number of translocations obtained were from crosses of Fl males (from normal male x irradiated female) with normal females while the highest from F Is resulting from crosses between both irradiated parents. Cytological changes observed in the testes of the Fl generation included emergence of vacuoles in place of germ cells, displacement of spermatocytes from the periphery to the center of the testes and disintegration of spermatocytes and spermatozoal bundles. However, the damages were not permanent as recovery were detected in testes from subsequent generations. It is likely that the effects of gamma irradiation on the karyotype and histology of the testis of the males are determined by the female parent as recovery

The prevalence of turner syndrome in girls presenting with coarctation of the aorta.

Science.gov (United States)

Wong, Sze Choong; Burgess, Trent; Cheung, Michael; Zacharin, Margaret

2014-02-01

To determine the prevalence of Turner syndrome in girls presenting with coarctation of the aorta (CoA). A total of 132 girls with known structural CoA was identified. Those girls who had no previous karyotype analysis performed were asked to participate in a research study in which a banded karyotype with 50-cell count was performed. Of 132 girls with CoA, 55 (41.7%) had karyotype analysis within 6 months of cardiac diagnosis. Three girls underwent karyotyping later because of clinical concerns. Of the 74 girls with CoA who had not had a karyotype, 38 (51.4%) consented to the study. Results were available for 37 girls. All were 46,XX. Five patients with Turner syndrome were identified in the 95 girls with CoA who had karyotype analysis (4 from early karyotype and 1 diagnosed later), which translated into a minimum prevalence of 5.3% of Turner syndrome in this group of girls with CoA. In addition, one infant with a 20-cell 46,XX karyotype had features of Turner syndrome. Our study demonstrated for the first time in a large cohort that 5.3% of girls presenting with CoA are found to have Turner syndrome when karyotyping is performed. Given the spectrum of preventable and treatable health problems after the diagnosis of Turner syndrome, we believe that all girls with CoA should have a karyotype analysis, ideally with at least 50-cell count, at the time of diagnosis of CoA. Copyright © 2014 Mosby, Inc. All rights reserved.

Abnormal sex chromosome constitution and longitudinal growth: serum levels of insulin-like growth factor (IGF)-I, IGF binding protein-3, luteinizing hormone, and testosterone in 109 males with 47,XXY, 47,XYY, or sex-determining region of the Y chromosome (SRY)-positive 46,XX karyotypes

DEFF Research Database (Denmark)

Aksglaede, L.; Skakkebaek, N.E.; Juul, A.

2008-01-01

CONTEXT: Growth is a highly complex process regulated by the interaction between sex steroids and the GH IGF-axis. However, other factors such as sex chromosome-related genes play independent roles. AIM: The aim of the study was to evaluate the role of abnormal chromosome constitution...... and elevated LH levels after puberty, whereas the sex hormone secretion of the 47,XYY boys remained normal. CONCLUSION: We found accelerated growth in early childhood in boys with 47,XXY and 47,XYY karyotypes, whereas 46,XX-males were shorter than controls. These abnormal growth patterns were not reflected...

De Novo CD5 Negative Blastic Mantle Cell Lymphoma Presented with Massive Bone Marrow Necrosis without Adenopathy or Organomegaly

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Ghaleb Elyamany

2015-01-01

Full Text Available The recent World Health Organization (WHO classification defines mantle cell lymphoma (MCL as a distinct entity characterized by a unique immunophenotype and a molecular hallmark of chromosomal translocation t(11;14(q13;q32. We report an unusual case of an advanced stage of CD5 negative MCL with a blastoid variant with a massive bone marrow (BM necrosis as an initial presenting feature, with no adenopathy or hepatosplenomegaly. The pathologic features showed blastoid variant of MCL and flow cytometry showed that the tumor cells were CD5−, CD19+, CD20+, FMC-7+, CD23−, and lambda light chain restricted. Chromosomal analysis, using karyotype and fluorescent in situ hybridization (FISH, demonstrated karyotypic abnormalities in addition to the t(11;14. Our case study may be reported as a unique case of CD5− blastic MCL with unusual presentation and findings which made the diagnosis of MCL difficult.

Non invasive blood flow measurement in cerebellum detects minimal hepatic encephalopathy earlier than psychometric tests.

Science.gov (United States)

Felipo, Vicente; Urios, Amparo; Giménez-Garzó, Carla; Cauli, Omar; Andrés-Costa, Maria-Jesús; González, Olga; Serra, Miguel A; Sánchez-González, Javier; Aliaga, Roberto; Giner-Durán, Remedios; Belloch, Vicente; Montoliu, Carmina

2014-09-07

To assess whether non invasive blood flow measurement by arterial spin labeling in several brain regions detects minimal hepatic encephalopathy. Blood flow (BF) was analyzed by arterial spin labeling (ASL) in different brain areas of 14 controls, 24 cirrhotic patients without and 16 cirrhotic patients with minimal hepatic encephalopathy (MHE). Images were collected using a 3 Tesla MR scanner (Achieva 3T-TX, Philips, Netherlands). Pulsed ASL was performed. Patients showing MHE were detected using the battery Psychometric Hepatic Encephalopathy Score (PHES) consisting of five tests. Different cognitive and motor functions were also assessed: alterations in selective attention were evaluated using the Stroop test. Patients and controls also performed visuo-motor and bimanual coordination tests. Several biochemical parameters were measured: serum pro-inflammatory interleukins (IL-6 and IL-18), 3-nitrotyrosine, cGMP and nitrates+nitrites in plasma, and blood ammonia. Bivariate correlations were evaluated. In patients with MHE, BF was increased in cerebellar hemisphere (P = 0.03) and vermis (P = 0.012) and reduced in occipital lobe (P = 0.017). BF in cerebellar hemisphere was also increased in patients without MHE (P = 0.02). Bimanual coordination was impaired in patients without MHE (P = 0.05) and much more in patients with MHE (P battery and with CFF. BF in cerebellar hemisphere correlates with plasma cGMP and nitric oxide (NO) metabolites. BF in vermis cerebellar also correlates with NO metabolites and with 3-nitrotyrosine. IL-18 in plasma correlates with BF in thalamus and occipital lobe. Non invasive BF determination in cerebellum using ASL may detect MHE earlier than the PHES. Altered NO-cGMP pathway seems to be associated to altered BF in cerebellum.