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Sample records for randomly selected clones

  1. Expressed sequence tags of randomly selected cDNA clones from Eucalyptus globulus-Pisolithus tinctorius ectomycorrhiza.

    Science.gov (United States)

    Tagu, D; Martin, F

    1995-01-01

    Random sequencing of cDNA clones from Eucalyptus globulus-Pisolithus tinctorius ectomycorrhizal tissues was carried out to generate expressed sequence tags (ESTs). Database comparisons revealed that 42% of the cDNAs corresponded to previously sequenced genes. These ESTs represent efficient molecular markers to analyze changes in gene expression during the formation of the ectomycorrhizal symbiosis.

  2. Productivity and fruit quality of Jonagold clones of home selection

    OpenAIRE

    К. П. Тарнавська

    2014-01-01

    New results of the clonal selection of apple tree (Malus domestica Borkh) conducted at Podillya Research Station of Horticultural Institute NAAS by method of state variety testing have been presented. By the results of the 6-year studying (2007 - 2012) of 20 new Jonagold clones of domestic selection their estimation was carried out according to the complex of such qualities as productivity, early ripening, marketability, taste qualities and durability of fruits. The following clones are defin...

  3. Field resistance of selected potato clones to Early blight

    OpenAIRE

    Novisel Veitía; Lourdes R. García; Idalmis Bermúdez-Caraballoso; Mayra Acosta- Suárez; Michel Leiva-Mora; Damaris Torres; Carlos Romero; Pedro Orellana

    2014-01-01

    Six potato clones, selected in vitro for their resistance to Alternaria solani Sor. culture filtrates, were evaluated for their field response to early blight infection. Field screening were performance under artificial inoculation and natural conditions. Early blight response was evaluated based on lesion size, disease severity, and area under disease progress curve (AUDPC). One clone displayed reduced lesion area (0.35 cm2) and AUDPC values compared to cv. `Desirée' (susceptible control) (0...

  4. Cloning

    Science.gov (United States)

    Cloning describes the processes used to create an exact genetic replica of another cell, tissue or organism. ... named Dolly. There are three different types of cloning: Gene cloning, which creates copies of genes or ...

  5. The clone selection studies on Siyah Gemre grape variety

    Directory of Open Access Journals (Sweden)

    Dilli Yıldız

    2015-01-01

    Full Text Available V. vinifera L.cv. “Siyah Gemre” is an important table grape variety of Mediterranean Region in Turkey. It is late sea- son, medium bunch density, round berry, red-black colored and seeded. The study was carried out to make clone selection for increasing the yield and quality in “Siyah Gemre” grape variety The project was completed in two stages. First one was selection nominees of mother clone vine and second was establishing of clonal collection vineyard. The first stage studies were carried out at grower vineyards of İsparta, Turkey surroundings where “Siyah Gemre” is grown wide spread, between 2001 and 2003. Clonal nominees were selected by using counting the cluster and shoot at the end of the project. After that, the clonal collection vineyard was established with spacing 3.0 m × 1.65 m in 2004. Twelve vines of each clonal nominees were grafted onto 110R rootstock. In the study the values of yield, number of cluster, weight of cluster, 100 berry weight, index of maturity, sensory analysis, weight of pruning and bud productivity were evaluated between 2007–2012. At the end of this study, according to the values of total point, five clone nominees were selected and among their 3, 19, 24 numbered clones were chosen in terms of total sensory analysis score, yield and stability, cluster and berry properties respectively.

  6. Field resistance of selected potato clones to Early blight

    Directory of Open Access Journals (Sweden)

    Novisel Veitía

    2014-10-01

    Full Text Available Six potato clones, selected in vitro for their resistance to Alternaria solani Sor. culture filtrates, were evaluated for their field response to early blight infection. Field screening were performance under artificial inoculation and natural conditions. Early blight response was evaluated based on lesion size, disease severity, and area under disease progress curve (AUDPC. One clone displayed reduced lesion area (0.35 cm2 and AUDPC values compared to cv. `Desirée' (susceptible control (0.58 cm2 but those values were higher than that of the resistant control Solanum chacoense `PI 275136' (0.14 cm2. On the other hand, no differences in lesion number were detected between the susceptible control and the selected clones. This variable showed values between 21.82 and 23.87 lesions in two leaves per plant. Although early blight resistance in potato is generally associated to late maturity, the mutant IBP-27 displayed increased resistance to early blight with medium-late maturity. The six clones presented medium-early to medium-late maturity, similar to parental cv. `Desirée' (vegetative cycle ranging from 90 to 110 days. One clone was found to have higher levels of resistant to early blight than cv. `Desirée' but lower than the levels of the resistant control S. chacoense. The resistance in this clone was characterized by the reduction in lesion area, disease severity, and AUDPC values in both artificial inoculation and natural infection screening.   Keywords: Alternaria solani,components of resistance, Solanum tuberosum

  7. A 'select and swap' strategy for the isolation of clones with tightly regulated transgenes.

    Science.gov (United States)

    Sullivan, M J; Carpenter, A J; Porter, A C

    2001-03-01

    Increasing numbers of biological problems are being addressed by genetic approaches that rely on inducible expression of transgenes. It is desirable that expression of such a transgene is tightly regulated, from close to zero expression in the 'off' state, to appreciable (at least physiological) expression in the 'on' state. Although there are many examples where tight regulation has been achieved, certain factors, including chromosomal position effects due to random integration of the transgene, often cause suboptimal inducibility and make the isolation of tightly regulated clones difficult and/or laborious. Here we describe a 'select and swap' strategy for the isolation, from a population of stable transfectants, of clones with tightly regulated transgenes. In this approach, a positively and negatively selectable, inducible marker gene is used to select for clones with optimal transgene regulation. After isolation of such clones, the marker gene is swapped with a linked gene of interest by the use of site-specific recombination. To test this strategy we introduced into human cells a plasmid with a tetracycline-inducible bacterial gpt gene linked to a promoterless luciferase gene, isolated clones with tight gpt expression and used the Cre/loxP site-specific recombination system to swap the gpt gene with the luciferase gene. We discuss ways for refining and developing the system and widening its applicability.

  8. Productivity and fruit quality of Jonagold clones of home selection

    Directory of Open Access Journals (Sweden)

    К. П. Тарнавська

    2014-03-01

    Full Text Available New results of the clonal selection of apple tree (Malus domestica Borkh conducted at Podillya Research Station of Horticultural Institute NAAS by method of state variety testing have been presented. By the results of the 6-year studying (2007 - 2012 of 20 new Jonagold clones of domestic selection their estimation was carried out according to the complex of such qualities as productivity, early ripening, marketability, taste qualities and durability of fruits. The following clones are defined to be the best: DP-16, DP-17, DP-18, DP-20. They start fruiting in the age of 2 or 3 years, productivity of the 5- or 6-year-old trees reaches 8,3–25,5 tons per hectare, quantity of the fruits of the highest and first grade is about 57–76% (in 2010–2012. Fruits of the mentioned clones are bigger than medium size (DP-16, big (DP-17, DP-18 and very big (DP-20; they have average similarity, excellent and very harmonious sour-sweet taste (8,3–8,7 points. Fruits of the best clones kept their quality for 202 – 220 days.

  9. Selection of new clones of linalool chemotype from genetic recombination in Lippia alba

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    Elcio Rodrigo Rufino

    2012-01-01

    Full Text Available The aromatic and medicinal species Lippia alba is vigorous and rugged native to the South America (Atlantic Rainforest. Because it is an allogamous and self-incompatible species, natural populations have high morphological and chemical variability. This work had as objective to conduct a preliminary screening to identify new promising clones from a novel (recombinant base population of Lippia alba with regard to its agronomic and phytochemical traits, using the linalool oil or chemotype as model. The two superior linalool clones, obtained by collection, were used as controls. Traits evaluated included: dry mass of leaves (DML, oil yield percentage (EOY%, oil production per plant (OP, and linalool percentage (LN%. Forty linalool chemotype clones were evaluated in three experiments, in a random block design with four replicates and four cuttings (clones per plot. Besides means comparisons, multivariate analysis was used in order to aid in the preliminary selection of clones. There were positive correlations from moderate to strong for DML vs. EOY%, OP vs. EOY% and DML vs. OP. Linalool clones superior or similar to both controls were identified for the DML, EOY%, OP, and LN% traits (univariate analyses, aimed at further validating experimentation. Five distinct groups were defined in the cluster analysis (UPGMA, each containing subgroups as well.

  10. Blocked Randomization with Randomly Selected Block Sizes

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    Jimmy Efird

    2010-12-01

    Full Text Available When planning a randomized clinical trial, careful consideration must be given to how participants are selected for various arms of a study. Selection and accidental bias may occur when participants are not assigned to study groups with equal probability. A simple random allocation scheme is a process by which each participant has equal likelihood of being assigned to treatment versus referent groups. However, by chance an unequal number of individuals may be assigned to each arm of the study and thus decrease the power to detect statistically significant differences between groups. Block randomization is a commonly used technique in clinical trial design to reduce bias and achieve balance in the allocation of participants to treatment arms, especially when the sample size is small. This method increases the probability that each arm will contain an equal number of individuals by sequencing participant assignments by block. Yet still, the allocation process may be predictable, for example, when the investigator is not blind and the block size is fixed. This paper provides an overview of blocked randomization and illustrates how to avoid selection bias by using random block sizes.

  11. Blocked randomization with randomly selected block sizes.

    Science.gov (United States)

    Efird, Jimmy

    2011-01-01

    When planning a randomized clinical trial, careful consideration must be given to how participants are selected for various arms of a study. Selection and accidental bias may occur when participants are not assigned to study groups with equal probability. A simple random allocation scheme is a process by which each participant has equal likelihood of being assigned to treatment versus referent groups. However, by chance an unequal number of individuals may be assigned to each arm of the study and thus decrease the power to detect statistically significant differences between groups. Block randomization is a commonly used technique in clinical trial design to reduce bias and achieve balance in the allocation of participants to treatment arms, especially when the sample size is small. This method increases the probability that each arm will contain an equal number of individuals by sequencing participant assignments by block. Yet still, the allocation process may be predictable, for example, when the investigator is not blind and the block size is fixed. This paper provides an overview of blocked randomization and illustrates how to avoid selection bias by using random block sizes.

  12. Selection of promising sweet potato clones using projective mapping.

    Science.gov (United States)

    Vicente, Esteban; Ares, Gastón; Rodríguez, Gustavo; Varela, Pablo; Bologna, Franco; Lado, Joanna

    2017-01-01

    Increasing demand for sweet potato in regions with temperate climates has triggered interest in the development of new cultivars. Breeding of this crop should consider sensory characteristics in order to meet consumers' expectations. This requires the application of simple and cost-effective methodologies that allow quality evaluation from a sensory perspective. With the objective of identifying the key sensory characteristics of different sweet potato genotypes, two commercial cultivars and seven clones were evaluated during three consecutive years using projective mapping by an untrained consumer panel. This methodology allowed the discrimination of the genotypes, identifying similarities and differences among groups based on sensory terms selected by the assessors. Genotypes were differentiated in terms of texture and flavor characteristics (firmness, moisture, smoothness, creaminess, flavor intensity, sweetness and bitterness). Materials for future crossings were identified. The evaluation of the sensory characteristics of sweet potato clones and cultivars using projective mapping is a quick, cost-effective and reliable tool for the selection of new advanced sweet potato clones with superior sensory characteristics compared to the reference cultivars INIA Arapey and Cuarí. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  13. Selective isolation of mammalian genes by TAR cloning.

    Science.gov (United States)

    Kouprina, Natalay; Larionov, Vladimir

    2006-05-01

    Transformation-associated recombination (TAR) cloning provides a unique tool for selective isolation of desired chromosome segments and full-size genes from complex genomes in the form of a circular yeast artificial chromosome (YAC) up to 250 kb in size. The method has a broad application for structural and functional genomics, long-range haplotyping, mutational analysis of gene families, characterization of chromosomal rearrangements, and evolutionary studies. This unit describes a procedure for gene isolation by TAR as well as a method for conversion of YAC-TAR isolates into a bacterial artificial chromosome (BAC) form.

  14. Analisis SIM Card Cloning Terhadap Algoritma Random Number Generator

    OpenAIRE

    Anwar, Nuril; Riadi, Imam; Luthfi, Ahmad

    2016-01-01

    . Crime in telecommunication sector has increased prevalently, especially with the use of mobile phone which is detrimental both for customers and the providers. In the GSM security system, several weaknesses are found concerning data security outside the network. SIM card clone is part of the security problem in which the data can be transferred to SIM card cloning media. SIM card cloning research can be presented in the form of SRES analysis algorithms A3 and A8 RAND to get Ki Auc for furth...

  15. Early selection of Eucalyptus clones in retrospective nursery test ...

    African Journals Online (AJOL)

    Within the framework of the eucalyptus breeding programme in the Congo, two retrospective tests were conducted using mature clones in the field and young cuttings under nursery conditions with two hybrids: 13 clones of Eucalyptus tereticornis* Eucalyptus grandis for the test TC 82-1B and 17 clones of Eucalyptus ...

  16. Randomized selection on the GPU

    Energy Technology Data Exchange (ETDEWEB)

    Monroe, Laura Marie [Los Alamos National Laboratory; Wendelberger, Joanne R [Los Alamos National Laboratory; Michalak, Sarah E [Los Alamos National Laboratory

    2011-01-13

    We implement here a fast and memory-sparing probabilistic top N selection algorithm on the GPU. To our knowledge, this is the first direct selection in the literature for the GPU. The algorithm proceeds via a probabilistic-guess-and-chcck process searching for the Nth element. It always gives a correct result and always terminates. The use of randomization reduces the amount of data that needs heavy processing, and so reduces the average time required for the algorithm. Probabilistic Las Vegas algorithms of this kind are a form of stochastic optimization and can be well suited to more general parallel processors with limited amounts of fast memory.

  17. Cloning

    Science.gov (United States)

    ... such as the liver, brain and heart. Other consequences include premature aging and problems with the immune system. Another potential ... cell dies. This is part of the natural aging process that seems to happen in all cell types. As a consequence, clones created from a cell taken from an ...

  18. Cost-effective HRMA pre-sequence typing of clone libraries; application to phage display selection

    National Research Council Canada - National Science Library

    Pepers, Barry A; Schut, Menno H; Vossen, Rolf Ham; van Ommen, Gert-Jan B; den Dunnen, Johan T; van Roon-Mom, Willeke Mc

    2009-01-01

    Methodologies like phage display selection, in vitro mutagenesis and the determination of allelic expression differences include steps where large numbers of clones need to be compared and characterised...

  19. IgE production after antigen-specific and cognate activation of HLA-DPw4-restricted T-cell clones, by 78% of randomly selected B-cell donors

    NARCIS (Netherlands)

    Baselmans, PJ; Pollabauer, EM; van Reijsen, FC; Heystek, HC; Hren, A; Stumptner, P; Tilanus, MGJ; Vooijs, WC; Mudde, GC

    The frequency of expression of the MHC class II antigen, HLA-DPw4, in the caucasoid population is approximately 78%, and is unmatched by phenotypic frequencies of other HLA class II molecules. Here we describe three human Der-P1-specific T-cell clones (TCC), restricted by the HLA-DPw4-variant

  20. Seleção de clones de batata-doce pelo procedimento REML/BLUP = Sweet potato clone selection by REML/BLUP procedure

    Directory of Open Access Journals (Sweden)

    Vanderley Borges

    2010-10-01

    Full Text Available Objetivou-se classificar e selecionar clones de batata-doce, utilizando-se a metodologia REML/BLUP. O experimento foi conduzido no município de Rio Largo, Estado de Alagoas, situado a 127 m de altitude, com latitude 9º27’S e longitude 35º27’W. Foram avaliados cinco clones (CL-2, CL-3, CL-4, CL-6 e CL-8 em delineamento experimental de blocos completos casualizados com oito repetições. As variáveis analisadas foram Número de Raízes Comerciais (NRC; Número de Raízes Não-Comerciais (NRNC; Número Total de Raízes (NTR; Peso da Parte Aérea (PPA; Peso Médio de Raízes Não-Comerciais (PMRNC; Comprimento de Raízes Comerciais (CRC; Peso Médio de Raízes Comerciais (PMRC; Diâmetro de Raízes Comerciais (DRC. A análisede deviance indicou que os clones diferenciam-se estatisticamente para NRNC, NTR, PMRNC, CRC e DRC. O CL-06 ocupou a primeira colocação para NRNC, NTR, PMRNC, PMRC, DRC; o CL-03, para PPA e CRC e o CL-02, para NRC. Pela classificação das médias genotípicas, o melhor clone foi o CL-06.The objective of this work was to classify and select sweet potato clones, using the REML/BLUP methodology. The study was carried out in Rio Largo, Alagoas State, located 127 m above sea level, 9º27’S and 35º27’W. Five clones were evaluated (CL-2, CL-3, CL-4, CL-6 and CL-8 in a randomized complete blocks design with eight replications. The analyzed variables were number of commercial roots (NCR, number of non-commercial roots (NNCR, total number of roots (TNR, aerial part weight (APW, average weight of noncommercial roots (AWNCR, commercial root length (CRL, average weight of commercial roots (AWCR, and diameter of commercial roots (DCR. The analysis of deviance showed that the clones differ statistically for NNCR, TNR, AWNCR, AWCR, CRL and DCR. CL-06 had the best NCRN, NNCR, TNR, AWNCR, AWCR, DCR; CL-03 for APW and CRL, and CL-02 for NCR. By the classification of genotypic averages, the best clone was CL-06.

  1. Seleção Preliminar de clones de aceroleira no estado do Ceará Preliminary selection of aceroleira clones in Ceará state

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    João Rodrigues de Paiva

    2003-10-01

    Full Text Available O aumento da lucratividade dos pomares de aceroleira por meio da utilização de cultivares com maior produtividade e conteúdo de vitamina C, atualmente, constitui-se no principal desafio do melhoramento genético. Com o objetivo de avaliar o desempenho de clones de aceroleira (Malpighia emarginata DC., sob cultivo em área de produtor, foi instalado em agosto de 1999 um experimento no delineamento de blocos ao acaso com 45 clones (tratamentos, três repetições e cinco plantas por parcela. A altura de planta e o diâmetro da copa foram medidos no primeiro e segundo ano de idade. A produção de frutos foi avaliada nos meses de agosto a dezembro no ano de 2000 e de janeiro a dezembro em 2001. A avaliação físico-química constou da determinação do conteúdo de vitamina C, sólidos solúveis totais (oBrix e peso médio do fruto (PMF. Entre as principais conclusões, destacam-se: há uma tendência de a produção dos clones se estender por todos os meses do ano, exceção feita aos meses de maio e julho, que não foram favoráveis a cerca de 53% dos clones; a seleção preliminar, considerando o desempenho satisfatório para as características morfológicas da planta e dos frutos, destaca os seguintes clones: I 13/2, I 51/1, II 26/4, III 56/4 e III 78/1; em 11% dos clones, os frutos mostram alto conteúdo de vitamina C, acima de 1.600 mg/100 g de polpa.The main objective to acerola breeding nowadays is to increase profitability of the orchards through the utilisation of high yield and high Vitamin C content cultivars. In order to evaluate the performance of acerola clones (Malpighia emarginata DC. planted in private orchard, an experiment was set up in August 1999 arranged as randomized block design with 45 clones, 3 replicates and 5 plants per plot. Plant height and canopy diameter were measured at plant ages of one and two years. Fruit yield was evaluated from August till December in the year 2000, and from January till December in 2001

  2. Genetic divergence and parent selection of sugarcane clones

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    Valéria Rosa Lopes

    2008-01-01

    Full Text Available The objective of this study was to estimate the genetic divergence of 140 sugarcane clones of the series RB97,in phase T3 of the Sugarcane Genetic Improvement Program of the Universidade Federal do Paraná, at three locations bymultivariate analysis, using the linear mixed model and grouping analysis by the Tocher procedure, based on Mahalanobis´generalized distance. The evaluated traits were number of stalks per plot, mass of ten stalks, Brix and Brix per plot in kg. Thenumber of groups varied according to the evaluated environment. Based on the results, combinations of one of the mostdivergent clones RB975008, RB975112, RB975019 RB975153 and RB975067 with any one of the most productive clonesRB975269, RB977533, RB975102, RB975317 and RB975038 are recommended.

  3. Altering the selection capabilities of common cloning vectors via restriction enzyme mediated gene disruption

    Science.gov (United States)

    2013-01-01

    Background The cloning of gene sequences forms the basis for many molecular biological studies. One important step in the cloning process is the isolation of bacterial transformants carrying vector DNA. This involves a vector-encoded selectable marker gene, which in most cases, confers resistance to an antibiotic. However, there are a number of circumstances in which a different selectable marker is required or may be preferable. Such situations can include restrictions to host strain choice, two phase cloning experiments and mutagenesis experiments, issues that result in additional unnecessary cloning steps, in which the DNA needs to be subcloned into a vector with a suitable selectable marker. Results We have used restriction enzyme mediated gene disruption to modify the selectable marker gene of a given vector by cloning a different selectable marker gene into the original marker present in that vector. Cloning a new selectable marker into a pre-existing marker was found to change the selection phenotype conferred by that vector, which we were able to demonstrate using multiple commonly used vectors and multiple resistance markers. This methodology was also successfully applied not only to cloning vectors, but also to expression vectors while keeping the expression characteristics of the vector unaltered. Conclusions Changing the selectable marker of a given vector has a number of advantages and applications. This rapid and efficient method could be used for co-expression of recombinant proteins, optimisation of two phase cloning procedures, as well as multiple genetic manipulations within the same host strain without the need to remove a pre-existing selectable marker in a previously genetically modified strain. PMID:23497512

  4. Random selection of Borel sets

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    Bernd Günther

    2010-10-01

    Full Text Available A theory of random Borel sets is presented, based on dyadic resolutions of compact metric spaces. The conditional expectation of the intersection of two independent random Borel sets is investigated. An example based on an embedding of Sierpinski’s universal curve into the space of Borel sets is given.

  5. Cloning and selection of reference genes for gene expression ...

    African Journals Online (AJOL)

    Full length mRNA sequences of Ac-β-actin and Ac-gapdh, and partial mRNA sequences of Ac-18SrRNA and Ac-ubiquitin were cloned from pineapple in this study. The four genes were tested as housekeeping genes in three experimental sets. GeNorm and NormFinder analysis revealed that β-actin was the most ...

  6. GENETIC DIVERGENCE AND MORPHO - AGRONOMIC PERFORMANCE OF JATROPHA CURCAS L. CLONES FOR SELECTION OF CLONAL VARIETIES

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    ADRIANA QUEIROZ DE ALMEIDA

    2016-01-01

    Full Text Available The knowledge about genetic diversity of jatropha crop is important for genetic conservation resources and breeding of this species. The aim of this study was to evaluate the genetic diversity and performance of jatropha clones through morphological characterization to selection of clonal varieties for biofuels production. The clones were obtained through shoot cuttings from previous selection in a population of half - sibs progenies. The morphoagronomic analyses of clones was carried out at 180 days after transplantation and were evaluated plant height, stem diameter, number of primary branches and number of secondary branches, number of bunches and number of fruits per plant. Evaluating clones performance, significant results were found for the number of secondary branches. About analysis of genetic diversity, the measures of dissimilarity genetic varied from 0.62 to 13.11, this way, the UFRBPR14 and UFRBPR15 clones were more divergent. The Tocher method was efficient to verify formation of four groups. The characteristics that most contributed to the divergence among clones were branches number, height and number of bunches, and, stem diameter had lower contribution. The jatropha clones differed only in the secondary branches number and multivariate analysis showed divergence among the jatropha clones with formation of four groups. Also, branches number, plant height and number of bunches were characteristic that contributed to genetic divergence.

  7. Development of a dual-expression vector facilitated with selection-free PCR recombination cloning strategy.

    Science.gov (United States)

    Cao, Liting; Zhou, Yancheng; Huang, Lin; Dong, Shiqi; Ma, Yue

    2017-12-01

    The conventional procedure for the construction of recombinant expression vector of a target gene includes PCR cloning and restriction enzyme mediated subcloning, which is time-consuming and sometimes troublesome because of the inefficiency of ligation. A variety of ligase-independent PCR cloning strategies have been developed, but they either involve complicated PCR procedures or need other DNA modifying enzymes. In this study, we report the design, and construction of an omnipotent expression vector pOmni, with which a target gene can be easily cloned through innovative selection-free PCR recombination cloning strategy with only one pair of primer and two times of PCR in one work day, without using any restriction enzymes, ligase and other DNA modifying enzymes. Furthermore, the target gene cloned in pOmni is ready to be high-efficiently expressed in either Escherichia coli cells or eukaryotic cells because of the elaborate design of compatible T7 promoter and CMV promoter expression elements in the vector. The cloning capability and reliability of selection-free PCR recombination cloning with pOmni were validated through cloning of 6 DNA fragments with length from 315 to 4557 bp, and the dual-expression function of the vector was verified through the cloning and expression of EGFP in E. coli BL21 and HeLa cells. pOmni developed in our study provides a powerful tool for gene cloning and expression, and is of special value for researches in which both prokaryotic and eukaryotic expression of a target gene are necessary.

  8. The assessment of physiology parameters of willow plants as a criterion for selection of prospective clones

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    Rodzkin Aleh I.

    2015-01-01

    Full Text Available Bioenergy production based on short rotation coppice willow plantations (SRC is an effective direction both for economic and environment profit. The yield of willow wood can amount to 10-15 tons per hectare of dry biomass per year and the cost of thus obtained energy is lower in comparison with other energy crops. In order to achieve high yield and profitability, the use of special willow clones is necessary. Species most often used in selection for biomass production are shrub type willows: Salix viminalis, Salix dasyclados and Salix schwerini, while the clones tested in this paper were also of tree species Salix alba. The productivity and some physiology characteristics of Serbian selection clones of Salix alba (Bačka, Volmianka and Drina and Swedish selection clone Jorr (Salix viminalis were investigated in greenhouses and in field conditions. As the result of testing three clones of Salix alba - Bačka, Volmianka and Drina, having special preferences and adaptability to different environmental conditions, these were included in State register of Republic of Belarus in 2013. In our experiment it was also satisfactory that specific properties of willows (intensity of transpiration and photosynthesis, water use efficiency and others, were conserved both in greenhouses and in field conditions. This factor gives opportunity to select prospective clones of willows at an early stage of ontogenesis for further testing.

  9. A general cloning system to selectively isolate any eukaryotic or prokaryotic genomic region in yeast

    Science.gov (United States)

    Noskov, Vladimir N; Kouprina, Natalay; Leem, Sun-Hee; Ouspenski, Ilia; Barrett, J Carl; Larionov, Vladimir

    2003-01-01

    Background Transformation-associated recombination (TAR) cloning in yeast is a unique method for selective isolation of large chromosomal fragments or entire genes from complex genomes. The technique involves homologous recombination, during yeast spheroplast transformation, between genomic DNA and a TAR vector that has short (~ 60 bp) 5' and 3' gene targeting sequences (hooks). Result TAR cloning requires that the cloned DNA fragment carry at least one autonomously replicating sequence (ARS) that can function as the origin of replication in yeast, which prevents wide application of the method. In this paper, we describe a novel TAR cloning system that allows isolation of genomic regions lacking yeast ARS-like sequences. ARS is inserted into the TAR vector along with URA3 as a counter-selectable marker. The hooks are placed between the TATA box and the transcription initiation site of URA3. Insertion of any sequence between hooks results in inactivation of URA3 expression. That inactivation confers resistance to 5-fluoroorotic acid, allowing selection of TAR cloning events against background vector recircularization events. Conclusion The new system greatly expands the area of application of TAR cloning by allowing isolation of any chromosomal region from eukaryotic and prokaryotic genomes regardless of the presence of autonomously replicating sequences. PMID:12720573

  10. A general cloning system to selectively isolate any eukaryotic or prokaryotic genomic region in yeast

    Directory of Open Access Journals (Sweden)

    Barrett J Carl

    2003-04-01

    Full Text Available Abstract Background Transformation-associated recombination (TAR cloning in yeast is a unique method for selective isolation of large chromosomal fragments or entire genes from complex genomes. The technique involves homologous recombination, during yeast spheroplast transformation, between genomic DNA and a TAR vector that has short (~ 60 bp 5' and 3' gene targeting sequences (hooks. Result TAR cloning requires that the cloned DNA fragment carry at least one autonomously replicating sequence (ARS that can function as the origin of replication in yeast, which prevents wide application of the method. In this paper, we describe a novel TAR cloning system that allows isolation of genomic regions lacking yeast ARS-like sequences. ARS is inserted into the TAR vector along with URA3 as a counter-selectable marker. The hooks are placed between the TATA box and the transcription initiation site of URA3. Insertion of any sequence between hooks results in inactivation of URA3 expression. That inactivation confers resistance to 5-fluoroorotic acid, allowing selection of TAR cloning events against background vector recircularization events. Conclusion The new system greatly expands the area of application of TAR cloning by allowing isolation of any chromosomal region from eukaryotic and prokaryotic genomes regardless of the presence of autonomously replicating sequences.

  11. A visual method for direct selection of high-producing Pichia pastoris clones

    Directory of Open Access Journals (Sweden)

    Liu Sheng

    2011-03-01

    Full Text Available Abstract Background The methylotrophic yeast, Pichia pastoris, offers the possibility to generate a high amount of recombinant proteins in a fast and easy way to use expression system. Being a single-celled microorganism, P. pastoris is easy to manipulate and grows rapidly on inexpensive media at high cell densities. A simple and direct method for the selection of high-producing clones can dramatically enhance the whole production process along with significant decrease in production costs. Results A visual method for rapid selection of high-producing clones based on mannanase reporter system was developed. The study explained that it was possible to use mannanase activity as a measure of the expression level of the protein of interest. High-producing target protein clones were directly selected based on the size of hydrolysis holes in the selected plate. As an example, the target gene (9elp-hal18 was expressed and purified in Pichia pastoris using this technology. Conclusions A novel methodology is proposed for obtaining the high-producing clones of proteins of interest, based on the mannanase reporter system. This system may be adapted to other microorganisms, such as Saccharomyces cerevisiae for the selection of clones.

  12. Use of randomly cloned DNA fragments for identification of Bacteroides thetaiotaomicron.

    OpenAIRE

    Salyers, A A; Lynn, S P; Gardner, J F

    1983-01-01

    Randomly cloned fragments of DNA from Bacteroides thetaiotaomicron were used as hybridization probes for differentiation of B. thetaiotaomicron from closely related Bacteroides species. HindIII digestion fragments of DNA from B. thetaiotaomicron (type strain) were inserted into plasmid pBR322 and labeled with [alpha-32P]dCTP by nick translation. These labeled plasmids were screened for hybridization to HindIII digests of chromosomal DNA from type strains of the following human colonic Bactero...

  13. Bifunctional lacZ alpha-ccdB genes for selective cloning of PCR products.

    Science.gov (United States)

    Gabant, P; Drèze, P L; Van Reeth, T; Szpirer, J; Szpirer, C

    1997-11-01

    The use of PCR-amplified DNA-fragments is a classical approach to generate recombinant DNA. To facilitate the cloning of PCR products, we have constructed two new pKIL vectors that allow selection of recombinants. The multiple cloning sites (MCS) of these plasmids contain two adjacent Aspel sites and a unique HindII site. Cleavage of these vectors with Aspel produce linearized molecules with a single thymidine nucleotide at the 3' ends allowing TA cloning of Taq-amplified fragments. On the other hand, cleavage with HindII can be used for the cloning of blunt-ended PCR products generated by other DNA polymerases. The LacZ alpha-CcdB fusion protein produced by these plasmids has retained both the CcdB killer activity and the ability to alpha-complement the truncated LacZ delta M15. This bifunctionality allowed us to show that small PCR products (< 1000 bp) that do not disrupt lacZ alpha efficiently do inactivate CcdB, which demonstrates that the CcdB-based selection is well adapted for cloning of PCR products, especially for small size fragments.

  14. Species selection and random drift in macroevolution.

    Science.gov (United States)

    Chevin, Luis-Miguel

    2016-03-01

    Species selection resulting from trait-dependent speciation and extinction is increasingly recognized as an important mechanism of phenotypic macroevolution. However, the recent bloom in statistical methods quantifying this process faces a scarcity of dynamical theory for their interpretation, notably regarding the relative contributions of deterministic versus stochastic evolutionary forces. I use simple diffusion approximations of birth-death processes to investigate how the expected and random components of macroevolutionary change depend on phenotype-dependent speciation and extinction rates, as can be estimated empirically. I show that the species selection coefficient for a binary trait, and selection differential for a quantitative trait, depend not only on differences in net diversification rates (speciation minus extinction), but also on differences in species turnover rates (speciation plus extinction), especially in small clades. The randomness in speciation and extinction events also produces a species-level equivalent to random genetic drift, which is stronger for higher turnover rates. I then show how microevolutionary processes including mutation, organismic selection, and random genetic drift cause state transitions at the species level, allowing comparison of evolutionary forces across levels. A key parameter that would be needed to apply this theory is the distribution and rate of origination of new optimum phenotypes along a phylogeny. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  15. Fundamental resource-allocating model in colleges and universities based on Immune Clone Algorithms

    Science.gov (United States)

    Ye, Mengdie

    2017-05-01

    In this thesis we will seek the combination of antibodies and antigens converted from the optimal course arrangement and make an analogy with Immune Clone Algorithms. According to the character of the Algorithms, we apply clone, clone gene and clone selection to arrange courses. Clone operator can combine evolutionary search and random search, global search and local search. By cloning and clone mutating candidate solutions, we can find the global optimal solution quickly.

  16. Improving randomness characterization through Bayesian model selection.

    Science.gov (United States)

    Díaz Hernández Rojas, Rafael; Solís, Aldo; Angulo Martínez, Alí M; U'Ren, Alfred B; Hirsch, Jorge G; Marsili, Matteo; Pérez Castillo, Isaac

    2017-06-08

    Random number generation plays an essential role in technology with important applications in areas ranging from cryptography to Monte Carlo methods, and other probabilistic algorithms. All such applications require high-quality sources of random numbers, yet effective methods for assessing whether a source produce truly random sequences are still missing. Current methods either do not rely on a formal description of randomness (NIST test suite) on the one hand, or are inapplicable in principle (the characterization derived from the Algorithmic Theory of Information), on the other, for they require testing all the possible computer programs that could produce the sequence to be analysed. Here we present a rigorous method that overcomes these problems based on Bayesian model selection. We derive analytic expressions for a model's likelihood which is then used to compute its posterior distribution. Our method proves to be more rigorous than NIST's suite and Borel-Normality criterion and its implementation is straightforward. We applied our method to an experimental device based on the process of spontaneous parametric downconversion to confirm it behaves as a genuine quantum random number generator. As our approach relies on Bayesian inference our scheme transcends individual sequence analysis, leading to a characterization of the source itself.

  17. Cloning and Expression of Randomly Mutated Bacillus subtilisα-Amylase Genes in HB101

    Directory of Open Access Journals (Sweden)

    Mohammed Rabbani

    2011-01-01

    Full Text Available The aim of this study was to isolate and express the randomly mutated α-amylase gene from B. subtilis strain 168. BS168F: 5′-gtgtcaagaatgtttgc-3′ and BS168R: 3′-gttttgttaaaagatga-5′ primers were used to amplify the amylase gene using the following cycle in error-prone PCR method: 94°C for 30 s, 40°C for 2 min, and 72°C for 2 min in 30 cycles that were followed with 72°C for 2 min as a post cycle. E. coli XL1 blue was used as host for plasmid construction. Amylase enzyme activity assay was performed using continuous spectrophotometric procedures. Results of sequencing showed that sequence was cloned from the first ATG and with the correct open reading frame. Having confirmed the integrity of the insert, the gene was ligated into expression vector pET-15b and then further confirmed using digestion analysis. Amylase activity showed 3 clones with higher enzymatic activity compared with the wild type. Error-prone PCR method produced a mutated gene that provides amylase activity much higher than that of wild type. Sequencing the mutated genes should shed light on the important region of the genes that could be manipulated in future studies.

  18. MEGAWHOP cloning: a method of creating random mutagenesis libraries via megaprimer PCR of whole plasmids.

    Science.gov (United States)

    Miyazaki, Kentaro

    2011-01-01

    MEGAWHOP allows for the cloning of DNA fragments into a vector and is used for conventional restriction digestion/ligation-based procedures. In MEGAWHOP, the DNA fragment to be cloned is used as a set of complementary primers that replace a homologous region in a template vector through whole-plasmid PCR. After synthesis of a nicked circular plasmid, the mixture is treated with DpnI, a dam-methylated DNA-specific restriction enzyme, to digest the template plasmid. The DpnI-treated mixture is then introduced into competent Escherichia coli cells to yield plasmids carrying replaced insert fragments. Plasmids produced by the MEGAWHOP method are virtually free of contamination by species without any inserts or with multiple inserts, and also the parent. Because the fragment is usually long enough to not interfere with hybridization to the template, various types of fragments can be used with mutations at any site (either known or unknown, random, or specific). By using fragments having homologous sequences at the ends (e.g., adaptor sequence), MEGAWHOP can also be used to recombine nonhomologous sequences mediated by the adaptors, allowing rapid creation of novel constructs and chimeric genes. Copyright © 2011 Elsevier Inc. All rights reserved.

  19. 32 CFR 1624.1 - Random selection procedures for induction.

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 6 2010-07-01 2010-07-01 false Random selection procedures for induction. 1624... SYSTEM INDUCTIONS § 1624.1 Random selection procedures for induction. (a) The Director of Selective Service shall from time to time establish a random selection sequence for induction by a drawing to be...

  20. Seleção de matrizes e clones de mangabeira para o cultivo in vitro Selection of parents and clones of mangabeira for in vitro cultivation

    Directory of Open Access Journals (Sweden)

    Luana de Lima Machado

    2004-05-01

    Full Text Available Altas taxas de mortalidade em viveiro de mudas de mangabeira (Hancornia speciosa impedem seu uso na reversão do processo de degradação das terras e na manutenção da produtividade e integridade ambiental do Cerrado. O objetivo deste trabalho foi selecionar matrizes e clones, provenientes de propagação sexuada e assexuada, com potencial de propagação in vitro, para produção de mudas de mangabeira. Foram coletados frutos de 11 matrizes e de cada matriz selecionaram-se 24 sementes em bom estado fitossanitário. Após a desinfecção, as sementes foram inoculadas em meio MS, sem reguladores de crescimento, obtendo-se uma média de germinação de 92,4%, e as matrizes não apresentaram diferença significativa entre si. Na fase de multiplicação, em meio MS, com os reguladores de crescimento BAP (6-benzilaminopurina e AIB (ácido indol-3-butírico, ambos na concentração de 1,28 mg L-1, a melhor matriz foi a C1 e o melhor clone foi o C1 15. Em todas as fases foi observada alta variabilidade, em menor porcentagem na matriz e maior porcentagem no clone dentro da matriz. A seleção deve ser realizada principalmente nos clones dentro da matriz.High tax of mortality of mangabeira (Hancornia speciosa seedlings in greenhouse conditions hinders its use on the reversion of the degradation of the natural vegetation, as well as on the preservation of the production and environmental integrity. The objective of this work was to select better mother plants and clones from sexual and assexual propagation, with potential to survive in vitro, for producing mangaba seedlings. Fruits were collected from 11 mother plants and from each plant, 24 seeds without aparent diseases were selected. After superficial desinfection, seeds were inoculated in MS medium without growth regulators and having a germination of 92.4% without significant difference between mother plants. On multiplication phase, with MS medium, with growth regulators BAP (6-benzilaminopurine

  1. Selection of new clones of linalool chemotype from genetic recombination in Lippia alba Seleção de novos clones de quimiotipo linalol em Lippia alba oriundos de recombinação genética

    Directory of Open Access Journals (Sweden)

    Elcio Rodrigo Rufino

    2012-01-01

    Full Text Available The aromatic and medicinal species Lippia alba is vigorous and rugged native to the South America (Atlantic Rainforest. Because it is an allogamous and self-incompatible species, natural populations have high morphological and chemical variability. This work had as objective to conduct a preliminary screening to identify new promising clones from a novel (recombinant base population of Lippia alba with regard to its agronomic and phytochemical traits, using the linalool oil or chemotype as model. The two superior linalool clones, obtained by collection, were used as controls. Traits evaluated included: dry mass of leaves (DML, oil yield percentage (EOY%, oil production per plant (OP, and linalool percentage (LN%. Forty linalool chemotype clones were evaluated in three experiments, in a random block design with four replicates and four cuttings (clones per plot. Besides means comparisons, multivariate analysis was used in order to aid in the preliminary selection of clones. There were positive correlations from moderate to strong for DML vs. EOY%, OP vs. EOY% and DML vs. OP. Linalool clones superior or similar to both controls were identified for the DML, EOY%, OP, and LN% traits (univariate analyses, aimed at further validating experimentation. Five distinct groups were defined in the cluster analysis (UPGMA, each containing subgroups as well.A espécie Lippia alba, aromática e medicinal, é nativa da América do Sul (Mata Atlântica e possui muito vigor e rusticidade. Por ser espécie alógama e autoincompatível, as populações naturais possuem elevada variabilidade morfológica e química. O presente trabalho teve por objetivo realizar uma triagem prévia para identificação de novos clones promissores, oriundos de uma população-base inédita (recombinante de Lippia alba quanto às características agronômicas e fitoquímicas, tendo como modelo o óleo ou quimiotipo linalol. Como controles, utilizaram-se os dois melhores clones linalol

  2. Soil Moisture and Turgidity of Selected Robusta Coffee Clones on Alluvial Plain with Seasonal Rainfall Pattern

    Directory of Open Access Journals (Sweden)

    Rudy Erwiyono

    2005-08-01

    Full Text Available Observation on the seasonal variations of hydrological condition and turgidity of selected Robusta coffee clones has been carried out in Kaliwining Experimental Station, Indonesian Coffee and Cocoa Research Institute in Jember. The aim was to evaluate the effect of hydrological variation on the coffee plants and the degree of soil moisture effect on plant performance. Experimental site overlays on alluvial plain, + 45 m a.s.l., 8o 15’ South with D rainfall type. Observation was conducted by survey method at the experimental plots of organic fertilizer and nitogen treatments on selected Robusta coffee clones derived from rooted cuttings, i.e. BP 436, BP 42, BP 936 and BP 358. Observation was only conducted at the experimental blocks of organic matter trials of 20 l/tree/year at nitrogen (Urea application of locally recommanded rate during the subsequent years of 1999 to 2001. Parameters observed included plant turgidity and soil moisture content of three different depths, i.e. 0—20, 20—40 and 40—60 cm and the weather. Observation was carried out in five replicates designed as blocks of barn manure treatment and N-fertilizer of recommended rate as basal fertilizer. The results showed that meteorological condition and soil moisture of experimental site through the years have seasonal patterns following the seasonal pattern of rainfall. Compared to other meteorological characteristics, relative humidity dominantly determined evaporation and plant turgidity. Plant turgi-dity was not only determined by soil moisture condition, but also atmospheric demand. When relative humidity (RH was relatively high, plant turgidity was relatively stable although soil moisture of surface layers was very low, and the reversal when soil moisture content was high plant turgidity was controlled by atmospheric demand (relative humidity. With a 3—4 dry month period, relative turgidity of the coffee plants was relatively stable above 82%, except when soil

  3. Isolation of cancer stem cells from three human glioblastoma cell lines: characterization of two selected clones.

    Directory of Open Access Journals (Sweden)

    Fortunata Iacopino

    Full Text Available Cancer stem cells (CSC were isolated via a non-adherent neurosphere assay from three glioma cell lines: LI, U87, and U373. Using a clonal assay, two clones (D2 and F11 were selected from spheres derived from LI cells and were characterized for the: expression of stem cell markers (CD133, Nestin, Musashi-1 and Sox2; proliferation; differentiation capability (determined by the expression of GalC, βIII-Tubulin and GFAP; Ca(2+ signaling and tumorigenicity in nude mice. Both D2 and F11 clones expressed higher levels of all stem cell markers with respect to the parental cell line. Clones grew more slowly than LI cells with a two-fold increase in duplication time. Markers of differentiation (βIII-Tubulin and GFAP were expressed at high levels in both LI cells and in neurospheres. The expression of Nestin, Sox2, and βIII-Tubulin was down-regulated in D2 and F11 when cultured in serum-containing medium, whereas Musashi-1 was increased. In this condition, duplication time of D2 and F11 increased without reaching that of LI cells. D2, F11 and parental cells did not express voltage-dependent Ca(2+-channels but they exhibited increased intracellular Ca(2+ levels in response to ATP. These Ca(2+ signals were larger in LI cells and in spheres cultured in serum-containing medium, while they were smaller in serum-free medium. The ATP treatment did not affect cell proliferation. Both D2 and F11 induced the appearance of tumors when ortotopically injected in athymic nude mice at a density 50-fold lower than that of LI cells. All these data indicate that both clones have characteristics of CSC and share the same stemness properties. The findings regarding the expression of differentiation markers and Ca(2+-channels show that both clones are unable to reach the terminal differentiation. Both D2 and F11 might represent a good model to improve the knowledge on CSC in glioblastoma and to identify new therapeutic approaches.

  4. [Cloning goat producing human lactoferrin with genetically modified donor cells selected by single or dual markers].

    Science.gov (United States)

    An, Liyou; Yuan, Yuguo; Yu, Baoli; Yang, Tingjia; Cheng, Yong

    2012-12-01

    We compared the efficiency of cloning goat using human lactoferrin (hLF) with genetically modified donor cells marked by single (Neo(r)) or double (Neo(r)/GFP) markers. Single marker expression vector (pBLC14) or dual markers expression vector (pAPLM) was delivered to goat fetal fibroblasts (GFF), and then the transgenic GFF was used as donor cells to produce transgenic goats. Respectively, 58.8% (20/34) and 86.7% (26/30) resistant cell lines confirmed the transgenic integration by PCR. Moreover, pAPLM cells lines were subcultured with several passages, only 20% (6/30) cell lines was observed fluorescence from each cell during the cell passage. Somatic cell nuclear transfer using the donor cells harbouring pBLC14 or pAPLM construct, resulting in a total of 806 reconstructed embryos, a pregnancy rate at 35 d (53.8%, 39.1%) and 60 d (26.9%, 21.7%), and an offspring birth rate (1.9%, 1.4%) with 5 and 7 newborn cloned goats, respectively. Transgene was confirmed by PCR and southern-blot in all cloned offspring. There were no significant differences at the reconstructed embryo fusion rates, pregnancy rates and the birth rate (P > 0.05) between single and double markers groups. The Neo(r)/GFP double markers could improve the reliability for accurately and efficiently selecting the genetically modified donor cells. No adverse effect was observed on the efficiency of transgenic goat production by SCNT using somatic cells transfected with double (Neo(r)/GFP) markers vector.

  5. Selection of sweet potato clones for the region Alto Vale do Jequitinhonha Seleção de clones de batata-doce para a região do Alto Vale do Jequitinhonha

    Directory of Open Access Journals (Sweden)

    Valter C de Andrade Júnior

    2009-09-01

    Full Text Available An experiment was carried out from December 2005 to July 2006, in the Universidade Federal dos Vales do Jequitinhonha e Mucuri (UFVJM, in Diamantina, Minas Gerais State, Brazil, aiming at selecting sweet potato clones for the Alto Vale do Jequitinhonha. We evaluated nine clones from the UFVJM germplasm bank, using cultivars Brazlândia Branca, Brazlândia Roxa, and Princesa as controls. The experimental design was blocks at random, with four replications. Plants were harvested seven months after transplanting. We assessed the fresh mass yield of vines and roots, as well as root shape and resistance to soil insects. Genotypes did not differ from each other for the fresh mass yield of vines (ranging from 3.81 to 11.76 t ha-1. The total yield of roots ranged from 22.0 to 45.4 t ha-1 and clones BD-06, BD-113-TO, BD-15, BD-38, BD-25, BD-61, and cultivar Princesa had statistically the highest figures. However, only clone BD-06 significantly overcame the control cultivars Brazlândia Branca and Brazlândia Roxa. Clone BD-06 had also the highest commercial yield of roots (38.58 t ha-1, statically similar to most of the other clones and cultivar Princesa (25.87 t ha-1, but superior to cultivars Brazlândia Branca and Brazlândia Roxa. Most of the clones tested, including clone BD-06, produced good shaped roots and were resistant to soil insects. Considering our results, clone BD-06 stood out as a good option for growing sweet potato in the Upper Valley of Jequitinhonha.Com o objetivo de selecionar clones de batata-doce para a região do alto Vale do Jequitinhonha, conduziu-se um experimento de dezembro de 2005 a julho de 2006, no CampusJK da Universidade Federal dos Vales do Jequitinhonha e Mucuri, UFVJM, município de Diamantina-MG. Foram avaliados nove clones de batata-doce pertencentes ao banco de germoplasma da UFVJM, juntamente com as cultivares Brazlândia Branca, Brazlândia Roxa e Princesa, utilizadas como testemunhas. O delineamento experimental

  6. Early selection of elite clones of an ornamental bromeliad in vitro Seleção precoce in vitro de clones elite de uma bromélia ornamental

    Directory of Open Access Journals (Sweden)

    Candida Elisa Manfio

    2010-07-01

    Full Text Available Orthophytum grossiorum is a typical bromeliad from Atlantic forestry threatened of extinction. The objectives of this research were to select O. grossiorum clones with ornamental values easy to propagate in vitro, and establish in vitro propagation protocols for these clones. The project was developed in three steps: germination and in vitro selection of seedlings responsive to BAP (6-benzylaminopurine, selection of clones with ornamental values, and establishment of protocol for in vitro propagation of the selected clones. In the first step only 18.33% of plantlets germinated in vitro were responsive to BAP. These plantlets were selected and replicated in vitro several times, each replicated plantlet constituting a clone. In the second step these clones were established ex vitro and surveyed for ornamental attributes. Five out of 11 clones were selected in this step. These clones presented distinct phenotypic traits and were considered of high ornamental quality. In the third step a protocol for in vitro propagation was developed for each selected clone.Orthophytum grossiorum é uma bromélia ameaçada de extinção típica de Mata Atlântica. Os objetivos deste trabalho foram selecionar clones de O. grossiorum com potencial ornamental e de fácil propagação in vitro e estabelecer protocolo de propagação in vitro para esses clones. O trabalho foi desenvolvido em três etapas: germinação e em seleção in vitro de plântulas responsivas a BAP (6-benzylaminopurine, seleção de clones com valores ornamentais e estabelecimento de protocolo para propagação in vitro dos clones selecionados. Na primeira etapa, foi observado que apenas 18.33% das plântulas germinadas in vitro eram responsivas a BAP. Essas plântulas foram selecionadas e reproduzidas em in vitro, e cada plântula selecionada e reproduzida constituiu um clone. Na segunda etapa, esses clones foram estabelecidos ex vitro e selecionados em relação aos atributos ornamentais

  7. Selective isolation of genomic loci from complex genomes by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae.

    Science.gov (United States)

    Kouprina, Natalay; Larionov, Vladimir

    2008-01-01

    Here, we describe a protocol for the selective isolation of any genomic fragment or gene of interest up to 250 kb in size from complex genomes as a circular yeast artificial chromosome (YAC). The method is based on transformation-associated recombination (TAR) in the yeast Saccharomyces cerevisiae between genomic DNA and a linearized TAR cloning vector containing targeting sequences homologous to a region of interest. Recombination between the vector and homologous sequences in the co-transformed mammalian DNA results in the establishment of a YAC that is able to propagate, segregate and be selected for in yeast. Yield of gene-positive clones varies from 1% to 5%. The entire procedure takes 2 weeks to complete once the TAR vector is constructed and genomic DNA is prepared. The TAR cloning method has a broad application in functional and comparative genomics, long-range haplotyping and characterization of chromosomal rearrangements, including copy number variations.

  8. Novel Zn2+-chelating peptides selected from a fimbria-displayed random peptide library

    DEFF Research Database (Denmark)

    Kjærgaard, Kristian; Schembri, Mark; Klemm, Per

    2001-01-01

    H adhesin. FimH is a component of the fimbrial organelle that can accommodate and display a diverse range of peptide sequences on the E. coli cell surface. In this study we have constructed a random peptide library in FimH. The library, consisting of similar to 40 million individual clones, was screened...... for peptide sequences that conferred on recombinant cells the ability to bind Zn2+. By serial selection, sequences that exhibited various degrees of binding affinity and specificity toward Zn2+ were enriched. None of the isolated sequences showed similarity to known Zn2+-binding proteins, indicating...

  9. In-Place Randomized Slope Selection

    DEFF Research Database (Denmark)

    Blunck, Henrik; Vahrenhold, Jan

    2006-01-01

    Slope selection is a well-known algorithmic tool used in the context of computing robust estimators for fitting a line to a collection P of n points in the plane. We demonstrate that it is possible to perform slope selection in expected O(nlogn) time using only constant extra space in addition to...

  10. Random effect selection in generalised linear models

    DEFF Research Database (Denmark)

    Denwood, Matt; Houe, Hans; Forkman, Björn

    We analysed abattoir recordings of meat inspection codes with possible relevance to onfarm animal welfare in cattle. Random effects logistic regression models were used to describe individual-level data obtained from 461,406 cattle slaughtered in Denmark. Our results demonstrate that the largest ...

  11. Stratified mass selection of promising Spondias mombin clones in a commercial crop

    Directory of Open Access Journals (Sweden)

    José Airton Rodrigues Nunes

    2011-01-01

    Full Text Available This study aimed to estimate genetic parameters and identify promising clones of Spondias mombin in ungraftedcommercial crop by stratified mass selection, based on the average of two harvests, using mixed models. The base populationgrowing on a private farm in Teresina/PI comprised 82 plants, which were evaluated in the growing seasons 2008 and 2009. Totaltitratable acidity (TTA, total soluble solids (Brix, Brix/TTA, fruit weight (FW, seed weight (SW, pulp yield (PuY, and processingyield (PrY were measured. Significant genetic variation among plants was detected for all traits. The coefficients of repeatabilitywere 0.97 (TTA, 0.39 (Brix, 0.86 (Brix/TTA, 0.84 (FW, 0.82 (SW, 0.35 (PuY, and 0.39 (PrY. The chemical were generally notcorrelated with the physical fruit traits. Ranking by predicted phenotypic values associated with PrY and Brix/TTA identified ninepromising plants (PrY>6.9% and Brix/TTA>10.

  12. Biochemical and molecular analysis of Camellia sinensis (L. O. Kuntze tea from the selected P/11/15 clone

    Directory of Open Access Journals (Sweden)

    Samynathan Ramkumar

    2016-06-01

    Full Text Available Green tea is one of the most important beverages consumed across the world and it possesses various phytotherapeutics. Polyphenol oxidase (PPO activity, total polyphenols, catechins, amino acid content and enzymatic antioxidants are considered to be potential parameters in tea characterization. P/11/15 clone (Camellia sinensis (L O. Kuntze was chosen to analyze the biochemical characterization and to analyze the gene expression pattern. The selected P/11/15 clone (C. sinensis (L O. Kuntze possess potent Polyphenol oxidase (49.62 U/mg of protein, sufficient catechin (20.75%, Polyphenol (20.01%, Peroxidase (450.08 μM of O2 formed min−1 g−1 dry weight, Catalase (1.20 μM H2O2 reduced min−1 mg−1 protein and Super Oxide Dismutase (45.11 U/mg proteins. Flavonoid gene expression reveals ANR (1.66% and F3H (1.02% were up regulated in the selected P/11/15 clone. The results obtained suggest that P/11/15 clone showed adequate enzyme levels, thus an increased antioxidant activity.

  13. Capacitance Regression Modelling Analysis on Latex from Selected Rubber Tree Clones

    Science.gov (United States)

    Rosli, A. D.; Hashim, H.; Khairuzzaman, N. A.; Mohd Sampian, A. F.; Baharudin, R.; Abdullah, N. E.; Sulaiman, M. S.; Kamaru'zzaman, M.

    2015-11-01

    This paper investigates the capacitance regression modelling performance of latex for various rubber tree clones, namely clone 2002, 2008, 2014 and 3001. Conventionally, the rubber tree clones identification are based on observation towards tree features such as shape of leaf, trunk, branching habit and pattern of seeds texture. The former method requires expert persons and very time-consuming. Currently, there is no sensing device based on electrical properties that can be employed to measure different clones from latex samples. Hence, with a hypothesis that the dielectric constant of each clone varies, this paper discusses the development of a capacitance sensor via Capacitance Comparison Bridge (known as capacitance sensor) to measure an output voltage of different latex samples. The proposed sensor is initially tested with 30ml of latex sample prior to gradually addition of dilution water. The output voltage and capacitance obtained from the test are recorded and analyzed using Simple Linear Regression (SLR) model. This work outcome infers that latex clone of 2002 has produced the highest and reliable linear regression line with determination coefficient of 91.24%. In addition, the study also found that the capacitive elements in latex samples deteriorate if it is diluted with higher volume of water.

  14. Sequential selection of random vectors under a sum constraint

    OpenAIRE

    Stanke, Mario

    2004-01-01

    We observe a sequence X1,X2,...,Xn of independent and identically distributed coordinatewise nonnegative d-dimensional random vectors. When a vector is observed it can either be selected or rejected but once made this decision is final. In each coordinate the sum of the selected vectors must not exceed a given constant. The problem is to find a selection policy that maximizes the expected number of selected vectors. For a general absolutely continuous distribution of t...

  15. A noncommercial polymerase chain reaction-based method to approach one hundred percent recombinant clone selection efficiency.

    Science.gov (United States)

    Shareef, Mohammed M; Dancea, Horatiu C; Gross, Jessica L; Myers, Tamara T; Griggs, Wendy W; Ahmed, Mansoor M; Sheldon, David G

    2008-11-01

    Molecular cloning is an important procedure in molecular biology, but this is often a rate-limiting step and can be very time-consuming, possibly due to low ligation efficiency. Here, we describe a simple polymerase chain reaction (PCR)-based strategy to approach 100% selection efficiency. The post-ligation mixture containing the recombinant was subjected to insert-specific primer-mediated PCR amplification using a high-fidelity DNA Pfu polymerase generating a plasmid containing staggered nicks. The PCR mixture was then digested with endonuclease DpnI, which digests the methylated and hemimethylated parental DNA template. The nicked vector was transformed into XL1 blue supercompetent cells where the nicks were repaired, thus amplifying and selecting only the newly amplified recombinant clones.

  16. Selective isolation of large chromosomal regions by transformation-associated recombination cloning for structural and functional analysis of mammalian genomes.

    Science.gov (United States)

    Kouprina, Natalay; Noskov, Vladimir N; Larionov, Vladimir

    2006-01-01

    Transformation-associated recombination (TAR) cloning allows selective isolation of full-size genes and genomic loci as circular yeast artificial chromosomes in yeast. The method has a broad application for structural and functional genomics, long-range haplotyping, characterization of chromosomal rearrangements, and evolutionary studies. This chapter describes a basic protocol of gene isolation by TAR, as well as a method of conversion of TAR isolates into bacterial artificial chromosomes.

  17. A simplified counter-selection recombineering protocol for creating fluorescent protein reporter constructs directly from C. elegans fosmid genomic clones

    Directory of Open Access Journals (Sweden)

    Hirani Nisha

    2013-01-01

    Full Text Available Abstract Background Recombineering is a genetic engineering tool that enables facile modification of large episomal clones, e.g. BACs, fosmids. We have previously adapted this technology to generate, directly from fosmid-based genomic clones, fusion gene reporter constructs designed to investigate gene expression patterns in C. elegans. In our adaptation a rpsL-tet(A positive/negative-selection cassette (RT-cassette is first inserted and then, under negative selection, seamlessly replaced with the desired sequence. We report here on the generation and application of a resource comprising two sets of constructs designed to facilitate this particular recombineering approach. Results Two complementary sets of constructs were generated. The first contains different fluorescent protein reporter coding sequences and derivatives while the second set of constructs, based in the copy-number inducible vector pCC1Fos, provide a resource designed to simplify RT-cassette-based recombineering. These latter constructs are used in pairs the first member of which provides a template for PCR-amplification of an RT-cassette while the second provides, as an excised restriction fragment, the desired fluorescent protein reporter sequence. As the RT-cassette is flanked by approximately 200 bp from the ends of the reporter sequence the subsequent negative selection replacement step is highly efficient. Furthermore, use of a restriction fragment minimizes artefacts negating the need for final clone sequencing. Utilizing this resource we generated single-, double- and triple-tagged fosmid-based reporters to investigate expression patterns of three C. elegans genes located on a single genomic clone. Conclusions We describe the generation and application of a resource designed to facilitate counter-selection recombineering of fosmid-based C. elegans genomic clones. By choosing the appropriate pair of ‘insertion’ and ‘replacement’ constructs recombineered products

  18. The result of a two-stages cross intra and interspecific selection of sugar cane crop potential clones

    Directory of Open Access Journals (Sweden)

    Herwati A.

    2017-06-01

    Full Text Available Sugarcane is one of strategic and important food commodities in Indonesia because it is the main source of sugar producers. Domestic sugar production in 2015 only reached 2.5 million tons, while its needs are 5.6 million tons which resulting in a shortage of 3.1 million tons to be met from import. The production in 2016 just reached 2.5 million tons causing the shortages that must be filled by import as much as 3.1 million tons. The Ministry of Agriculture has a program for sugar self-sufficiency that is expected to be achieved by 2014 with production is expected to reach 5.7 million tons. The discrepancy between production levels at this time with the target in 2014 still quite wide. The target accession can be reached by intensification and land extension or expansion. The availability of land development with the availability of adequate water has to face obstacles competing with rice plant as the main staple food. In 2007 more than 60% sugar cane crop was in dry land (Hadisaputro, et al., 2008. The expansion of dry land still has an opportunity to be developed in various ways such as the availability of sugar cane varieties with drought resistant. The research objectives are to accomplish the drought resistant selection in the field to the result of crossbreeding clones in 2014 (MLG-14. The activities implemented in KP. Karangploso, Malang, started on January until December 2016. The research materials are 51 crop clones of two stage selection which 7 varieties are PSDK, PSJT 941, PS 881, PSJK, VMC 76-16, GLAGAH, ERIANTHUS, CENING, BL, and PS 881 as a control. Using a randomized block design with three replication were planted in plots consisting of three arc along the 5 m. The PKP range (from center to center of arc are 100 cm length. The range between replications is 2.5 – 3 cm length. The seeds form is a one eye mule (bud set. Furthermore, after 1.5 month old, the seeds were selected based on its uniformly conditions and then planted in

  19. A novel Gateway®-compatible binary vector allows direct selection of recombinant clones in Agrobacterium tumefaciens

    Directory of Open Access Journals (Sweden)

    Traore Sy

    2011-12-01

    Full Text Available Abstract Background Cloning genes into plasmid vectors is one of the key steps for studying gene function. Recently, Invitrogen™ developed a convenient Gateway® cloning system based on the site-specific DNA recombination properties of bacteriophage lambda and the cytotoxic protein ccdB, which is lethal to most E. coli strains. The ccdB protein, however, is not toxic to Agrobacterium tumefaciens, an important player often used for studying gene function in planta. This limits the direct application of the Gateway® cloning system in plant transformation-mediated research. Results In this study, we constructed a novel Gateway®-compatible destination vector, pEG101-SacB/R, by replacing the ccdB gene with a SacB-SacR gene cassette as the negative selectable marker. Conclusion Our results demonstrate that the new pEG101-SacB/R destination vector can be used for Gateway® cloning in Agrobacterium tumefaciens. pEG101-SacB/R will be a valuable tool for high-throughput functional analysis of genes in planta.

  20. A novel Gateway®-compatible binary vector allows direct selection of recombinant clones in Agrobacterium tumefaciens.

    Science.gov (United States)

    Traore, Sy Mamadou; Zhao, Bingyu

    2011-12-07

    Cloning genes into plasmid vectors is one of the key steps for studying gene function. Recently, Invitrogen™ developed a convenient Gateway® cloning system based on the site-specific DNA recombination properties of bacteriophage lambda and the cytotoxic protein ccdB, which is lethal to most E. coli strains. The ccdB protein, however, is not toxic to Agrobacterium tumefaciens, an important player often used for studying gene function in planta. This limits the direct application of the Gateway® cloning system in plant transformation-mediated research. In this study, we constructed a novel Gateway®-compatible destination vector, pEG101-SacB/R, by replacing the ccdB gene with a SacB-SacR gene cassette as the negative selectable marker. Our results demonstrate that the new pEG101-SacB/R destination vector can be used for Gateway® cloning in Agrobacterium tumefaciens. pEG101-SacB/R will be a valuable tool for high-throughput functional analysis of genes in planta.

  1. A novel sandwich hybridization method for selecting cDNAs from large genomic regions: Identification of cDNAs from the cloned genomic DNA spanning the XLRP locus

    Energy Technology Data Exchange (ETDEWEB)

    Yan, D.; McHenry, C.; Fujita, R. [Univ. of Michigan, Ann Arbor, MI (United States)] [and others

    1994-09-01

    We have developed an efficient hybridization-based cDNA-selection method. A sandwich of three species - single-stranded cDNA, tagged RNA derived from genomic DNA, and biotinylated RNA complementary to the tag - allows specific retention of hybrids on an avidin-matrix. Previously, using model experiments, we demonstrated highly specific and efficient selection of a retinal gene, NRL, from complex mixtures of cDNA clones, using a sub-library from a 5 kb NRL genomic clone. We have now applied this selection strategy to isolate cDNAs from human adult retina and fetal eye libraries, with the {open_quotes}genomic RNA{close_quotes} derived from two YAC clones (OTC-C and 55B) spanning the region of X-linked retinitis pigmentosa (XLRP) locus RP3 at Xp21.1. Effectiveness of the selection-method was monitored by enrichment of TCTEX-1L gene that maps within the 55B YAC. Of the 15 selected cDNA clones that hybridized to the 55B YAC DNA, five appear to the map to specific cosmid clones derived from the 55B YAC. Inserts in these selected cDNA clones range from 0.5 to 2.3 kb in size. Additional clones are now being isolated and characterized. This procedure should be independent of the size or complexity of genomic DNA being used for selection, allow for the isolation of full-length cDNAs, and may have wider application.

  2. Chemical composition and enzymatic digestibility of sugarcane clones selected for varied lignin content

    Directory of Open Access Journals (Sweden)

    Masarin Fernando

    2011-12-01

    Full Text Available Abstract Background The recalcitrance of lignocellulosic materials is a major limitation for their conversion into fermentable sugars. Lignin depletion in new cultivars or transgenic plants has been identified as a way to diminish this recalcitrance. In this study, we assessed the success of a sugarcane breeding program in selecting sugarcane plants with low lignin content, and report the chemical composition and agronomic characteristics of eleven experimental hybrids and two reference samples. The enzymatic digestion of untreated and chemically delignified samples was evaluated to advance the performance of the sugarcane residue (bagasse in cellulosic-ethanol production processes. Results The ranges for the percentages of glucan, hemicellulose, lignin, and extractive (based on oven-dry biomass of the experimental hybrids and reference samples were 38% to 43%, 25% to 32%, 17% to 24%, and 1.6% to 7.5%, respectively. The samples with the smallest amounts of lignin did not produce the largest amounts of total polysaccharides. Instead, a variable increase in the mass of a number of components, including extractives, seemed to compensate for the reduction in lignin content. Hydroxycinnamic acids accounted for a significant part of the aromatic compounds in the samples, with p-coumaric acid predominating, whereas ferulic acid was present only in low amounts. Hydroxycinnamic acids with ester linkage to the hemicelluloses varied from 2.3% to 3.6%. The percentage of total hydroxycinnamic acids (including the fraction linked to lignin through ether linkages varied from 5.0% to 9.2%, and correlated to some extent with the lignin content. These clones released up to 31% of glucose after 72 hours of digestion with commercial cellulases, whereas chemically delignified samples led to cellulose conversion values of more than 80%. However, plants with lower lignin content required less delignification to reach higher efficiencies of cellulose conversion during

  3. Evaluation of field performance of poplar clones using selected competition indices.

    Science.gov (United States)

    Chandler Brodie; D.S. DeBell

    2004-01-01

    Use of competition indices in the analysis of forestry experiments may improve detection and understanding of treatment effects, and thereby improve the application of results. In this paper, we compared the performance of eight indices in an analysis of a spacing trial of four Populus clones planted in pure and mixed clonal plots. Indices were...

  4. Selectivity and sparseness in randomly connected balanced networks.

    Directory of Open Access Journals (Sweden)

    Cengiz Pehlevan

    Full Text Available Neurons in sensory cortex show stimulus selectivity and sparse population response, even in cases where no strong functionally specific structure in connectivity can be detected. This raises the question whether selectivity and sparseness can be generated and maintained in randomly connected networks. We consider a recurrent network of excitatory and inhibitory spiking neurons with random connectivity, driven by random projections from an input layer of stimulus selective neurons. In this architecture, the stimulus-to-stimulus and neuron-to-neuron modulation of total synaptic input is weak compared to the mean input. Surprisingly, we show that in the balanced state the network can still support high stimulus selectivity and sparse population response. In the balanced state, strong synapses amplify the variation in synaptic input and recurrent inhibition cancels the mean. Functional specificity in connectivity emerges due to the inhomogeneity caused by the generative statistical rule used to build the network. We further elucidate the mechanism behind and evaluate the effects of model parameters on population sparseness and stimulus selectivity. Network response to mixtures of stimuli is investigated. It is shown that a balanced state with unselective inhibition can be achieved with densely connected input to inhibitory population. Balanced networks exhibit the "paradoxical" effect: an increase in excitatory drive to inhibition leads to decreased inhibitory population firing rate. We compare and contrast selectivity and sparseness generated by the balanced network to randomly connected unbalanced networks. Finally, we discuss our results in light of experiments.

  5. Selection of new clones of linalool chemotype from genetic recombination in Lippia alba

    OpenAIRE

    Rufino,Elcio Rodrigo; Siqueira,Walter José; Marques,Márcia Ortiz Maio; Colombo, Carlos Augusto; Azevedo Filho, Joaquim Adelino; Martins,Antônio Lúcio Melo

    2012-01-01

    The aromatic and medicinal species Lippia alba is vigorous and rugged native to the South America (Atlantic Rainforest). Because it is an allogamous and self-incompatible species, natural populations have high morphological and chemical variability. This work had as objective to conduct a preliminary screening to identify new promising clones from a novel (recombinant) base population of Lippia alba with regard to its agronomic and phytochemical traits, using the linalool oil or chemotype as ...

  6. On-farm testing of selected cassava clones | Saleh | African Crop ...

    African Journals Online (AJOL)

    ... une évaluation participative des essais. Les fermiers ont préféré les clones ZNZ/98/036, ZNZ/98/034 et ZNZ/98/084 à cause de la concentration en sucre, la résistance aux maladies, les rendements des raciness, et le contenu en matière sèche. Mots clés: Maladies, Manihot esculenta, pestes. African Crop Science Journal ...

  7. Fast, Randomized Join-Order Selection - Why Use Transformations?

    NARCIS (Netherlands)

    C.A. Galindo-Legaria; A.J. Pellenkoft (Jan); M.L. Kersten (Martin)

    1994-01-01

    textabstractWe study the effectiveness of probabilistic selection of join-query evaluation plans, without reliance on tree transformation rules. Instead, each candidate plan is chosen uniformly at random from the space of valid evaluation orders. This leads to a transformation-free strategy where a

  8. The reliability of randomly selected final year pharmacy students in ...

    African Journals Online (AJOL)

    Employing ANOVA, factorial experimental analysis, and the theory of error, reliability studies were conducted on the assessment of the drug product chloroquine phosphate tablets. The G–Study employed equal numbers of the factors for uniform control, and involved three analysts (randomly selected final year Pharmacy ...

  9. Avoid Early Selection for Growth Rate in Cottonwood

    Science.gov (United States)

    D. T. Cooper; Robert B. Ferguson

    1971-01-01

    A sample of 37 cottonwood clones from a selection program was compared with a sample of 40 random clones in a 14-year test at two sites near Stoneville, Mississippi. Throughout the test period, the select sample was slightly better in mean growth rate, but this difference decreased with age. Performance of ''blue tag" clones selected at age 5 and planted...

  10. Local randomization in neighbor selection improves PRM roadmap quality

    KAUST Repository

    McMahon, Troy

    2012-10-01

    Probabilistic Roadmap Methods (PRMs) are one of the most used classes of motion planning methods. These sampling-based methods generate robot configurations (nodes) and then connect them to form a graph (roadmap) containing representative feasible pathways. A key step in PRM roadmap construction involves identifying a set of candidate neighbors for each node. Traditionally, these candidates are chosen to be the k-closest nodes based on a given distance metric. In this paper, we propose a new neighbor selection policy called LocalRand(k,K\\'), that first computes the K\\' closest nodes to a specified node and then selects k of those nodes at random. Intuitively, LocalRand attempts to benefit from random sampling while maintaining the higher levels of local planner success inherent to selecting more local neighbors. We provide a methodology for selecting the parameters k and K\\'. We perform an experimental comparison which shows that for both rigid and articulated robots, LocalRand results in roadmaps that are better connected than the traditional k-closest policy or a purely random neighbor selection policy. The cost required to achieve these results is shown to be comparable to k-closest. © 2012 IEEE.

  11. Desempenho de clones de seringueira da série IAC 300 selecionados para a região noroeste do Estado de São Paulo Performance of Hevea clones from IAC 300 series selected in the northwestern region of São Paulo State, Brazil

    Directory of Open Access Journals (Sweden)

    Paulo de Souza Gonçalves

    2001-04-01

    Full Text Available É apresentado o desempenho de 19 novos clones de seringueira [Hevea brasiliensis (Willd. exAdr. de Juss. Muell. Arg.], resultantes de hibridações conduzidas no Instituto Agronômico e avaliados em experimento de pequena escala, tendo o clone RRIM 600 como testemunha. O experimento em campo obedeceu ao delineamento em blocos ao acaso, com três repetições. Com relação à produção de borracha seca, o clone IAC 40 apresentou a maior média (62,22 g/árvore/sangria nos três anos de avaliação, seguido pelo IAC 301 (57,67 g/árvore/sangria e pelo IAC 300 (50,61 g/árvore/sangria, com produções 154%, 138% e 123% superiores em relação ao RRIM 600 (41,04 g/árvore/sangria. Todos os clones selecionados foram vigorosos, com perímetro do caule na abertura do painel variando de 37,81 cm (IAC 317 a 50,90 cm (IAC 315. A porcentagem de plantas aptas a sangria variou de 20,0% (IAC 317 a 100% (IAC 315. Todos os clones apresentaram baixas incidências de quebra pelo vento e de secamento do painel. Não foi detectada nenhuma doença foliar em caráter epidêmico. Dos clones estudados, 15 apresentaram alta resistência à antracnose do painel, e foram superiores ao RRIM 600; os outros cinco apresentaram resistência moderada semelhante ao RRIM 600.The present paper shows the performance of 19 rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss. Muell. Arg.] originated from Hevea breeding programme conducted at the Instituto Agronômico de Campinas (IAC and evaluated in a small scale trial in the northwestern of São Paulo State, Brazil. The old popular clone RRIM 600 of Malaysian origin was used as control. The trial was laid out in a randomized block design with three replications. Concerned to yielding the clone IAC 40 recorded highest yield (62.22 g/tree/tap over three years of tapping which was followed by IAC 301 (57.67 g/tree/tap and IAC 300 (50.61 g/tree/tap yielding 154%, 138% and 123% superior to the control clone and RRIM 600 whereas

  12. Selecting a phoneme-to-grapheme mapping: Random or weighted selection?

    Directory of Open Access Journals (Sweden)

    Binna Lee

    2015-05-01

    Our findings demonstrate that random selection underestimates MOA’s PG correspondences whereas weighted selection predicts higher PG correspondences than he produces. To explain his intermediate spelling performance on PPEs, we will test additional approaches to weighing the relative probability of PG mappings, including using log frequencies, separating consonant and vowel status, and considering the number of grapheme options in each phoneme.

  13. Size-selection of cDNA libraries for the cloning of cDNAs after suppression subtractive hybridization.

    Science.gov (United States)

    Lévesque, V; Fayad, T; Ndiaye, K; Nahé Diouf, M; Lussier, J G

    2003-07-01

    Here we describe the establishment of size-selected cDNA libraries for the cloning of full-length cDNAs that were initially identified by suppression subtractive hybridization (SSH) technology as being differentially expressed. First, the SSH-cDNA fragments were used as 32P-probes to verify their level and differential pattern of expression by virtual Northern and to establish their corresponding full-length cDNA size. Second, cDNAs were separated by size on agarose gels and used to construct size-selected cDNA plasmid libraries, which were then screened by colony hybridization with the SSH-cDNA fragments. We conclude that the described approach complements SSH technology by allowing efficient cloning and characterization of the corresponding full-length cDNA from any desired cell type or species. This approach will give researchers the ability to specifically target and study differentially expressed genes in an efficient manner for functional genomic studies.

  14. Selection for altruism through random drift in variable size populations.

    Science.gov (United States)

    Houchmandzadeh, Bahram; Vallade, Marcel

    2012-05-10

    Altruistic behavior is defined as helping others at a cost to oneself and a lowered fitness. The lower fitness implies that altruists should be selected against, which is in contradiction with their widespread presence is nature. Present models of selection for altruism (kin or multilevel) show that altruistic behaviors can have 'hidden' advantages if the 'common good' produced by altruists is restricted to some related or unrelated groups. These models are mostly deterministic, or assume a frequency dependent fitness. Evolutionary dynamics is a competition between deterministic selection pressure and stochastic events due to random sampling from one generation to the next. We show here that an altruistic allele extending the carrying capacity of the habitat can win by increasing the random drift of "selfish" alleles. In other terms, the fixation probability of altruistic genes can be higher than those of a selfish ones, even though altruists have a smaller fitness. Moreover when populations are geographically structured, the altruists advantage can be highly amplified and the fixation probability of selfish genes can tend toward zero. The above results are obtained both by numerical and analytical calculations. Analytical results are obtained in the limit of large populations. The theory we present does not involve kin or multilevel selection, but is based on the existence of random drift in variable size populations. The model is a generalization of the original Fisher-Wright and Moran models where the carrying capacity depends on the number of altruists.

  15. Selection for altruism through random drift in variable size populations

    Directory of Open Access Journals (Sweden)

    Houchmandzadeh Bahram

    2012-05-01

    Full Text Available Abstract Background Altruistic behavior is defined as helping others at a cost to oneself and a lowered fitness. The lower fitness implies that altruists should be selected against, which is in contradiction with their widespread presence is nature. Present models of selection for altruism (kin or multilevel show that altruistic behaviors can have ‘hidden’ advantages if the ‘common good’ produced by altruists is restricted to some related or unrelated groups. These models are mostly deterministic, or assume a frequency dependent fitness. Results Evolutionary dynamics is a competition between deterministic selection pressure and stochastic events due to random sampling from one generation to the next. We show here that an altruistic allele extending the carrying capacity of the habitat can win by increasing the random drift of “selfish” alleles. In other terms, the fixation probability of altruistic genes can be higher than those of a selfish ones, even though altruists have a smaller fitness. Moreover when populations are geographically structured, the altruists advantage can be highly amplified and the fixation probability of selfish genes can tend toward zero. The above results are obtained both by numerical and analytical calculations. Analytical results are obtained in the limit of large populations. Conclusions The theory we present does not involve kin or multilevel selection, but is based on the existence of random drift in variable size populations. The model is a generalization of the original Fisher-Wright and Moran models where the carrying capacity depends on the number of altruists.

  16. Effect of clone selection, nitrogen supply, leaf damage and mycorrhizal fungi on stilbene and emodin production in knotweed

    Directory of Open Access Journals (Sweden)

    Nývltová Zora

    2011-05-01

    Full Text Available Abstract Background Fallopia japonica and its hybrid, F. xbohemica, due to their fast spread, are famous as nature threats rather than blessings. Their fast growth rate, height, coverage, efficient nutrient translocation between tillers and organs and high phenolic production, may be perceived either as dangerous or beneficial features that bring about the elimination of native species or a life-supporting source. To the best of our knowledge, there have not been any studies aimed at increasing the targeted production of medically desired compounds by these remarkable plants. We designed a two-year pot experiment to determine the extent to which stilbene (resveratrol, piceatannol, resveratrolosid, piceid and astringins and emodin contents of F. japonica, F. sachalinensis and two selected F. xbohemica clones are affected by soil nitrogen (N supply, leaf damage and mycorrhizal inoculation. Results 1 Knotweeds are able to grow on substrates with extremely low nitrogen content and have a high efficiency of N translocation. The fast-spreading hybrid clones store less N in their rhizomes than the parental species. 2 The highest concentrations of stilbenes were found in the belowground biomass of F. japonica. However, because of the high belowground biomass of one clone of F. xbohemica, this hybrid produced more stilbenes per plant than F. japonica. 3 Leaf damage increased the resveratrol and emodin contents in the belowground biomass of the non-inoculated knotweed plants. 4 Although knotweed is supposed to be a non-mycorrhizal species, its roots are able to host the fungi. Inoculation with mycorrhizal fungi resulted in up to 2% root colonisation. 5 Both leaf damage and inoculation with mycorrhizal fungi elicited an increase of the piceid (resveratrol-glucoside content in the belowground biomass of F. japonica. However, the mycorrhizal fungi only elicited this response in the absence of leaf damage. Because the leaf damage suppressed the effect of the

  17. Genetic alterations of hepatocellular carcinoma by random amplified polymorphic DNA analysis and cloning sequencing of tumor differential DNA fragment

    Science.gov (United States)

    Xian, Zhi-Hong; Cong, Wen-Ming; Zhang, Shu-Hui; Wu, Meng-Chao

    2005-01-01

    AIM: To study the genetic alterations and their association with clinicopathological characteristics of hepatocellular carcinoma (HCC), and to find the tumor related DNA fragments. METHODS: DNA isolated from tumors and corresponding noncancerous liver tissues of 56 HCC patients was amplified by random amplified polymorphic DNA (RAPD) with 10 random 10-mer arbitrary primers. The RAPD bands showing obvious differences in tumor tissue DNA corresponding to that of normal tissue were separated, purified, cloned and sequenced. DNA sequences were analyzed and compared with GenBank data. RESULTS: A total of 56 cases of HCC were demonstrated to have genetic alterations, which were detected by at least one primer. The detestability of genetic alterations ranged from 20% to 70% in each case, and 17.9% to 50% in each primer. Serum HBV infection, tumor size, histological grade, tumor capsule, as well as tumor intrahepatic metastasis, might be correlated with genetic alterations on certain primers. A band with a higher intensity of 480 bp or so amplified fragments in tumor DNA relative to normal DNA could be seen in 27 of 56 tumor samples using primer 4. Sequence analysis of these fragments showed 91% homology with Homo sapiens double homeobox protein DUX10 gene. CONCLUSION: Genetic alterations are a frequent event in HCC, and tumor related DNA fragments have been found in this study, which may be associated with hepatocarcin-ogenesis. RAPD is an effective method for the identification and analysis of genetic alterations in HCC, and may provide new information for further evaluating the molecular mechanism of hepatocarcinogenesis. PMID:15996039

  18. The versatility of heart-cutting and comprehensive two-dimensional liquid chromatography in monoclonal antibody clone selection.

    Science.gov (United States)

    Sandra, Koen; Steenbeke, Mieke; Vandenheede, Isabel; Vanhoenacker, Gerd; Sandra, Pat

    2017-11-10

    In recent years, two-dimensional liquid chromatography (2D-LC) has seen an enormous evolution and one of the fields where it is being widely adopted is in the analysis of therapeutic monoclonal antibodies (mAbs). We here further add to the many flavours of this powerful technology. Workflows based on heart-cutting (LC-LC) and comprehensive (LC×LC) 2D-LC are described that allow to guide the clone selection process in mAb and biosimilar development. Combining Protein A affinity chromatography in the first dimension with size exclusion (SEC), cation exchange (CEX) or reversed-phase liquid chromatography-mass spectrometry (RPLC-MS) in the second dimension simultaneously allows to assess mAb titer and critical structural aspects such as aggregation, fragmentation, charge heterogeneity, molecular weight (MW), amino acid sequence and glycosylation. Complementing the LC-LC measurements at intact protein level with LC×LC based peptide mapping provides the necessary information to make clear decisions on which clones to take further into development. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Cotton leaf curl Multan betasatellite strains cloned from Gossypium barbadense further supports selection due to host resistance.

    Science.gov (United States)

    Azhar, Muhammad Tehseen; Akhtar, Sohail; Mansoor, Shahid

    2012-10-01

    The cotton leaf curl Multan betasatellite encodes an essential pathogenicity determinant involved in induction of disease symptoms. We have shown recently that a recombinant betasatellite with a satellite conserved region derived from the tomato leaf curl betasatellite, is prevalent in the Punjab province and is associated with the breakdown of resistance in cotton to cotton leaf curl disease. We intended to see if the betasatellite that was associated with the first epidemic is still being maintained in some other hosts. We cloned betasatellite from G. barbadense, a cotton species highly susceptible to the disease. We found that both the original and recombinant betasatellite are associated with this cotton species. These findings strengthen our hypothesis that the recombinant betasatellite now prevalent on commercial cotton has been selected due to its ability to cross the host resistance barrier.

  20. Interference-aware random beam selection for spectrum sharing systems

    KAUST Repository

    Abdallah, Mohamed M.

    2012-09-01

    Spectrum sharing systems have been introduced to alleviate the problem of spectrum scarcity by allowing secondary unlicensed networks to share the spectrum with primary licensed networks under acceptable interference levels to the primary users. In this paper, we develop interference-aware random beam selection schemes that provide enhanced throughput for the secondary link under the condition that the interference observed at the primary link is within a predetermined acceptable value. For a secondary transmitter equipped with multiple antennas, our schemes select a random beam, among a set of power- optimized orthogonal random beams, that maximizes the capacity of the secondary link while satisfying the interference constraint at the primary receiver for different levels of feedback information describing the interference level at the primary receiver. For the proposed schemes, we develop a statistical analysis for the signal-to-noise and interference ratio (SINR) statistics as well as the capacity of the secondary link. Finally, we present numerical results that study the effect of system parameters including number of beams and the maximum transmission power on the capacity of the secondary link attained using the proposed schemes. © 2012 IEEE.

  1. Seleção de clones experimentais de cupuaçu para características agroindustriais via modelos mistos. = Selection of experimental clones of cupuaçu for the agro industry using mixed models.

    Directory of Open Access Journals (Sweden)

    Maria Clideana Cabral Maia

    2011-04-01

    Full Text Available As estatísticas REML/BLUP são análises mais detalhadas e podem ser usadas como critérios seletivos na rotina dos programas de melhoramento do cupuaçu. O objetivo desse trabalho é a seleção de clones experimentais pré-melhorados para características agroindustriais via modelos mistos. Os experimentos incluíram oito clones experimentais, obtidos a partir de seleção massal estratificada em área de produtor com base na produtividade, características tecnológicas e sanidade das matrizes. Para a avaliação foram considerados variáveis de componentes primários da produção (peso do fruto – g e peso da polpa – g; caracteres agroindustriais comprimento do fruto – cm, diâmetro do fruto – cm, diâmetro da casca – mm, peso de sementes – g, número de sementes, firmeza do fruto, °Brix, pH e vitamina C. Foram estimados via modelos mistos os componentes de variância por REML individual e os componentes de médias (BLUP individual. Os dados foram analisados através da metodologia REML/BLUP (Maximum Restricted Likelihood/ Best Linear Unbiased Prediction com o emprego do software Selegen. Os melhores clones (27, 29 e 31 com destaque para o clone 29 apresentando maiores ganhos genéticos com médias finais superiores a média geral para as variáveis comprimento de fruto, diâmetro do fruto, peso de fruto, firmezado fruto, diâmetro de casca, peso de polpa, peso de sementes, °Brix, pH e vitamina C. A variável peso de fruto apresentou alta correlação genética com diâmetro de fruto, peso de polpa e peso de sementes. O atributo diâmetro do fruto pode ser usado para extrapolar resultados para os demais caracteres por ser de medição mais fácil e menosfactível de erros. Os clones 27, 29 e 31 por suas características agroindustriais favoráveis podem fazer parte da composição de um pomar comercial. = The statistical methods REML/BLUP are detailed analyses and can be used as selective criterions in the routine of breeding

  2. Unbiased split variable selection for random survival forests using maximally selected rank statistics.

    Science.gov (United States)

    Wright, Marvin N; Dankowski, Theresa; Ziegler, Andreas

    2017-04-15

    The most popular approach for analyzing survival data is the Cox regression model. The Cox model may, however, be misspecified, and its proportionality assumption may not always be fulfilled. An alternative approach for survival prediction is random forests for survival outcomes. The standard split criterion for random survival forests is the log-rank test statistic, which favors splitting variables with many possible split points. Conditional inference forests avoid this split variable selection bias. However, linear rank statistics are utilized by default in conditional inference forests to select the optimal splitting variable, which cannot detect non-linear effects in the independent variables. An alternative is to use maximally selected rank statistics for the split point selection. As in conditional inference forests, splitting variables are compared on the p-value scale. However, instead of the conditional Monte-Carlo approach used in conditional inference forests, p-value approximations are employed. We describe several p-value approximations and the implementation of the proposed random forest approach. A simulation study demonstrates that unbiased split variable selection is possible. However, there is a trade-off between unbiased split variable selection and runtime. In benchmark studies of prediction performance on simulated and real datasets, the new method performs better than random survival forests if informative dichotomous variables are combined with uninformative variables with more categories and better than conditional inference forests if non-linear covariate effects are included. In a runtime comparison, the method proves to be computationally faster than both alternatives, if a simple p-value approximation is used. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  3. The signature of positive selection at randomly chosen loci.

    Science.gov (United States)

    Przeworski, Molly

    2002-03-01

    In Drosophila and humans, there are accumulating examples of loci with a significant excess of high-frequency-derived alleles or high levels of linkage disequilibrium, relative to a neutral model of a random-mating population of constant size. These are features expected after a recent selective sweep. Their prevalence suggests that positive directional selection may be widespread in both species. However, as I show here, these features do not persist long after the sweep ends: The high-frequency alleles drift to fixation and no longer contribute to polymorphism, while linkage disequilibrium is broken down by recombination. As a result, loci chosen without independent evidence of recent selection are not expected to exhibit either of these features, even if they have been affected by numerous sweeps in their genealogical history. How then can we explain the patterns in the data? One possibility is population structure, with unequal sampling from different subpopulations. Alternatively, positive selection may not operate as is commonly modeled. In particular, the rate of fixation of advantageous mutations may have increased in the recent past.

  4. Blind Measurement Selection: A Random Matrix Theory Approach

    KAUST Repository

    Elkhalil, Khalil

    2016-12-14

    This paper considers the problem of selecting a set of $k$ measurements from $n$ available sensor observations. The selected measurements should minimize a certain error function assessing the error in estimating a certain $m$ dimensional parameter vector. The exhaustive search inspecting each of the $n\\\\choose k$ possible choices would require a very high computational complexity and as such is not practical for large $n$ and $k$. Alternative methods with low complexity have recently been investigated but their main drawbacks are that 1) they require perfect knowledge of the measurement matrix and 2) they need to be applied at the pace of change of the measurement matrix. To overcome these issues, we consider the asymptotic regime in which $k$, $n$ and $m$ grow large at the same pace. Tools from random matrix theory are then used to approximate in closed-form the most important error measures that are commonly used. The asymptotic approximations are then leveraged to select properly $k$ measurements exhibiting low values for the asymptotic error measures. Two heuristic algorithms are proposed: the first one merely consists in applying the convex optimization artifice to the asymptotic error measure. The second algorithm is a low-complexity greedy algorithm that attempts to look for a sufficiently good solution for the original minimization problem. The greedy algorithm can be applied to both the exact and the asymptotic error measures and can be thus implemented in blind and channel-aware fashions. We present two potential applications where the proposed algorithms can be used, namely antenna selection for uplink transmissions in large scale multi-user systems and sensor selection for wireless sensor networks. Numerical results are also presented and sustain the efficiency of the proposed blind methods in reaching the performances of channel-aware algorithms.

  5. Pediatric selective mutism therapy: a randomized controlled trial.

    Science.gov (United States)

    Esposito, Maria; Gimigliano, Francesca; Barillari, Maria R; Precenzano, Francesco; Ruberto, Maria; Sepe, Joseph; Barillari, Umberto; Gimigliano, Raffaele; Militerni, Roberto; Messina, Giovanni; Carotenuto, Marco

    2017-10-01

    Selective mutism (SM) is a rare disease in children coded by DSM-5 as an anxiety disorder. Despite the disabling nature of the disease, there is still no specific treatment. The aims of this study were to verify the efficacy of six-month standard psychomotor treatment and the positive changes in lifestyle, in a population of children affected by SM. Randomized controlled trial registered in the European Clinical Trials Registry (EuDract 2015-001161-36). University third level Centre (Child and Adolescent Neuropsychiatry Clinic). Study population was composed by 67 children in group A (psychomotricity treatment) (35 M, mean age 7.84±1.15) and 71 children in group B (behavioral and educational counseling) (37 M, mean age 7.75±1.36). Psychomotor treatment was administered by trained child therapists in residential settings three times per week. Each child was treated for the whole period by the same therapist and all the therapists shared the same protocol. The standard psychomotor session length is of 45 minutes. At T0 and after 6 months (T1) of treatments, patients underwent a behavioral and SM severity assessment. To verify the effects of the psychomotor management, the Child Behavior Checklist questionnaire (CBCL) and Selective Mutism Questionnaire (SMQ) were administered to the parents. After 6 months of psychomotor treatment SM children showed a significant reduction among CBCL scores such as in social relations, anxious/depressed, social problems and total problems (Ppsychomotricity a safe and efficacy therapy for pediatric selective mutism.

  6. Optimizing Event Selection with the Random Grid Search

    Energy Technology Data Exchange (ETDEWEB)

    Bhat, Pushpalatha C. [Fermilab; Prosper, Harrison B. [Florida State U.; Sekmen, Sezen [Kyungpook Natl. U.; Stewart, Chip [Broad Inst., Cambridge

    2017-06-29

    The random grid search (RGS) is a simple, but efficient, stochastic algorithm to find optimal cuts that was developed in the context of the search for the top quark at Fermilab in the mid-1990s. The algorithm, and associated code, have been enhanced recently with the introduction of two new cut types, one of which has been successfully used in searches for supersymmetry at the Large Hadron Collider. The RGS optimization algorithm is described along with the recent developments, which are illustrated with two examples from particle physics. One explores the optimization of the selection of vector boson fusion events in the four-lepton decay mode of the Higgs boson and the other optimizes SUSY searches using boosted objects and the razor variables.

  7. What is Cloning?

    Science.gov (United States)

    Donate Home Cloning What is Cloning What is Cloning Clones are organisms that are exact genetic copies. ... clones made through modern cloning technologies. How Is Cloning Done? Many people first heard of cloning when ...

  8. Effects of Heavy Metals and Arbuscular Mycorrhiza on the Leaf Proteome of a Selected Poplar Clone: A Time Course Analysis

    Science.gov (United States)

    Lingua, Guido; Bona, Elisa; Todeschini, Valeria; Cattaneo, Chiara; Marsano, Francesco; Berta, Graziella; Cavaletto, Maria

    2012-01-01

    Arbuscular mycorrhizal (AM) fungi establish a mutualistic symbiosis with the roots of most plant species. While receiving photosynthates, they improve the mineral nutrition of the plant and can also increase its tolerance towards some pollutants, like heavy metals. Although the fungal symbionts exclusively colonize the plant roots, some plant responses can be systemic. Therefore, in this work a clone of Populus alba L., previously selected for its tolerance to copper and zinc, was used to investigate the effects of the symbiosis with the AM fungus Glomus intraradices on the leaf protein expression. Poplar leaf samples were collected from plants maintained in a glasshouse on polluted (copper and zinc contaminated) or unpolluted soil, after four, six and sixteen months of growth. For each harvest, about 450 proteins were reproducibly separated on 2DE maps. At the first harvest the most relevant effect on protein modulation was exerted by the AM fungi, at the second one by the metals, and at the last one by both treatments. This work demonstrates how importantly the time of sampling affects the proteome responses in perennial plants. In addition, it underlines the ability of a proteomic approach, targeted on protein identification, to depict changes in a specific pattern of protein expression, while being still far from elucidating the biological function of each protein. PMID:22761694

  9. Genetic variability in residual feed intake in rainbow trout clones and testing of indirect selection criteria (Open Access publication

    Directory of Open Access Journals (Sweden)

    Chatain Béatrice

    2008-11-01

    Full Text Available Abstract Little is known about the genetic basis of residual feed intake (RFI variation in fish, since this trait is highly sensitive to environmental influences, and feed intake of individuals is difficult to measure accurately. The purpose of this work was (i to assess the genetic variability of RFI estimated by an X-ray technique and (ii to develop predictive criteria for RFI. Two predictive criteria were tested: loss of body weight during feed deprivation and compensatory growth during re-feeding. Ten heterozygous rainbow trout clones were used. Individual intake and body weight were measured three times at threeweek intervals. Then, individual body weight was recorded after two cycles of a three-week feed deprivation followed by a three-week re-feeding. The ratio of the genetic variance to the phenotypic variance was found high to moderate for growth, feed intake, and RFI (VG/VP = 0.63 ± 0.11, 0.29 ± 0.11, 0.29 ± 0.09, respectively. The index that integrates performances achieved during deprivation and re-feeding periods explained 59% of RFI variations. These results provide a basis for further studies on the origin of RFI differences and show that indirect criteria are good candidates for future selective breeding programs.

  10. Effects of heavy metals and arbuscular mycorrhiza on the leaf proteome of a selected poplar clone: a time course analysis.

    Directory of Open Access Journals (Sweden)

    Guido Lingua

    Full Text Available Arbuscular mycorrhizal (AM fungi establish a mutualistic symbiosis with the roots of most plant species. While receiving photosynthates, they improve the mineral nutrition of the plant and can also increase its tolerance towards some pollutants, like heavy metals. Although the fungal symbionts exclusively colonize the plant roots, some plant responses can be systemic. Therefore, in this work a clone of Populus alba L., previously selected for its tolerance to copper and zinc, was used to investigate the effects of the symbiosis with the AM fungus Glomus intraradices on the leaf protein expression. Poplar leaf samples were collected from plants maintained in a glasshouse on polluted (copper and zinc contaminated or unpolluted soil, after four, six and sixteen months of growth. For each harvest, about 450 proteins were reproducibly separated on 2DE maps. At the first harvest the most relevant effect on protein modulation was exerted by the AM fungi, at the second one by the metals, and at the last one by both treatments. This work demonstrates how importantly the time of sampling affects the proteome responses in perennial plants. In addition, it underlines the ability of a proteomic approach, targeted on protein identification, to depict changes in a specific pattern of protein expression, while being still far from elucidating the biological function of each protein.

  11. GC-MS Metabolite Profiling of Extreme Southern Pinot noir Wines: Effects of Vintage, Barrel Maturation, and Fermentation Dominate over Vineyard Site and Clone Selection.

    Science.gov (United States)

    Schueuermann, Claudia; Khakimov, Bekzod; Engelsen, Søren Balling; Bremer, Phil; Silcock, Patrick

    2016-03-23

    Wine is an extremely complex beverage that contains a multitude of volatile and nonvolatile compounds. This study investiged the effect of vineyard site and grapevine clone on the volatile profiles of commercially produced Pinot noir wines from central Otago, New Zealand. Volatile metabolites in Pinot noir wines produced from five grapevine clones grown on six vineyard sites in close proximity, over two consecutive vintages, were surveyed using gas chromatography-mass spectrometry (GC-MS). The raw GC-MS data were processed using parallel factor analysis (PARAFAC2), and final metabolite data were analyzed by principal component analysis (PCA). Winemaking conditions, vintage, and barrel maturation were found to be the most dominant factors. The effects of vineyard site and clone were mostly vintage dependent. Although four compounds including β-citronellol, homovanillyl alcohol, N-(3-methylbutyl)acetamide, and N-(2-phenylethyl)acetamide discriminated the vineyard sites independent of vintage, Pinot noir wines from different clones were only partially discriminated by PCA, and marker compound selection remained challenging.

  12. CRISPR-Cas9-Edited Site Sequencing (CRES-Seq): An Efficient and High-Throughput Method for the Selection of CRISPR-Cas9-Edited Clones.

    Science.gov (United States)

    Veeranagouda, Yaligara; Debono-Lagneaux, Delphine; Fournet, Hamida; Thill, Gilbert; Didier, Michel

    2018-01-16

    The emergence of clustered regularly interspaced short palindromic repeats-Cas9 (CRISPR-Cas9) gene editing systems has enabled the creation of specific mutants at low cost, in a short time and with high efficiency, in eukaryotic cells. Since a CRISPR-Cas9 system typically creates an array of mutations in targeted sites, a successful gene editing project requires careful selection of edited clones. This process can be very challenging, especially when working with multiallelic genes and/or polyploid cells (such as cancer and plants cells). Here we described a next-generation sequencing method called CRISPR-Cas9 Edited Site Sequencing (CRES-Seq) for the efficient and high-throughput screening of CRISPR-Cas9-edited clones. CRES-Seq facilitates the precise genotyping up to 96 CRISPR-Cas9-edited sites (CRES) in a single MiniSeq (Illumina) run with an approximate sequencing cost of $6/clone. CRES-Seq is particularly useful when multiple genes are simultaneously targeted by CRISPR-Cas9, and also for screening of clones generated from multiallelic genes/polyploid cells. © 2018 by John Wiley & Sons, Inc. Copyright © 2018 John Wiley & Sons, Inc.

  13. Selection strategy and the design of hybrid oligonucleotide primers for RACE-PCR: cloning a family of toxin-like sequences from Agelena orientalis

    Directory of Open Access Journals (Sweden)

    Lipkin Alexey

    2007-05-01

    Full Text Available Abstract Background the use of specific but partially degenerate primers for nucleic acid hybridisations and PCRs amplification of known or unknown gene families was first reported well over a decade ago and the technique has been used widely since then. Results here we report a novel and successful selection strategy for the design of hybrid partially degenerate primers for use with RT-PCR and RACE-PCR for the identification of unknown gene families. The technique (named PaBaLiS has proven very effective as it allowed us to identify and clone a large group of mRNAs encoding neurotoxin-like polypeptide pools from the venom of Agelena orientalis species of spider. Our approach differs radically from the generally accepted CODEHOP principle first reported in 1998. Most importantly, our method has proven very efficient by performing better than an independently generated high throughput EST cloning programme. Our method yielded nearly 130 non-identical sequences from Agelena orientalis, whilst the EST cloning technique yielded only 48 non-identical sequences from 2100 clones obtained from the same Agelena material. In addition to the primer design approach reported here, which is almost universally applicable to any PCR cloning application, our results also indicate that venom of Agelena orientalis spider contains a much larger family of related toxin-like sequences than previously thought. Conclusion with upwards of 100,000 species of spider thought to exist, and a propensity for producing diverse peptide pools, many more peptides of pharmacological importance await discovery. We envisage that some of these peptides and their recombinant derivatives will provide a new range of tools for neuroscience research and could also facilitate the development of a new generation of analgesic drugs and insecticides.

  14. Event selection with a Random Forest in IceCube

    Energy Technology Data Exchange (ETDEWEB)

    Ruhe, Tim [TU, Dortmund (Germany); Collaboration: IceCube-Collaboration

    2011-07-01

    The Random Forest method is a multivariate algorithm that can be used for classification and regression respectively. The Random Forest implemented in the RapidMiner learning environment has been used for training and validation on data and Monte Carlo simulations of the IceCube neutrino telescope. Latest results are presented.

  15. Seleção de clones de batata-doce resistentes a Meloidogyne incognita raça 1 Selection of sweetpotato clones resistant to Meloidogyne incognita race 1

    Directory of Open Access Journals (Sweden)

    Aline Marchese

    2010-09-01

    Full Text Available O objetivo deste trabalho foi selecionar clones de batata-doce (Ipomoea batatas resistentes à raça 1 de Meloidogyne incognita e avaliar a eficiência do método de seleção empregado, pela estimação dos coeficientes de variação genética e ambiental e das herdabilidades no sentido amplo. Foram utilizados 123 genótipos de batata-doce, entre os quais quatro cultivares comerciais - Brazlândia Rosada, Brazlândia Roxa, Brazlândia Branca e Palmas -, e 119 acessos previamente selecionados no programa de melhoramento vegetal da Universidade Federal de Lavras. O delineamento experimental utilizado foi o de blocos aumentados, com três tratamentos comuns: as cultivares de batata-doce Brazlândia Branca e Palmas, e a cultivar de tomate Santa Clara, suscetível ao nematoide. A classificação dos níveis de resistência foi realizada de acordo com o fator de reprodução do nematoide e o índice de reprodução relativo à cultivar Santa Clara, de tomateiro. A relação entre os coeficientes de variação genética e ambiental e as herdabilidades no sentido amplo foram altas, tanto para o fator de reprodução quanto para o índice de reprodução dos nematoides, o que demonstra a eficiência do método empregado para a seleção de genótipos resistentes. Foram identificados 57 genótipos promissores de batata-doce, resistentes à raça 1 de M. incognita, e selecionados para continuar no programa de melhoramento.The objective of this work was to select sweetpotato (Ipomoea batatas resistant clones to Meloidogyne incognita race 1, and to assess the efficiency of the selection method deployed, through the estimation of genetic and environmental coefficients of variation, and broad-sense heritabilities. Genotypes assessed comprised 123 sweetpotato entries altogether, including four commercial cultivars - Brazlândia Rosada, Brazlândia Roxa, Brazlândia Branca, Palmas - and 119 clones previously selected by the Universidade Federal de Lavras

  16. A new structural class of subtype-selective inhibitor of cloned excitatory amino acid transporter, EAAT2

    DEFF Research Database (Denmark)

    Bräuner-Osborne, Hans; Hermit, M B; Nielsen, B

    2000-01-01

    We have studied the pharmacological effects of (RS)-2-amino-3-(3-hydroxy-5-methylisoxazol-4-yl)propionic acid (AMPA) and the enantiomers of (RS)-2-amino-3-(3-hydroxy-1,2, 5-thiadiazol-4-yl)propionic acid (TDPA) on cloned human excitatory amino acid transporter subtypes 1, 2 and 3 (EAAT1...

  17. From selective full-length genes isolation by TAR cloning in yeast to their expression from HAC vectors in human cells.

    Science.gov (United States)

    Kouprina, Natalay; Lee, Nicholas C O; Kononenko, Artem V; Samoshkin, Alexander; Larionov, Vladimir

    2015-01-01

    Transformation-associated recombination (TAR) cloning allows selective isolation of full-length genes and genomic loci as large circular Yeast Artificial Chromosomes (YACs) in yeast. The method has a broad application for structural and functional genomics, long-range haplotyping, characterization of chromosomal rearrangements, and evolutionary studies. In this paper, we describe a basic protocol for gene isolation by TAR as well as a method to convert TAR isolates into Bacterial Artificial Chromosomes (BACs) using a retrofitting vector. The retrofitting vector contains a 3' HPRT-loxP cassette to allow subsequent gene loading into a unique loxP site of the HAC-based (Human Artificial Chromosome) gene delivery vector. The benefit of combining the TAR gene cloning technology with the HAC gene delivery system for gene expression studies is discussed.

  18. Assessment of genetic diversity in different clones of Dalbergia ...

    African Journals Online (AJOL)

    Genetic diversity of forty (40) clones of Dalbergia sissoo Roxb was analyzed using randomly amplified polymorphic DNA (RAPD) markers by selecting 30 decamer primers, which were later reduced to 10 based on the preliminary PCR amplification. A total of 129 distinct DNA fragments (bands) were amplified, of which 104 ...

  19. Kualitas Umbi Beberapa Klon Kentang (Solanum Tuberosum L.) Dataran Medium Untuk Keripik* [Tuber Quality of Some Potato (Solanum Tuberosum L.) Clones of Medium Altitude Area for Chips Making

    OpenAIRE

    Asgar, Ali

    2013-01-01

    Quality testing of several potato clones (Solanum tuberosum L.) planted at mid level area for potato chips. Objective of the research is to test the quality of clones/cultivars resulted from selection. Quality test of 8 selective clones was conducted from November 2010 to February 2011 in post-harvest laboratory of Research Institute for Vegetables Lembang. Research was arranged in randomized complete block design with 4 replications. Treatments consisted of 1) klon 395195.7, 2) klon 397073.7...

  20. Seleção de clones de batata para microclimas de altitude no Planalto Central Selection of potato cultivars for high altitude microclimates in Central Brazil

    Directory of Open Access Journals (Sweden)

    Nei Peixoto

    2002-09-01

    Full Text Available Iniciou-se em 1986, em Anápolis, um programa de desenvolvimento de cultivares de batata adaptadas ao clima de altitude do Brasil Central, partindo-se de 15.000 genótipos, resultantes de 200 famílias obtidas pela Embrapa Hortaliças em 1985 e 1986. No primeiro ciclo, em 1986, foram selecionados 5.000 genótipos, considerando-se aspectos fenológicos, incidência de doenças, qualidade dos tubérculos e potencial de produção. Esses mesmos critérios foram adotados nas gerações posteriores, selecionando-se, anualmente, 15-20% de genótipos superiores. Em 1990 avaliaram-se 52 destes clones, tendo como testemunhas as cultivares Achat e Bintje; Destes foram selecionados 28 clones promissores que foram submetidos à cultura de ápices caulinares e à indexação para os vírus PLRV, PVY e PVX na Embrapa Hortaliças. No período de 1995 a 1997 foram avaliados em Goiás, nos municípios de Anápolis, Morrinhos, Pirenópolis e Urutaí, e em Jaboticabal. Os dados foram submetidos à análise de variância, e aqueles referentes a 14 genótipos em 7 ambientes, à regressão pelo método de Eberhart & Russell. Os clones BAT 2, BAT 3, BAT 4, BAT 19, BAT 27 e BAT 28 destacaram-se entre os mais produtivos, considerando-se, também, as características de tubérculos para o consumo. Os genótipos responderam proporcionalmente à melhoria do ambiente. O clone BAT 19 foi o mais estável.A potato selection program was done in Anapolis, State of Goias, Brazil, beginning in 1986 with 15,000 genotypes, resulting from 200 crosses obtained by Embrapa Hortaliças in 1985 and 1986. In the first selection cycle, in 1986, 5,000 genotypes were selected, considering plant growth and development, disease incidence, tuber quality and yield potential. These criteria were also adopted in further generations, when 15 to 20% of the best genotypes were yearly selected. In 1990 52 of the selected genotypes were evaluated in comparison with the cultivars Achat and Bintje. The

  1. Study on MAX-MIN Ant System with Random Selection in Quadratic Assignment Problem

    Science.gov (United States)

    Iimura, Ichiro; Yoshida, Kenji; Ishibashi, Ken; Nakayama, Shigeru

    Ant Colony Optimization (ACO), which is a type of swarm intelligence inspired by ants' foraging behavior, has been studied extensively and its effectiveness has been shown by many researchers. The previous studies have reported that MAX-MIN Ant System (MMAS) is one of effective ACO algorithms. The MMAS maintains the balance of intensification and diversification concerning pheromone by limiting the quantity of pheromone to the range of minimum and maximum values. In this paper, we propose MAX-MIN Ant System with Random Selection (MMASRS) for improving the search performance even further. The MMASRS is a new ACO algorithm that is MMAS into which random selection was newly introduced. The random selection is one of the edgechoosing methods by agents (ants). In our experimental evaluation using ten quadratic assignment problems, we have proved that the proposed MMASRS with the random selection is superior to the conventional MMAS without the random selection in the viewpoint of the search performance.

  2. Academic Cloning.

    Science.gov (United States)

    Sikula, John P.; Sikula, Andrew F.

    1980-01-01

    The authors define "cloning" as an integral feature of all educational systems, citing teaching practices which reward students for closely reproducing the teacher's thoughts and/or behaviors and administrative systems which tend to promote like-minded subordinates. They insist, however, that "academic cloning" is not a totally…

  3. Three-stage biochemical selection: cloning of prototype class IIS/IIC/IIG restriction endonuclease-methyltransferase TsoI from the thermophile Thermus scotoductus.

    Science.gov (United States)

    Skowron, Piotr M; Vitkute, Jolanta; Ramanauskaite, Danute; Mitkaite, Goda; Jezewska-Frackowiak, Joanna; Zebrowska, Joanna; Zylicz-Stachula, Agnieszka; Lubys, Arvydas

    2013-08-06

    In continuing our research into the new family of bifunctional restriction endonucleases (REases), we describe the cloning of the tsoIRM gene. Currently, the family includes six thermostable enzymes: TaqII, Tth111II, TthHB27I, TspGWI, TspDTI, TsoI, isolated from various Thermus sp. and two thermolabile enzymes: RpaI and CchII, isolated from mesophilic bacteria Rhodopseudomonas palustris and Chlorobium chlorochromatii, respectively. The enzymes have several properties in common. They are large proteins (molecular size app. 120 kDa), coded by fused genes, with the REase and methyltransferase (MTase) in a single polypeptide, where both activities are affected by S-adenosylmethionine (SAM). They recognize similar asymmetric cognate sites and cleave at a distance of 11/9 nt from the recognition site. Thus far, we have cloned and characterised TaqII, Tth111II, TthHB27I, TspGWI and TspDTI. TsoI REase, which originate from thermophilic Thermus scotoductus RFL4 (T. scotoductus), was cloned in Escherichia coli (E. coli) using two rounds of biochemical selection of the T. scotoductus genomic library for the TsoI methylation phenotype. DNA sequencing of restriction-resistant clones revealed the common open reading frame (ORF) of 3348 bp, coding for a large polypeptide of 1116 aminoacid (aa) residues, which exhibited a high level of similarity to Tth111II (50% identity, 60% similarity). The ORF was PCR-amplified, subcloned into a pET21 derivative under the control of a T7 promoter and was subjected to the third round of biochemical selection in order to isolate error-free clones. Induction experiments resulted in synthesis of an app. 125 kDa protein, exhibiting TsoI-specific DNA cleavage. Also, the wild-type (wt) protein was purified and reaction optima were determined. Previously we identified and cloned the Thermus family RM genes using a specially developed method based on partial proteolysis of thermostable REases. In the case of TsoI the classic biochemical selection

  4. Three-stage biochemical selection: cloning of prototype class IIS/IIC/IIG restriction endonuclease-methyltransferase TsoI from the thermophile Thermus scotoductus

    Science.gov (United States)

    2013-01-01

    Background In continuing our research into the new family of bifunctional restriction endonucleases (REases), we describe the cloning of the tsoIRM gene. Currently, the family includes six thermostable enzymes: TaqII, Tth111II, TthHB27I, TspGWI, TspDTI, TsoI, isolated from various Thermus sp. and two thermolabile enzymes: RpaI and CchII, isolated from mesophilic bacteria Rhodopseudomonas palustris and Chlorobium chlorochromatii, respectively. The enzymes have several properties in common. They are large proteins (molecular size app. 120 kDa), coded by fused genes, with the REase and methyltransferase (MTase) in a single polypeptide, where both activities are affected by S-adenosylmethionine (SAM). They recognize similar asymmetric cognate sites and cleave at a distance of 11/9 nt from the recognition site. Thus far, we have cloned and characterised TaqII, Tth111II, TthHB27I, TspGWI and TspDTI. Results TsoI REase, which originate from thermophilic Thermus scotoductus RFL4 (T. scotoductus), was cloned in Escherichia coli (E. coli) using two rounds of biochemical selection of the T. scotoductus genomic library for the TsoI methylation phenotype. DNA sequencing of restriction-resistant clones revealed the common open reading frame (ORF) of 3348 bp, coding for a large polypeptide of 1116 aminoacid (aa) residues, which exhibited a high level of similarity to Tth111II (50% identity, 60% similarity). The ORF was PCR-amplified, subcloned into a pET21 derivative under the control of a T7 promoter and was subjected to the third round of biochemical selection in order to isolate error-free clones. Induction experiments resulted in synthesis of an app. 125 kDa protein, exhibiting TsoI-specific DNA cleavage. Also, the wild-type (wt) protein was purified and reaction optima were determined. Conclusions Previously we identified and cloned the Thermus family RM genes using a specially developed method based on partial proteolysis of thermostable REases. In the case of TsoI the

  5. Why Clone?

    Science.gov (United States)

    ... to clone agricultural animals, such as cattle and pigs, that are efficient producers of high-quality milk ... risks involved. Visit Teach.Genetics Cite this page Feedback Disclaimer Permissions Policy Privacy Policy Copyright © University of ...

  6. Directional random oligonucleotide primed (DROP) global amplification of cDNA: its application to subtractive cDNA cloning.

    OpenAIRE

    Hampson, I N; Hampson, L; Dexter, T M

    1996-01-01

    We describe a method of global PCR amplification of cDNA such that the strand sense is maintained. The products of this process are random primed fragments ranging in size from 100 to 500 bp which facilitates uniform PCR amplification of total cDNA. Directional incorporation of a T7 RNA polymerase initiator/promoter sequence allows efficient synthesis of total sense RNA from this material and the use of a biotinylated primer permits the separation of single-stranded cDNA. Isolation of these p...

  7. In vivo selection of randomly mutated retroviral genomes

    NARCIS (Netherlands)

    Berkhout, B.; Klaver, B.

    1993-01-01

    Darwinian evolution, that is the outgrowth of the fittest variants in a population, usually applies to living organisms over long periods of time. Recently, in vitro selection/amplification techniques have been developed that allow for the rapid evolution of functionally active nucleic acids from a

  8. Assessing the accuracy and stability of variable selection methods for random forest modeling in ecology

    Science.gov (United States)

    Random forest (RF) modeling has emerged as an important statistical learning method in ecology due to its exceptional predictive performance. However, for large and complex ecological datasets there is limited guidance on variable selection methods for RF modeling. Typically, e...

  9. Cloning, clones and clonal disease.

    Science.gov (United States)

    Luzzatto, L

    2000-01-01

    In the past, cloning has been familiar to plant breeders because many plants can be easily reproduced in this way, bypassing the lengthy process of cross-fertilisation. Recently, the concept of cloning has become popular in human biology and medicine on two accounts. First, individual genes can be cloned from the enormous complexity of the DNA that makes up the human genetic material. It is expected that, within a few years, all the estimated 100,000 human genes will be isolated by this approach. This should make it possible to identify all the genes that determine the individual characteristics of human beings, including those responsible for causing human diseases or for making people more or less susceptible to pick up diseases from the environment. Cloned genes made into pharmaceutical products are already in use for treating a variety of diseases, from hormonal deficiencies to certain types of anaemia.

  10. The frequency of drugs in randomly selected drivers in Denmark

    DEFF Research Database (Denmark)

    Simonsen, Kirsten Wiese; Steentoft, Anni; Hels, Tove

    Introduction Driving under the influence of alcohol and drugs is a global problem. In Denmark as well as in other countries there is an increasing focus on impaired driving. Little is known about the occurrence of psychoactive drugs in the general traffic. Therefore the European commission...... initiated the DRUID project. This roadside study is the Danish part of the EU-project DRUID (Driving under the Influence of Drugs, Alcohol, and Medicines) and included three representative regions in Denmark. Methods Oral fluid samples (n = 3002) were collected randomly from drivers using a sampling scheme...... stratified by time, season, and road type. The oral fluid samples were screened for 29 illegal and legal psychoactive substances and metabolites as well as ethanol. Results Fourteen (0.5%) drivers were positive for ethanol (alone or in combination with drugs) at concentrations above 0.53 g/l, which...

  11. Sample Selection in Randomized Experiments: A New Method Using Propensity Score Stratified Sampling

    Science.gov (United States)

    Tipton, Elizabeth; Hedges, Larry; Vaden-Kiernan, Michael; Borman, Geoffrey; Sullivan, Kate; Caverly, Sarah

    2014-01-01

    Randomized experiments are often seen as the "gold standard" for causal research. Despite the fact that experiments use random assignment to treatment conditions, units are seldom selected into the experiment using probability sampling. Very little research on experimental design has focused on how to make generalizations to well-defined…

  12. Pseudo cluster randomization dealt with selection bias and contamination in clinical trials

    NARCIS (Netherlands)

    Teerenstra, S.; Melis, R.J.F.; Peer, P.G.M.; Borm, G.F.

    2006-01-01

    BACKGROUND AND OBJECTIVES: When contamination is present, randomization on a patient level leads to dilution of the treatment effect. The usual solution is to randomize on a cluster level, but at the cost of efficiency and more importantly, this may introduce selection bias. Furthermore, it may slow

  13. Acceptance sampling using judgmental and randomly selected samples

    Energy Technology Data Exchange (ETDEWEB)

    Sego, Landon H.; Shulman, Stanley A.; Anderson, Kevin K.; Wilson, John E.; Pulsipher, Brent A.; Sieber, W. Karl

    2010-09-01

    We present a Bayesian model for acceptance sampling where the population consists of two groups, each with different levels of risk of containing unacceptable items. Expert opinion, or judgment, may be required to distinguish between the high and low-risk groups. Hence, high-risk items are likely to be identifed (and sampled) using expert judgment, while the remaining low-risk items are sampled randomly. We focus on the situation where all observed samples must be acceptable. Consequently, the objective of the statistical inference is to quantify the probability that a large percentage of the unsampled items in the population are also acceptable. We demonstrate that traditional (frequentist) acceptance sampling and simpler Bayesian formulations of the problem are essentially special cases of the proposed model. We explore the properties of the model in detail, and discuss the conditions necessary to ensure that required samples sizes are non-decreasing function of the population size. The method is applicable to a variety of acceptance sampling problems, and, in particular, to environmental sampling where the objective is to demonstrate the safety of reoccupying a remediated facility that has been contaminated with a lethal agent.

  14. SIMULTANEOUS SELECTION FOR GENOTYPIC PRODUCTION, ADAPTABILITY, AND STABILITY IN CASHEW CLONES BY MIXED MODELS SELEÇÃO SIMULTÂNEA PARA PRODUÇÃO, ADAPTABILIDADE E ESTABILIDADE GENOTÍPICAS EM CLONES DE CAJUEIRO, VIA MODELOS MISTOS

    Directory of Open Access Journals (Sweden)

    José Jaime Vasconcelos Cavalcanti

    2009-01-01

    genotypic adaptability and stability. The experiments were set up employing a complete block design, with eleven treatments, three repetitions and five plants per plot. The results showed an alteration in the clone order, in the different environments, as reflected from the genotypic correlation of average magnitude (0.58. The heritability of clones presented moderate to high magnitude for the different traits, indicating excellent possibilities for selection, allowing selective accuracy of 83%. The methods MHVG, PRVG, and MHPRVG can be part of selective criteria in the cashew breeding program.

     

    KEY-WORDS: Anacardium occidentale; genotype x environment interaction; BLUP/REML.

  1. Selective cloning, characterization, and production of the Culicoides nubeculosus salivary gland allergen repertoire associated with equine insect bite hypersensitivity.

    Science.gov (United States)

    Schaffartzik, Anna; Marti, Eliane; Torsteinsdottir, Sigurbjörg; Mellor, Philip S; Crameri, Reto; Rhyner, Claudio

    2011-02-15

    Salivary gland proteins of Culicoides spp. have been suggested to be among the main allergens inducing IgE-mediated insect bite hypersensitivity (IBH), an allergic dermatitis of the horse. The aim of our study was to identify, produce and characterize IgE-binding salivary gland proteins of Culicoides nubeculosus relevant for IBH by phage surface display technology. A cDNA library constructed with mRNA derived from C. nubeculosus salivary glands was displayed on the surface of filamentous phage M13 and enriched for clones binding serum IgE of IBH-affected horses. Ten cDNA inserts encoding putative salivary gland allergens were isolated and termed Cul n 2 to Cul n 11. However, nine cDNA sequences coded for truncated proteins as determined by database searches. The cDNA sequences were amplified by PCR, subcloned into high level expression vectors and expressed as hexahistidine-tagged fusion proteins in Escherichia coli. Preliminary ELISA results obtained with these fusions confirmed the specific binding to serum IgE of affected horses. Therefore, the putative complete open reading frames derived from BLAST analyses were isolated by RACE-PCR and subcloned into expression vectors. The full length proteins expressed in Escherichia coli showed molecular masses in the range of 15.5-68.7 kDa in SDS-PAGE in good agreement with the masses calculated from the predicted protein sequences. Western blot analyses of all recombinant allergens with a serum pool of IBH-affected horses showed their ability to specifically bind serum IgE of sensitized horses, and ELISA determinations yielded individual horse recognition patterns with a frequency of sensitization ranging from 13 to 57%, depending on the allergen tested. The in vivo relevance of eight of the recombinant allergens was demonstrated in intradermal skin testing. For the two characterized allergens Cul n 6 and Cul n 11, sensitized horses were not available for intradermal tests. Control horses without clinical signs of IBH

  2. Phenotypic stability and genetic gains in six-year girth growth of Hevea clones

    Directory of Open Access Journals (Sweden)

    Paulo de Souza Gonçalves

    1999-07-01

    Full Text Available Rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss. Müell. Arg.] budgrafts of seven clones were evaluated on five contrasting sites in the plateau region of the São Paulo State, Brazil. The objective of this work was to study the phenotypic stability for girth growth. The experimental design was a randomized block design with three replications and seven treatments. Analysis of variance of girth at six-year plant growth indicated a highly significant clone x site interaction. Only linear sites and clone x site components of clone x year interaction were significant, indicating that the performance of clones over sites for this trait could be predicted. The clones GT 1 and PB 235 showed the greatest stability in relation to girth growth, with foreseen responses to change, introduced in the sites. The clones PB 235 and IAN 873 showed significative difference in relation to regression coefficient, representing clones with specific adaptability on favorable and unfavorable sites respectively. The clone GT 1 became the most promissory one in the study of stability and adaptability even showing low girth growth. Expected genetic gains from planting sites, along with estimates of clonal variance and repeatability of clonal means are generally greatest or close to the greatest when selection is done at the same site.

  3. Quality Evalution of Potato Clones as Processed Material Cultivated in Lembang

    Science.gov (United States)

    Rahayu, S. T.; Handayani, T.; Levianny, P. S.

    2017-03-01

    Potatoes are widely grown in the temperate as well as tropical zones and are the fourth largest staple crop in the world after maize, wheat and rice. The study aimed to evaluate the quality of several potato clones as raw material on potato based products (chips and boiled). The study was conducted at Indonesian Vegetable Research Institute, Lembang about 1200 m asl height, in 2016. The design used was a randomized complete block design with three replications. The samples tested were 5 clones selection (clones number 1,2,3,4,10). In this study, variety Granola (Clone number 6) and Atlantic (Clone number 7) were used as a susceptible control, meanwhile the Katahdin (Clone number 8) and SP 951 (Clone number 9) were used as the resistant control. Chemical properties tested were starch, reduction sugar, water content, specific gravity, and Total Soluble Solute (TSS). The organoleptic assessment method used was hedonic test with scale of 1-5 (very like until very dislike) which had been done by 15 untrained panelists. Data was statisticaly analized by Duncan’s test (5%). Clone 1 and 2 were preferred by panelist as raw material for potato chips, which got score of ‘very like’ until ‘like’ for color, size, taste, and texture parameters. Although there was no significant difference on color and size parameters for all samples of that boiled potato there, however, clone no 8 can be considered as the most favourite based on taste and texture parameters.

  4. SNP selection and classification of genome-wide SNP data using stratified sampling random forests.

    Science.gov (United States)

    Wu, Qingyao; Ye, Yunming; Liu, Yang; Ng, Michael K

    2012-09-01

    For high dimensional genome-wide association (GWA) case-control data of complex disease, there are usually a large portion of single-nucleotide polymorphisms (SNPs) that are irrelevant with the disease. A simple random sampling method in random forest using default mtry parameter to choose feature subspace, will select too many subspaces without informative SNPs. Exhaustive searching an optimal mtry is often required in order to include useful and relevant SNPs and get rid of vast of non-informative SNPs. However, it is too time-consuming and not favorable in GWA for high-dimensional data. The main aim of this paper is to propose a stratified sampling method for feature subspace selection to generate decision trees in a random forest for GWA high-dimensional data. Our idea is to design an equal-width discretization scheme for informativeness to divide SNPs into multiple groups. In feature subspace selection, we randomly select the same number of SNPs from each group and combine them to form a subspace to generate a decision tree. The advantage of this stratified sampling procedure can make sure each subspace contains enough useful SNPs, but can avoid a very high computational cost of exhaustive search of an optimal mtry, and maintain the randomness of a random forest. We employ two genome-wide SNP data sets (Parkinson case-control data comprised of 408 803 SNPs and Alzheimer case-control data comprised of 380 157 SNPs) to demonstrate that the proposed stratified sampling method is effective, and it can generate better random forest with higher accuracy and lower error bound than those by Breiman's random forest generation method. For Parkinson data, we also show some interesting genes identified by the method, which may be associated with neurological disorders for further biological investigations.

  5. An efficient method of wavelength interval selection based on random frog for multivariate spectral calibration

    Science.gov (United States)

    Yun, Yong-Huan; Li, Hong-Dong; Wood, Leslie R. E.; Fan, Wei; Wang, Jia-Jun; Cao, Dong-Sheng; Xu, Qing-Song; Liang, Yi-Zeng

    2013-07-01

    Wavelength selection is a critical step for producing better prediction performance when applied to spectral data. Considering the fact that the vibrational and rotational spectra have continuous features of spectral bands, we propose a novel method of wavelength interval selection based on random frog, called interval random frog (iRF). To obtain all the possible continuous intervals, spectra are first divided into intervals by moving window of a fix width over the whole spectra. These overlapping intervals are ranked applying random frog coupled with PLS and the optimal ones are chosen. This method has been applied to two near-infrared spectral datasets displaying higher efficiency in wavelength interval selection than others. The source code of iRF can be freely downloaded for academy research at the website: http://code.google.com/p/multivariate-calibration/downloads/list.

  6. Survival of the fittest clone: Pro-apoptotic protein Noxa controls selection of lymphocytes under competitive conditions

    NARCIS (Netherlands)

    Wensveen, F.M.

    2010-01-01

    Darwinistic selection, or ‘survival of the fittest’, is based on intrinsic capacity, relative to that of its competitors in a given niche. This process drives the generation of species by allowing survival of organisms in with favorable, specialized characteristics for a certain niche. However, mere

  7. Delay line length selection in generating fast random numbers with a chaotic laser.

    Science.gov (United States)

    Zhang, Jianzhong; Wang, Yuncai; Xue, Lugang; Hou, Jiayin; Zhang, Beibei; Wang, Anbang; Zhang, Mingjiang

    2012-04-10

    The chaotic light signals generated by an external cavity semiconductor laser have been experimentally demonstrated to extract fast random numbers. However, the photon round-trip time in the external cavity can cause the occurrence of the periodicity in random sequences. To overcome it, the exclusive-or operation on corresponding random bits in samples of the chaotic signal and its time-delay signal from a chaotic laser is required. In this scheme, the proper selection of delay length is a key issue. By doing a large number of experiments and theoretically analyzing the interplay between the Runs test and the threshold value of the autocorrelation function, we find when the corresponding delay time of autocorrelation trace with the correlation coefficient of less than 0.007 is considered as the delay time between the chaotic signal and its time-delay signal, streams of random numbers can be generated with verified randomness.

  8. In vitro Embryogenesis Derived from Shoot Tips in Mass Propagation of Two Selected-Clones of Phalaenopsis

    Directory of Open Access Journals (Sweden)

    Budi WINARTO

    2016-09-01

    Full Text Available Phalaenopsis is of high economic value and market demand in Indonesia; however, orchid products are mostly imported from other countries. ‘Kristina Dwi’ (KD 69.274 and ‘Dedeh’ (D 802.28 are two selected clones with high potential utilized and developed commercially. To support their commercialization, a reliable in vitro propagation protocol is essential.  In the current study, an in vitro mass propagation protocol for KD 69.274 and D 802.28 clones was successfully established using shoot tips as explant sources. A high number of embryos, up to 8.2 embryos per explant, with 58.5% explant regeneration, and 3.5 regenerated-explants in average were regenerated from shoot tips of KD 69.274 clone cultured on  half-strength Murashige and Skoog (MS medium, with full strength micro, Fe-chellate and vitamin containing 0.5 mg/L thidiazuruon (TDZ and 0.25 mg/L N6-benzyladenine (BA. The initial embryos were proliferated by culturing embryos individually on half-strength MS medium with 0.13 mg/L TDZ and 0.25 mg/L BA and resulted in high embryo regeneration up to 91.4%, with 10.2 embryos per explant and no embryo browning. The embryos were multiplied under periodical subcultures of 3 months each, resulting in gradual increasing number of embryos from the first subculture till the fifth subculture, with 23.6 embryos produced, then declined afterward. The embryos were easily germinated on half-strength MS medium with full strength of vitamin and hormone free, with 73.9% embryo germination and 14.9 germinated embryos. Healthy plantlets were stimulated on the same medium with 2 g/L activated charcoal (AC and successfully acclimatized on Cycas rumphii bulk, with 88.3% survival plantlets. Finally, it can be summarized that a new in vitro mass propagation protocol, as new alternative choice for Phalaenopsis propagation, was successfully established.

  9. Human Cloning

    Science.gov (United States)

    2006-07-20

    research group, headed by Douglas Melton and Kevin Eggan, submitted their proposal to a Harvard committee composed of ethicists, scientists and public...United States. Although the company offered no proof of its claim, Dr . Brigette Boisselier, Managing Director of Clonaid, stated that genetic tests would...a year of the Dolly announcement, concerns over human cloning were heightened when Dr . Richard Seed, a Chicago scientist, announced on January 7

  10. Characterization of a recombinant humanized anti-cocaine monoclonal antibody produced from multiple clones for the selection of a master cell bank candidate.

    Science.gov (United States)

    Wetzel, Hanna N; Webster, Rose P; Saeed, Fatima O; Kirley, Terence L; Ball, William J; Norman, Andrew B

    2017-06-03

    We have generated a humanized anti-cocaine monoclonal antibody (mAb), which is at an advanced stage of pre-clinical development. We report here in vitro binding affinity studies, and in vivo pharmacokinetic and efficacy studies of the recombinant mAb. The overall aim was to characterize the recombinant antibody from each of the three highest producing transfected clones and to select one to establish a master cell bank. In mAb pharmacokinetic studies, after injection with h2E2 (120 mg/kg iv) blood was collected from the tail tip of mice over 28 days. Antibody concentrations were quantified using ELISA. The h2E2 concentration as a function of time was fit using a two-compartment pharmacokinetic model. To test in vivo efficacy, mice were injected with h2E2 (120 mg/kg iv), then one hour later injected with an equimolar dose of cocaine. Blood and brain were collected 5 min after cocaine administration. Cocaine concentrations were quantified using LC/MS. The affinity of the antibody for cocaine was determined using a [3H] cocaine binding assay. All three antibodies had long elimination half-lives, 2-5 nM Kd for cocaine, and prevented cocaine's entry into the brain by sequestering it in the plasma. Pharmacokinetic and radioligand binding assays supported designation of the highest producing clone 85 as the master cell bank candidate. Overall, the recombinant h2E2 showed favorable binding properties, pharmacokinetics, and in vivo efficacy. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. Molecular cloning, characterization and positively selected sites of the glutathione S-transferase family from Locusta migratoria.

    Directory of Open Access Journals (Sweden)

    Xueyao Zhang

    Full Text Available Glutathione S-transferases (GSTs are multifunctional enzymes that are involved in the metabolism of endogenous and exogenous compounds and are related to insecticide resistance. The purpose of this study was to provide new information on the molecular characteristics and the positive selection of locust GSTs. Based on the transcriptome database, we sequenced 28 cytosolic GSTs and 4 microsomal GSTs from the migratory locust (Locusta migratoria. We assigned the 28 cytosolic GSTs into 6 classes--sigma, epsilon, delta, theta, omega and zeta, and the 4 microsomal GSTs into 2 subclasses--insect and MGST3. The tissue- and stage-expression patterns of the GSTs differed at the mRNA level. Further, the substrate specificities and kinetic constants of the cytosolic GSTs differed markedly at the protein level. The results of likelihood ratio tests provided strong evidence for positive selection in the delta class. The result of Bayes Empirical Bayes analysis identified 4 amino acid sites in the delta class as positive selection sites. These sites were located on the protein surface. Our findings will facilitate the elucidation of the molecular characteristics and evolutionary aspects of insect GST superfamily.

  12. Five Year Field Evaluation of Prosopis alba Clones on pH 9–10 Soils in Argentina Selected for Growth in the Greenhouse at Seawater Salinities (45 dS m−1

    Directory of Open Access Journals (Sweden)

    Mauricio Ewens

    2012-03-01

    Full Text Available Prosopis alba seedlings, that grew at the 45 dS m−1 salinity level in a previous study of growth and survival of Argentine and Peruvian Prosopis, were propagated by rooting cuttings and established in a seed orchard/long term evaluation trial on soils with low salinity (EC 5.1–7.5 dS m−1 but high pH (8.9 to 10.2. A pH gradient occurred in the field with values ranging from pH 9.4 in block 1 to pH 10.3 in block 5. After five years growth, almost all of the clones had a mean height greater than 4 m and one clone was more than 5 m. Ten of the 21 tested clones had significantly greater biomass growth than the three seed propagated check varieties. The broad-sense (i.e., clone mean heritability was estimated to be 0.45 for biomass, 0.53 for diameter and 0.59 for height indicating that strong genetic gains should be possible by selecting and vegetatively propagating the best genotypes. In the block with the highest pH values, two clones that appear to be P. alba × P. ruscifolia hybrids (i.e., P. vinallilo had the greatest biomass. Correlations between growth during the last two months in the high salinity hydroponic greenhouse selection system and growth in the field were significant (R2 = 0.262 and positive, although the relationship was negative for putative P. vinallilo clones (R2 = 0.938. The several fold increase in biomass of some of the clones over the three check varieties, suggests that the greenhouse screen was successful in identifying superior salt tolerant clones. Apparently whether the greenhouse seedlings had lesser (~1 cm to greater (~3 cm height growth was not as important as just having a healthy live apical meristem. The observed salt tolerance of the putative P. vinalillo clones may prove useful as rootstocks for recently described high pod producing P. alba clones.

  13. [Scientific ethics of human cloning].

    Science.gov (United States)

    Valenzuela, Carlos Y

    2005-01-01

    True cloning is fission, budding or other types of asexual reproduction. In humans it occurs in monozygote twinning. This type of cloning is ethically and religiously good. Human cloning can be performed by twinning (TWClo) or nuclear transfer (NTClo). Both methods need a zygote or a nuclear transferred cell, obtained in vitro (IVTec). They are under the IVTec ethics. IVTecs use humans (zygotes, embryos) as drugs or things; increase the risk of malformations; increase development and size of abnormalities and may cause long-term changes. Cloning for preserving extinct (or almost extinct) animals or humans when sexual reproduction is not possible is ethically valid. The previous selection of a phenotype in human cloning violates some ethical principles. NTClo for reproductive or therapeutic purposes is dangerous since it increases the risk for nucleotide or chromosome mutations, de-programming or re-programming errors, aging or malignancy of the embryo cells thus obtained.

  14. Two-year Randomized Clinical Trial Of Self-etching Adhesives And Selective Enamel Etching

    OpenAIRE

    Pena, MR; Rodrigues CE; JA; Ely; Giannini, C.; Reis, M; AF

    2016-01-01

    Objective: The aim of this randomized, controlled prospective clinical trial was to evaluate the clinical effectiveness of restoring noncarious cervical lesions with two self-etching adhesive systems applied with or without selective enamel etching. Methods: A one-step self-etching adhesive (Xeno V+) and a two-step self-etching system (Clearfil SE Bond) were used. The effectiveness of phosphoric acid selective etching of enamel margins was also evaluated. Fifty-six cavities were restored with...

  15. Hebbian Learning in a Random Network Captures Selectivity Properties of the Prefrontal Cortex.

    Science.gov (United States)

    Lindsay, Grace W; Rigotti, Mattia; Warden, Melissa R; Miller, Earl K; Fusi, Stefano

    2017-11-08

    Complex cognitive behaviors, such as context-switching and rule-following, are thought to be supported by the prefrontal cortex (PFC). Neural activity in the PFC must thus be specialized to specific tasks while retaining flexibility. Nonlinear "mixed" selectivity is an important neurophysiological trait for enabling complex and context-dependent behaviors. Here we investigate (1) the extent to which the PFC exhibits computationally relevant properties, such as mixed selectivity, and (2) how such properties could arise via circuit mechanisms. We show that PFC cells recorded from male and female rhesus macaques during a complex task show a moderate level of specialization and structure that is not replicated by a model wherein cells receive random feedforward inputs. While random connectivity can be effective at generating mixed selectivity, the data show significantly more mixed selectivity than predicted by a model with otherwise matched parameters. A simple Hebbian learning rule applied to the random connectivity, however, increases mixed selectivity and enables the model to match the data more accurately. To explain how learning achieves this, we provide analysis along with a clear geometric interpretation of the impact of learning on selectivity. After learning, the model also matches the data on measures of noise, response density, clustering, and the distribution of selectivities. Of two styles of Hebbian learning tested, the simpler and more biologically plausible option better matches the data. These modeling results provide clues about how neural properties important for cognition can arise in a circuit and make clear experimental predictions regarding how various measures of selectivity would evolve during animal training. SIGNIFICANCE STATEMENT The prefrontal cortex is a brain region believed to support the ability of animals to engage in complex behavior. How neurons in this area respond to stimuli-and in particular, to combinations of stimuli ("mixed

  16. Selecting Optimal Parameters of Random Linear Network Coding for Wireless Sensor Networks

    DEFF Research Database (Denmark)

    Heide, Janus; Zhang, Qi; Fitzek, Frank

    2013-01-01

    This work studies how to select optimal code parameters of Random Linear Network Coding (RLNC) in Wireless Sensor Networks (WSNs). With Rateless Deluge [1] the authors proposed to apply Network Coding (NC) for Over-the-Air Programming (OAP) in WSNs, and demonstrated that with NC a significant...

  17. Tehran Air Pollutants Prediction Based on Random Forest Feature Selection Method

    Science.gov (United States)

    Shamsoddini, A.; Aboodi, M. R.; Karami, J.

    2017-09-01

    Air pollution as one of the most serious forms of environmental pollutions poses huge threat to human life. Air pollution leads to environmental instability, and has harmful and undesirable effects on the environment. Modern prediction methods of the pollutant concentration are able to improve decision making and provide appropriate solutions. This study examines the performance of the Random Forest feature selection in combination with multiple-linear regression and Multilayer Perceptron Artificial Neural Networks methods, in order to achieve an efficient model to estimate carbon monoxide and nitrogen dioxide, sulfur dioxide and PM2.5 contents in the air. The results indicated that Artificial Neural Networks fed by the attributes selected by Random Forest feature selection method performed more accurate than other models for the modeling of all pollutants. The estimation accuracy of sulfur dioxide emissions was lower than the other air contaminants whereas the nitrogen dioxide was predicted more accurate than the other pollutants.

  18. TEHRAN AIR POLLUTANTS PREDICTION BASED ON RANDOM FOREST FEATURE SELECTION METHOD

    Directory of Open Access Journals (Sweden)

    A. Shamsoddini

    2017-09-01

    Full Text Available Air pollution as one of the most serious forms of environmental pollutions poses huge threat to human life. Air pollution leads to environmental instability, and has harmful and undesirable effects on the environment. Modern prediction methods of the pollutant concentration are able to improve decision making and provide appropriate solutions. This study examines the performance of the Random Forest feature selection in combination with multiple-linear regression and Multilayer Perceptron Artificial Neural Networks methods, in order to achieve an efficient model to estimate carbon monoxide and nitrogen dioxide, sulfur dioxide and PM2.5 contents in the air. The results indicated that Artificial Neural Networks fed by the attributes selected by Random Forest feature selection method performed more accurate than other models for the modeling of all pollutants. The estimation accuracy of sulfur dioxide emissions was lower than the other air contaminants whereas the nitrogen dioxide was predicted more accurate than the other pollutants.

  19. Classification of epileptic EEG signals based on simple random sampling and sequential feature selection.

    Science.gov (United States)

    Ghayab, Hadi Ratham Al; Li, Yan; Abdulla, Shahab; Diykh, Mohammed; Wan, Xiangkui

    2016-06-01

    Electroencephalogram (EEG) signals are used broadly in the medical fields. The main applications of EEG signals are the diagnosis and treatment of diseases such as epilepsy, Alzheimer, sleep problems and so on. This paper presents a new method which extracts and selects features from multi-channel EEG signals. This research focuses on three main points. Firstly, simple random sampling (SRS) technique is used to extract features from the time domain of EEG signals. Secondly, the sequential feature selection (SFS) algorithm is applied to select the key features and to reduce the dimensionality of the data. Finally, the selected features are forwarded to a least square support vector machine (LS_SVM) classifier to classify the EEG signals. The LS_SVM classifier classified the features which are extracted and selected from the SRS and the SFS. The experimental results show that the method achieves 99.90, 99.80 and 100 % for classification accuracy, sensitivity and specificity, respectively.

  20. Personal name in Igbo Culture: A dataset on randomly selected personal names and their statistical analysis.

    Science.gov (United States)

    Okagbue, Hilary I; Opanuga, Abiodun A; Adamu, Muminu O; Ugwoke, Paulinus O; Obasi, Emmanuela C M; Eze, Grace A

    2017-12-01

    This data article contains the statistical analysis of Igbo personal names and a sample of randomly selected of such names. This was presented as the following: 1). A simple random sampling of some Igbo personal names and their respective gender associated with each name. 2). The distribution of the vowels, consonants and letters of alphabets of the personal names. 3). The distribution of name length. 4). The distribution of initial and terminal letters of Igbo personal names. The significance of the data was discussed.

  1. Selection of new clones of linalool chemotype from genetic recombination in Lippia alba Seleção de novos clones de quimiotipo linalol em Lippia alba oriundos de recombinação genética

    OpenAIRE

    Elcio Rodrigo Rufino; Walter José Siqueira; Márcia Ortiz Maio Marques; Carlos Augusto Colombo; Joaquim Adelino de Azevedo Filho; Antônio Lúcio Melo Martins

    2012-01-01

    The aromatic and medicinal species Lippia alba is vigorous and rugged native to the South America (Atlantic Rainforest). Because it is an allogamous and self-incompatible species, natural populations have high morphological and chemical variability. This work had as objective to conduct a preliminary screening to identify new promising clones from a novel (recombinant) base population of Lippia alba with regard to its agronomic and phytochemical traits, using the linalool oil or chemotype as ...

  2. Simulated Performance Evaluation of a Selective Tracker Through Random Scenario Generation

    DEFF Research Database (Denmark)

    Hussain, Dil Muhammad Akbar

    2006-01-01

      The paper presents a simulation study on the performance of a target tracker using selective track splitting filter algorithm through a random scenario implemented on a digital signal processor.  In a typical track splitting filter all the observation which fall inside a likelihood ellipse...... are used for update, however, in our proposed selective track splitting filter less number of observations are used for track update.  Much of the previous performance work [1] has been done on specific (deterministic) scenarios. One of the reasons for considering the specific scenarios, which were...

  3. Classification of epileptic EEG signals based on simple random sampling and sequential feature selection

    OpenAIRE

    Ghayab, Hadi Ratham Al; Li, Yan; Abdulla, Shahab; Diykh, Mohammed; Wan, Xiangkui

    2016-01-01

    Electroencephalogram (EEG) signals are used broadly in the medical fields. The main applications of EEG signals are the diagnosis and treatment of diseases such as epilepsy, Alzheimer, sleep problems and so on. This paper presents a new method which extracts and selects features from multi-channel EEG signals. This research focuses on three main points. Firstly, simple random sampling (SRS) technique is used to extract features from the time domain of EEG signals. Secondly, the sequential fea...

  4. Hybrid sequencing approach applied to human fecal metagenomic clone libraries revealed clones with potential biotechnological applications.

    Directory of Open Access Journals (Sweden)

    Mária Džunková

    Full Text Available Natural environments represent an incredible source of microbial genetic diversity. Discovery of novel biomolecules involves biotechnological methods that often require the design and implementation of biochemical assays to screen clone libraries. However, when an assay is applied to thousands of clones, one may eventually end up with very few positive clones which, in most of the cases, have to be "domesticated" for downstream characterization and application, and this makes screening both laborious and expensive. The negative clones, which are not considered by the selected assay, may also have biotechnological potential; however, unfortunately they would remain unexplored. Knowledge of the clone sequences provides important clues about potential biotechnological application of the clones in the library; however, the sequencing of clones one-by-one would be very time-consuming and expensive. In this study, we characterized the first metagenomic clone library from the feces of a healthy human volunteer, using a method based on 454 pyrosequencing coupled with a clone-by-clone Sanger end-sequencing. Instead of whole individual clone sequencing, we sequenced 358 clones in a pool. The medium-large insert (7-15 kb cloning strategy allowed us to assemble these clones correctly, and to assign the clone ends to maintain the link between the position of a living clone in the library and the annotated contig from the 454 assembly. Finally, we found several open reading frames (ORFs with previously described potential medical application. The proposed approach allows planning ad-hoc biochemical assays for the clones of interest, and the appropriate sub-cloning strategy for gene expression in suitable vectors/hosts.

  5. Statistical inference of selection and divergence from a time-dependent Poisson random field model.

    Directory of Open Access Journals (Sweden)

    Amei Amei

    Full Text Available We apply a recently developed time-dependent Poisson random field model to aligned DNA sequences from two related biological species to estimate selection coefficients and divergence time. We use Markov chain Monte Carlo methods to estimate species divergence time and selection coefficients for each locus. The model assumes that the selective effects of non-synonymous mutations are normally distributed across genetic loci but constant within loci, and synonymous mutations are selectively neutral. In contrast with previous models, we do not assume that the individual species are at population equilibrium after divergence. Using a data set of 91 genes in two Drosophila species, D. melanogaster and D. simulans, we estimate the species divergence time t(div = 2.16 N(e (or 1.68 million years, assuming the haploid effective population size N(e = 6.45 x 10(5 years and a mean selection coefficient per generation μ(γ = 1.98/N(e. Although the average selection coefficient is positive, the magnitude of the selection is quite small. Results from numerical simulations are also presented as an accuracy check for the time-dependent model.

  6. Selection bias and subject refusal in a cluster-randomized controlled trial

    Directory of Open Access Journals (Sweden)

    Rochelle Yang

    2017-07-01

    Full Text Available Abstract Background Selection bias and non-participation bias are major methodological concerns which impact external validity. Cluster-randomized controlled trials are especially prone to selection bias as it is impractical to blind clusters to their allocation into intervention or control. This study assessed the impact of selection bias in a large cluster-randomized controlled trial. Methods The Improved Cardiovascular Risk Reduction to Enhance Rural Primary Care (ICARE study examined the impact of a remote pharmacist-led intervention in twelve medical offices. To assess eligibility, a standardized form containing patient demographics and medical information was completed for each screened patient. Eligible patients were approached by the study coordinator for recruitment. Both the study coordinator and the patient were aware of the site’s allocation prior to consent. Patients who consented or declined to participate were compared across control and intervention arms for differing characteristics. Statistical significance was determined using a two-tailed, equal variance t-test and a chi-square test with adjusted Bonferroni p-values. Results were adjusted for random cluster variation. Results There were 2749 completed screening forms returned to research staff with 461 subjects who had either consented or declined participation. Patients with poorly controlled diabetes were found to be significantly more likely to decline participation in intervention sites compared to those in control sites. A higher mean diastolic blood pressure was seen in patients with uncontrolled hypertension who declined in the control sites compared to those who declined in the intervention sites. However, these findings were no longer significant after adjustment for random variation among the sites. After this adjustment, females were now found to be significantly more likely to consent than males (odds ratio = 1.41; 95% confidence interval = 1.03, 1

  7. Cloning-free CRISPR

    Directory of Open Access Journals (Sweden)

    Mandana Arbab

    2015-11-01

    Full Text Available We present self-cloning CRISPR/Cas9 (scCRISPR, a technology that allows for CRISPR/Cas9-mediated genomic mutation and site-specific knockin transgene creation within several hours by circumventing the need to clone a site-specific single-guide RNA (sgRNA or knockin homology construct for each target locus. We introduce a self-cleaving palindromic sgRNA plasmid and a short double-stranded DNA sequence encoding the desired locus-specific sgRNA into target cells, allowing them to produce a locus-specific sgRNA plasmid through homologous recombination. scCRISPR enables efficient generation of gene knockouts (∼88% mutation rate at approximately one-sixth the cost of plasmid-based sgRNA construction with only 2 hr of preparation for each targeted site. Additionally, we demonstrate efficient site-specific knockin of GFP transgenes without any plasmid cloning or genome-integrated selection cassette in mouse and human embryonic stem cells (2%–4% knockin rate through PCR-based addition of short homology arms. scCRISPR substantially lowers the bar on mouse and human transgenesis.

  8. Evaluación y selección preliminar por rendimiento de tubérculo y potencial industrial de 36 clones de papa (Solanum tuberosum L. Preliminary evaluation and selection of yield and industrial potential of 36 potato clones (Solanum tuberosum L.

    Directory of Open Access Journals (Sweden)

    Perilla C. Alexánder

    2002-08-01

    augmented designs analysis in randomized bloc s, in order to choose the clones for several variables and not for one as the traditional analysis. With the macro in the analysis procedure, were found 19 clones, 7 are superior in the group of the evaluated variables: the clones 6.5 and 12.59 are recommended for processing in french fries, 2.14, 6.8, 11.35, 12.62 y 12.71 for chips. Between 7 clones mentioned stand out 6.8 and 2.14 for present an less susceptibility to late blight and, the clon 6.5 for having less time in the ripen of tuber (15 days less than Capiro.

  9. Evaluation of Quantitative and Qualitative Traits of 18 Potato Clones

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    A. R Bolandi

    2016-10-01

    to those of check. Based on results of this experiment, the clones 397003-7, 396151-27 and 397045-100 could be selected for Ardebil region. The objective of this research was to evaluate the quantitative and qualitative traits of cultivars and advanced potato clones in spring cultivation (Jolge-e-Rokh region. Materials and Methods In this research, 18 potato clones for the quantitative and qualitative traits were compared with three check cultivars including: Agria (suitable for French-fries, Marfona (suitable for boiled eating and Lady Rosetta (suitable for chips in Jolge-Rokh Agriculture Research Station, the location 35'¸ 50° north latitude and 59° east longitude and 1721 m above sea level, in crop year 2011. Experimental design was Randomized Complete Block Design (RCBD with three replications. Treatment consisted of 18 advanced potato clones: 396151-8, 397045-4, 397045-10, TP12-13, TP21-29, TP12-8, 397007-16, 397007-17, 396140-6, 397009-8, 397015-14, 397003-7, 396151-27, 397045-100, 397097-9, 396151-20, 397045-7 and 69 indigenous with three control cultivars (Agria, Marfona and Lady Rosetta. Tubers were planted on two rows with 6 meters length. Distance between row and plants on the row were 75 and 25 cm, respectively. Area of each plot was 9 square meter. The evaluated characters were total yield, marketable yield, eye number, dry matter percentage, tuber number per plant, tuber weight per plant and mean of tuber weight. In order to measure total yield, after maturity, and remove the aerial organs, all of the tubers were harvested and the fresh weight was obtained. After removal of the tumor in bad shape, with soft rot and smaller than 30 mm that cannot be sold as part of the marketable yield, rest of them were used to measure marketable yield. Tuber dry matter percentage (TDM% was determined from the relationship between fresh and dry weights of sub-sample of 8-10 thinly sliced tubers dried for 48 h at 80° C. Data were analyzed using SAS 9.1 software. The

  10. Simple Cloning by Prolonged Overlap Extension-PCR with Application to the Preparation of Large-Size Random Gene Mutagenesis Library in Escherichia coli.

    Science.gov (United States)

    Zhong, Chao; You, Chun; Wei, Ping; Zhang, Yi-Heng Percival

    2017-01-01

    We developed a simple method (simple cloning) for subcloning DNA fragments into any location of a targeted vector without the need of restriction enzyme, ligase, exonuclease, or recombinase in Escherichia coli. This technology can be applied to common E. coli hosts (e.g., DH5α, JM109, TOP10, BL21(DE3)). The protocol includes three steps: (1) generate DNA insert and linear vector backbone by regular high-fidelity PCR, where these two DNA fragments contain 3' and 5' overlapping termini; (2) generate DNA multimers based on these two DNA fragments by using prolonged overlap extension-PCR (POE-PCR) without primers added; and (3) transform POE-PCR product to competent Escherichia coli cells directly, yielding the desired plasmid. Simple cloning provides a new cloning method with great simplicity and flexibility. Furthermore, this new method can be modified for the preparation of a large-size mutant library for directed evolution in E. coli. Using this method, it is very easy to generate a mutant library with a size of more than 10(7) per 50 μL of the POE-PCR product within 1 day.

  11. Effect of non-random mating on genomic and BLUP selection schemes

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    Nirea Kahsay G

    2012-04-01

    Full Text Available Abstract Background The risk of long-term unequal contribution of mating pairs to the gene pool is that deleterious recessive genes can be expressed. Such consequences could be alleviated by appropriately designing and optimizing breeding schemes i.e. by improving selection and mating procedures. Methods We studied the effect of mating designs, random, minimum coancestry and minimum covariance of ancestral contributions on rate of inbreeding and genetic gain for schemes with different information sources, i.e. sib test or own performance records, different genetic evaluation methods, i.e. BLUP or genomic selection, and different family structures, i.e. factorial or pair-wise. Results Results showed that substantial differences in rates of inbreeding due to mating design were present under schemes with a pair-wise family structure, for which minimum coancestry turned out to be more effective to generate lower rates of inbreeding. Specifically, substantial reductions in rates of inbreeding were observed in schemes using sib test records and BLUP evaluation. However, with a factorial family structure, differences in rates of inbreeding due mating designs were minor. Moreover, non-random mating had only a small effect in breeding schemes that used genomic evaluation, regardless of the information source. Conclusions It was concluded that minimum coancestry remains an efficient mating design when BLUP is used for genetic evaluation or when the size of the population is small, whereas the effect of non-random mating is smaller in schemes using genomic evaluation.

  12. Repetibilidade e número de colheitas para seleção de clones de cana-de-açúcar Repeatability and harvest numbers in selecting sugarcane clones

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    Adésio Ferreira

    2005-08-01

    Full Text Available Os objetivos deste trabalho foram estabelecer estimativas dos coeficientes de repetibilidade (r e determinar a previsibilidade (R² e o número de medições necessárias das características toneladas de colmos por hectare, toneladas de sacarose no caldo da cana por hectare e teor de sacarose dos colmos, pol porcento cana, em genótipos de cana-de-açúcar. O delineamento experimental utilizado foi o de blocos casualizados, com três repetições em quatro experimentos e quatro repetições nos demais experimentos. As estimativas de repetibilidade foram obtidas pelos métodos estatísticos da análise de variância, componentes principais com base na matriz de correlações e análise estrutural (correlação, r - médio. As estimativas dos coeficientes de repetibilidade revelaram valores muito semelhantes. A repetibilidade média geral nas três características foi superior a 0,60, demonstrando regularidade do desempenho dos genótipos nas várias medições (cortes e confiabilidade na discriminação genotípica superior a 87%. Verificou-se, nas três características, a necessidade do emprego de no mínimo três cortes, para que a seleção possa ser praticada com previsibilidade do valor real do genótipo acima de 80%.This work aimed at the establishment of the repeatability coefficients (r, determination of the predictability degree (R² and the needed measurement numbers for tons of cane per hectare, percentage of pol (sucrose in the juice of cane and tons of pol in the juice of cane per hectare in sugarcane genotypes. A randomized block experimental design, with three replicates in four experiments and four replicates in the other experiments was used. The repeatability estimates were obtained by the statistical methods: anova; main components based on correlation matrix; and structural analysis (correlation, average r. The estimates of the repeatability coefficients showed values with very similar magnitude. The general average

  13. Emulsion PCR: a high efficient way of PCR amplification of random DNA libraries in aptamer selection.

    Directory of Open Access Journals (Sweden)

    Keke Shao

    Full Text Available Aptamers are short RNA or DNA oligonucleotides which can bind with different targets. Typically, they are selected from a large number of random DNA sequence libraries. The main strategy to obtain aptamers is systematic evolution of ligands by exponential enrichment (SELEX. Low efficiency is one of the limitations for conventional PCR amplification of random DNA sequence library in aptamer selection because of relative low products and high by-products formation efficiency. Here, we developed emulsion PCR for aptamer selection. With this method, the by-products formation decreased tremendously to an undetectable level, while the products formation increased significantly. Our results indicated that by-products in conventional PCR amplification were from primer-product and product-product hybridization. In emulsion PCR, we can completely avoid the product-product hybridization and avoid the most of primer-product hybridization if the conditions were optimized. In addition, it also showed that the molecule ratio of template to compartment was crucial to by-product formation efficiency in emulsion PCR amplification. Furthermore, the concentration of the Taq DNA polymerase in the emulsion PCR mixture had a significant impact on product formation efficiency. So, the results of our study indicated that emulsion PCR could improve the efficiency of SELEX.

  14. Human cloning 2001.

    Science.gov (United States)

    Healy, David L; Weston, Gareth; Pera, Martin F; Rombauts, Luk; Trounson, Alan O

    2002-05-01

    This review summaries human cloning from a clinical perspective. Natural human clones, that is, monozygotic twins, are increasing in the general community. Iatrogenic human clones have been produced for decades in infertile couples given fertility treatment such as ovulation induction. A clear distinction must be made between therapeutic cloning using embryonic stem cells and reproductive cloning attempts. Unlike the early clinical years of in vitro fertilization, with cloning there is no animal model that is safe and dependable. Until there is such a model, 'Dolly'-style human cloning is medically unacceptable.

  15. Cloning of observables

    OpenAIRE

    Ferraro, Alessandro; Galbiati, Matteo; Paris, Matteo G. A.

    2005-01-01

    We introduce the concept of cloning for classes of observables and classify cloning machines for qubit systems according to the number of parameters needed to describe the class under investigation. A no-cloning theorem for observables is derived and the connections between cloning of observables and joint measurements of noncommuting observables are elucidated. Relationships with cloning of states and non-demolition measurements are also analyzed.

  16. Assessing the accuracy and stability of variable selection methods for random forest modeling in ecology.

    Science.gov (United States)

    Fox, Eric W; Hill, Ryan A; Leibowitz, Scott G; Olsen, Anthony R; Thornbrugh, Darren J; Weber, Marc H

    2017-07-01

    Random forest (RF) modeling has emerged as an important statistical learning method in ecology due to its exceptional predictive performance. However, for large and complex ecological data sets, there is limited guidance on variable selection methods for RF modeling. Typically, either a preselected set of predictor variables are used or stepwise procedures are employed which iteratively remove variables according to their importance measures. This paper investigates the application of variable selection methods to RF models for predicting probable biological stream condition. Our motivating data set consists of the good/poor condition of n = 1365 stream survey sites from the 2008/2009 National Rivers and Stream Assessment, and a large set (p = 212) of landscape features from the StreamCat data set as potential predictors. We compare two types of RF models: a full variable set model with all 212 predictors and a reduced variable set model selected using a backward elimination approach. We assess model accuracy using RF's internal out-of-bag estimate, and a cross-validation procedure with validation folds external to the variable selection process. We also assess the stability of the spatial predictions generated by the RF models to changes in the number of predictors and argue that model selection needs to consider both accuracy and stability. The results suggest that RF modeling is robust to the inclusion of many variables of moderate to low importance. We found no substantial improvement in cross-validated accuracy as a result of variable reduction. Moreover, the backward elimination procedure tended to select too few variables and exhibited numerous issues such as upwardly biased out-of-bag accuracy estimates and instabilities in the spatial predictions. We use simulations to further support and generalize results from the analysis of real data. A main purpose of this work is to elucidate issues of model selection bias and instability to ecologists interested in

  17. PReFerSim: fast simulation of demography and selection under the Poisson Random Field model.

    Science.gov (United States)

    Ortega-Del Vecchyo, Diego; Marsden, Clare D; Lohmueller, Kirk E

    2016-11-15

    The Poisson Random Field (PRF) model has become an important tool in population genetics to study weakly deleterious genetic variation under complicated demographic scenarios. Currently, there are no freely available software applications that allow simulation of genetic variation data under this model. Here we present PReFerSim, an ANSI C program that performs forward simulations under the PRF model. PReFerSim models changes in population size, arbitrary amounts of inbreeding, dominance and distributions of selective effects. Users can track summaries of genetic variation over time and output trajectories of selected alleles. PReFerSim is freely available at: https://github.com/LohmuellerLab/PReFerSim CONTACT: klohmueller@ucla.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  18. AN APPROACH FOR CLONE DETECTION IN DOCUMENTATION REUSE

    Directory of Open Access Journals (Sweden)

    D. V. Lutsiv

    2014-07-01

    Full Text Available The paper focuses on the searching method for repetitions in DocBook/DRL or plain text documents. An algorithm has been designed based on software clone detection. The algorithm supports filtering results: clones are rejected if clone length in the group is less than 5 symbols, intersection of clone groups is eliminated, meaningfulness clones are removed, the groups containing clones consisting only of XML are eliminated. Remaining search is supported: found clones are extracted from the documentation, and clone search is repeated. One step is proved to be enough. Adaptive reuse technique of Paul Bassett – Stan Jarzabek has been implemented. A software tool has been developed on the basis of the algorithm. The tool supports setting parameters for repetitions detection and visualization of the obtained results. The tool is integrated into DocLine document development environment, and provides refactoring of documents using found clones. The Clone Miner clone detection utility is used for clones search. The method has been evaluated for Linux Kernel Documentation (29 documents, 25000 lines. Five semantic kinds of clones have been selected: terms (abbreviations, one word and two word terms, hyperlinks, license agreements, functionality description, and code examples. 451 meaningful clone groups have been found, average clone length is 4.43 tokens, and average number of clones in a group is 3.56.

  19. Selective oropharyngeal decontamination versus selective digestive decontamination in critically ill patients: a meta-analysis of randomized controlled trials

    Directory of Open Access Journals (Sweden)

    Zhao D

    2015-07-01

    Full Text Available Di Zhao,1,* Jian Song,2,* Xuan Gao,3 Fei Gao,4 Yupeng Wu,2 Yingying Lu,5 Kai Hou1 1Department of Neurosurgery, The First Hospital of Hebei Medical University, 2Department of Neurosurgery, 3Department of Neurology, The Second Hospital of Hebei Medical University, 4Hebei Provincial Procurement Centers for Medical Drugs and Devices, 5Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang People’s Republic of China *These authors contributed equally to this work Background: Selective digestive decontamination (SDD and selective oropharyngeal decontamination (SOD are associated with reduced mortality and infection rates among patients in intensive care units (ICUs; however, whether SOD has a superior effect than SDD remains uncertain. Hence, we conducted a meta-analysis of randomized controlled trials (RCTs to compare SOD with SDD in terms of clinical outcomes and antimicrobial resistance rates in patients who were critically ill. Methods: RCTs published in PubMed, Embase, and Web of Science were systematically reviewed to compare the effects of SOD and SDD in patients who were critically ill. Outcomes included day-28 mortality, length of ICU stay, length of hospital stay, duration of mechanical ventilation, ICU-acquired bacteremia, and prevalence of antibiotic-resistant Gram-negative bacteria. Results were expressed as risk ratio (RR with 95% confidence intervals (CIs, and weighted mean differences (WMDs with 95% CIs. Pooled estimates were performed using a fixed-effects model or random-effects model, depending on the heterogeneity among studies. Results: A total of four RCTs involving 23,822 patients met the inclusion criteria and were included in this meta-analysis. Among patients whose admitting specialty was surgery, cardiothoracic surgery (57.3% and neurosurgery (29.7% were the two main types of surgery being performed. Pooled results showed that SOD had similar effects as SDD in day-28 mortality (RR =1

  20. Ethnopharmacological versus random plant selection methods for the evaluation of the antimycobacterial activity

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    Danilo R. Oliveira

    2011-05-01

    Full Text Available The municipality of Oriximiná, Brazil, has 33 quilombola communities in remote areas, endowed with wide experience in the use of medicinal plants. An ethnobotanical survey was carried out in five of these communities. A free-listing method directed for the survey of species locally indicated against Tuberculosis and lung problems was also applied. Data were analyzed by quantitative techniques: saliency index and major use agreement. Thirty four informants related 254 ethnospecies. Among these, 43 were surveyed for possible antimycobacterial activity. As a result of those informations, ten species obtained from the ethnodirected approach (ETHNO and eighteen species obtained from the random approach (RANDOM were assayed against Mycobacterium tuberculosis by the microdilution method, using resazurin as an indicator of cell viability. The best results for antimycobacterial activity were obtained of some plants selected by the ethnopharmacological approach (50% ETHNO x 16,7% RANDOM. These results can be even more significant if we consider that the therapeutic success obtained among the quilombola practice is complex, being the use of some plants acting as fortifying agents, depurative, vomitory, purgative and bitter remedy, especially to infectious diseases, of great importance to the communities in the curing or recovering of health as a whole.

  1. Random forest variable selection in spatial malaria transmission modelling in Mpumalanga Province, South Africa.

    Science.gov (United States)

    Kapwata, Thandi; Gebreslasie, Michael T

    2016-11-16

    Malaria is an environmentally driven disease. In order to quantify the spatial variability of malaria transmission, it is imperative to understand the interactions between environmental variables and malaria epidemiology at a micro-geographic level using a novel statistical approach. The random forest (RF) statistical learning method, a relatively new variable-importance ranking method, measures the variable importance of potentially influential parameters through the percent increase of the mean squared error. As this value increases, so does the relative importance of the associated variable. The principal aim of this study was to create predictive malaria maps generated using the selected variables based on the RF algorithm in the Ehlanzeni District of Mpumalanga Province, South Africa. From the seven environmental variables used [temperature, lag temperature, rainfall, lag rainfall, humidity, altitude, and the normalized difference vegetation index (NDVI)], altitude was identified as the most influential predictor variable due its high selection frequency. It was selected as the top predictor for 4 out of 12 months of the year, followed by NDVI, temperature and lag rainfall, which were each selected twice. The combination of climatic variables that produced the highest prediction accuracy was altitude, NDVI, and temperature. This suggests that these three variables have high predictive capabilities in relation to malaria transmission. Furthermore, it is anticipated that the predictive maps generated from predictions made by the RF algorithm could be used to monitor the progression of malaria and assist in intervention and prevention efforts with respect to malaria.

  2. Random forest variable selection in spatial malaria transmission modelling in Mpumalanga Province, South Africa

    Directory of Open Access Journals (Sweden)

    Thandi Kapwata

    2016-11-01

    Full Text Available Malaria is an environmentally driven disease. In order to quantify the spatial variability of malaria transmission, it is imperative to understand the interactions between environmental variables and malaria epidemiology at a micro-geographic level using a novel statistical approach. The random forest (RF statistical learning method, a relatively new variable-importance ranking method, measures the variable importance of potentially influential parameters through the percent increase of the mean squared error. As this value increases, so does the relative importance of the associated variable. The principal aim of this study was to create predictive malaria maps generated using the selected variables based on the RF algorithm in the Ehlanzeni District of Mpumalanga Province, South Africa. From the seven environmental variables used [temperature, lag temperature, rainfall, lag rainfall, humidity, altitude, and the normalized difference vegetation index (NDVI], altitude was identified as the most influential predictor variable due its high selection frequency. It was selected as the top predictor for 4 out of 12 months of the year, followed by NDVI, temperature and lag rainfall, which were each selected twice. The combination of climatic variables that produced the highest prediction accuracy was altitude, NDVI, and temperature. This suggests that these three variables have high predictive capabilities in relation to malaria transmission. Furthermore, it is anticipated that the predictive maps generated from predictions made by the RF algorithm could be used to monitor the progression of malaria and assist in intervention and prevention efforts with respect to malaria.

  3. Selecting the appropriate pacing mode for patients with sick sinus syndrome: evidence from randomized clinical trials.

    Science.gov (United States)

    Albertsen, A E; Nielsen, J C

    2003-12-01

    Several observational studies have indicated that selection of pacing mode may be important for the clinical outcome in patients with symptomatic bradycardia, affecting the development of atrial fibrillation (AF), thromboembolism, congestive heart failure, mortality and quality of life. In this paper we present and discuss the most recent data from six randomized trials on mode selection in patients with sick sinus syndrome (SSS). In pacing mode selection, VVI(R) pacing is the least attractive solution, increasing the incidence of AF and-as compared with AAI(R) pacing, also the incidence of heart failure, thromboembolism and death. VVI(R) pacing should not be used as the primary pacing mode in patients with SSS, who haven't chronic AF. AAIR pacing is superior to DDDR pacing, reducing AF and preserving left ventricular function. Single site right ventricular pacing-VVI(R) or DDD(R) mode-causes an abnormal ventricular activation and contraction (called ventricular desynchronization), which results in a reduced left ventricular function. Despite the risk of AV block, we consider AAIR pacing to be the optimal pacing mode for isolated SSS today and an algorithm to select patients for AAIR pacing is suggested. Trials on new pacemaker algorithms minimizing right ventricular pacing as well as trials testing alternative pacing sites and multisite pacing to reduce ventricular desynchronization can be expected within the next years.

  4. Cloning cattle: the methods in the madness.

    Science.gov (United States)

    Oback, Björn; Wells, David N

    2007-01-01

    Somatic cell nuclear transfer (SCNT) is much more widely and efficiently practiced in cattle than in any other species, making this arguably the most important mammal cloned to date. While the initial objective behind cattle cloning was commercially driven--in particular to multiply genetically superior animals with desired phenotypic traits and to produce genetically modified animals-researchers have now started to use bovine SCNT as a tool to address diverse questions in developmental and cell biology. In this paper, we review current cattle cloning methodologies and their potential technical or biological pitfalls at any step of the procedure. In doing so, we focus on one methodological parameter, namely donor cell selection. We emphasize the impact of epigenetic and genetic differences between embryonic, germ, and somatic donor cell types on cloning efficiency. Lastly, we discuss adult phenotypes and fitness of cloned cattle and their offspring and illustrate some of the more imminent commercial cattle cloning applications.

  5. Geography and genography: prediction of continental origin using randomly selected single nucleotide polymorphisms

    Directory of Open Access Journals (Sweden)

    Ramoni Marco F

    2007-03-01

    Full Text Available Abstract Background Recent studies have shown that when individuals are grouped on the basis of genetic similarity, group membership corresponds closely to continental origin. There has been considerable debate about the implications of these findings in the context of larger debates about race and the extent of genetic variation between groups. Some have argued that clustering according to continental origin demonstrates the existence of significant genetic differences between groups and that these differences may have important implications for differences in health and disease. Others argue that clustering according to continental origin requires the use of large amounts of genetic data or specifically chosen markers and is indicative only of very subtle genetic differences that are unlikely to have biomedical significance. Results We used small numbers of randomly selected single nucleotide polymorphisms (SNPs from the International HapMap Project to train naïve Bayes classifiers for prediction of ancestral continent of origin. Predictive accuracy was tested on two independent data sets. Genetically similar groups should be difficult to distinguish, especially if only a small number of genetic markers are used. The genetic differences between continentally defined groups are sufficiently large that one can accurately predict ancestral continent of origin using only a minute, randomly selected fraction of the genetic variation present in the human genome. Genotype data from only 50 random SNPs was sufficient to predict ancestral continent of origin in our primary test data set with an average accuracy of 95%. Genetic variations informative about ancestry were common and widely distributed throughout the genome. Conclusion Accurate characterization of ancestry is possible using small numbers of randomly selected SNPs. The results presented here show how investigators conducting genetic association studies can use small numbers of arbitrarily

  6. Joint random beam and spectrum selection for spectrum sharing systems with partial channel state information

    KAUST Repository

    Abdallah, Mohamed M.

    2013-11-01

    In this work, we develop joint interference-aware random beam and spectrum selection scheme that provide enhanced performance for the secondary network under the condition that the interference observed at the primary receiver is below a predetermined acceptable value. We consider a secondary link composed of a transmitter equipped with multiple antennas and a single-antenna receiver sharing the same spectrum with a set of primary links composed of a single-antenna transmitter and a single-antenna receiver. The proposed schemes jointly select a beam, among a set of power-optimized random beams, as well as the primary spectrum that maximizes the signal-to-interference-plus-noise ratio (SINR) of the secondary link while satisfying the primary interference constraint. In particular, we consider the case where the interference level is described by a q-bit description of its magnitude, whereby we propose a technique to find the optimal quantizer thresholds in a mean square error (MSE) sense. © 2013 IEEE.

  7. Interference-aware random beam selection schemes for spectrum sharing systems

    KAUST Repository

    Abdallah, Mohamed

    2012-10-19

    Spectrum sharing systems have been recently introduced to alleviate the problem of spectrum scarcity by allowing secondary unlicensed networks to share the spectrum with primary licensed networks under acceptable interference levels to the primary users. In this work, we develop interference-aware random beam selection schemes that provide enhanced performance for the secondary network under the condition that the interference observed by the receivers of the primary network is below a predetermined/acceptable value. We consider a secondary link composed of a transmitter equipped with multiple antennas and a single-antenna receiver sharing the same spectrum with a primary link composed of a single-antenna transmitter and a single-antenna receiver. The proposed schemes select a beam, among a set of power-optimized random beams, that maximizes the signal-to-interference-plus-noise ratio (SINR) of the secondary link while satisfying the primary interference constraint for different levels of feedback information describing the interference level at the primary receiver. For the proposed schemes, we develop a statistical analysis for the SINR statistics as well as the capacity and bit error rate (BER) of the secondary link.

  8. Feature selection for outcome prediction in oesophageal cancer using genetic algorithm and random forest classifier.

    Science.gov (United States)

    Paul, Desbordes; Su, Ruan; Romain, Modzelewski; Sébastien, Vauclin; Pierre, Vera; Isabelle, Gardin

    2017-09-01

    The outcome prediction of patients can greatly help to personalize cancer treatment. A large amount of quantitative features (clinical exams, imaging, …) are potentially useful to assess the patient outcome. The challenge is to choose the most predictive subset of features. In this paper, we propose a new feature selection strategy called GARF (genetic algorithm based on random forest) extracted from positron emission tomography (PET) images and clinical data. The most relevant features, predictive of the therapeutic response or which are prognoses of the patient survival 3 years after the end of treatment, were selected using GARF on a cohort of 65 patients with a local advanced oesophageal cancer eligible for chemo-radiation therapy. The most relevant predictive results were obtained with a subset of 9 features leading to a random forest misclassification rate of 18±4% and an areas under the of receiver operating characteristic (ROC) curves (AUC) of 0.823±0.032. The most relevant prognostic results were obtained with 8 features leading to an error rate of 20±7% and an AUC of 0.750±0.108. Both predictive and prognostic results show better performances using GARF than using 4 other studied methods. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. AQUA Cloning: A Versatile and Simple Enzyme-Free Cloning Approach.

    Directory of Open Access Journals (Sweden)

    Hannes M Beyer

    Full Text Available Assembly cloning is increasingly replacing conventional restriction enzyme and DNA-ligase-dependent cloning methods for reasons of efficiency and performance. Here, we describe AQUA (advanced quick assembly, a simple and versatile seamless assembly cloning approach. We demonstrate the applicability and versatility of AQUA Cloning in selected proof-of-principle applications including targeted insertion-, deletion- and site-directed point-mutagenesis, and combinatorial cloning. Furthermore, we show the one pot de novo assembly of multiple DNA fragments into a single circular plasmid encoding a complex light- and chemically-regulated Boolean A NIMPLY B logic operation. AQUA Cloning harnesses intrinsic in vivo processing of linear DNA fragments with short regions of homology of 16 to 32 bp mediated by Escherichia coli. It does not require any kits, enzymes or preparations of reagents and is the simplest assembly cloning protocol to date.

  10. Mouse cloning using a drop of peripheral blood.

    Science.gov (United States)

    Kamimura, Satoshi; Inoue, Kimiko; Ogonuki, Narumi; Hirose, Michiko; Oikawa, Mami; Yo, Masahiro; Ohara, Osamu; Miyoshi, Hiroyuki; Ogura, Atsuo

    2013-08-01

    Somatic cell nuclear transfer (SCNT) is a unique technology that produces cloned animals from single cells. It is desirable from a practical viewpoint that donor cells can be collected noninvasively and used readily for nuclear transfer. The present study was undertaken to determine whether peripheral blood cells freshly collected from living mice could be used for SCNT. We collected a drop of peripheral blood (15-45 μl) from the tail of a donor. A nucleated cell (leukocyte) suspension was prepared by lysing the red blood cells. Following SCNT using randomly selected leukocyte nuclei, cloned offspring were born at a 2.8% birth rate. Fluorescence-activated cell sorting revealed that granulocytes/monocytes and lymphocytes could be roughly distinguished by their sizes, the former being significantly larger. We then cloned putative granulocytes/monocytes and lymphocytes separately and obtained 2.1% and 1.7% birth rates, respectively (P > 0.05). Because the use of lymphocyte nuclei inevitably results in the birth of offspring with DNA rearrangements, we applied granulocyte/monocyte cloning to two genetically modified strains and two recombinant inbred strains. Normal-looking offspring were obtained from all four strains tested. The present study clearly indicated that genetic copies of mice could be produced using a drop of peripheral blood from living donors. This strategy will be applied to the rescue of infertile founder animals or a "last-of-line" animal possessing invaluable genetic resources.

  11. Physiological and transcriptional responses of two contrasting Populus clones to nitrogen stress.

    Science.gov (United States)

    Wang, Xiaoli; Li, Xiaodong; Zhang, Sheng; Korpelainen, Helena; Li, Chunyang

    2016-05-01

    The aim of this study was to reveal mechanisms responsible for nitrogen (N) stress in two contrasting Populus clones. Leaves of Nanlin 1388 (N stress-insensitive clone hybrids of Populus deltoides Bart.CV. × Populus euramericana (Dode) Guineir CV) and Nanlin 895 (N stress-sensitive clone hybrids of Populus deltoides Bart.CV. × Populus euramericana (Dode) Guineir CV) were harvested and analyzed. Different responses visible in photosynthesis, N and carbon contents, physiological traits, and chlorophyll were observed. The Solexa/Illumina's digital gene expression system was used to investigate differentially expressed miRNAs and mRNAs under N stress. Target profiling, and biological network and function analyses were also performed. Randomly selected mRNAs and miRNAs were validated by quantitative reverse transcription polymerase chain reaction. In all, 110 Nanlin 1388 and 122 Nanlin 895 miRNAs were differentially expressed, among which 34 and 23 miRNAs were newly found in the two clones, respectively. Under N stress, a total of 329 and 98 mRNAs were regulated in N stress-insensitive and -sensitive clones, respectively. Notably, the miR396 family and its regulated mRNAs were altered in both clones under N stress, while miR646 was regulated only in the N stress-insensitive clone (Nanlin 1388), and miR156, miR319 and miR393 in the N stress-sensitive clone (Nanlin 895). Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses also proved several clone-specific functions and pathways. These findings may be significant for understanding the genetic responses of Populus to N stress. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  12. Does the Use of a Decision Aid Improve Decision Making in Prosthetic Heart Valve Selection? A Multicenter Randomized Trial

    NARCIS (Netherlands)

    Korteland, Nelleke M.; Ahmed, Yunus; Koolbergen, David R.; Brouwer, Marjan; de Heer, Frederiek; Kluin, Jolanda; Bruggemans, Eline F.; Klautz, Robert J. M.; Stiggelbout, Anne M.; Bucx, Jeroen J. J.; Roos-Hesselink, Jolien W.; Polak, Peter; Markou, Thanasie; van den Broek, Inge; Ligthart, Rene; Bogers, Ad J. J. C.; Takkenberg, Johanna J. M.

    2017-01-01

    A Dutch online patient decision aid to support prosthetic heart valve selection was recently developed. A multicenter randomized controlled trial was conducted to assess whether use of the patient decision aid results in optimization of shared decision making in prosthetic heart valve selection. In

  13. Selective outcome reporting and sponsorship in randomized controlled trials in IVF and ICSI.

    Science.gov (United States)

    Braakhekke, M; Scholten, I; Mol, F; Limpens, J; Mol, B W; van der Veen, F

    2017-10-01

    Are randomized controlled trials (RCTs) on IVF and ICSI subject to selective outcome reporting and is this related to sponsorship? There are inconsistencies, independent from sponsorship, in the reporting of primary outcome measures in the majority of IVF and ICSI trials, indicating selective outcome reporting. RCTs are subject to bias at various levels. Of these biases, selective outcome reporting is particularly relevant to IVF and ICSI trials since there is a wide variety of outcome measures to choose from. An established cause of reporting bias is sponsorship. It is, at present, unknown whether RCTs in IVF/ICSI are subject to selective outcome reporting and whether this is related with sponsorship. We systematically searched RCTs on IVF and ICSI published between January 2009 and March 2016 in MEDLINE, EMBASE, the Cochrane Central Register of Controlled Trials and the publisher subset of PubMed. We analysed 415 RCTs. Per included RCT, we extracted data on impact factor of the journal, sample size, power calculation, and trial registry and thereafter data on primary outcome measure, the direction of trial results and sponsorship. Of the 415 identified RCTs, 235 were excluded for our primary analysis, because the sponsorship was not reported. Of the 180 RCTs included in our analysis, 7 trials did not report on any primary outcome measure and 107 of the remaining 173 trials (62%) reported on surrogate primary outcome measures. Of the 114 registered trials, 21 trials (18%) provided primary outcomes in their manuscript that were different from those in the trial registry. This indicates selective outcome reporting. We found no association between selective outcome reporting and sponsorship. We ran additional analyses to include the trials that had not reported sponsorship and found no outcomes that differed from our primary analysis. Since the majority of the trials did not report on sponsorship, there is a risk on sampling bias. IVF and ICSI trials are subject, to

  14. Evaluación de patógenos en clones de lulo (Solanum quitoense Lam. Pathogenity evaluation on Solanum quitoense Lam. Clones

    Directory of Open Access Journals (Sweden)

    Consuelo Montes Rojas

    2010-04-01

    consisted of a complete randomized block design with 4 repetitions, the working sampling plot consisted on 6 plants arranged in triangles at distances of 2 m within rows, the inter row distance was 2,5 m. The incidence and severity percentages of damage were evaluated to determine the disease effects. The first incidence was evaluated as the affected plants percentage and severity, as percentage of plant tissue affected by the pathogen. The most limiting diseases for the 42 clones were Phytophthora infestans, which produced mortality more than 40%; Fusarium oxysporum affected 12 of the evaluated clons; Colletotrichum sp. affecting 21 clones which were classified as tolerant and fairly tolerant; and Cladosporium sp., affecting 21 clones and were classified as susceptible, while the clons PL19, PL24, PL11, PL35 were considered fairly tolerant. The clones JY E1 (52.2%, PH E 1 (45.8%, VM E2 (45.8% were selected by survival; by tolerance to Fusarium oxysporum the clones PL35, PL11, PL24, PL8, PL19, 120052, 120043, ORE1, AGE1; and the clones SER 7, SER 15, SER 9, SEC 31, and SEC 27, were selected due to their fair tolerance to Phytophthora infestans, and Colletotrichum sp and their fair resistance against nematodes, proving to be vigorous and productive.

  15. Active classifier selection for RGB-D object categorization using a Markov random field ensemble method

    Science.gov (United States)

    Durner, Maximilian; Márton, Zoltán.; Hillenbrand, Ulrich; Ali, Haider; Kleinsteuber, Martin

    2017-03-01

    In this work, a new ensemble method for the task of category recognition in different environments is presented. The focus is on service robotic perception in an open environment, where the robot's task is to recognize previously unseen objects of predefined categories, based on training on a public dataset. We propose an ensemble learning approach to be able to flexibly combine complementary sources of information (different state-of-the-art descriptors computed on color and depth images), based on a Markov Random Field (MRF). By exploiting its specific characteristics, the MRF ensemble method can also be executed as a Dynamic Classifier Selection (DCS) system. In the experiments, the committee- and topology-dependent performance boost of our ensemble is shown. Despite reduced computational costs and using less information, our strategy performs on the same level as common ensemble approaches. Finally, the impact of large differences between datasets is analyzed.

  16. Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches

    Energy Technology Data Exchange (ETDEWEB)

    Chandonia, John-Marc; Brenner, Steven E.

    2004-07-14

    The structural genomics project is an international effort to determine the three-dimensional shapes of all important biological macromolecules, with a primary focus on proteins. Target proteins should be selected according to a strategy which is medically and biologically relevant, of good value, and tractable. As an option to consider, we present the Pfam5000 strategy, which involves selecting the 5000 most important families from the Pfam database as sources for targets. We compare the Pfam5000 strategy to several other proposed strategies that would require similar numbers of targets. These include including complete solution of several small to moderately sized bacterial proteomes, partial coverage of the human proteome, and random selection of approximately 5000 targets from sequenced genomes. We measure the impact that successful implementation of these strategies would have upon structural interpretation of the proteins in Swiss-Prot, TrEMBL, and 131 complete proteomes (including 10 of eukaryotes) from the Proteome Analysis database at EBI. Solving the structures of proteins from the 5000 largest Pfam families would allow accurate fold assignment for approximately 68 percent of all prokaryotic proteins (covering 59 percent of residues) and 61 percent of eukaryotic proteins (40 percent of residues). More fine-grained coverage which would allow accurate modeling of these proteins would require an order of magnitude more targets. The Pfam5000 strategy may be modified in several ways, for example to focus on larger families, bacterial sequences, or eukaryotic sequences; as long as secondary consideration is given to large families within Pfam, coverage results vary only slightly. In contrast, focusing structural genomics on a single tractable genome would have only a limited impact in structural knowledge of other proteomes: a significant fraction (about 30-40 percent of the proteins, and 40-60 percent of the residues) of each proteome is classified in small

  17. Clinical outcome of intracytoplasmic injection of spermatozoa morphologically selected under high magnification: a prospective randomized study.

    Science.gov (United States)

    Balaban, Basak; Yakin, Kayhan; Alatas, Cengiz; Oktem, Ozgur; Isiklar, Aycan; Urman, Bulent

    2011-05-01

    Recent evidence shows that the selection of spermatozoa based on the analysis of morphology under high magnification (×6000) may have a positive impact on embryo development in cases with severe male factor infertility and/or previous implantation failures. The objective of this prospective randomized study was to compare the clinical outcome of 87 intracytoplasmic morphologically selected sperm injection (IMSI) cycles with 81 conventional intracytoplasmic sperm injection (ICSI) cycles in an unselected infertile population. IMSI did not provide a significant improvement in the clinical outcome compared with ICSI although there were trends for higher implantation (28.9% versus 19.5%), clinical pregnancy (54.0% versus 44.4%) and live birth rates (43.7% versus 38.3%) in the IMSI group. However, severe male factor patients benefited from the IMSI procedure as shown by significantly higher implantation rates compared with their counterparts in the ICSI group (29.6% versus 15.2%, P=0.01). These results suggest that IMSI may improve IVF success rates in a selected group of patients with male factor infertility. New technological developments enable the real time examination of motile spermatozoa with an inverted light microscope equipped with high-power differential interference contrast optics, enhanced by digital imaging. High magnification (over ×6000) provides the identification of spermatozoa with a normal nucleus and nuclear content. Intracytoplasmic injection of spermatozoa selected according to fine nuclear morphology under high magnification may improve the clinical outcome in cases with severe male factor infertility. Copyright © 2010 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

  18. The egg-sharing model for human therapeutic cloning research: managing donor selection criteria, the proportion of shared oocytes allocated to research, and amount of financial subsidy given to the donor.

    Science.gov (United States)

    Heng, Boon Chin; Tong, Guo Qing; Stojkovic, Miodrag

    2006-01-01

    Recent advances in human therapeutic cloning made by Hwang and colleagues have opened up new avenues of therapy for various human diseases. However, the major bottleneck of this new technology is the severe shortage of human donor oocytes. Egg-sharing in return for subsidized fertility treatment has been suggested as an ethically justifiable and practical solution to overcome the shortage of donor oocytes for therapeutic cloning. Because the utilization of shared oocytes in therapeutic cloning research does not result in any therapeutic benefit to a second party, this would necessitate a different management strategy compared to their use for the assisted conception of infertile women who are unable to produce any oocytes of their own. It is proposed that the pool of prospective egg-sharers in therapeutic cloning research be limited only to younger women (below 30 years of age) with indications for either male partner sub-fertility or tubal blockage. With regards to the proportion of the shared gametes being allocated to research, a threshold number of retrieved oocytes should be set that if not exceeded, would result in the patient being automatically removed from the egg-sharing scheme. Any excess supernumerary oocyte above this threshold number can be contributed to science, and allocation should be done in a randomized manner. Perhaps, a total of 10 retrieved oocytes from the patient may be considered a suitable threshold, since the chances of conception are unlikely to be impaired. With regards to the amount of subsidy being given to the patient, it is suggested that the proportion of financial subsidy should be equal to the proportion of the patient's oocytes being allocated to research. No doubt, the promise of future therapeutic benefit may be offered to the patient instead of financial subsidy. However, this is ethically controversial because therapeutic cloning has not yet been demonstrated to be a viable model of clinical therapy and any promises made to

  19. A Comparison of Dietary Habits between Recreational Runners and a Randomly Selected Adult Population in Slovenia.

    Science.gov (United States)

    Škof, Branko; Rotovnik Kozjek, Nada

    2015-09-01

    The aim of the study was to compare the dietary habits of recreational runners with those of a random sample of the general population. We also wanted to determine the influence of gender, age and sports performance of recreational runners on their basic diet and compliance with recommendations in sports nutrition. The study population consisted of 1,212 adult Slovenian recreational runners and 774 randomly selected residents of Slovenia between the ages of 18 and 65 years. The data on the dietary habits of our subjects was gathered by means of two questionnaires. The following parameters were evaluated: the type of diet, a food pattern, and the frequency of consumption of individual food groups, the use of dietary supplements, fluid intake, and alcohol consumption. Recreational runners had better compliance with recommendations for healthy nutrition than the general population. This pattern increased with the runner's age and performance level. Compared to male runners, female runners ate more regularly and had a more frequent consumption of food groups associated with a healthy diet (fruit, vegetables, whole grain foods, and low-fat dairy products). The consumption of simple sugars and use of nutritional supplements by well-trained runners was inadequate with values recommended for physically active individuals. Recreational runners are an exemplary population group that actively seeks to adopt a healthier lifestyle.

  20. Radiographic methods used before removal of mandibular third molars among randomly selected general dental clinics.

    Science.gov (United States)

    Matzen, Louise H; Petersen, Lars B; Wenzel, Ann

    2016-01-01

    To assess radiographic methods and diagnostically sufficient images used before removal of mandibular third molars among randomly selected general dental clinics. Furthermore, to assess factors predisposing for an additional radiographic examination. 2 observers visited 18 randomly selected clinics in Denmark and studied patient files, including radiographs of patients who had their mandibular third molar(s) removed. The radiographic unit and type of receptor were registered. A diagnostically sufficient image was defined as the whole tooth and mandibular canal were displayed in the radiograph (yes/no). Overprojection between the tooth and mandibular canal (yes/no) and patient-reported inferior alveolar nerve sensory disturbances (yes/no) were recorded. Regression analyses tested if overprojection between the third molar and the mandibular canal and an insufficient intraoral image predisposed for additional radiographic examination(s). 1500 mandibular third molars had been removed; 1090 had intraoral, 468 had panoramic and 67 had CBCT examination. 1000 teeth were removed after an intraoral examination alone, 433 after panoramic examination and 67 after CBCT examination. 90 teeth had an additional examination after intraoral. Overprojection between the tooth and mandibular canal was a significant factor (p < 0.001, odds ratio = 3.56) for an additional examination. 63.7% of the intraoral images were sufficient and 36.3% were insufficient, with no significant difference between images performed with phosphor plates and solid-state sensors (p = 0.6). An insufficient image predisposed for an additional examination (p = 0.008, odds ratio = 1.8) but was only performed in 11% of the cases. Most mandibular third molars were removed based on an intraoral examination although 36.3% were insufficient.

  1. Control group selection in critical care randomized controlled trials evaluating interventional strategies: An ethical assessment.

    Science.gov (United States)

    Silverman, Henry J; Miller, Franklin G

    2004-03-01

    Ethical concern has been raised with critical care randomized controlled trials in which the standard of care reflects a broad range of clinical practices. Commentators have argued that trials without an unrestricted control group, in which standard practices are implemented at the discretion of the attending physician, lack the ability to redefine the standard of care and might expose subjects to excessive harms due to an inability to stop early. To develop a framework for analyzing control group selection for critical care trials. Ethical analysis. A key ethical variable in trial design is the extent with which the control group adequately reflects standard care practices. Such a control group might incorporate either the "unrestricted" practices of physicians or a protocol that specifies and restricts the parameters of standard practices. Control group selection should be determined with respect to the following ethical objectives of trial design: 1) clinical value, 2) scientific validity, 3) efficiency and feasibility, and 4) protection of human subjects. Because these objectives may conflict, control group selection will involve trade-offs and compromises. Trials using a protocolized rather than an unrestricted standard care control group will likely have enhanced validity. However, if the protocolized control group lacks representativeness to standard care practices, then trials that use such groups will offer less clinical value and could provide less assurance of protecting subjects compared with trials that use unrestricted control groups. For trials evaluating contrasting strategies that do not adequately represent standard practices, use of a third group that is more representative of standard practices will enhance clinical value and increase the ability to stop early if needed to protect subjects. These advantages might come at the expense of efficiency and feasibility. Weighing and balancing the competing ethical objectives of trial design should be

  2. Pathotypes in the Entomophaga grylli species complex of grasshopper pathogens differentiated with random amplification of polymorphic DNA and cloned-DNA probes.

    OpenAIRE

    Bidochka, M J; Walsh, S R; Ramos, M E; Leger, R J; Silver, J C; Roberts, D W

    1995-01-01

    The zygomycetous fungus Entomophaga grylli is a pathogen that shows host-specific variance to grasshopper subfamilies. Three pathotypes of the E. grylli species complex were differentiated by three molecular techniques. In the first method, the three pathotypes showed different fragment patterns generated by random amplifica- tion of polymorphic DNA (RAPD). There was little or no interisolate variability in RAPD fragment patterns within each pathotype. Passage of an isolate of pathotype 3, or...

  3. Empirical Results on Cloning and Clone Detection

    OpenAIRE

    Wagner, Stefan

    2015-01-01

    Cloning means the use of copy-paste as method in developing software artefacts. This practice has several problems, such as unnecessary increase of these artefacts, and thereby increased comprehension and change efforts, as well as potential inconsistencies. The automatic detection of clones has been a topic for research for several years now and we have made huge progress in terms of precision and recall. This led to a series of empirical analyses we have performed on the effects and the amo...

  4. The adverse effect of selective cyclooxygenase-2 inhibitor on random skin flap survival in rats.

    Directory of Open Access Journals (Sweden)

    Haiyong Ren

    Full Text Available BACKGROUND: Cyclooxygenase-2(COX-2 inhibitors provide desired analgesic effects after injury or surgery, but evidences suggested they also attenuate wound healing. The study is to investigate the effect of COX-2 inhibitor on random skin flap survival. METHODS: The McFarlane flap model was established in 40 rats and evaluated within two groups, each group gave the same volume of Parecoxib and saline injection for 7 days. The necrotic area of the flap was measured, the specimens of the flap were stained with haematoxylin-eosin(HE for histologic analysis. Immunohistochemical staining was performed to analyse the level of VEGF and COX-2 . RESULTS: 7 days after operation, the flap necrotic area ratio in study group (66.65 ± 2.81% was significantly enlarged than that of the control group(48.81 ± 2.33%(P <0.01. Histological analysis demonstrated angiogenesis with mean vessel density per mm(2 being lower in study group (15.4 ± 4.4 than in control group (27.2 ± 4.1 (P <0.05. To evaluate the expression of COX-2 and VEGF protein in the intermediate area II in the two groups by immunohistochemistry test .The expression of COX-2 in study group was (1022.45 ± 153.1, and in control group was (2638.05 ± 132.2 (P <0.01. The expression of VEGF in the study and control groups were (2779.45 ± 472.0 vs (4938.05 ± 123.6(P <0.01.In the COX-2 inhibitor group, the expressions of COX-2 and VEGF protein were remarkably down-regulated as compared with the control group. CONCLUSION: Selective COX-2 inhibitor had adverse effect on random skin flap survival. Suppression of neovascularization induced by low level of VEGF was supposed to be the biological mechanism.

  5. Rapid selection of accessible and cleavable sites in RNA by Escherichia coli RNase P and random external guide sequences

    OpenAIRE

    Lundblad, Eirik W.; Xiao, Gaoping; Ko, Jae-hyeong; Altman, Sidney

    2008-01-01

    A method of inhibiting the expression of particular genes by using external guide sequences (EGSs) has been improved in its rapidity and specificity. Random EGSs that have 14-nt random sequences are used in the selection procedure for an EGS that attacks the mRNA for a gene in a particular location. A mixture of the random EGSs, the particular target RNA, and RNase P is used in the diagnostic procedure, which, after completion, is analyzed in a gel with suitable control lanes. Within a few ho...

  6. Spiked pepper: selection of clones toward cropping on the edaphoclimatic conditions from Belém, Brazil Pimenta-de-macaco: seleção de clones para plantio nas condições edafoclimáticas de Belém

    Directory of Open Access Journals (Sweden)

    José Maria D Gaia

    2010-12-01

    Full Text Available Spiked pepper presents a high yield of essential oil with useful biological properties for human health and agriculture. In order to evaluate the morphoagronomic variability and, afterwards, to select genotypes for plant breeding and cultivation, thirteen clones were propagated. Thus, spiked pepper cuttings were rooted under greenhouse, transferred to a nursery and, afterwards, planted at the experimental area. The evaluations were carried out in two harvest seasons. The evaluated morphoagronomic traits were number of leaves per branch, leaf length, leaf width, diameter of the oldest branch, plant height, number of orthotropic branches, number of plagiotropic branches, internode length, fresh and dry matter, yield of essential oil and dillapiole content. The analysis of variance and the Scott-Knott test were utilized for data analysis and comparisons among clones and parentals were carried out through genetic and experimental variation coefficients. Fresh matter (first season, number of orthotropic branches and diameter of the the oldest branch (second season presented variability. The Scott-Knott test detected variability for fresh matter, dillapiole content (first season, diameter of the oldest branch and number of orthotropic branches (second season. The yield of essential oil and the dillapiole content were higher for the clones than for the parentals. In conclusion, the clones showed adaptability to the soil and climate conditions of Belém, Pará State, Brazil; the harvest time influenced the oil yield and the dillapiole content; the variance analysis evidenced uniformity and productivity for the evaluated clones, suggesting they can be recommended for cultivation on small-scale production systems in this location.Pimenta-de-macaco é uma espécie com elevado teor de óleo essencial em que se constatam propriedades biológicas utilizáveis na agricultura e saúde humana. Com o objetivo de avaliar a variabilidade morfoagronômica e

  7. Random genetic drift, natural selection, and noise in human cranial evolution.

    Science.gov (United States)

    Roseman, Charles C

    2016-08-01

    This study assesses the extent to which relationships among groups complicate comparative studies of adaptation in recent human cranial variation and the extent to which departures from neutral additive models of evolution hinder the reconstruction of population relationships among groups using cranial morphology. Using a maximum likelihood evolutionary model fitting approach and a mixed population genomic and cranial data set, I evaluate the relative fits of several widely used models of human cranial evolution. Moreover, I compare the goodness of fit of models of cranial evolution constrained by genomic variation to test hypotheses about population specific departures from neutrality. Models from population genomics are much better fits to cranial variation than are traditional models from comparative human biology. There is not enough evolutionary information in the cranium to reconstruct much of recent human evolution but the influence of population history on cranial variation is strong enough to cause comparative studies of adaptation serious difficulties. Deviations from a model of random genetic drift along a tree-like population history show the importance of environmental effects, gene flow, and/or natural selection on human cranial variation. Moreover, there is a strong signal of the effect of natural selection or an environmental factor on a group of humans from Siberia. The evolution of the human cranium is complex and no one evolutionary process has prevailed at the expense of all others. A holistic unification of phenome, genome, and environmental context, gives us a strong point of purchase on these problems, which is unavailable to any one traditional approach alone. Am J Phys Anthropol 160:582-592, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  8. CURE-SMOTE algorithm and hybrid algorithm for feature selection and parameter optimization based on random forests.

    Science.gov (United States)

    Ma, Li; Fan, Suohai

    2017-03-14

    The random forests algorithm is a type of classifier with prominent universality, a wide application range, and robustness for avoiding overfitting. But there are still some drawbacks to random forests. Therefore, to improve the performance of random forests, this paper seeks to improve imbalanced data processing, feature selection and parameter optimization. We propose the CURE-SMOTE algorithm for the imbalanced data classification problem. Experiments on imbalanced UCI data reveal that the combination of Clustering Using Representatives (CURE) enhances the original synthetic minority oversampling technique (SMOTE) algorithms effectively compared with the classification results on the original data using random sampling, Borderline-SMOTE1, safe-level SMOTE, C-SMOTE, and k-means-SMOTE. Additionally, the hybrid RF (random forests) algorithm has been proposed for feature selection and parameter optimization, which uses the minimum out of bag (OOB) data error as its objective function. Simulation results on binary and higher-dimensional data indicate that the proposed hybrid RF algorithms, hybrid genetic-random forests algorithm, hybrid particle swarm-random forests algorithm and hybrid fish swarm-random forests algorithm can achieve the minimum OOB error and show the best generalization ability. The training set produced from the proposed CURE-SMOTE algorithm is closer to the original data distribution because it contains minimal noise. Thus, better classification results are produced from this feasible and effective algorithm. Moreover, the hybrid algorithm's F-value, G-mean, AUC and OOB scores demonstrate that they surpass the performance of the original RF algorithm. Hence, this hybrid algorithm provides a new way to perform feature selection and parameter optimization.

  9. Noise-induced hearing loss in randomly selected New York dairy farmers.

    Science.gov (United States)

    May, J J; Marvel, M; Regan, M; Marvel, L H; Pratt, D S

    1990-01-01

    To understand better the effects of noise levels associated with dairy farming, we randomly selected 49 full-time dairy farmers from an established cohort. Medical and occupational histories were taken and standard audiometric testing was done. Forty-six males (94%) and three females (6%) with a mean age of 43.5 (+/- 13) years and an average of 29.4 (+/- 14) years in farming were tested. Pure Tone Average thresholds (PTA4) at 0.5, 1.0, 2.0, and 3.0 kHz plus High Frequency Average thresholds (HFA3) at 3.0, 4.0, and 6.0 kHz were calculated. Subjects with a loss of greater than or equal to 20 db in either ear were considered abnormal. Eighteen subjects (37%) had abnormal PTA4S and 32 (65%) abnormal HFA3S. The left ear was more severely affected in both groups (p less than or equal to .05, t-test). Significant associations were found between hearing loss and years worked (odds ratio 4.1, r = .53) and age (odds ratio 4.1, r = .59). No association could be found between hearing loss and measles; mumps; previous ear infections; or use of power tools, guns, motorcycles, snowmobiles, or stereo headphones. Our data suggest that among farmers, substantial hearing loss occurs especially in the high-frequency ranges. Presbycusis is an important confounding variable.

  10. Modeling Slotted Aloha as a Stochastic Game with Random Discrete Power Selection Algorithms

    Directory of Open Access Journals (Sweden)

    Rachid El-Azouzi

    2009-01-01

    Full Text Available We consider the uplink case of a cellular system where bufferless mobiles transmit over a common channel to a base station, using the slotted aloha medium access protocol. We study the performance of this system under several power differentiation schemes. Indeed, we consider a random set of selectable transmission powers and further study the impact of priorities given either to new arrival packets or to the backlogged ones. Later, we address a general capture model where a mobile transmits successfully a packet if its instantaneous SINR (signal to interferences plus noise ratio is lager than some fixed threshold. Under this capture model, we analyze both the cooperative team in which a common goal is jointly optimized as well as the noncooperative game problem where mobiles reach to optimize their own objectives. Furthermore, we derive the throughput and the expected delay and use them as the objectives to optimize and provide a stability analysis as alternative study. Exhaustive performance evaluations were carried out, we show that schemes with power differentiation improve significantly the individual as well as global performances, and could eliminate in some cases the bi-stable nature of slotted aloha.

  11. Desempenho de clones de seringueira da série IAC 300 na região do planalto de São Paulo Performance of IAC 300 rubber clones in the plateau of São Paulo State, Brazil

    Directory of Open Access Journals (Sweden)

    Paulo de Souza Gonçalves

    2002-02-01

    Full Text Available O objetivo deste trabalho foi selecionar clones de seringueira (Hevea spp. promissores para a região do planalto do Estado de São Paulo. De uma população de 70 clones, de polinização controlada, integrantes do experimento de avaliação em pequena escala, foram avaliados 16 da série IAC 300. O experimento foi instalado na Estação Experimental de Pindorama, no espaçamento de 7 x 3 m, em delineamento de blocos casualizados, com três repetições, tendo os clones RRIM 600 e GT 1 como testemunhas. Quanto à produção de borracha seca, destacaram-se oito e dez clones superiores ao RRIM 600 e GT 1, respectivamente. Todos os clones avaliados apresentaram-se vigorosos em relação ao perímetro do caule na abertura do painel. Sete deles mostraram alta resistência; sete, resistência moderada, e dois, suscetíveis à antracnose do painel. Sugere-se sua avaliação em experimentos de grande escala, para avaliar, além da produção, os demais caracteres secundários, em diferentes ambientes, para futuras recomendações em larga escala para o Estado de São Paulo.The present paper shows the results of the selection of IAC 300 serial promising clones of rubber tree (Hevea spp. for the plateau region of São Paulo State, Brazil. Eighteen clones were selected from a population of 70 clones resulted of controlled pollination, all evaluated in a small scale trial. The trial was laid out in randomized block design with three replications following the 7.0 m x 3.0 m spacing at the Experimental Station of Pindorama. The clones RRIM 600 and GT 1 were used as control. Regarding to yield, eight and ten clones showed superiority to RRIM 600 and GT 1, respectively. All the selected clones showed to be vigorous regarding to the girth by the panel opening. Seven clones showed high resistance, seven with moderate resistance, and two were susceptible to the anthracnose panel canker. A complementary evaluation in large scale trials is to evaluate, besides

  12. Statement on Human Cloning

    Science.gov (United States)

    ... as our understanding of this technology advances. Support Stem Cell Research (including Research Cloning) AAAS supports stem cell research, including the use of nuclear transplantation techniques (also ...

  13. Gateway Recombinational Cloning.

    Science.gov (United States)

    Reece-Hoyes, John S; Walhout, Albertha J M

    2018-01-02

    The Gateway recombinatorial cloning system was developed for cloning multiple DNA fragments in parallel (e.g., in 96-well formats) in a standardized manner using the same enzymes. Gateway cloning is based on the highly specific integration and excision reactions of bacteriophage λ into and out of the Escherichia coli genome. Because the sites of recombination (" att " sites) are much longer (25-242 bp) than restriction sites, they are extremely unlikely to occur by chance in DNA fragments. Therefore, the same recombination enzyme can be used to robustly clone many different fragments of variable size in parallel reactions. © 2018 Cold Spring Harbor Laboratory Press.

  14. The prevalence of symptoms associated with pulmonary tuberculosis in randomly selected children from a high burden community

    OpenAIRE

    Marais, B.; Obihara, C; Gie, R.; Schaaf, H; Hesseling, A.; Lombard, C.; Enarson, D; Bateman, E; Beyers, N

    2005-01-01

    Background: Diagnosis of childhood tuberculosis is problematic and symptom based diagnostic approaches are often promoted in high burden settings. This study aimed (i) to document the prevalence of symptoms associated with tuberculosis among randomly selected children living in a high burden community, and (ii) to compare the prevalence of these symptoms in children without tuberculosis to those in children with newly diagnosed tuberculosis.

  15. Rapid selection of accessible and cleavable sites in RNA by Escherichia coli RNase P and random external guide sequences.

    Science.gov (United States)

    Lundblad, Eirik W; Xiao, Gaoping; Ko, Jae-Hyeong; Altman, Sidney

    2008-02-19

    A method of inhibiting the expression of particular genes by using external guide sequences (EGSs) has been improved in its rapidity and specificity. Random EGSs that have 14-nt random sequences are used in the selection procedure for an EGS that attacks the mRNA for a gene in a particular location. A mixture of the random EGSs, the particular target RNA, and RNase P is used in the diagnostic procedure, which, after completion, is analyzed in a gel with suitable control lanes. Within a few hours, the procedure is complete. The action of EGSs designed by an older method is compared with EGSs designed by the random EGS method on mRNAs from two bacterial pathogens.

  16. CloneAssistant 1.0: a stand-alone software for automated cloning primer design.

    Science.gov (United States)

    Shao, Chaogang; Meng, Yijun; Lv, Shaolei; Zhong, Wei; Wang, Zheyu; Chen, Ming

    2010-11-01

    "CloneAssistant 1.0" is a stand-alone software compatible with the current Windows operating systems, which can automatically design cloning primers with full consideration of the sequence information of vectors and genes, cloning strategies, the principles of primer design, reading frames, position effects, and enzymatic reaction conditions for users. Five internal XML (extensible markup language) databases [restriction enzymes, plasmids, universal buffers, PCR (polymerase chain reaction) protection bases, and an MCS (multiple cloning site) double digest interference database] were established to serve as the basic support for "CloneAssistant 1.0". The primer pairs designed are sorted according to the difficulty of the follow-up experiments. Once a primer pair is selected by the user, detailed experimental guidance for this primer pair will be provided. In addition, "CloneAssistant 1.0" can be used for restriction map analysis, ORF (open reading frame) finding, sequence alignment and complementary analysis, translation, restriction enzyme and universal buffer queries, and isocaudamer analysis. "CloneAssistant 1.0" makes gene clone design much easier, and it can be freely downloaded from http://bis.zju.edu.cn/clone. Copyright © 2010 Elsevier B.V. All rights reserved.

  17. Do Clones Dream of Love? Images of Clones in Popular Culture

    Directory of Open Access Journals (Sweden)

    Dragana Antonijević

    2016-02-01

    Full Text Available Fantasies about clones, cyborgs and androids have become part and parcel of the mythology of modern times – the mythologies of the biotechnological era in which the achievements of genetic engineering have inflamed fears of possible abuse of scientific knowledge and the consequences of such abuse. The paper considers the phenomenon of reproductive cloning of human beings as it is represented in popular culture, especially film as it is one of the most important sources of representations and constructions of ideas about clones. After the introductory consideration of this phenomenon in scientific, ethical and media debates which are imbued with rejection of reproductive cloning, I have analyzed the different uses of the clone motif in selected movies. I have examined the structure and content of the genre formula of "social melodrama" which is present in films about clones, and have analyzed the mythical patterns pertaining to the topic of cloning, such as the myth of immortality, the myth of twins, the myth of the uniqueness of human kind etc. Ultimately, the nature and origins of the fear of clones and disgust that clones cause have been examined, and it has been shown that they mostly boil down to the fear of the dehumanization of human beings, the fear of the loss of difference and the transgression of biological, sociocultural and metaphysical boundaries.

  18. Differential privacy-based evaporative cooling feature selection and classification with relief-F and random forests.

    Science.gov (United States)

    Le, Trang T; Simmons, W Kyle; Misaki, Masaya; Bodurka, Jerzy; White, Bill C; Savitz, Jonathan; McKinney, Brett A

    2017-09-15

    Classification of individuals into disease or clinical categories from high-dimensional biological data with low prediction error is an important challenge of statistical learning in bioinformatics. Feature selection can improve classification accuracy but must be incorporated carefully into cross-validation to avoid overfitting. Recently, feature selection methods based on differential privacy, such as differentially private random forests and reusable holdout sets, have been proposed. However, for domains such as bioinformatics, where the number of features is much larger than the number of observations p≫n , these differential privacy methods are susceptible to overfitting. We introduce private Evaporative Cooling, a stochastic privacy-preserving machine learning algorithm that uses Relief-F for feature selection and random forest for privacy preserving classification that also prevents overfitting. We relate the privacy-preserving threshold mechanism to a thermodynamic Maxwell-Boltzmann distribution, where the temperature represents the privacy threshold. We use the thermal statistical physics concept of Evaporative Cooling of atomic gases to perform backward stepwise privacy-preserving feature selection. On simulated data with main effects and statistical interactions, we compare accuracies on holdout and validation sets for three privacy-preserving methods: the reusable holdout, reusable holdout with random forest, and private Evaporative Cooling, which uses Relief-F feature selection and random forest classification. In simulations where interactions exist between attributes, private Evaporative Cooling provides higher classification accuracy without overfitting based on an independent validation set. In simulations without interactions, thresholdout with random forest and private Evaporative Cooling give comparable accuracies. We also apply these privacy methods to human brain resting-state fMRI data from a study of major depressive disorder. Code

  19. Bayesian dose selection design for a binary outcome using restricted response adaptive randomization.

    Science.gov (United States)

    Meinzer, Caitlyn; Martin, Renee; Suarez, Jose I

    2017-09-08

    In phase II trials, the most efficacious dose is usually not known. Moreover, given limited resources, it is difficult to robustly identify a dose while also testing for a signal of efficacy that would support a phase III trial. Recent designs have sought to be more efficient by exploring multiple doses through the use of adaptive strategies. However, the added flexibility may potentially increase the risk of making incorrect assumptions and reduce the total amount of information available across the dose range as a function of imbalanced sample size. To balance these challenges, a novel placebo-controlled design is presented in which a restricted Bayesian response adaptive randomization (RAR) is used to allocate a majority of subjects to the optimal dose of active drug, defined as the dose with the lowest probability of poor outcome. However, the allocation between subjects who receive active drug or placebo is held constant to retain the maximum possible power for a hypothesis test of overall efficacy comparing the optimal dose to placebo. The design properties and optimization of the design are presented in the context of a phase II trial for subarachnoid hemorrhage. For a fixed total sample size, a trade-off exists between the ability to select the optimal dose and the probability of rejecting the null hypothesis. This relationship is modified by the allocation ratio between active and control subjects, the choice of RAR algorithm, and the number of subjects allocated to an initial fixed allocation period. While a responsive RAR algorithm improves the ability to select the correct dose, there is an increased risk of assigning more subjects to a worse arm as a function of ephemeral trends in the data. A subarachnoid treatment trial is used to illustrate how this design can be customized for specific objectives and available data. Bayesian adaptive designs are a flexible approach to addressing multiple questions surrounding the optimal dose for treatment efficacy

  20. Using ArcMap, Google Earth, and Global Positioning Systems to select and locate random households in rural Haiti

    Directory of Open Access Journals (Sweden)

    Wampler Peter J

    2013-01-01

    Full Text Available Abstract Background A remote sensing technique was developed which combines a Geographic Information System (GIS; Google Earth, and Microsoft Excel to identify home locations for a random sample of households in rural Haiti. The method was used to select homes for ethnographic and water quality research in a region of rural Haiti located within 9 km of a local hospital and source of health education in Deschapelles, Haiti. The technique does not require access to governmental records or ground based surveys to collect household location data and can be performed in a rapid, cost-effective manner. Methods The random selection of households and the location of these households during field surveys were accomplished using GIS, Google Earth, Microsoft Excel, and handheld Garmin GPSmap 76CSx GPS units. Homes were identified and mapped in Google Earth, exported to ArcMap 10.0, and a random list of homes was generated using Microsoft Excel which was then loaded onto handheld GPS units for field location. The development and use of a remote sensing method was essential to the selection and location of random households. Results A total of 537 homes initially were mapped and a randomized subset of 96 was identified as potential survey locations. Over 96% of the homes mapped using Google Earth imagery were correctly identified as occupied dwellings. Only 3.6% of the occupants of mapped homes visited declined to be interviewed. 16.4% of the homes visited were not occupied at the time of the visit due to work away from the home or market days. A total of 55 households were located using this method during the 10 days of fieldwork in May and June of 2012. Conclusions The method used to generate and field locate random homes for surveys and water sampling was an effective means of selecting random households in a rural environment lacking geolocation infrastructure. The success rate for locating households using a handheld GPS was excellent and only

  1. Using ArcMap, Google Earth, and Global Positioning Systems to select and locate random households in rural Haiti.

    Science.gov (United States)

    Wampler, Peter J; Rediske, Richard R; Molla, Azizur R

    2013-01-18

    A remote sensing technique was developed which combines a Geographic Information System (GIS); Google Earth, and Microsoft Excel to identify home locations for a random sample of households in rural Haiti. The method was used to select homes for ethnographic and water quality research in a region of rural Haiti located within 9 km of a local hospital and source of health education in Deschapelles, Haiti. The technique does not require access to governmental records or ground based surveys to collect household location data and can be performed in a rapid, cost-effective manner. The random selection of households and the location of these households during field surveys were accomplished using GIS, Google Earth, Microsoft Excel, and handheld Garmin GPSmap 76CSx GPS units. Homes were identified and mapped in Google Earth, exported to ArcMap 10.0, and a random list of homes was generated using Microsoft Excel which was then loaded onto handheld GPS units for field location. The development and use of a remote sensing method was essential to the selection and location of random households. A total of 537 homes initially were mapped and a randomized subset of 96 was identified as potential survey locations. Over 96% of the homes mapped using Google Earth imagery were correctly identified as occupied dwellings. Only 3.6% of the occupants of mapped homes visited declined to be interviewed. 16.4% of the homes visited were not occupied at the time of the visit due to work away from the home or market days. A total of 55 households were located using this method during the 10 days of fieldwork in May and June of 2012. The method used to generate and field locate random homes for surveys and water sampling was an effective means of selecting random households in a rural environment lacking geolocation infrastructure. The success rate for locating households using a handheld GPS was excellent and only rarely was local knowledge required to identify and locate households. This

  2. Cloning-free CRISPR

    NARCIS (Netherlands)

    Arbab, Mandana; Srinivasan, Sharanya; Hashimoto, Tatsunori; Geijsen, Niels; Sherwood, Richard I

    2015-01-01

    We present self-cloning CRISPR/Cas9 (scCRISPR), a technology that allows for CRISPR/Cas9-mediated genomic mutation and site-specific knockin transgene creation within several hours by circumventing the need to clone a site-specific single-guide RNA (sgRNA) or knockin homology construct for each

  3. Cloning, killing, and identity.

    Science.gov (United States)

    McMahan, J

    1999-01-01

    One potentially valuable use of cloning is to provide a source of tissues or organs for transplantation. The most important objection to this use of cloning is that a human clone would be the sort of entity that it would be seriously wrong to kill. I argue that entities of the sort that you and I essentially are do not begin to exist until around the seventh month of fetal gestation. Therefore to kill a clone prior to that would not be to kill someone like you or me but would be only to prevent one of us from existing. And even after one of us begins to exist, the objections to killing it remain comparatively weak until its psychological capacities reach a certain level of maturation. These claims support the permissibility of killing a clone during the early stages of its development in order to use its organs for transplantation. PMID:10226909

  4. Generation of Aptamers from A Primer-Free Randomized ssDNA Library Using Magnetic-Assisted Rapid Aptamer Selection

    Science.gov (United States)

    Tsao, Shih-Ming; Lai, Ji-Ching; Horng, Horng-Er; Liu, Tu-Chen; Hong, Chin-Yih

    2017-04-01

    Aptamers are oligonucleotides that can bind to specific target molecules. Most aptamers are generated using random libraries in the standard systematic evolution of ligands by exponential enrichment (SELEX). Each random library contains oligonucleotides with a randomized central region and two fixed primer regions at both ends. The fixed primer regions are necessary for amplifying target-bound sequences by PCR. However, these extra-sequences may cause non-specific bindings, which potentially interfere with good binding for random sequences. The Magnetic-Assisted Rapid Aptamer Selection (MARAS) is a newly developed protocol for generating single-strand DNA aptamers. No repeat selection cycle is required in the protocol. This study proposes and demonstrates a method to isolate aptamers for C-reactive proteins (CRP) from a randomized ssDNA library containing no fixed sequences at 5‧ and 3‧ termini using the MARAS platform. Furthermore, the isolated primer-free aptamer was sequenced and binding affinity for CRP was analyzed. The specificity of the obtained aptamer was validated using blind serum samples. The result was consistent with monoclonal antibody-based nephelometry analysis, which indicated that a primer-free aptamer has high specificity toward targets. MARAS is a feasible platform for efficiently generating primer-free aptamers for clinical diagnoses.

  5. The basic science and mathematics of random mutation and natural selection.

    Science.gov (United States)

    Kleinman, Alan

    2014-12-20

    The mutation and natural selection phenomenon can and often does cause the failure of antimicrobial, herbicidal, pesticide and cancer treatments selection pressures. This phenomenon operates in a mathematically predictable behavior, which when understood leads to approaches to reduce and prevent the failure of the use of these selection pressures. The mathematical behavior of mutation and selection is derived using the principles given by probability theory. The derivation of the equations describing the mutation and selection phenomenon is carried out in the context of an empirical example. Copyright © 2014 John Wiley & Sons, Ltd.

  6. BIOETHICS AND HUMAN CLONING

    Directory of Open Access Journals (Sweden)

    Željko Kaluđerović

    2011-12-01

    Full Text Available In this paper the authors analyze the process of negotiating and beginning of the United Nations Declaration on Human Cloning as well as the paragraphs of the very Declaration. The negotiation was originally conceived as a clear bioethical debate that should have led to a general agreement to ban human cloning. However, more often it had been discussed about human rights, cultural, civil and religious differences between people and about priorities in case of eventual conflicts between different value systems. In the end, a non-binding Declaration on Human Cloning had been adopted, full of numerous compromises and ambiguous formulations, that relativized the original intention of proposer states. According to authors, it would have been better if bioethical discussion and eventual regulations on cloning mentioned in the following text had been left over to certain professional bodies, and only after the public had been fully informed about it should relevant supranational organizations have taken that into consideration.

  7. Main: Clone Detail [KOME

    Lifescience Database Archive (English)

    Full Text Available Clone Detail Mapping Pseudomolecule data detail Detail information Mapping to the T...IGR japonica Pseudomolecules kome_mapping_pseudomolecule_data_detail.zip kome_mapping_pseudomolecule_data_detail ...

  8. Unified Approach to Universal Cloning and Phase-Covariant Cloning

    OpenAIRE

    Hu, Jia-Zhong; Yu, Zong-Wen; Wang, Xiang-Bin

    2008-01-01

    We analyze the problem of approximate quantum cloning when the quantum state is between two latitudes on the Bloch's sphere. We present an analytical formula for the optimized 1-to-2 cloning. The formula unifies the universal quantum cloning (UQCM) and the phase covariant quantum cloning.

  9. Enzyme free cloning for high throughput gene cloning and expression

    NARCIS (Netherlands)

    de Jong, R.N.; Daniëls, M.; Kaptein, R.|info:eu-repo/dai/nl/074334603; Folkers, G.E.|info:eu-repo/dai/nl/162277202

    2006-01-01

    Structural and functional genomics initiatives significantly improved cloning methods over the past few years. Although recombinational cloning is highly efficient, its costs urged us to search for an alternative high throughput (HTP) cloning method. We implemented a modified Enzyme Free Cloning

  10. Novel random peptide libraries displayed on AAV serotype 9 for selection of endothelial cell-directed gene transfer vectors.

    Science.gov (United States)

    Varadi, K; Michelfelder, S; Korff, T; Hecker, M; Trepel, M; Katus, H A; Kleinschmidt, J A; Müller, O J

    2012-08-01

    We have demonstrated the potential of random peptide libraries displayed on adeno-associated virus (AAV)2 to select for AAV2 vectors with improved efficiency for cell type-directed gene transfer. AAV9, however, may have advantages over AAV2 because of a lower prevalence of neutralizing antibodies in humans and more efficient gene transfer in vivo. Here we provide evidence that random peptide libraries can be displayed on AAV9 and can be utilized to select for AAV9 capsids redirected to the cell type of interest. We generated an AAV9 peptide display library, which ensures that the displayed peptides correspond to the packaged genomes and performed four consecutive selection rounds on human coronary artery endothelial cells in vitro. This screening yielded AAV9 library capsids with distinct peptide motifs enabling up to 40-fold improved transduction efficiencies compared with wild-type (wt) AAV9 vectors. Incorporating sequences selected from AAV9 libraries into AAV2 capsids could not increase transduction as efficiently as in the AAV9 context. To analyze the potential on endothelial cells in the intact natural vascular context, human umbilical veins were incubated with the selected AAV in situ and endothelial cells were isolated. Fluorescence-activated cell sorting analysis revealed a 200-fold improved transduction efficiency compared with wt AAV9 vectors. Furthermore, AAV9 vectors with targeting sequences selected from AAV9 libraries revealed an increased transduction efficiency in the presence of human intravenous immunoglobulins, suggesting a reduced immunogenicity. We conclude that our novel AAV9 peptide library is functional and can be used to select for vectors for future preclinical and clinical gene transfer applications.

  11. Emotional reactions to human reproductive cloning.

    Science.gov (United States)

    May, Joshua

    2016-01-01

    Extant surveys of people's attitudes towards human reproductive cloning focus on moral judgements alone, not emotional reactions or sentiments. This is especially important given that some (especially Leon Kass) have argued against such cloning on the ground that it engenders widespread negative emotions, like disgust, that provide a moral guide. To provide some data on emotional reactions to human cloning, with a focus on repugnance, given its prominence in the literature. This brief mixed-method study measures the self-reported attitudes and emotions (positive or negative) towards cloning from a sample of participants in the USA. Most participants condemned cloning as immoral and said it should be illegal. The most commonly reported positive sentiment was by far interest/curiosity. Negative emotions were much more varied, but anxiety was the most common. Only about a third of participants selected disgust or repugnance as something they felt, and an even smaller portion had this emotion come to mind prior to seeing a list of options. Participants felt primarily interested and anxious about human reproductive cloning. They did not primarily feel disgust or repugnance. This provides initial empirical evidence that such a reaction is not appropriately widespread. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  12. The Jackprot Simulation Couples Mutation Rate with Natural Selection to Illustrate How Protein Evolution Is Not Random

    Science.gov (United States)

    Espinosa, Avelina; Bai, Chunyan Y.

    2016-01-01

    Protein evolution is not a random process. Views which attribute randomness to molecular change, deleterious nature to single-gene mutations, insufficient geological time, or population size for molecular improvements to occur, or invoke “design creationism” to account for complexity in molecular structures and biological processes, are unfounded. Scientific evidence suggests that natural selection tinkers with molecular improvements by retaining adaptive peptide sequence. We used slot-machine probabilities and ion channels to show biological directionality on molecular change. Because ion channels reside in the lipid bilayer of cell membranes, their residue location must be in balance with the membrane's hydrophobic/philic nature; a selective “pore” for ion passage is located within the hydrophobic region. We contrasted the random generation of DNA sequence for KcsA, a bacterial two-transmembrane-domain (2TM) potassium channel, from Streptomyces lividans, with an under-selection scenario, the “jackprot,” which predicted much faster evolution than by chance. We wrote a computer program in JAVA APPLET version 1.0 and designed an online interface, The Jackprot Simulation http://faculty.rwu.edu/cbai/JackprotSimulation.htm, to model a numerical interaction between mutation rate and natural selection during a scenario of polypeptide evolution. Winning the “jackprot,” or highest-fitness complete-peptide sequence, required cumulative smaller “wins” (rewarded by selection) at the first, second, and third positions in each of the 161 KcsA codons (“jackdons” that led to “jackacids” that led to the “jackprot”). The “jackprot” is a didactic tool to demonstrate how mutation rate coupled with natural selection suffices to explain the evolution of specialized proteins, such as the complex six-transmembrane (6TM) domain potassium, sodium, or calcium channels. Ancestral DNA sequences coding for 2TM-like proteins underwent nucleotide

  13. The Jackprot Simulation Couples Mutation Rate with Natural Selection to Illustrate How Protein Evolution Is Not Random.

    Science.gov (United States)

    Paz-Y-Miño C, Guillermo; Espinosa, Avelina; Bai, Chunyan Y

    2011-09-01

    Protein evolution is not a random process. Views which attribute randomness to molecular change, deleterious nature to single-gene mutations, insufficient geological time, or population size for molecular improvements to occur, or invoke "design creationism" to account for complexity in molecular structures and biological processes, are unfounded. Scientific evidence suggests that natural selection tinkers with molecular improvements by retaining adaptive peptide sequence. We used slot-machine probabilities and ion channels to show biological directionality on molecular change. Because ion channels reside in the lipid bilayer of cell membranes, their residue location must be in balance with the membrane's hydrophobic/philic nature; a selective "pore" for ion passage is located within the hydrophobic region. We contrasted the random generation of DNA sequence for KcsA, a bacterial two-transmembrane-domain (2TM) potassium channel, from Streptomyces lividans, with an under-selection scenario, the "jackprot," which predicted much faster evolution than by chance. We wrote a computer program in JAVA APPLET version 1.0 and designed an online interface, The Jackprot Simulation http://faculty.rwu.edu/cbai/JackprotSimulation.htm, to model a numerical interaction between mutation rate and natural selection during a scenario of polypeptide evolution. Winning the "jackprot," or highest-fitness complete-peptide sequence, required cumulative smaller "wins" (rewarded by selection) at the first, second, and third positions in each of the 161 KcsA codons ("jackdons" that led to "jackacids" that led to the "jackprot"). The "jackprot" is a didactic tool to demonstrate how mutation rate coupled with natural selection suffices to explain the evolution of specialized proteins, such as the complex six-transmembrane (6TM) domain potassium, sodium, or calcium channels. Ancestral DNA sequences coding for 2TM-like proteins underwent nucleotide "edition" and gene duplications to generate the 6

  14. Pseudo cluster randomization: a treatment allocation method to minimize contamination and selection bias.

    NARCIS (Netherlands)

    Borm, G.F.; Melis, R.J.F.; Teerenstra, S.; Peer, P.G.M.

    2005-01-01

    In some clinical trials, treatment allocation on a patient level is not feasible, and whole groups or clusters of patients are allocated to the same treatment. If, for example, a clinical trial is investigating the efficacy of various patient coaching methods and randomization is done on a patient

  15. Induction/Engineering, Detection, Selection, and Expansion of Clinical-Grade Human Antigen-Specific CD8+ Cytotoxic T Cell Clones for Adoptive Immunotherapy

    Directory of Open Access Journals (Sweden)

    Matjaž Jeras

    2010-01-01

    Full Text Available Adoptive transfer of effector antigen-specific immune cells is becoming a promising treatment option in allogeneic transplantation, infectious diseases, cancer, and autoimmune disorders. Within this context, the important role of CD8+ cytotoxic T cells (CTLs is objective of intensive studies directed to their in vivo and ex vivo induction, detection, selection, expansion, and therapeutic effectiveness. Additional questions that are being addressed by the scientific community are related to the establishment and maintenance of their longevity and memory state as well as to defining critical conditions underlying their transitions between discrete, but functionally different subtypes. In this article we review and comment latest approaches and techniques used for preparing large amounts of antigen-specific CTLs, suitable for clinical use.

  16. The influence of alternative plant propagation and stand establishment techniques on survival and growth of eastern cottonwood (Populus deltoids Bartr.) clones

    Science.gov (United States)

    Donald J. Kaczmarek; Randall Rousseau; Jeff A. Wright; Brian Wachelka

    2014-01-01

    Four eastern cottonwood clones, including standard operational clone ST66 and three advanced clonal selections were produced and included in a test utilizing five different plant propagation methods. Despite relatively large first-year growth differences among clones, all clones demonstrated similar responses to the treatments and clone × cutting treatment interactions...

  17. Presence of psychoactive substances in oral fluid from randomly selected drivers in Denmark

    DEFF Research Database (Denmark)

    Simonsen, K. Wiese; Steentoft, A.; Hels, Tove

    2012-01-01

    This roadside study is the Danish part of the EU-project DRUID (Driving under the Influence of Drugs, Alcohol, and Medicines) and included three representative regions in Denmark. Oral fluid samples (n = 3002) were collected randomly from drivers using a sampling scheme stratified by time, season...... of narcotic drugs. It can be concluded that driving under the influence of drugs is as serious a road safety problem as drunk driving.......This roadside study is the Danish part of the EU-project DRUID (Driving under the Influence of Drugs, Alcohol, and Medicines) and included three representative regions in Denmark. Oral fluid samples (n = 3002) were collected randomly from drivers using a sampling scheme stratified by time, season...

  18. Presence of psychoactive substances in oral fluid from randomly selected drivers in Denmark

    DEFF Research Database (Denmark)

    Simonsen, Kirsten Wiese; Steentoft, Anni; Hels, Tove

    2012-01-01

    This roadside study is the Danish part of the EU-project DRUID (Driving under the Influence of Drugs, Alcohol, and Medicines) and included three representative regions in Denmark. Oral fluid samples (n = 3002) were collected randomly from drivers using a sampling scheme stratified by time, season....... It can be concluded that driving under the influence of drugs is as serious a road safety problem as drunk driving.......This roadside study is the Danish part of the EU-project DRUID (Driving under the Influence of Drugs, Alcohol, and Medicines) and included three representative regions in Denmark. Oral fluid samples (n = 3002) were collected randomly from drivers using a sampling scheme stratified by time, season...

  19. Feature selection and classification of mechanical fault of an induction motor using random forest classifier

    Directory of Open Access Journals (Sweden)

    Raj Kumar Patel

    2016-09-01

    Full Text Available Fault detection and diagnosis is the most important technology in condition-based maintenance (CBM system for rotating machinery. This paper experimentally explores the development of a random forest (RF classifier, a recently emerged machine learning technique, for multi-class mechanical fault diagnosis in bearing of an induction motor. Firstly, the vibration signals are collected from the bearing using accelerometer sensor. Parameters from the vibration signal are extracted in the form of statistical features and used as input feature for the classification problem. These features are classified through RF classifiers for four class problems. The prime objective of this paper is to evaluate effectiveness of random forest classifier on bearing fault diagnosis. The obtained results compared with the existing artificial intelligence techniques, neural network. The analysis of results shows the better performance and higher accuracy than the well existing techniques.

  20. Generating in vivo cloning vectors for parallel cloning of large gene clusters by homologous recombination.

    Directory of Open Access Journals (Sweden)

    Jeongmin Lee

    Full Text Available A robust method for the in vivo cloning of large gene clusters was developed based on homologous recombination (HR, requiring only the transformation of PCR products into Escherichia coli cells harboring a receiver plasmid. Positive clones were selected by an acquired antibiotic resistance, which was activated by the recruitment of a short ribosome-binding site plus start codon sequence from the PCR products to the upstream position of a silent antibiotic resistance gene in receiver plasmids. This selection was highly stringent and thus the cloning efficiency of the GFPuv gene (size: 0.7 kb was comparable to that of the conventional restriction-ligation method, reaching up to 4.3 × 10(4 positive clones per μg of DNA. When we attempted parallel cloning of GFPuv fusion genes (size: 2.0 kb and carotenoid biosynthesis pathway clusters (sizes: 4 kb, 6 kb, and 10 kb, the cloning efficiency was similarly high regardless of the DNA size, demonstrating that this would be useful for the cloning of large DNA sequences carrying multiple open reading frames. However, restriction analyses of the obtained plasmids showed that the selected cells may contain significant amounts of receiver plasmids without the inserts. To minimize the amount of empty plasmid in the positive selections, the sacB gene encoding a levansucrase was introduced as a counter selection marker in receiver plasmid as it converts sucrose to a toxic levan in the E. coli cells. Consequently, this method yielded completely homogeneous plasmids containing the inserts via the direct transformation of PCR products into E. coli cells.

  1. Selective nerve root blocks vs. caudal epidural injection for single level prolapsed lumbar intervertebral disc - A prospective randomized study.

    Science.gov (United States)

    Singh, Sudhir; Kumar, Sanjiv; Chahal, Gaurav; Verma, Reetu

    2017-01-01

    Chronic lumbar radiculopathy has a lifetime prevalence of 5.3% in men and 3.7% in women. It usually resolves spontaneously, but up to 30% cases will have pronounced symptoms even after one year. A prospective randomized single-blind study was conducted to compare the efficacy of caudal epidural steroid injection and selective nerve root block in management of pain and disability in cases of lumbar disc herniation. Eighty patients with confirmed single-level lumbar disc herniation were equally divided in two groups: (a) caudal epidural and (b) selective nerve root block group, by a computer-generated random allocation method. The caudal group received three injections of steroid mixed with local anesthetics while selective nerve root block group received single injection of steroid mixed with local anesthetic agent. Patients were assessed for pain relief and reduction in disability. In SNRB group, pain reduced by more than 50% up till 6 months, while in caudal group more than 50% reduction of pain was maintained till 1 year. The reduction in ODI in SNRB group was 52.8% till 3 months, 48.6% till 6 months, and 46.7% at 1 year, while in caudal group the improvement was 59.6%, 64.6%, 65.1%, and 65.4% at corresponding follow-up periods, respectively. Caudal epidural block is an easy and safe method with better pain relief and improvement in functional disability than selective nerve root block. Selective nerve root block injection is technically more demanding and has to be given by a skilled anesthetist.

  2. Inverse fusion PCR cloning.

    Directory of Open Access Journals (Sweden)

    Markus Spiliotis

    Full Text Available Inverse fusion PCR cloning (IFPC is an easy, PCR based three-step cloning method that allows the seamless and directional insertion of PCR products into virtually all plasmids, this with a free choice of the insertion site. The PCR-derived inserts contain a vector-complementary 5'-end that allows a fusion with the vector by an overlap extension PCR, and the resulting amplified insert-vector fusions are then circularized by ligation prior transformation. A minimal amount of starting material is needed and experimental steps are reduced. Untreated circular plasmid, or alternatively bacteria containing the plasmid, can be used as templates for the insertion, and clean-up of the insert fragment is not urgently required. The whole cloning procedure can be performed within a minimal hands-on time and results in the generation of hundreds to ten-thousands of positive colonies, with a minimal background.

  3. Optimal asymptotic cloning machines

    Science.gov (United States)

    Chiribella, Giulio; Yang, Yuxiang

    2014-06-01

    We pose the question whether the asymptotic equivalence between quantum cloning and quantum state estimation, valid at the single-clone level, still holds when all clones are examined globally. We conjecture that the answer is affirmative and present a large amount of evidence supporting our conjecture, developing techniques to derive optimal asymptotic cloners and proving their equivalence with estimation in virtually all scenarios considered in the literature. Our analysis covers the case of arbitrary finite sets of states, arbitrary families of coherent states, arbitrary phase- and multiphase-covariant sets of states, and two-qubit maximally entangled states. In all these examples we observe that the optimal asymptotic cloners enjoy a universality property, consisting in the fact that scaling of their fidelity does not depend on the specific details of the input states, but only on the number of free parameters needed to specify them.

  4. Selection of locations of knots for linear splines in random regression test-day models.

    Science.gov (United States)

    Jamrozik, J; Bohmanova, J; Schaeffer, L R

    2010-04-01

    Using spline functions (segmented polynomials) in regression models requires the knowledge of the location of the knots. Knots are the points at which independent linear segments are connected. Optimal positions of knots for linear splines of different orders were determined in this study for different scenarios, using existing estimates of covariance functions and an optimization algorithm. The traits considered were test-day milk, fat and protein yields, and somatic cell score (SCS) in the first three lactations of Canadian Holsteins. Two ranges of days in milk (from 5 to 305 and from 5 to 365) were taken into account. In addition, four different populations of Holstein cows, from Australia, Canada, Italy and New Zealand, were examined with respect to first lactation (305 days) milk only. The estimates of genetic and permanent environmental covariance functions were based on single- and multiple-trait test-day models, with Legendre polynomials of order 4 as random regressions. A differential evolution algorithm was applied to find the best location of knots for splines of orders 4 to 7 and the criterion for optimization was the goodness-of-fit of the spline covariance function. Results indicated that the optimal position of knots for linear splines differed between genetic and permanent environmental effects, as well as between traits and lactations. Different populations also exhibited different patterns of optimal knot locations. With linear splines, different positions of knots should therefore be used for different effects and traits in random regression test-day models when analysing milk production traits.

  5. The Cloning of America.

    Science.gov (United States)

    Dobson, Judith E.; Dobson, Russell L.

    1981-01-01

    Proposes that the U.S. school system purports to prize human variability, but many educators are engaged in activities that seek to homogenize students. Describes these activities, including diagnosis, labeling, ability grouping, and positive reinforcement. Presents suggestions for counselors to combat sources of cloning and self-validation. (RC)

  6. Applications of quantum cloning

    Science.gov (United States)

    Pomarico, E.; Sanguinetti, B.; Sekatski, P.; Zbinden, H.; Gisin, N.

    2011-10-01

    Quantum Cloning Machines (QCMs) allow for the copying of information, within the limits imposed by quantum mechanics. These devices are particularly interesting in the high-gain regime, i.e., when one input qubit generates a state of many output qubits. In this regime, they allow for the study of certain aspects of the quantum to classical transition. The understanding of these aspects is the root of the two recent applications that we will review in this paper: the first one is the Quantum Cloning Radiometer, a device which is able to produce an absolute measure of spectral radiance. This device exploits the fact that in the quantum regime information can be copied with only finite fidelity, whereas when a state becomes macroscopic, this fidelity gradually increases to 1. Measuring the fidelity of the cloning operation then allows to precisely determine the absolute spectral radiance of the input optical source. We will then discuss whether a Quantum Cloning Machine could be used to produce a state visible by the naked human eye, and the possibility of a Bell Experiment with humans playing the role of detectors.

  7. Self-Cloning CRISPR

    NARCIS (Netherlands)

    Arbab, M.; Sherwood, R. I.

    2016-01-01

    CRISPR/Cas9-gene editing has emerged as a revolutionary technology to easily modify specific genomic loci by designing complementary sgRNA sequences and introducing these into cells along with Cas9. Self-cloning CRISPR/Cas9 (scCRISPR) uses a self-cleaving palindromic sgRNA plasmid (sgPal) that

  8. Secure the Clones

    Science.gov (United States)

    Jensen, Thomas; Kirchner, Florent; Pichardie, David

    Exchanging mutable data objects with untrusted code is a delicate matter because of the risk of creating a data space that is accessible by an attacker. Consequently, secure programming guidelines for Java stress the importance of using defensive copying before accepting or handing out references to an internal mutable object. However, implementation of a copy method (like clone()) is entirely left to the programmer. It may not provide a sufficiently deep copy of an object and is subject to overriding by a malicious sub-class. Currently no language-based mechanism supports secure object cloning. This paper proposes a type-based annotation system for defining modular copy policies for class-based object-oriented programs. A copy policy specifies the maximally allowed sharing between an object and its clone. We present a static enforcement mechanism that will guarantee that all classes fulfill their copy policy, even in the presence of overriding of copy methods, and establish the semantic correctness of the overall approach in Coq. The mechanism has been implemented and experimentally evaluated on clone methods from several Java libraries.

  9. A Seminar on Human Cloning: Cloning in Reproductive Medicine

    OpenAIRE

    Illmensee, Karl

    2001-01-01

    This review article summarizes the historical development of mammalian cloning, presents current advances and presumed risk factors in the field of reproductive cloning, discusses possible clinical applications of therapeutic and diagnostic cloning and outlines prospective commercial trends in pharmacytical cloning. Predictable progress in biotechnology and stem cell engineering should prove to be advantageous for patients' health and for novel benefits in reproductive and regenerative medicine.

  10. A Randomized Controlled Trial of Cognitive Debiasing Improves Assessment and Treatment Selection for Pediatric Bipolar Disorder

    Science.gov (United States)

    Jenkins, Melissa M.; Youngstrom, Eric A.

    2015-01-01

    Objective This study examined the efficacy of a new cognitive debiasing intervention in reducing decision-making errors in the assessment of pediatric bipolar disorder (PBD). Method The study was a randomized controlled trial using case vignette methodology. Participants were 137 mental health professionals working in different regions of the US (M=8.6±7.5 years of experience). Participants were randomly assigned to a (1) brief overview of PBD (control condition), or (2) the same brief overview plus a cognitive debiasing intervention (treatment condition) that educated participants about common cognitive pitfalls (e.g., base-rate neglect; search satisficing) and taught corrective strategies (e.g., mnemonics, Bayesian tools). Both groups evaluated four identical case vignettes. Primary outcome measures were clinicians’ diagnoses and treatment decisions. The vignette characters’ race/ethnicity was experimentally manipulated. Results Participants in the treatment group showed better overall judgment accuracy, p < .001, and committed significantly fewer decision-making errors, p < .001. Inaccurate and somewhat accurate diagnostic decisions were significantly associated with different treatment and clinical recommendations, particularly in cases where participants missed comorbid conditions, failed to detect the possibility of hypomania or mania in depressed youths, and misdiagnosed classic manic symptoms. In contrast, effects of patient race were negligible. Conclusions The cognitive debiasing intervention outperformed the control condition. Examining specific heuristics in cases of PBD may identify especially problematic mismatches between typical habits of thought and characteristics of the disorder. The debiasing intervention was brief and delivered via the Web; it has the potential to generalize and extend to other diagnoses as well as to various practice and training settings. PMID:26727411

  11. Genome-wide association data classification and SNPs selection using two-stage quality-based Random Forests.

    Science.gov (United States)

    Nguyen, Thanh-Tung; Huang, Joshua; Wu, Qingyao; Nguyen, Thuy; Li, Mark

    2015-01-01

    Single-nucleotide polymorphisms (SNPs) selection and identification are the most important tasks in Genome-wide association data analysis. The problem is difficult because genome-wide association data is very high dimensional and a large portion of SNPs in the data is irrelevant to the disease. Advanced machine learning methods have been successfully used in Genome-wide association studies (GWAS) for identification of genetic variants that have relatively big effects in some common, complex diseases. Among them, the most successful one is Random Forests (RF). Despite of performing well in terms of prediction accuracy in some data sets with moderate size, RF still suffers from working in GWAS for selecting informative SNPs and building accurate prediction models. In this paper, we propose to use a new two-stage quality-based sampling method in random forests, named ts-RF, for SNP subspace selection for GWAS. The method first applies p-value assessment to find a cut-off point that separates informative and irrelevant SNPs in two groups. The informative SNPs group is further divided into two sub-groups: highly informative and weak informative SNPs. When sampling the SNP subspace for building trees for the forest, only those SNPs from the two sub-groups are taken into account. The feature subspaces always contain highly informative SNPs when used to split a node at a tree. This approach enables one to generate more accurate trees with a lower prediction error, meanwhile possibly avoiding overfitting. It allows one to detect interactions of multiple SNPs with the diseases, and to reduce the dimensionality and the amount of Genome-wide association data needed for learning the RF model. Extensive experiments on two genome-wide SNP data sets (Parkinson case-control data comprised of 408,803 SNPs and Alzheimer case-control data comprised of 380,157 SNPs) and 10 gene data sets have demonstrated that the proposed model significantly reduced prediction errors and outperformed

  12. The First Human Cloned Embryo.

    Science.gov (United States)

    Cibelli, Jose B.; Lanza, Robert P.; West, Michael D.; Ezzell, Carol

    2002-01-01

    Describes a process known as parthenogenesis which produces cloned, early-stage embryos and human embryos generated only from eggs. Speculates that this technology puts therapeutic cloning within reach. (DDR)

  13. [Nuclear transfer and therapeutic cloning].

    Science.gov (United States)

    Xu, Xiao-Ming; Lei, An-Min; Hua, Jin-Lian; Dou, Zhong-Ying

    2005-03-01

    Nuclear transfer and therapeutic cloning have widespread and attractive prospects in animal agriculture and biomedical applications. We reviewed that the quality of oocytes and nuclear reprogramming of somatic donor cells were the main reasons of the common abnormalities in cloned animals and the low efficiency of cloning and showed the problems and outlets in therapeutic cloning, such as some basic problems in nuclear transfer affected clinical applications of therapeutic cloning. Study on isolation and culture of nuclear transfer embryonic stem (ntES) cells and specific differentiation of ntES cells into important functional cells should be emphasized and could enhance the efficiency. Adult stem cells could help to cure some great diseases, but could not replace therapeutic cloning. Ethics also impeded the development of therapeutic cloning. It is necessary to improve many techniques and reinforce the research of some basic theories, then somatic nuclear transfer and therapeutic cloning may apply to agriculture reproduction and benefit to human life better.

  14. Animal Cloning and Food Safety

    Science.gov (United States)

    ... Home For Consumers Consumer Updates Animal Cloning and Food Safety Share Tweet Linkedin Pin it More sharing options ... on clones of livestock animals to evaluate the safety of food from these animals. The resulting report, called a ...

  15. Role of selective V2-receptor-antagonism in septic shock: a randomized, controlled, experimental study

    OpenAIRE

    Rehberg, Sebastian; Ertmer, Christian; Lange, Matthias; Morelli, Andrea; Whorton, Elbert; Strohhäcker, Anne-Katrin; Dünser, Martin Wolfgang; Lipke, Erik; Kampmeier, Tim G; Aken, Hugo; Traber, Daniel L; Westphal, Martin

    2010-01-01

    ABSTRACT : INTRODUCTION : V2-receptor (V2R) stimulation potentially aggravates sepsis-induced vasodilation, fluid accumulation and microvascular thrombosis. Therefore, the present study was performed to determine the effects of a first-line therapy with the selective V2R-antagonist (Propionyl1-D-Tyr(Et)2-Val4-Abu6-Arg8,9)-Vasopressin on cardiopulmonary hemodynamics and organ function vs. the mixed V1aR/V2R-agonist arginine vasopressin (AVP) or placebo in an established ovine model of septic s...

  16. Conflicts of Interest, Selective Inertia, and Research Malpractice in Randomized Clinical Trials: An Unholy Trinity.

    Science.gov (United States)

    Berger, Vance W

    2015-08-01

    Recently a great deal of attention has been paid to conflicts of interest in medical research, and the Institute of Medicine has called for more research into this important area. One research question that has not received sufficient attention concerns the mechanisms of action by which conflicts of interest can result in biased and/or flawed research. What discretion do conflicted researchers have to sway the results one way or the other? We address this issue from the perspective of selective inertia, or an unnatural selection of research methods based on which are most likely to establish the preferred conclusions, rather than on which are most valid. In many cases it is abundantly clear that a method that is not being used in practice is superior to the one that is being used in practice, at least from the perspective of validity, and that it is only inertia, as opposed to any serious suggestion that the incumbent method is superior (or even comparable), that keeps the inferior procedure in use, to the exclusion of the superior one. By focusing on these flawed research methods we can go beyond statements of potential harm from real conflicts of interest, and can more directly assess actual (not potential) harm.

  17. HUMAN CLONING AND FDA REGULATION

    OpenAIRE

    Vosk, Ted

    1998-01-01

    In the February 27, 1997 issue of the journal Nature scientists from Scotland's Roslin Institute reported their successful efforts to clone an adult sheep using differentiated somatic cells from the animal. The clone, named Dolly, was the first instance of the successful cloning of an adult mammal. The shock waves created by the possible ramifications of this development were immediately felt around the world. For the first time, the cloning of an adult human being was no longer being conside...

  18. Participant-selected music and physical activity in older adults following cardiac rehabilitation: a randomized controlled trial.

    Science.gov (United States)

    Clark, Imogen N; Baker, Felicity A; Peiris, Casey L; Shoebridge, Georgie; Taylor, Nicholas F

    2017-03-01

    To evaluate effects of participant-selected music on older adults' achievement of activity levels recommended in the physical activity guidelines following cardiac rehabilitation. A parallel group randomized controlled trial with measurements at Weeks 0, 6 and 26. A multisite outpatient rehabilitation programme of a publicly funded metropolitan health service. Adults aged 60 years and older who had completed a cardiac rehabilitation programme. Experimental participants selected music to support walking with guidance from a music therapist. Control participants received usual care only. The primary outcome was the proportion of participants achieving activity levels recommended in physical activity guidelines. Secondary outcomes compared amounts of physical activity, exercise capacity, cardiac risk factors, and exercise self-efficacy. A total of 56 participants, mean age 68.2 years (SD = 6.5), were randomized to the experimental ( n = 28) and control groups ( n = 28). There were no differences between groups in proportions of participants achieving activity recommended in physical activity guidelines at Week 6 or 26. Secondary outcomes demonstrated between-group differences in male waist circumference at both measurements (Week 6 difference -2.0 cm, 95% CI -4.0 to 0; Week 26 difference -2.8 cm, 95% CI -5.4 to -0.1), and observed effect sizes favoured the experimental group for amounts of physical activity (d = 0.30), exercise capacity (d = 0.48), and blood pressure (d = -0.32). Participant-selected music did not increase the proportion of participants achieving recommended amounts of physical activity, but may have contributed to exercise-related benefits.

  19. Content analysis of a stratified random selection of JVME articles: 1974-2004.

    Science.gov (United States)

    Olson, Lynne E

    2011-01-01

    A content analysis was performed on a random sample (N = 168) of 25% of the articles published in the Journal of Veterinary Medical Education (JVME) per year from 1974 through 2004. Over time, there were increased numbers of authors per paper, more cross-institutional collaborations, greater prevalence of references or endnotes, and lengthier articles, which could indicate a trend toward publications describing more complex or complete work. The number of first authors that could be identified as female was greatest for the most recent time period studied (2000-2004). Two different categorization schemes were created to assess the content of the publications. The first categorization scheme identified the most frequently published topics as admissions, descriptions of courses, the effect of changing teaching methods, issues facing the profession, and examples of uses of technology. The second categorization scheme identified the subset of articles that described medical education research on the basis of the purpose of the research, which represented only 14% of the sample articles (24 of 168). Of that group, only three of 24, or 12%, represented studies based on a firm conceptual framework that could be confirmed or refuted by the study's results. The results indicate that JVME is meeting its broadly based mission and that publications in the veterinary medical education literature have features common to publications in medicine and medical education.

  20. Capturing the Flatness of a peer-to-peer lending network through random and selected perturbations

    Science.gov (United States)

    Karampourniotis, Panagiotis D.; Singh, Pramesh; Uparna, Jayaram; Horvat, Emoke-Agnes; Szymanski, Boleslaw K.; Korniss, Gyorgy; Bakdash, Jonathan Z.; Uzzi, Brian

    Null models are established tools that have been used in network analysis to uncover various structural patterns. They quantify the deviance of an observed network measure to that given by the null model. We construct a null model for weighted, directed networks to identify biased links (carrying significantly different weights than expected according to the null model) and thus quantify the flatness of the system. Using this model, we study the flatness of Kiva, a large international crownfinancing network of borrowers and lenders, aggregated to the country level. The dataset spans the years from 2006 to 2013. Our longitudinal analysis shows that flatness of the system is reducing over time, meaning the proportion of biased inter-country links is growing. We extend our analysis by testing the robustness of the flatness of the network in perturbations on the links' weights or the nodes themselves. Examples of such perturbations are event shocks (e.g. erecting walls) or regulatory shocks (e.g. Brexit). We find that flatness is unaffected by random shocks, but changes after shocks target links with a large weight or bias. The methods we use to capture the flatness are based on analytics, simulations, and numerical computations using Shannon's maximum entropy. Supported by ARL NS-CTA.

  1. Benefits of Selected Physical Exercise Programs in Detention: A Randomized Controlled Study

    Directory of Open Access Journals (Sweden)

    Claudia Battaglia

    2013-10-01

    Full Text Available The aim of the study was to determine which kind of physical activity could be useful to inmate populations to improve their health status and fitness levels. A repeated measure design was used to evaluate the effects of two different training protocols on subjects in a state of detention, tested pre- and post-experimental protocol.Seventy-five male subjects were enrolled in the studyand randomly allocated to three groups: the cardiovascular plus resistance training protocol group (CRT (n = 25; mean age 30.9 ± 8.9 years,the high-intensity strength training protocol group (HIST (n = 25; mean age 33.9 ± 6.8 years, and a control group (C (n = 25; mean age 32.9 ± 8.9 years receiving no treatment. All subjects underwent a clinical assessmentandfitness tests. MANOVA revealed significant multivariate effects on group (p < 0.01 and group-training interaction (p < 0.05. CRT protocol resulted the most effective protocol to reach the best outcome in fitness tests. Both CRT and HIST protocols produced significant gains in the functional capacity (cardio-respiratory capacity and cardiovascular disease risk decrease of incarcerated males. The significant gains obtained in functional capacity reflect the great potential of supervised exercise interventions for improving the health status of incarcerated people.

  2. Sequence and expression of a microspore cDNA clone with homology to a ribosomal protein

    Directory of Open Access Journals (Sweden)

    Michael P. Turcich

    2014-01-01

    Full Text Available A cDNA library was made to RNA from corn anthers containing developing pollen at the uninucleate microspore stage. A randomly selected clone from this library which contained an insert (531 bp was isolated and sequenced. An open reading frame of 330 bp was located. Computer alignments of the putative amino acid sequence with sequences from GenBank and the SwissProt protein databases indicated homology to L12, an acidic ribosomal protein. RNA blot analysis showed highest levels of this mRNA in mature pollen. The significance of this observation in light of the known biochemistry of ribosome synthesis in developing pollen is discussed.

  3. Reduced plasma aldosterone concentrations in randomly selected patients with insulin-dependent diabetes mellitus.

    LENUS (Irish Health Repository)

    Cronin, C C

    2012-02-03

    Abnormalities of the renin-angiotensin system have been reported in patients with diabetes mellitus and with diabetic complications. In this study, plasma concentrations of prorenin, renin, and aldosterone were measured in a stratified random sample of 110 insulin-dependent (Type 1) diabetic patients attending our outpatient clinic. Fifty-four age- and sex-matched control subjects were also examined. Plasma prorenin concentration was higher in patients without complications than in control subjects when upright (geometric mean (95% confidence intervals (CI): 75.9 (55.0-105.6) vs 45.1 (31.6-64.3) mU I-1, p < 0.05). There was no difference in plasma prorenin concentration between patients without and with microalbuminuria and between patients without and with background retinopathy. Plasma renin concentration, both when supine and upright, was similar in control subjects, in patients without complications, and in patients with varying degrees of diabetic microangiopathy. Plasma aldosterone was suppressed in patients without complications in comparison to control subjects (74 (58-95) vs 167 (140-199) ng I-1, p < 0.001) and was also suppressed in patients with microvascular disease. Plasma potassium was significantly higher in patients than in control subjects (mean +\\/- standard deviation: 4.10 +\\/- 0.36 vs 3.89 +\\/- 0.26 mmol I-1; p < 0.001) and plasma sodium was significantly lower (138 +\\/- 4 vs 140 +\\/- 2 mmol I-1; p < 0.001). We conclude that plasma prorenin is not a useful early marker for diabetic microvascular disease. Despite apparently normal plasma renin concentrations, plasma aldosterone is suppressed in insulin-dependent diabetic patients.

  4. Recombinational Cloning Using Gateway and In-Fusion Cloning Schemes

    Science.gov (United States)

    Throop, Andrea L.; LaBaer, Joshua

    2015-01-01

    The comprehensive study of protein structure and function, or proteomics, depends on the obtainability of full-length cDNAs in species-specific expression vectors and subsequent functional analysis of the expressed protein. Recombinational cloning is a universal cloning technique based on site-specific recombination that is independent of the insert DNA sequence of interest, which differentiates this method from the classical restriction enzyme-based cloning methods. Recombinational cloning enables rapid and efficient parallel transfer of DNA inserts into multiple expression systems. This unit summarizes strategies for generating expression-ready clones using the most popular recombinational cloning technologies, including the commercially available Gateway® (Life Technologies) and In-Fusion® (Clontech) cloning technologies. PMID:25827088

  5. A Permutation Importance-Based Feature Selection Method for Short-Term Electricity Load Forecasting Using Random Forest

    Directory of Open Access Journals (Sweden)

    Nantian Huang

    2016-09-01

    Full Text Available The prediction accuracy of short-term load forecast (STLF depends on prediction model choice and feature selection result. In this paper, a novel random forest (RF-based feature selection method for STLF is proposed. First, 243 related features were extracted from historical load data and the time information of prediction points to form the original feature set. Subsequently, the original feature set was used to train an RF as the original model. After the training process, the prediction error of the original model on the test set was recorded and the permutation importance (PI value of each feature was obtained. Then, an improved sequential backward search method was used to select the optimal forecasting feature subset based on the PI value of each feature. Finally, the optimal forecasting feature subset was used to train a new RF model as the final prediction model. Experiments showed that the prediction accuracy of RF trained by the optimal forecasting feature subset was higher than that of the original model and comparative models based on support vector regression and artificial neural network.

  6. Effectiveness of a selective, personality-targeted prevention program for adolescent alcohol use and misuse: a cluster randomized controlled trial.

    Science.gov (United States)

    Conrod, Patricia J; O'Leary-Barrett, Maeve; Newton, Nicola; Topper, Lauren; Castellanos-Ryan, Natalie; Mackie, Clare; Girard, Alain

    2013-03-01

    Selective school-based alcohol prevention programs targeting youth with personality risk factors for addiction and mental health problems have been found to reduce substance use and misuse in those with elevated personality profiles. To report 24-month outcomes of the Teacher-Delivered Personality-Targeted Interventions for Substance Misuse Trial (Adventure trial) in which school staff were trained to provide interventions to students with 1 of 4 high-risk (HR) profiles: anxiety sensitivity, hopelessness, impulsivity, and sensation seeking and to examine the indirect herd effects of this program on the broader low-risk (LR) population of students who were not selected for intervention. Cluster randomized controlled trial. Secondary schools in London, United Kingdom. A total of 1210 HR and 1433 LR students in the ninth grade (mean [SD] age, 13.7 [0.33] years). Schools were randomized to provide brief personality-targeted interventions to HR youth or treatment as usual (statutory drug education in class). Participants were assessed for drinking, binge drinking, and problem drinking before randomization and at 6-monthly intervals for 2 years. Two-part latent growth models indicated long-term effects of the intervention on drinking rates (β = -0.320, SE = 0.145, P = .03) and binge drinking rates (β = -0.400, SE = 0.179, P = .03) and growth in binge drinking (β = -0.716, SE = 0.274, P = .009) and problem drinking (β = -0.452, SE = 0.193, P = .02) for HR youth. The HR youth were also found to benefit from the interventions during the 24-month follow-up on drinking quantity (β = -0.098, SE = 0.047, P = .04), growth in drinking quantity (β = -0.176, SE = 0.073, P = .02), and growth in binge drinking frequency (β = -0.183, SE = 0.092, P = .047). Some herd effects in LR youth were observed, specifically on drinking rates (β = -0.259, SE = 0.132, P = .049) and growth of binge drinking (β = -0.244, SE = 0.073, P = .001), during the 24-month follow-up. Findings further

  7. Buffalo embryos produced by handmade cloning from oocytes selected using brilliant cresyl blue staining have better developmental competence and quality and are closer to embryos produced by in vitro fertilization in terms of their epigenetic status and gene expression pattern.

    Science.gov (United States)

    Mohapatra, Sushil K; Sandhu, Anjit; Neerukattu, Venkata S; Singh, Karn P; Selokar, Naresh L; Singla, Suresh K; Chauhan, Manmohan S; Manik, Radhey S; Palta, Prabhat

    2015-04-01

    We compared handmade cloned (HMC) buffalo blastocysts produced from oocytes stained with Brilliant Cresyl Blue (BCB) and classified into those with blue (BCB+) or colorless cytoplasm (BCB-). The blastocyst rate was higher (p<0.001) for BCB+ than for BCB- oocytes (43.41 ± 2.54 vs. 22.74 ± 1.76%). BCB+ blastocysts had inner cell mass (ICM) cell number, ICM-to-trophectoderm ratio, global level of H3K18ac, apoptotic index, and expression level of BCL-XL, but not that of CASPASE-3, similar to that of blastocysts produced through in vitro fertilization (IVF), which was higher (p<0.05) than that of BCB- blastocysts. The global level of H3K9me2, which was similar in BCB+ and BCB- blastocysts, was higher (p<0.01) than that in IVF blastocysts. The expression level of OCT4 and SOX2 was higher (p<0.05) and that of GATA2 was lower (p<0.05) in BCB+ than that in BCB- blastocysts, whereas that of DNMT1, DNMT3a, NANOG, and CDX2 was not significantly different between the two groups. The expression level of DNMT1, OCT4, NANOG, and SOX2 was lower (p<0.05) and that of CDX2 was higher (p<0.05) in BCB+ than in IVF blastocysts. In conclusion, because BCB+ blastocysts have better developmental competence and are closer to IVF blastocysts in terms of quality, epigenetic status, and gene expression than BCB- blastocysts, BCB staining can be used effectively for selection of developmentally competent oocytes for HMC.

  8. YAC clone information - RGP physicalmap | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available 08/lsdba.nbdc00318-06-002 Description of data contents YAC clones selected with DNA markers Data file File name: rgp_physical...map_yac_clones.zip File URL: ftp://ftp.biosciencedbc.jp/archive/rgp-physicalmap/LATEST/rgp_physical...sciencedbc.jp/togodb/view/rgp_physicalmap_yac_clones#en Data acquisition method YAC clones selected with RGP...rom. No. Chromosome number Region Region number Physical map image The file name of rice physical map Order ...bout This Database Database Description Download License Update History of This Database Site Policy | Contact Us YAC clone information - RGP physicalmap | LSDB Archive ...

  9. Three concepts of cloning in human beings.

    Science.gov (United States)

    Cui, Ke-Hui

    2005-07-01

    Human cloning, organ cloning and tissue cloning are various types of cloning that occur at different levels with different methodologies. According to three standards of terminology for an embryo (fertilization through germ cells, development in the uterus and having the potential to produce a human life), tissue cloning and type I organ cloning will not produce an embryo. In contrast, human cloning and type II organ cloning will produce an embryo. Thus, only non-germinal tissue cloning and type I organ cloning are beyond the ethical question and will not change human beings as a species. Using cloned tissues to make new tissues or organs is promising for the future of medicine.

  10. Preference option randomized design (PORD) for comparative effectiveness research: Statistical power for testing comparative effect, preference effect, selection effect, intent-to-treat effect, and overall effect.

    Science.gov (United States)

    Heo, Moonseong; Meissner, Paul; Litwin, Alain H; Arnsten, Julia H; McKee, M Diane; Karasz, Alison; McKinley, Paula; Rehm, Colin D; Chambers, Earle C; Yeh, Ming-Chin; Wylie-Rosett, Judith

    2017-01-01

    Comparative effectiveness research trials in real-world settings may require participants to choose between preferred intervention options. A randomized clinical trial with parallel experimental and control arms is straightforward and regarded as a gold standard design, but by design it forces and anticipates the participants to comply with a randomly assigned intervention regardless of their preference. Therefore, the randomized clinical trial may impose impractical limitations when planning comparative effectiveness research trials. To accommodate participants' preference if they are expressed, and to maintain randomization, we propose an alternative design that allows participants' preference after randomization, which we call a "preference option randomized design (PORD)". In contrast to other preference designs, which ask whether or not participants consent to the assigned intervention after randomization, the crucial feature of preference option randomized design is its unique informed consent process before randomization. Specifically, the preference option randomized design consent process informs participants that they can opt out and switch to the other intervention only if after randomization they actively express the desire to do so. Participants who do not independently express explicit alternate preference or assent to the randomly assigned intervention are considered to not have an alternate preference. In sum, preference option randomized design intends to maximize retention, minimize possibility of forced assignment for any participants, and to maintain randomization by allowing participants with no or equal preference to represent random assignments. This design scheme enables to define five effects that are interconnected with each other through common design parameters-comparative, preference, selection, intent-to-treat, and overall/as-treated-to collectively guide decision making between interventions. Statistical power functions for testing

  11. Optimally cloned binary coherent states

    Science.gov (United States)

    Müller, C. R.; Leuchs, G.; Marquardt, Ch.; Andersen, U. L.

    2017-10-01

    Binary coherent state alphabets can be represented in a two-dimensional Hilbert space. We capitalize this formal connection between the otherwise distinct domains of qubits and continuous variable states to map binary phase-shift keyed coherent states onto the Bloch sphere and to derive their quantum-optimal clones. We analyze the Wigner function and the cumulants of the clones, and we conclude that optimal cloning of binary coherent states requires a nonlinearity above second order. We propose several practical and near-optimal cloning schemes and compare their cloning fidelity to the optimal cloner.

  12. Characterization of forage and extrusa clones dwarf elephant grass under rotational stocking

    Directory of Open Access Journals (Sweden)

    Tatiana Pires Pereira

    2014-10-01

    Full Text Available The objective of this trial was to evaluate the behavior ingestive of crossbred heifers and chemical characteristics of the material from two clones of dwarf elephant grass (BRS Kurumi ‘and CNPGL 01/03/00 submitted to different management strategies through sampling of forage (whole plant extrusa and manual hand plucking. The experiment was conducted at Embrapa Dairy Cattle, Coronel Pacheco, MG. We used a completely randomized design with factorial (2x2x2 with three replications. The treatments consisted of two clones of elephant grass (BRS Kurumi ‘and CNPGL 01/03/00, two light interception at the entrance of the animals (90 and 95% and two heights of post-grazing residue (30 and 50 cm with three replications. The chemical analysis showed that the methodology manual grazing simulation enables an acceptable estimate of the forage selected by grazing animals and the sampling of the whole plant is not selected by the animal diet. To harvest extrusa rate evaluation and mass bit, fractions and chemical composition of the plant of the ingested material was taken. Characteristics, structural and nutritional value of clone BRS ‘Kurumi’ facilitated greater forage intake by the animal, suggesting its use in grazing systems.

  13. Single-chain lipopeptide vaccines for the induction of virus-specific cytotoxic T cell responses in randomly selected populations.

    Science.gov (United States)

    Gras-Masse, H

    2001-12-01

    Effective vaccine development is now taking advantage of the rapidly accumulating information concerning the molecular basis of a protective immune response. Analysts and medicinal chemists have joined forces with immunologists and taken up the clear challenge of identifying immunologically active structural elements and synthesizing them in pure, reproducible forms. Current literature reveals the growing interest for extremely reductionist approaches aiming at producing totally synthetic vaccines that would be fully defined at the molecular level and particularly safe. The sequential information contained in these formulations tends to be minimized to those epitopes which elicit neutralizing antibodies, or cell-mediated responses. In the following review, we describe some of our results in developing fully synthetic, clinically acceptable lipopeptide vaccines for inducing cytotoxic T lymphocytes (CTL) responses in randomly selected populations.

  14. Experimental alternatives for evaluation of progenies and clones in eucalyptus breeding programs

    Directory of Open Access Journals (Sweden)

    Souza Elaine Aparecida de

    2003-01-01

    Full Text Available The feasibility of using augmented block designs and spatial analysis methods for early stage selection in eucalyptus breeding programs was tested. A total of 113 half-sib progenies of Eucalyptus urophylla and eight clones were evaluated in an 11 x 11 triple lattice experiment at two locations: Posto da Mata (Bahia, Brazil and São Mateus (Minas Gerais, Brazil. Four checks were randomly allocated within each block. Plots consisted of 15 m long rows containing 6 plants spaced 3 m apart. The girth at breast height (cm/plant was evaluated at 19 and 26 months of age. Variance analyses were performed according to the following methods: lattice design, randomized complete block design, augmented block design, Papadakis method, moving means method, and check plots. Comparisons among different methods were based on the magnitude of experimental errors and precision of the estimates of genetic and phenotypic parameters. General results indicated that augmented block design is useful to evaluate progenies and clones in early selection in eucalyptus breeding programs using moderate and low selection intensities. However, this design is not suitable for estimating genetic and phenotypic parameters due to its low precision. Check plots, nearest neighbour, Papadakis (1937, and moving means methods were efficient in removing the heterogeneity within blocks. These efficiencies were compared to that in lattice analysis for estimation of genetic and phenotypic parameters.

  15. Selecting Optimal Random Forest Predictive Models: A Case Study on Predicting the Spatial Distribution of Seabed Hardness

    Science.gov (United States)

    Li, Jin; Tran, Maggie; Siwabessy, Justy

    2016-01-01

    Spatially continuous predictions of seabed hardness are important baseline environmental information for sustainable management of Australia’s marine jurisdiction. Seabed hardness is often inferred from multibeam backscatter data with unknown accuracy and can be inferred from underwater video footage at limited locations. In this study, we classified the seabed into four classes based on two new seabed hardness classification schemes (i.e., hard90 and hard70). We developed optimal predictive models to predict seabed hardness using random forest (RF) based on the point data of hardness classes and spatially continuous multibeam data. Five feature selection (FS) methods that are variable importance (VI), averaged variable importance (AVI), knowledge informed AVI (KIAVI), Boruta and regularized RF (RRF) were tested based on predictive accuracy. Effects of highly correlated, important and unimportant predictors on the accuracy of RF predictive models were examined. Finally, spatial predictions generated using the most accurate models were visually examined and analysed. This study confirmed that: 1) hard90 and hard70 are effective seabed hardness classification schemes; 2) seabed hardness of four classes can be predicted with a high degree of accuracy; 3) the typical approach used to pre-select predictive variables by excluding highly correlated variables needs to be re-examined; 4) the identification of the important and unimportant predictors provides useful guidelines for further improving predictive models; 5) FS methods select the most accurate predictive model(s) instead of the most parsimonious ones, and AVI and Boruta are recommended for future studies; and 6) RF is an effective modelling method with high predictive accuracy for multi-level categorical data and can be applied to ‘small p and large n’ problems in environmental sciences. Additionally, automated computational programs for AVI need to be developed to increase its computational efficiency and

  16. Selecting Optimal Random Forest Predictive Models: A Case Study on Predicting the Spatial Distribution of Seabed Hardness.

    Directory of Open Access Journals (Sweden)

    Jin Li

    Full Text Available Spatially continuous predictions of seabed hardness are important baseline environmental information for sustainable management of Australia's marine jurisdiction. Seabed hardness is often inferred from multibeam backscatter data with unknown accuracy and can be inferred from underwater video footage at limited locations. In this study, we classified the seabed into four classes based on two new seabed hardness classification schemes (i.e., hard90 and hard70. We developed optimal predictive models to predict seabed hardness using random forest (RF based on the point data of hardness classes and spatially continuous multibeam data. Five feature selection (FS methods that are variable importance (VI, averaged variable importance (AVI, knowledge informed AVI (KIAVI, Boruta and regularized RF (RRF were tested based on predictive accuracy. Effects of highly correlated, important and unimportant predictors on the accuracy of RF predictive models were examined. Finally, spatial predictions generated using the most accurate models were visually examined and analysed. This study confirmed that: 1 hard90 and hard70 are effective seabed hardness classification schemes; 2 seabed hardness of four classes can be predicted with a high degree of accuracy; 3 the typical approach used to pre-select predictive variables by excluding highly correlated variables needs to be re-examined; 4 the identification of the important and unimportant predictors provides useful guidelines for further improving predictive models; 5 FS methods select the most accurate predictive model(s instead of the most parsimonious ones, and AVI and Boruta are recommended for future studies; and 6 RF is an effective modelling method with high predictive accuracy for multi-level categorical data and can be applied to 'small p and large n' problems in environmental sciences. Additionally, automated computational programs for AVI need to be developed to increase its computational efficiency and

  17. Ultra-low background DNA cloning system.

    Directory of Open Access Journals (Sweden)

    Kenta Goto

    Full Text Available Yeast-based in vivo cloning is useful for cloning DNA fragments into plasmid vectors and is based on the ability of yeast to recombine the DNA fragments by homologous recombination. Although this method is efficient, it produces some by-products. We have developed an "ultra-low background DNA cloning system" on the basis of yeast-based in vivo cloning, by almost completely eliminating the generation of by-products and applying the method to commonly used Escherichia coli vectors, particularly those lacking yeast replication origins and carrying an ampicillin resistance gene (Amp(r. First, we constructed a conversion cassette containing the DNA sequences in the following order: an Amp(r 5' UTR (untranslated region and coding region, an autonomous replication sequence and a centromere sequence from yeast, a TRP1 yeast selectable marker, and an Amp(r 3' UTR. This cassette allowed conversion of the Amp(r-containing vector into the yeast/E. coli shuttle vector through use of the Amp(r sequence by homologous recombination. Furthermore, simultaneous transformation of the desired DNA fragment into yeast allowed cloning of this DNA fragment into the same vector. We rescued the plasmid vectors from all yeast transformants, and by-products containing the E. coli replication origin disappeared. Next, the rescued vectors were transformed into E. coli and the by-products containing the yeast replication origin disappeared. Thus, our method used yeast- and E. coli-specific "origins of replication" to eliminate the generation of by-products. Finally, we successfully cloned the DNA fragment into the vector with almost 100% efficiency.

  18. pPCV, a versatile vector for cloning PCR products.

    Science.gov (United States)

    Janner, Christiane R; Brito, Ana Lívia P; Moraes, Lidia Maria P; Reis, Viviane Cb; Torres, Fernando Ag

    2013-01-01

    The efficiency of PCR product cloning depends on the nature of the DNA polymerase employed because amplicons may have blunt-ends or 3' adenosines overhangs. Therefore, for amplicon cloning, available commercial vectors are either blunt-ended or have a single 3' overhanging thymidine. The aim of this work was to offer in a single vector the ability to clone both types of PCR products. For that purpose, a minimal polylinker was designed to include restriction sites for EcoRV and XcmI which enable direct cloning of amplicons bearing blunt-ends or A-overhangs, respectively, still offering blue/white selection. When tested, the resulting vector, pPCV, presented high efficiency cloning of both types of amplicons.

  19. Randomized trial of switching from prescribed non-selective non-steroidal anti-inflammatory drugs to prescribed celecoxib

    DEFF Research Database (Denmark)

    Macdonald, Thomas M; Hawkey, Chris J; Ford, Ian

    2017-01-01

    BACKGROUND: Selective cyclooxygenase-2 inhibitors and conventional non-selective non-steroidal anti-inflammatory drugs (nsNSAIDs) have been associated with adverse cardiovascular (CV) effects. We compared the CV safety of switching to celecoxib vs. continuing nsNSAID therapy in a European setting....... METHOD: Patients aged 60 years and over with osteoarthritis or rheumatoid arthritis, free from established CV disease and taking chronic prescribed nsNSAIDs, were randomized to switch to celecoxib or to continue their previous nsNSAID. The primary endpoint was hospitalization for non-fatal myocardial...... expected developed an on-treatment (OT) primary CV event and the rate was similar for celecoxib, 0.95 per 100 patient-years, and nsNSAIDs, 0.86 per 100 patient-years (HR = 1.12, 95% confidence interval, 0.81-1.55; P = 0.50). Comparable intention-to-treat (ITT) rates were 1.14 per 100 patient...

  20. Ethical issues in animal cloning.

    Science.gov (United States)

    Fiester, Autumn

    2005-01-01

    The issue of human reproductive cloning has recently received a great deal attention in public discourse. Bioethicists, policy makers, and the media have been quick to identify the key ethical issues involved in human reproductive cloning and to argue, almost unanimously, for an international ban on such attempts. Meanwhile, scientists have proceeded with extensive research agendas in the cloning of animals. Despite this research, there has been little public discussion of the ethical issues raised by animal cloning projects. Polling data show that the public is decidedly against the cloning of animals. To understand the public's reaction and fill the void of reasoned debate about the issue, we need to review the possible objections to animal cloning and assess the merits of the anti-animal cloning stance. Some objections to animal cloning (e.g., the impact of cloning on the population of unwanted animals) can be easily addressed, while others (e.g., the health of cloned animals) require more serious attention by the public and policy makers.

  1. K-Ras(G12D)-selective inhibitory peptides generated by random peptide T7 phage display technology.

    Science.gov (United States)

    Sakamoto, Kotaro; Kamada, Yusuke; Sameshima, Tomoya; Yaguchi, Masahiro; Niida, Ayumu; Sasaki, Shigekazu; Miwa, Masanori; Ohkubo, Shoichi; Sakamoto, Jun-Ichi; Kamaura, Masahiro; Cho, Nobuo; Tani, Akiyoshi

    2017-03-11

    Amino-acid mutations of Gly 12 (e.g. G12D, G12V, G12C) of V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (K-Ras), the most promising drug target in cancer therapy, are major growth drivers in various cancers. Although over 30 years have passed since the discovery of these mutations in most cancer patients, effective mutated K-Ras inhibitors have not been marketed. Here, we report novel and selective inhibitory peptides to K-Ras(G12D). We screened random peptide libraries displayed on T7 phage against purified recombinant K-Ras(G12D), with thorough subtraction of phages bound to wild-type K-Ras, and obtained KRpep-2 (Ac-RRCPLYISYDPVCRR-NH 2 ) as a consensus sequence. KRpep-2 showed more than 10-fold binding- and inhibition-selectivity to K-Ras(G12D), both in SPR analysis and GDP/GTP exchange enzyme assay. K D and IC 50 values were 51 and 8.9 nM, respectively. After subsequent sequence optimization, we successfully generated KRpep-2d (Ac-RRRRCPLYISYDPVCRRRR-NH 2 ) that inhibited enzyme activity of K-Ras(G12D) with IC 50  = 1.6 nM and significantly suppressed ERK-phosphorylation, downstream of K-Ras(G12D), along with A427 cancer cell proliferation at 30 μM peptide concentration. To our knowledge, this is the first report of a K-Ras(G12D)-selective inhibitor, contributing to the development and study of K-Ras(G12D)-targeting drugs. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Lessons learned from cloning dogs.

    Science.gov (United States)

    Kim, M J; Oh, H J; Kim, G A; Park, J E; Park, E J; Jang, G; Ra, J C; Kang, S K; Lee, B C

    2012-08-01

    The aim of this article is to review dog cloning research and to suggest its applications based on a discussion about the normality of cloned dogs. Somatic cell nuclear transfer was successfully used for production of viable cloned puppies despite limited understanding of in vitro dog embryo production. Cloned dogs have similar growth characteristics to those born from natural fertilization, with no evidence of serious adverse effects. The offspring of cloned dogs also have similar growth performance and health to those of naturally bred puppies. Therefore, cloning in domestic dogs can be applied as an assisted reproductive technique to conserve endangered species, to treat sterile canids or aged dogs, to improve reproductive performance of valuable individuals and to generate disease model animals. © 2012 Blackwell Verlag GmbH.

  3. ROOT MORPHOLOGY AND NUTRIENT UPTAKE KINETICS BY AUSTRALIAN CEDAR CLONES

    Directory of Open Access Journals (Sweden)

    RAQUEL OLIVEIRA BATISTA

    2016-01-01

    Full Text Available Evaluation of root morphology and kinetic parameters assist in the characterization of genotypes in nutrient uptake efficiency. This study characterized Australian cedar clones concerning their nutrient uptake capacity at the seedling stage through root morphology and the kinetics of P, K, Ca, and Mg uptake. The experiment was conducted using a nutrient solution in a greenhouse and growth chamber. Four Australian cedar clones (HE, XF, XD, and XE, provided by Bela Forest View ( Empresa Florestal Bela Vista , were tested using a completely randomized design with five repetitions, totaling 20 experimental plots. The length, volume, surface area, average diameter, and root length per diameter class, as well as the uptake parameters V max , K m , C min , and the estimated inflow of P, K, Ca, and Mg, were determined. The root morphological characteristics varied between Australian cedar clones; clone XD exhibited the largest root system development. The uptake efficiency of P, K, Ca, and Mg varied between cedar Australian clones. When availability differed, clones XE and XF exhibited greater plasticity in the uptake of P and K respectively, and similar results were found for clone HE in the uptake of Ca and Mg.

  4. MOLECULAR CLONING OF OVINE cDNA LEPTIN GENE

    OpenAIRE

    CLAUDIA TEREZIA SOCOL; VLAIC A.; VIORICA COSIER

    2013-01-01

    An efficient bacterial transformation system suitable for cloning the coding sequence of the ovine leptin gene in E. coli DH5α host cells using the pGEMT easy vector it is described in this paper. The necessity of producing leptin is based on the fact that the role of this molecule in the animal and human organism is still unknown, leptin not existing as commercial product on the Romanian market. The results obtained in the bacterial transformation, cloning, recombinant clones selection, cont...

  5. Relationship between Physiological Characteristic and Bean Quality on Some Cocoa Clones (Theobroma cacao L.

    Directory of Open Access Journals (Sweden)

    Indah Anita Sari

    2015-12-01

    Full Text Available Photosynthesis is one of the physiological process that influence the bean weight and this process related with the efectiveness of the stomata character and chlorophyll content in the leaves. The research was conducted at Kaliwining Research Station, Indonesian Coffee and Cocoa Research Institute. Design of experiment was randomized complete block design (RCBD consisted of six clones as treatment were Sulawesi 1, Sulawesi 2, Sca 6, ICS 60, TSH 858, ICCRI 03, PA 300. Each treatment was replicated three times.  Stomata resistance diffusion, tranpiration,the content of chlorophyll a, chlorophyll b, chlorophyll total (a+b, bean number and bean weight were observed. The resuts  of experiment showed that  difference in chlorophyll a, chlorophyll b, chlorophyll total (a+b, stomata resistance diffusion, bean number and bean weight existed within  six clones tested. Transpiration rate did not show the significantly different between six clones tested. Sulawesi 1 showed the highest content of chlorophyll a and  ICS 60 and ICCRI 03 showed higher content of chlorophyll b than the other clones. Chlorophyll a, b and total (a+b showed positively influence on bean number and bean weight. Transpiration rate had negatively influence to bean number per pod, on the otherhand it showed positively influence to bean weight. Chlorophyll total (a+b showed high genetic variance (σg2, high phenotypic variance (σf2  and high estimated value of heritability (H.  The chlorophyll a,b had moderate genetic variance, moderate phenotypic variance and high of estimated value of heritability.  Chlorophyll total (a+b could be used a selection criteria based on the value of correlation, genetic variance, phenotypic variance and estimated value of heritability would give high opportunity in selection process. 

  6. Human cloning and child welfare.

    Science.gov (United States)

    Burley, J; Harris, J

    1999-01-01

    In this paper we discuss an objection to human cloning which appeals to the welfare of the child. This objection varies according to the sort of harm it is expected the clone will suffer. The three formulations of it that we will consider are: 1. Clones will be harmed by the fearful or prejudicial attitudes people may have about or towards them (H1); 2. Clones will be harmed by the demands and expectations of parents or genotype donors (H2); 3. Clones will be harmed by their own awareness of their origins, for example the knowledge that the genetic donor is a stranger (H3). We will show why these three versions of the child welfare objection do not necessarily supply compelling reasons to ban human reproductive cloning. The claim that we will develop and defend in the course of our discussion is that even if it is the case that a cloned child will suffer harms of the type H1-H3, it is none the less permissible to conceive by cloning so long as these cloning-induced welfare deficits are not such as to blight the existence of the resultant child, whoever this may be. PMID:10226914

  7. Efficiency and response of conilon coffee clones to phosphorus fertilization

    Directory of Open Access Journals (Sweden)

    Lima Deleon Martins

    2013-06-01

    Full Text Available Studies on nutritional efficiency of phosphorus in conilon coffee plants are important tools to unravel the high limitation that natural low levels of this nutrient in soil impose to these species cultivars. Therefore, this study aimed at evaluating the nutritional efficiency and the response to phosphorus of conilon coffee clones. Plants were managed during 150 days in pots containing 10 dm³ of soil, in greenhouse. A factorial scheme 13 x 2 was used, with three replications, being the factors: 13 clones constituting the clonal cultivar "Vitória Incaper 8142" and two levels of phosphate fertilization (0% and 150% of the P2O5 usualy recommended, in a completely randomized design (CRD. The results indicate a differentiated response of dry matter production and of phosphorus content on each level of phosphate fertilization for the conilon coffee clones and that CV-04, CV-05 and CV-08 clones are nutritionally efficient and responsive to the phosphate fertilization.

  8. Selectivity of Chemoresistive Sensors Made of Chemically Functionalized Carbon Nanotube Random Networks for Volatile Organic Compounds (VOC

    Directory of Open Access Journals (Sweden)

    Jean-François Feller

    2014-01-01

    Full Text Available Different grades of chemically functionalized carbon nanotubes (CNT have been processed by spraying layer-by-layer (sLbL to obtain an array of chemoresistive transducers for volatile organic compound (VOC detection. The sLbL process led to random networks of CNT less conductive, but more sensitive to vapors than filtration under vacuum (bucky papers. Shorter CNT were also found to be more sensitive due to the less entangled and more easily disconnectable conducting networks they are making. Chemical functionalization of the CNT’ surface is changing their selectivity towards VOC, which makes it possible to easily discriminate methanol, chloroform and tetrahydrofuran (THF from toluene vapors after the assembly of CNT transducers into an array to make an e-nose. Interestingly, the amplitude of the CNT transducers’ responses can be enhanced by a factor of five (methanol to 100 (chloroform by dispersing them into a polymer matrix, such as poly(styrene (PS, poly(carbonate (PC or poly(methyl methacrylate (PMMA. COOH functionalization of CNT was found to penalize their dispersion in polymers and to decrease the sensors’ sensitivity. The resulting conductive polymer nanocomposites (CPCs not only allow for a more easy tuning of the sensors’ selectivity by changing the chemical nature of the matrix, but they also allow them to adjust their sensitivity by changing the average gap between CNT (acting on quantum tunneling in the CNT network. Quantum resistive sensors (QRSs appear promising for environmental monitoring and anticipated disease diagnostics that are both based on VOC analysis.

  9. Transformation-associated recombination (TAR) cloning for genomics studies and synthetic biology.

    Science.gov (United States)

    Kouprina, Natalay; Larionov, Vladimir

    2016-09-01

    Transformation-associated recombination (TAR) cloning represents a unique tool for isolation and manipulation of large DNA molecules. The technique exploits a high level of homologous recombination in the yeast Sacharomyces cerevisiae. So far, TAR cloning is the only method available to selectively recover chromosomal segments up to 300 kb in length from complex and simple genomes. In addition, TAR cloning allows the assembly and cloning of entire microbe genomes up to several Mb as well as engineering of large metabolic pathways. In this review, we summarize applications of TAR cloning for functional/structural genomics and synthetic biology.

  10. Optimal Subset Selection of Time-Series MODIS Images and Sample Data Transfer with Random Forests for Supervised Classification Modelling

    Directory of Open Access Journals (Sweden)

    Fuqun Zhou

    2016-10-01

    Full Text Available Nowadays, various time-series Earth Observation data with multiple bands are freely available, such as Moderate Resolution Imaging Spectroradiometer (MODIS datasets including 8-day composites from NASA, and 10-day composites from the Canada Centre for Remote Sensing (CCRS. It is challenging to efficiently use these time-series MODIS datasets for long-term environmental monitoring due to their vast volume and information redundancy. This challenge will be greater when Sentinel 2–3 data become available. Another challenge that researchers face is the lack of in-situ data for supervised modelling, especially for time-series data analysis. In this study, we attempt to tackle the two important issues with a case study of land cover mapping using CCRS 10-day MODIS composites with the help of Random Forests’ features: variable importance, outlier identification. The variable importance feature is used to analyze and select optimal subsets of time-series MODIS imagery for efficient land cover mapping, and the outlier identification feature is utilized for transferring sample data available from one year to an adjacent year for supervised classification modelling. The results of the case study of agricultural land cover classification at a regional scale show that using only about a half of the variables we can achieve land cover classification accuracy close to that generated using the full dataset. The proposed simple but effective solution of sample transferring could make supervised modelling possible for applications lacking sample data.

  11. Biased random key genetic algorithm with insertion and gender selection for capacitated vehicle routing problem with time windows

    Science.gov (United States)

    Rochman, Auliya Noor; Prasetyo, Hari; Nugroho, Munajat Tri

    2017-06-01

    Vehicle Routing Problem (VRP) often occurs when the manufacturers need to distribute their product to some customers/outlets. The distribution process is typically restricted by the capacity of the vehicle and the working hours at the distributor. This type of VRP is also known as Capacitated Vehicle Routing Problem with Time Windows (CVRPTW). A Biased Random Key Genetic Algorithm (BRKGA) was designed and coded in MATLAB to solve the CVRPTW case of soft drink distribution. The standard BRKGA was then modified by applying chromosome insertion into the initial population and defining chromosome gender for parent undergoing crossover operation. The performance of the established algorithms was then compared to a heuristic procedure for solving a soft drink distribution. Some findings are revealed (1) the total distribution cost of BRKGA with insertion (BRKGA-I) results in a cost saving of 39% compared to the total cost of heuristic method, (2) BRKGA with the gender selection (BRKGA-GS) could further improve the performance of the heuristic method. However, the BRKGA-GS tends to yield worse results compared to that obtained from the standard BRKGA.

  12. Sequence-Based Prediction of RNA-Binding Proteins Using Random Forest with Minimum Redundancy Maximum Relevance Feature Selection

    Directory of Open Access Journals (Sweden)

    Xin Ma

    2015-01-01

    Full Text Available The prediction of RNA-binding proteins is one of the most challenging problems in computation biology. Although some studies have investigated this problem, the accuracy of prediction is still not sufficient. In this study, a highly accurate method was developed to predict RNA-binding proteins from amino acid sequences using random forests with the minimum redundancy maximum relevance (mRMR method, followed by incremental feature selection (IFS. We incorporated features of conjoint triad features and three novel features: binding propensity (BP, nonbinding propensity (NBP, and evolutionary information combined with physicochemical properties (EIPP. The results showed that these novel features have important roles in improving the performance of the predictor. Using the mRMR-IFS method, our predictor achieved the best performance (86.62% accuracy and 0.737 Matthews correlation coefficient. High prediction accuracy and successful prediction performance suggested that our method can be a useful approach to identify RNA-binding proteins from sequence information.

  13. A preliminary investigation of the jack-bean urease inhibition by randomly selected traditionally used herbal medicine.

    Science.gov (United States)

    Biglar, Mahmood; Soltani, Khadijeh; Nabati, Farzaneh; Bazl, Roya; Mojab, Faraz; Amanlou, Massoud

    2012-01-01

    Helicobacter pylori (H. pylori) infection leads to different clinical and pathological outcomes in humans, including chronic gastritis, peptic ulcer disease and gastric neoplasia and even gastric cancer and its eradiation dependst upon multi-drug therapy. The most effective therapy is still unknown and prompts people to make great efforts to find better and more modern natural or synthetic anti-H. pylori agents. In this report 21 randomly selected herbal methanolic extracts were evaluated for their effect on inhibition of Jack-bean urease using the indophenol method as described by Weatherburn. The inhibition potency was measured by UV spectroscopy technique at 630 nm which attributes to released ammonium. Among these extracts, five showed potent inhibitory activities with IC50 ranges of 18-35 μg/mL. These plants are Matricaria disciforme (IC50:35 μg/mL), Nasturtium officinale (IC50:18 μg/mL), Punica granatum (IC50:30 μg/mL), Camelia sinensis (IC50:35 μg/mL), Citrus aurantifolia (IC50:28 μg/mL).

  14. A brief, web-based personalized feedback selective intervention for college student marijuana use: a randomized clinical trial.

    Science.gov (United States)

    Lee, Christine M; Neighbors, Clayton; Kilmer, Jason R; Larimer, Mary E

    2010-06-01

    Despite clear need, brief web-based interventions for marijuana-using college students have not been evaluated in the literature. The current study was designed to evaluate a brief, web-based personalized feedback intervention for at-risk marijuana users transitioning to college. All entering first-year students were invited to complete a brief questionnaire. Participants meeting criteria completed a baseline assessment (N = 341) and were randomly assigned to web-based personalized feedback or assessment-only control conditions. Participants completed 3-month (95.0%) and 6-month (94.4%) follow-up assessments. Results indicated that although there was no overall intervention effect, moderator analyses found promising effects for those with a family history of drug problems and, to a smaller extent, students who were higher in contemplation of changing marijuana use at baseline. Implications of these findings for selective intervention of college marijuana use and web-based interventions in general are discussed. (PsycINFO Database Record (c) 2010 APA, all rights reserved).

  15. Optimal Subset Selection of Time-Series MODIS Images and Sample Data Transfer with Random Forests for Supervised Classification Modelling.

    Science.gov (United States)

    Zhou, Fuqun; Zhang, Aining

    2016-10-25

    Nowadays, various time-series Earth Observation data with multiple bands are freely available, such as Moderate Resolution Imaging Spectroradiometer (MODIS) datasets including 8-day composites from NASA, and 10-day composites from the Canada Centre for Remote Sensing (CCRS). It is challenging to efficiently use these time-series MODIS datasets for long-term environmental monitoring due to their vast volume and information redundancy. This challenge will be greater when Sentinel 2-3 data become available. Another challenge that researchers face is the lack of in-situ data for supervised modelling, especially for time-series data analysis. In this study, we attempt to tackle the two important issues with a case study of land cover mapping using CCRS 10-day MODIS composites with the help of Random Forests' features: variable importance, outlier identification. The variable importance feature is used to analyze and select optimal subsets of time-series MODIS imagery for efficient land cover mapping, and the outlier identification feature is utilized for transferring sample data available from one year to an adjacent year for supervised classification modelling. The results of the case study of agricultural land cover classification at a regional scale show that using only about a half of the variables we can achieve land cover classification accuracy close to that generated using the full dataset. The proposed simple but effective solution of sample transferring could make supervised modelling possible for applications lacking sample data.

  16. Identification of a novel clone, ST736, among Enterococcus faecium clinical isolates and its association with daptomycin nonsusceptibility.

    Science.gov (United States)

    Wang, Guiqing; Kamalakaran, Sitharthan; Dhand, Abhay; Huang, Weihua; Ojaimi, Caroline; Zhuge, Jian; Yee, Leslie Lee; Mayigowda, Pramod; Surendraiah, Pavan Kumar Makam; Dimitrova, Nevenka; Fallon, John T

    2014-08-01

    Resistance to daptomycin in enterococcal clinical isolates remains rare but is being increasingly reported in the United States and worldwide. There are limited data on the genetic relatedness and microbiological and clinical characteristics of daptomycin-nonsusceptible enterococcal clinical isolates. In this study, we assessed the population genetics of daptomycin-nonsusceptible Enterococcus faecium (DNSE) clinical isolates by multilocus sequence typing (MLST) and whole-genome sequencing analysis. Forty-two nonduplicate DNSE isolates and 43 randomly selected daptomycin-susceptible E. faecium isolates were included in the analysis. All E. faecium isolates were recovered from patients at a tertiary care medical center in suburban New York City from May 2009 through December 2013. The daptomycin MICs of the DNSE isolates ranged from 6 to >256 μg/ml. Three major clones of E. faecium (ST18, ST412, and ST736) were identified among these clinical isolates by MLST and whole-genome sequence-based analysis. A newly recognized clone, ST736, was seen in 32 of 42 (76.2%) DNSE isolates and in only 14 of 43 (32.6%) daptomycin-susceptible E. faecium isolates (P faecium clone ST736 and daptomycin nonsusceptibility. The identification and potential spread of this novel E. faecium clone and its association with daptomycin nonsusceptibility constitute a challenge for patient management and infection control at our medical center. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  17. [The discrete horror of cloning].

    Science.gov (United States)

    Guibourg, Ricardo A

    2009-01-01

    The author raises the topic of cloning after the decision of the Argentine government, which concerned for the "dignity of the human person", passed a decree of need and urgency, No. 200/97 (Annex), prohibiting cloning experiments with human beings. Therefore, considering that the topic is so terribly urgent and necessary, the author feels it is timely to consider it.

  18. Genome flux in tomato cell clones cultured in vitro in different physiological equilibria. II. A RAPD analysis of variability.

    Science.gov (United States)

    Bogani, P; Simoni, A; Lio', P; Scialpi, A; Buiatti, M

    1996-10-01

    An analysis of the effect of changing physiological conditions on genome evolution in tomato cell populations has been carried out on long-term in vitro cultured clones grown on different auxin-cytokinin equilibria or selected for low-high competence for active defense against Fusarium oxysporum f.sp. lycopersici. RAPD analysis, confirmed through pattern rehybridization, was used as a random tool to measure the genetic variability. Through the use of a modified ANOVA, variation was shown to depend on both the initial genotype and the physiological conditions. Pattern correlation analysis through a mutual information algorithm suggested the fixation of RAPD patterns specific to physiological equilibria. The results are discussed in view of the possible relevance for evolution at hierarchical levels higher than cell populations. Key words : tomato clones, somaclonal variation, RAPD, coadaptation.

  19. Enumeration of Escherichia coli cells on chicken carcasses as a potential measure of microbial process control in a random selection of slaughter establishments in the United States

    Science.gov (United States)

    The purpose of this study was to evaluate whether the measurement of Escherichia coli levels at two points during the chicken slaughter process has utility as a measure of quality control. A one year long survey was conducted during 2004 and 2005 in 20 randomly selected United States chicken slaught...

  20. Impact of amoxicillin therapy on resistance selection in patients with community-acquired lower respiratory tract infections : A randomized, placebo-controlled study

    NARCIS (Netherlands)

    Malhotra-Kumar, Surbhi; Van Heirstraeten, Liesbet; Coenen, Samuel; Lammens, Christine; Adriaenssens, Niels; Kowalczyk, Anna; Godycki-Cwirko, Maciek; Bielicka, Zuzana; Hupkova, Helena; Lannering, Christina; Mölstad, Sigvard; Fernandez-Vandellos, Patricia; Torres, Antoni; Parizel, Maxim; Ieven, Margareta; Butler, Chris C.; Verheij, Theo; Little, Paul; Goossens, Hermanon; Frimodt-Møller, Niels; Bruno, Pascale; Hering, Iris; Lemiengre, Marieke; Loens, Katherine; Malmvall, Bo Eric; Muras, Magdalena; Romano, Nuria Sanchez; Prat, Matteu Serra; Svab, Igor; Swain, Jackie; Tarsia, Paolo; Leus, Frank; Veen, Robert; Worby, Tricia

    2016-01-01

    Objectives: To determine the effect of amoxicillin treatment on resistance selection in patients with community-acquired lower respiratory tract infections in a randomized, placebo-controlled trial. Methods: Patients were prescribed amoxicillin 1 g, three times daily (n = 52) or placebo (n = 50) for

  1. The Long-Term Effectiveness of a Selective, Personality-Targeted Prevention Program in Reducing Alcohol Use and Related Harms: A Cluster Randomized Controlled Trial

    Science.gov (United States)

    Newton, Nicola C.; Conrod, Patricia J.; Slade, Tim; Carragher, Natacha; Champion, Katrina E.; Barrett, Emma L.; Kelly, Erin V.; Nair, Natasha K.; Stapinski, Lexine; Teesson, Maree

    2016-01-01

    Background: This study investigated the long-term effectiveness of Preventure, a selective personality-targeted prevention program, in reducing the uptake of alcohol, harmful use of alcohol, and alcohol-related harms over a 3-year period. Methods: A cluster randomized controlled trial was conducted to assess the effectiveness of Preventure.…

  2. FastCloning: a highly simplified, purification-free, sequence- and ligation-independent PCR cloning method

    Directory of Open Access Journals (Sweden)

    Lu Jia

    2011-10-01

    Full Text Available Abstract Background Although a variety of methods and expensive kits are available, molecular cloning can be a time-consuming and frustrating process. Results Here we report a highly simplified, reliable, and efficient PCR-based cloning technique to insert any DNA fragment into a plasmid vector or into a gene (cDNA in a vector at any desired position. With this method, the vector and insert are PCR amplified separately, with only 18 cycles, using a high fidelity DNA polymerase. The amplified insert has the ends with ~16-base overlapping with the ends of the amplified vector. After DpnI digestion of the mixture of the amplified vector and insert to eliminate the DNA templates used in PCR reactions, the mixture is directly transformed into competent E. coli cells to obtain the desired clones. This technique has many advantages over other cloning methods. First, it does not need gel purification of the PCR product or linearized vector. Second, there is no need of any cloning kit or specialized enzyme for cloning. Furthermore, with reduced number of PCR cycles, it also decreases the chance of random mutations. In addition, this method is highly effective and reproducible. Finally, since this cloning method is also sequence independent, we demonstrated that it can be used for chimera construction, insertion, and multiple mutations spanning a stretch of DNA up to 120 bp. Conclusion Our FastCloning technique provides a very simple, effective, reliable, and versatile tool for molecular cloning, chimera construction, insertion of any DNA sequences of interest and also for multiple mutations in a short stretch of a cDNA.

  3. Animal cloning: problems and prospects.

    Science.gov (United States)

    Wells, D N

    2005-04-01

    An efficient animal cloning technology would provide many new opportunities for livestock agriculture, human medicine, and animal conservation. Nuclear cloning involves the production of animals that are genetically identical to the donor cells used in a technique known as nuclear transfer (NT). However, at present it is an inefficient process: in cattle, only around 6% of the embryos transferred to the reproductive tracts of recipient cows result in healthy, longterm surviving clones. Of concern are the high losses throughout gestation, during birth and in the post-natal period through to adulthood. Many of the pregnancy losses relate to failure of the placenta to develop and function correctly. Placental dysfunction may also have an adverse influence on postnatal health. These anomalies are probably due to incorrect epigenetic reprogramming of the donor genome following NT, leading to inappropriate patterns of gene expression during the development of clones. Whilst some physiological tests on surviving clones suggest normality, other reports indicate a variety of post-natal clone-associated abnormalities. This variability in outcome may reflect species-specific and/or cloning methodological differences. Importantly, to date it appears that these clone-associated phenotypes are not transmitted to offspring following sexual reproduction. This indicates that they represent epigenetic errors, rather than genetic errors, which are corrected during gametogenesis. Whilst this needs confirmation at the molecular level, it provides initial confidence in the first application of NT in agriculture, namely, the production of small numbers of cloned sires from genetically elite bulls, for natural mating, to effectively disseminate genetic gain. In addition to the animal welfare concerns with the technology, the underlying health of the animals and the consequential effect on food safety are critical aspects that require investigation to gain regulatory and consumer

  4. A Fosmid Cloning Strategy for Detecting the Widest Possible Spectrum of Microbes from the International Space Station Drinking Water System

    Directory of Open Access Journals (Sweden)

    Sangdun Choi

    2012-12-01

    Full Text Available In this study, fosmid cloning strategies were used to assess the microbial populations in water from the International Space Station (ISS drinking water system (henceforth referred to as Prebiocide and Tank A water samples. The goals of this study were: to compare the sensitivity of the fosmid cloning strategy with that of traditional culture-based and 16S rRNA-based approaches and to detect the widest possible spectrum of microbial populations during the water purification process. Initially, microbes could not be cultivated, and conventional PCR failed to amplify 16S rDNA fragments from these low biomass samples. Therefore, randomly primed rolling-circle amplification was used to amplify any DNA that might be present in the samples, followed by size selection by using pulsed-field gel electrophoresis. The amplified high-molecular-weight DNA from both samples was cloned into fosmid vectors. Several hundred clones were randomly selected for sequencing, followed by Blastn/Blastx searches. Sequences encoding specific genes from Burkholderia, a species abundant in the soil and groundwater, were found in both samples. Bradyrhizobium and Mesorhizobium, which belong to rhizobia, a large community of nitrogen fixers often found in association with plant roots, were present in the Prebiocide samples. Ralstonia, which is prevalent in soils with a high heavy metal content, was detected in the Tank A samples. The detection of many unidentified sequences suggests the presence of potentially novel microbial fingerprints. The bacterial diversity detected in this pilot study using a fosmid vector approach was higher than that detected by conventional 16S rRNA gene sequencing.

  5. Mathematical design of prokaryotic clone-based microarrays

    NARCIS (Netherlands)

    Pieterse, B.; Quirijns, E.J.; Schuren, F.H.J.; Werf, M.J. van der

    2005-01-01

    Background: Clone-based microarrays, on which each spot represents a random genomic fragment, are a good alternative to open reading frame-based microarrays, especially for microorganisms for which the complete genome sequence is not available. Since the generation of a genomic DNA library is a

  6. Mathematical design of prokaryotic clone-based microarrays

    NARCIS (Netherlands)

    Pieterse, B.; Quirijns, E.J.; Schuren, F.H.J.; Werf, van der M.J.

    2005-01-01

    Background - Clone-based microarrays, on which each spot represents a random genomic fragment, are a good alternative to open reading frame-based microarrays, especially for microorganisms for which the complete genome sequence is not available. Since the generation of a genomic DNA library is a

  7. Probabilistic cloning of coherent states without a phase reference

    DEFF Research Database (Denmark)

    Müller, Christian R.; Wittmann, Christoffer; Marek, Petr

    2012-01-01

    We present a probabilistic cloning scheme operating independently of any phase reference. The scheme is based solely on a phase-randomized displacement and photon counting, omitting the need for nonclassical resources and nonlinear materials. In an experimental implementation, we employ the schem...

  8. Surveillance for cancer recurrence in long-term young breast cancer survivors randomly selected from a statewide cancer registry.

    Science.gov (United States)

    Jones, Tarsha; Duquette, Debra; Underhill, Meghan; Ming, Chang; Mendelsohn-Victor, Kari E; Anderson, Beth; Milliron, Kara J; Copeland, Glenn; Janz, Nancy K; Northouse, Laurel L; Duffy, Sonia M; Merajver, Sofia D; Katapodi, Maria C

    2018-01-20

    This study examined clinical breast exam (CBE) and mammography surveillance in long-term young breast cancer survivors (YBCS) and identified barriers and facilitators to cancer surveillance practices. Data collected with a self-administered survey from a statewide, randomly selected sample of YBCS diagnosed with invasive breast cancer or ductal carcinoma in situ younger than 45 years old, stratified by race (Black vs. White/Other). Multivariate logistic regression models identified predictors of annual CBEs and mammograms. Among 859 YBCS (n = 340 Black; n = 519 White/Other; mean age = 51.0 ± 5.9; diagnosed 11.0 ± 4.0 years ago), the majority (> 85%) reported an annual CBE and a mammogram. Black YBCS in the study were more likely to report lower rates of annual mammography and more barriers accessing care compared to White/Other YBCS. Having a routine source of care, confidence to use healthcare services, perceived expectations from family members and healthcare providers to engage in cancer surveillance, and motivation to comply with these expectations were significant predictors of having annual CBEs and annual mammograms. Cost-related lack of access to care was a significant barrier to annual mammograms. Routine source of post-treatment care facilitated breast cancer surveillance above national average rates. Persistent disparities regarding access to mammography surveillance were identified for Black YBCS, primarily due to lack of access to routine source of care and high out-of-pocket costs. Public health action targeting cancer surveillance in YBCS should ensure routine source of post-treatment care and address cost-related barriers. Clinical Trials Registration Number: NCT01612338.

  9. Evaluation of Randomly Selected Completed Medical Records Sheets in Teaching Hospitals of Jahrom University of Medical Sciences, 2009

    Directory of Open Access Journals (Sweden)

    Mohammad Parsa Mahjob

    2011-06-01

    Full Text Available Background and objective: Medical record documentation, often use to protect the patients legal rights, also providing information for medical researchers, general studies, education of health care staff and qualitative surveys is used. There is a need to control the amount of data entered in the medical record sheets of patients, considering the completion of these sheets is often carried out after completion of service delivery to the patients. Therefore, in this study the prevalence of completeness of medical history, operation reports, and physician order sheets by different documentaries in Jahrom teaching hospitals during year 2009 was analyzed. Methods and Materials: In this descriptive / retrospective study, the 400 medical record sheets of the patients from two teaching hospitals affiliated to Jahrom medical university was randomly selected. The tool of data collection was a checklist based on the content of medical history sheet, operation report and physician order sheets. The data were analyzed by SPSS (Version10 software and Microsoft Office Excel 2003. Results: Average of personal (Demography data entered in medical history, physician order and operation report sheets which is done by department's secretaries were 32.9, 35.8 and 40.18 percent. Average of clinical data entered by physician in medical history sheet is 38 percent. Surgical data entered by the surgeon in operation report sheet was 94.77 percent. Average of data entered by operation room's nurse in operation report sheet was 36.78 percent; Average of physician order data in physician order sheet entered by physician was 99.3 percent. Conclusion: According to this study, the rate of completed record papers reviewed by documentary in Jahrom teaching hospitals were not desirable and in some cases were very weak and incomplete. This deficiency was due to different reason such as medical record documentaries negligence, lack of adequate education for documentaries, High work

  10. Sexual selection has minimal impact on effective population sizes in species with high rates of random offspring mortality: An empirical demonstration using fitness distributions.

    Science.gov (United States)

    Pischedda, Alison; Friberg, Urban; Stewart, Andrew D; Miller, Paige M; Rice, William R

    2015-10-01

    The effective population size (N(e)) is a fundamental parameter in population genetics that influences the rate of loss of genetic diversity. Sexual selection has the potential to reduce N(e) by causing the sex-specific distributions of individuals that successfully reproduce to diverge. To empirically estimate the effect of sexual selection on N(e), we obtained fitness distributions for males and females from an outbred, laboratory-adapted population of Drosophila melanogaster. We observed strong sexual selection in this population (the variance in male reproductive success was ∼14 times higher than that for females), but found that sexual selection had only a modest effect on N(e), which was 75% of the census size. This occurs because the substantial random offspring mortality in this population diminishes the effects of sexual selection on N(e), a result that necessarily applies to other high fecundity species. The inclusion of this random offspring mortality creates a scaling effect that reduces the variance/mean ratios for male and female reproductive success and causes them to converge. Our results demonstrate that measuring reproductive success without considering offspring mortality can underestimate Ne and overestimate the genetic consequences of sexual selection. Similarly, comparing genetic diversity among different genomic components may fail to detect strong sexual selection. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

  11. Construction and selection of subtracted cDNA library of mouse hepatocarcinoma cell lines with different lymphatic metastasis potential

    Science.gov (United States)

    Hou, Li; Tang, Jan-Wu; Cui, Xiao-Nan; Wang, Bo; Song, Bo; Sun, Lei

    2004-01-01

    AIM: In order to elucidate the molecular mechanism of lymphatic metastasis of hepatocarcinoma, we detected the difference of gene expression between mouse hepatocarcinoma cell lines Hca-F and Hca-P with different lymphatic metastasis potential. METHODS: cDNA of Hca-F cells was used as a tester and cDNA of Hca-P cells was used as a driver. cDNAs highly expressed in Hca-F cells were isolated by the suppression subtractive hybridization (SSH) method. The isolated cDNA was cloned into T/A cloning vector. The ligation products were transformed into DH5 α competent cells. Individual clones were randomly selected and used for PCR amplification. Vector DNA from positive clones was isolated for sequencing. RESULTS: There were 800 positive clones in amplified subtracted cDNA library. Random analysis of 160 clones with PCR showed that 95% of the clones contained 100-700 bp inserts. Analysis of 20 sequenced cDNA clones randomly picked from the SSH library revealed 4 known genes (mouse heat shock protein 84 ku, DNA helicase, ribosomal protein S13 ,ethanol induced 6 gene) and 3 expressed sequence tags (ESTs). Four cDNAs showed no homology and presumably represent novel genes. CONCLUSION: A subtracted cDNA library of differentially expressed genes in mouse heptocarcinoma cell lines with different lymphatic metastasis potential was successfully constructed with SSH and T/A cloning techniques. The library is efficient and lays a solid foundation for searching new lymphatic metastasis related genes. The expression of mouse heat shock protein gene, DNA helicase and other 4 novel gene may be different between mouse heptocarcinoma cell lines with different lymphatic metastasis potential. PMID:15285011

  12. Human cloning: can it be made safe?

    Science.gov (United States)

    Rhind, Susan M; Taylor, Jane E; De Sousa, Paul A; King, Tim J; McGarry, Michelle; Wilmut, Ian

    2003-11-01

    There are continued claims of attempts to clone humans using nuclear transfer, despite the serious problems that have been encountered in cloning other mammals. It is known that epigenetic and genetic mechanisms are involved in clone failure, but we still do not know exactly how. Human reproductive cloning is unethical, but the production of cells from cloned embryos could offer many potential benefits. So, can human cloning be made safe?

  13. Quantum Cloning Machines and the Applications

    OpenAIRE

    Fan, Heng; Wang, Yi-Nan; Jing, Li; Yue, Jie-Dong; Shi, Han-Duo; Zhang, Yong-Liang; Mu, Liang-Zhu

    2013-01-01

    No-cloning theorem is fundamental for quantum mechanics and for quantum information science that states an unknown quantum state cannot be cloned perfectly. However, we can try to clone a quantum state approximately with the optimal fidelity, or instead, we can try to clone it perfectly with the largest probability. Thus various quantum cloning machines have been designed for different quantum information protocols. Specifically, quantum cloning machines can be designed to analyze the securit...

  14. Melhoramento da cana-de-açúcar: IX: evaluation of clones obtained in 1980 and 1981 hybridizations, selected in Ribeirão Preto region, state of São Paulo, Brazil Sugarcane breeding: IX

    Directory of Open Access Journals (Sweden)

    Marcos Guimarães de Andrade Landell

    1995-01-01

    Full Text Available Testaram-se doze clones de cana-de-açúcar, obtidos de hibridações realizadas em Camamu (BA, em 1980 e 1981, em três ensaios na região de Ribeirão Preto (SP. Além do delineamento em blocos ao acaso, com seis repetições, efetuou-se a análise estatística com a média das três colheitas (1.°, 2.° e 3.° cortes, tomando as variedades SP70-1143, NA56-79 e IAC64-257 como testemunhas-padrão. Entre os caracteres agroindustriais avaliados estão: a produtividade de cana e açúcar, pol % cana, fibra %, intensidade de florescimento, índice de infestação de broca-do-colmo (Diatraea saccharalis e a reação à ferrugem (Puccinia melanocephala. O melhor clone foi o IAC80-2094, indicado para início de safra, com boa produção e bom teor de fibra, mas de florescimento intenso e suscetibilidade à ferrugem. O IAC81-2004 também apresentou bons resultados, caracterizando-se como precoce, com bom teor de fibra e boa resistência à broca-do-colmo. Em condições naturais de campo, porém, sua desvantagem é a grande incidência de "chicotes" de carvão. Apesar de ambos os clones apresentarem características agroindustriais vantajosas, desaconselha-se que sejam incluídos no estudo de manejo parietal para outras regiões paulistas, em função dos problemas fitossanitários citados.A number of sugarcane clones obtained in crosses made in 1980 and 1981, was tested in three locations with Oxisol soils at Ribeirão Preto region. The commercial varieties SP70-1143, NA56-79 and IAC64-257 were used as controls in trials and evaluated for agricultural and industrial traits on the average of three harvests. The best clone in the experiments was IAC80-2094, which has been indicated for early harvest period with good yield and fiber content, but with heavy tasseling and susceptibility to rust. Other early maturing clone was IAC81-2004, which showes good fiber content and stem borer tolerance, however it does show, in natural conditions in the field

  15. Photonic quantum simulator for unbiased phase covariant cloning

    Science.gov (United States)

    Knoll, Laura T.; López Grande, Ignacio H.; Larotonda, Miguel A.

    2018-01-01

    We present the results of a linear optics photonic implementation of a quantum circuit that simulates a phase covariant cloner, using two different degrees of freedom of a single photon. We experimentally simulate the action of two mirrored 1→ 2 cloners, each of them biasing the cloned states into opposite regions of the Bloch sphere. We show that by applying a random sequence of these two cloners, an eavesdropper can mitigate the amount of noise added to the original input state and therefore, prepare clones with no bias, but with the same individual fidelity, masking its presence in a quantum key distribution protocol. Input polarization qubit states are cloned into path qubit states of the same photon, which is identified as a potential eavesdropper in a quantum key distribution protocol. The device has the flexibility to produce mirrored versions that optimally clone states on either the northern or southern hemispheres of the Bloch sphere, as well as to simulate optimal and non-optimal cloning machines by tuning the asymmetry on each of the cloning machines.

  16. Limitations on Cloning in Classical Mechanics

    OpenAIRE

    Fenyes, Aaron

    2010-01-01

    In this paper, we show that a result precisely analogous to the traditional quantum no-cloning theorem holds in classical mechanics. This classical no-cloning theorem does not prohibit classical cloning, we argue, because it is based on a too-restrictive definition of cloning. Using a less popular, more inclusive definition of cloning, we give examples of classical cloning processes. We also prove that a cloning machine must be at least as complicated as the object it is supposed to clone.

  17. Boron mobility in eucalyptus clones Mobilidade de Boro em clones de eucalipto

    Directory of Open Access Journals (Sweden)

    Jackson Freitas Brilhante de São José

    2009-12-01

    Full Text Available Understanding the magnitude of B mobility in eucalyptus may help to select clones that are more efficient for B use and to design new practices of B fertilization. This study consisted of five experiments with three eucalyptus clones (129, 57 and 58 where the response to and mobility of B were evaluated. Results indicated that clone 129 was less sensitive to B deficiency than clones 68 and 57, apparently due to its ability to translocate B previously absorbed via root systems to younger tissues when B in solution became limiting. Translocation also occurred when B was applied as boric acid only once to a single mature leaf, resulting in higher B concentration in roots, stems and younger leaves. The growth of B-deficient plants was also recovere by a single foliar application of B to a mature leaf. This mobility was greater, when foliar-applied B was supplied in complexed (boric acid + manitol than in non-complexed form (boric acid alone. When the root system of clone 129 was split in two solution compartments, B supplied to one root compartment was translocated to the shoot and back to the roots in the other compartment, improving the B status and growth. Thus, it appears that B is relatively mobile in eucalyptus, especially in clone 129, and its higher mobility could be due to the presence of an organic compound such as manitol, able to complex B.O entendimento da magnitude da mobilidade de B no eucalipto é importante, devido a sua utilidade para a seleção de clones mais eficiente para esse micronutriente, além da projeção de novas práticas de fertilização de B. Este estudo envolveu cinco experimentos com três clones de eucalipto (129, 57 e 68, em que foram avaliadas a resposta e a mobilidade de B. Os resultados indicaram que o clone 129 foi menos sensível à deficiência de B do que os clones 68 e 57, aparentemente, em razão da sua maior habilidade de translocar B, previamente absorvido via sistema radicular, para tecidos jovens

  18. Therapeutic cloning in the mouse

    Science.gov (United States)

    Mombaerts, Peter

    2003-01-01

    Nuclear transfer technology can be applied to produce autologous differentiated cells for therapeutic purposes, a concept termed therapeutic cloning. Countless articles have been published on the ethics and politics of human therapeutic cloning, reflecting the high expectations from this new opportunity for rejuvenation of the aging or diseased body. Yet the research literature on therapeutic cloning, strictly speaking, is comprised of only four articles, all in the mouse. The efficiency of derivation of embryonic stem cell lines via nuclear transfer is remarkably consistent among these reports. However, the efficiency is so low that, in its present form, the concept is unlikely to become widespread in clinical practice. PMID:12949262

  19. Human therapeutic cloning (NTSC): applying research from mammalian reproductive cloning.

    Science.gov (United States)

    French, Andrew J; Wood, Samuel H; Trounson, Alan O

    2006-01-01

    Human therapeutic cloning or nuclear transfer stem cells (NTSC) to produce patient-specific stem cells, holds considerable promise in the field of regenerative medicine. The recent withdrawal of the only scientific publications claiming the successful generation of NTSC lines afford an opportunity to review the available research in mammalian reproductive somatic cell nuclear transfer (SCNT) with the goal of progressing human NTSC. The process of SCNT is prone to epigenetic abnormalities that contribute to very low success rates. Although there are high mortality rates in some species of cloned animals, most surviving clones have been shown to have normal phenotypic and physiological characteristics and to produce healthy offspring. This technology has been applied to an increasing number of mammals for utility in research, agriculture, conservation, and biomedicine. In contrast, attempts at SCNT to produce human embryonic stem cells (hESCs) have been disappointing. Only one group has published reliable evidence of success in deriving a cloned human blastocyst, using an undifferentiated hESC donor cell, and it failed to develop into a hESC line. When optimal conditions are present, it appears that in vitro development of cloned and parthenogenetic embryos, both of which may be utilized to produce hESCs, may be similar to in vitro fertilized embryos. The derivation of ESC lines from cloned embryos is substantially more efficient than the production of viable offspring. This review summarizes developments in mammalian reproductive cloning, cell-to-cell fusion alternatives, and strategies for oocyte procurement that may provide important clues facilitating progress in human therapeutic cloning leading to the successful application of cell-based therapies utilizing autologous hESC lines.

  20. Birth of clones of the world's first cloned dog.

    Science.gov (United States)

    Kim, Min Jung; Oh, Hyun Ju; Kim, Geon A; Setyawan, Erif Maha Nugraha; Choi, Yoo Bin; Lee, Seok Hee; Petersen-Jones, Simon M; Ko, CheMyong J; Lee, Byeong Chun

    2017-11-10

    Animal cloning has gained popularity as a method to produce genetically identical animals or superior animals for research or industrial uses. However, the long-standing question of whether a cloned animal undergoes an accelerated aging process is yet to be answered. As a step towards answering this question, we compared longevity and health of Snuppy, the world's first cloned dog, and its somatic cell donor, Tai, a male Afghan hound. Briefly, both Snuppy and Tai were generally healthy until both developed cancer to which they succumbed at the ages of 10 and 12 years, respectively. The longevity of both the donor and the cloned dog was close to the median lifespan of Afghan hounds which is reported to be 11.9 years. Here, we report creation of 4 clones using adipose-derived mesenchymal stem cells from Snuppy as donor cells. Clinical and molecular follow-up of these reclones over their lives will provide us with a unique opportunity to study the health and longevity of cloned animals compared with their cell donors.

  1. Cloning humans? Biological, ethical, and social considerations.

    Science.gov (United States)

    Ayala, Francisco J

    2015-07-21

    There are, in mankind, two kinds of heredity: biological and cultural. Cultural inheritance makes possible for humans what no other organism can accomplish: the cumulative transmission of experience from generation to generation. In turn, cultural inheritance leads to cultural evolution, the prevailing mode of human adaptation. For the last few millennia, humans have been adapting the environments to their genes more often than their genes to the environments. Nevertheless, natural selection persists in modern humans, both as differential mortality and as differential fertility, although its intensity may decrease in the future. More than 2,000 human diseases and abnormalities have a genetic causation. Health care and the increasing feasibility of genetic therapy will, although slowly, augment the future incidence of hereditary ailments. Germ-line gene therapy could halt this increase, but at present, it is not technically feasible. The proposal to enhance the human genetic endowment by genetic cloning of eminent individuals is not warranted. Genomes can be cloned; individuals cannot. In the future, therapeutic cloning will bring enhanced possibilities for organ transplantation, nerve cells and tissue healing, and other health benefits.

  2. Human cloning and 'posthuman' society.

    Science.gov (United States)

    Blackford, Russell

    2005-01-01

    Since early 1997, when the creation of Dolly the sheep by somatic cell nuclear transfer was announced in Nature, numerous government reports, essays, articles and books have considered the ethical problems and policy issues surrounding human reproductive cloning. In this article, I consider what response a modern liberal society should give to the prospect of human cloning, if it became safe and practical. Some opponents of human cloning have argued that permitting it would place us on a slippery slope to a repugnant future society, comparable to that portrayed in Aldous Huxley's novel, Brave New World. I conclude that, leaving aside concerns about safety, none of the psychological or social considerations discussed in this article provides an adequate policy justification for invoking the state's coercive powers to prevent human cloning.

  3. Human Cloning: Let's Discuss It.

    Science.gov (United States)

    Taras, Loretta; Stavroulakis, Anthea M.; Ortiz, Mary T.

    1999-01-01

    Describes experiences with holding discussions on cloning at a variety of levels in undergraduate biology courses. Discusses teaching methods used and student reactions to the discussions. Contains 12 references. (WRM)

  4. Expression cloning screening of a unique and full-length set of cDNA clones is an efficient method for identifying genes involved in Xenopus neurogenesis.

    Science.gov (United States)

    Voigt, Jana; Chen, Jun-An; Gilchrist, Mike; Amaya, Enrique; Papalopulu, Nancy

    2005-03-01

    Functional screens, where a large numbers of cDNA clones are assayed for certain biological activity, are a useful tool in elucidating gene function. In Xenopus, gain of function screens are performed by pool screening, whereby RNA transcribed in vitro from groups of cDNA clones, ranging from thousands to a hundred, are injected into early embryos. Once an activity is detected in a pool, the active clone is identified by sib-selection. Such screens are intrinsically biased towards potent genes, whose RNA is active at low quantities. To improve the sensitivity and efficiency of a gain of function screen we have bioinformatically processed an arrayed and EST sequenced set of 100,000 gastrula and neurula cDNA clones, to create a unique and full-length set of approximately 2500 clones. Reducing the redundancy and excluding truncated clones from the starting clone set reduced the total number of clones to be screened, in turn allowing us to reduce the pool size to just eight clones per pool. We report that the efficiency of screening this clone set is five-fold higher compared to a redundant set derived from the same libraries. We have screened 960 cDNA clones from this set, for genes that are involved in neurogenesis. We describe the overexpression phenotypes of 18 single clones, the majority of which show a previously uncharacterised phenotype and some of which are completely novel. In situ hybridisation analysis shows that a large number of these genes are specifically expressed in neural tissue. These results demonstrate the effectiveness of a unique full-length set of cDNA clones for uncovering players in a developmental pathway.

  5. Insights on bovine genetic engineering and cloning

    Directory of Open Access Journals (Sweden)

    Fabiana F. Bressan

    2013-12-01

    Full Text Available Transgenic technology has become an essential tool for the development of animal biotechnologies, and animal cloning through somatic cell nuclear transfer (SCNT enabled the generation of genetically modified animals utilizing previously modified and selected cell lineages as nuclei donors, assuring therefore the generation of homogeneous herds expressing the desired modification. The present study aimed to discuss the use of SCNT as an important methodology for the production of transgenic herds, and also some recent insights on genetic modification of nuclei donors and possible effects of gene induction of pluripotency on SCNT.

  6. Islamic perspectives on human cloning.

    Science.gov (United States)

    Sadeghi, Mahmoud

    2007-01-01

    The present paper seeks to assess various views from Islamic jurists relating to human cloning, which is one of the controversial topics in the recent past. Taking Islamic jurisprudence principles, such as the rule of necessity for self preservation and respect for human beings, the rule of la darar wa la dirar ('the necessity to refrain from causing harm to oneself and others') and the rule of usr wa haraj, one may indicate that if human cloning could not be prohibited, as such, it could still be opposed because it gives way to various harmful consequences, which include family disorder, chaos in the clone's family relationships, physical and mental diseases for clones and suffering of egg donors and surrogate mothers. However with due attention to the fact that the reasons behind the prohibition of abortion only restrict the destruction of human embryos in their post-implantation stages, human cloning for biomedical research and exploitation of stem cells from cloned embryos at the blastocyst stage for therapeutic purposes would be acceptable.

  7. Cloning goes to the movies.

    Science.gov (United States)

    Cormick, Craig

    2006-10-01

    Public attitude research conducted by Biotechnology Australia shows that one of the major sources of information on human reproductive cloning is movies. Traditionally, understanding of new and emerging technologies has come through the mass media but human cloning, being so widely addressed through the popular culture of movies, is more effectively defined by Hollywood than the news media or science media. But how well are the science and social issues of cloning portrayed in box office hits such as The Island, Multiplicity, Star Wars: Attack of the Clones and Jurassic Park? These movies have enormous reach and undoubted influence, and are therefore worth analyzing in some detail. This study looks at 33 movies made between 1971 and 2005 that address human reproductive cloning, and it categorizes the films based on their genre and potential influence. Yet rather than simply rating the quality of the science portrayed, the study compares the key messages in these movies with public attitudes towards cloning, to examine the correlations.

  8. Artificial cloning of domestic animals.

    Science.gov (United States)

    Keefer, Carol L

    2015-07-21

    Domestic animals can be cloned using techniques such as embryo splitting and nuclear transfer to produce genetically identical individuals. Although embryo splitting is limited to the production of only a few identical individuals, nuclear transfer of donor nuclei into recipient oocytes, whose own nuclear DNA has been removed, can result in large numbers of identical individuals. Moreover, clones can be produced using donor cells from sterile animals, such as steers and geldings, and, unlike their genetic source, these clones are fertile. In reality, due to low efficiencies and the high costs of cloning domestic species, only a limited number of identical individuals are generally produced, and these clones are primarily used as breed stock. In addition to providing a means of rescuing and propagating valuable genetics, somatic cell nuclear transfer (SCNT) research has contributed knowledge that has led to the direct reprogramming of cells (e.g., to induce pluripotent stem cells) and a better understanding of epigenetic regulation during embryonic development. In this review, I provide a broad overview of the historical development of cloning in domestic animals, of its application to the propagation of livestock and transgenic animal production, and of its scientific promise for advancing basic research.

  9. Affinity selection of Nipah and Hendra virus-related vaccine candidates from a complex random peptide library displayed on bacteriophage virus-like particles

    Energy Technology Data Exchange (ETDEWEB)

    Peabody, David S.; Chackerian, Bryce; Ashley, Carlee; Carnes, Eric; Negrete, Oscar

    2017-01-24

    The invention relates to virus-like particles of bacteriophage MS2 (MS2 VLPs) displaying peptide epitopes or peptide mimics of epitopes of Nipah Virus envelope glycoprotein that elicit an immune response against Nipah Virus upon vaccination of humans or animals. Affinity selection on Nipah Virus-neutralizing monoclonal antibodies using random sequence peptide libraries on MS2 VLPs selected peptides with sequence similarity to peptide sequences found within the envelope glycoprotein of Nipah itself, thus identifying the epitopes the antibodies recognize. The selected peptide sequences themselves are not necessarily identical in all respects to a sequence within Nipah Virus glycoprotein, and therefore may be referred to as epitope mimics VLPs displaying these epitope mimics can serve as vaccine. On the other hand, display of the corresponding wild-type sequence derived from Nipah Virus and corresponding to the epitope mapped by affinity selection, may also be used as a vaccine.

  10. Towards Clone Detection in UML Domain Models

    DEFF Research Database (Denmark)

    Störrle, Harald

    2010-01-01

    , we discuss how model clones arise by analyzing several practical scenarios. We propose a formal definition of models and clones, that allows us to specify a generic clone detection algorithm. Through a thorough analysis of the detail structure of sample UML domain models, recommendations for clone...

  11. Ants farm subterranean aphids mostly in single clone groups

    DEFF Research Database (Denmark)

    Ivens, Aniek B.F.; Kronauer, Daniel Jan Christoph; Pen, Ido

    2012-01-01

    mutualisms have been studied in sufficient genetic detail to address these issues, so we decided to characterize symbiont diversity in the complex mutualism between multiple root aphid species and Lasius flavus ants. After showing elsewhere that three of these aphid species have low dispersal and mostly...... if not exclusively asexual reproduction, we here investigate aphid diversity within and between ant nest mounds. Results The three focal species (Geoica utricularia, Forda marginata and Tetraneura ulmi) had considerable clonal diversity at the population level. Yet more than half of the ant mounds contained just...... a single aphid species, a significantly higher percentage than expected from a random distribution. Over 60% of these single-species mounds had a single aphid clone, and clones tended to persist across subsequent years. Whenever multiple species/clones co-occurred in the same mound, they were spatially...

  12. Restriction enzyme body doubles and PCR cloning: on the general use of type IIs restriction enzymes for cloning.

    Science.gov (United States)

    Tóth, Eszter; Huszár, Krisztina; Bencsura, Petra; Kulcsár, Péter István; Vodicska, Barbara; Nyeste, Antal; Welker, Zsombor; Tóth, Szilvia; Welker, Ervin

    2014-01-01

    The procedure described here allows the cloning of PCR fragments containing a recognition site of the restriction endonuclease (Type IIP) used for cloning in the sequence of the insert. A Type IIS endonuclease--a Body Double of the Type IIP enzyme--is used to generate the same protruding palindrome. Thus, the insert can be cloned to the Type IIP site of the vector without digesting the PCR product with the same Type IIP enzyme. We achieve this by incorporating the recognition site of a Type IIS restriction enzyme that cleaves the DNA outside of its recognition site in the PCR primer in such a way that the cutting positions straddle the desired overhang sequence. Digestion of the PCR product by the Body Double generates the required overhang. Hitherto the use of Type IIS restriction enzymes in cloning reactions has only been used for special applications, the approach presented here makes Type IIS enzymes as useful as Type IIP enzymes for general cloning purposes. To assist in finding Body Double enzymes, we summarised the available Type IIS enzymes which are potentially useful for Body Double cloning and created an online program (http://group.szbk.u-szeged.hu/welkergr/body_double/index.html) for the selection of suitable Body Double enzymes and the design of the appropriate primers.

  13. [Mystery and problems of cloning].

    Science.gov (United States)

    Nikitin, V A

    2010-01-01

    The attention of investigators is attracted to the fact that, in spite of great efforts in mammalian cloning, advances that have been made in this area of research are not great, and cloned animals have developmental pathologies often incompatible with life and/or reproduction ability. It is yet not clear what technical or biological factors underlie this, and how they are connected or interact with each other, which is more realistic strategically. There is a great number of articles dealing with the influence of cloning with the nuclear transfer on genetic and epigenetic reprogramming of donor cells. At the same time we can see the practical absence of analytical investigations concerning the technology of cloning as such, its weak points, and possible sources of cellular trauma in the course of microsurgery of nuclear transfer or twinning. This article discusses step by step several nuclear transfer techniques and the methods of dividing early preimplanted embryos for twinning with the aim to reveal possible sources of cell damage during micromanipulation that may have negative influence on the development of cloned organisms. Several new author's technologies based on the study of cell biophysical characteristics are described, which allow one to avoid cellular trauma during manipulation and minimize the possibility of cell damage at any rate.

  14. [Cloning and law in Hungary].

    Science.gov (United States)

    Julesz, Máté

    2015-03-01

    Reproductive human cloning is prohibited in Hungary, as in many other countries. Therapeutic human cloning is not prohibited, just like in many other countries. Stem cell therapy is also allowed. Article III, paragraph (3) of the Hungarian basic law (constitution) strictly forbids total human cloning. Article 1 of the Additional Protocol to the Oviedo Convention, on the Prohibition of Cloning Human Beings (1998) stipulates that any intervention seeking to create a human being genetically identical to another human being, whether living or dead, is prohibited. In Hungary, according to Article 174 of the Criminal Code, total human cloning constitutes a crime. Article 180, paragraph (3) of the Hungarian Act on Health declares that embryos shall not be brought about for research purposes; research shall be conducted only on embryos brought about for reproductive purposes when this is authorized by the persons entitled to decide upon its disposal, or when the embryo is damaged. Article 180, paragraph (5) of the Hungarian Act on Health stipulates that multiple individuals who genetically conform to one another shall not be brought about. According to Article 181, paragraph (1) of the Hungarian Act on Health, an embryo used for research shall be kept alive for not longer than 14 days, not counting the time it was frozen for storage and the time period of research.

  15. Multiple factors affect pest and pathogen damage on 31 Populus clones in South Carolina

    Science.gov (United States)

    David R. Coyle; Mark D. Coleman; Jaclin A. Durant; Lee A. Newman

    2006-01-01

    Populus species and hybrids have many practical applications, but there is a paucity of data regarding selections that perform well in the southeastern US. We compared pest susceptibility of 31 Populus clones over 3 years in South Carolina, USA. Cuttings were planted in spring 2001 on two study sites. Clones planted in the...

  16. Bias in the prediction of genetic gain due to mass and half-sib selection in random mating populations

    Directory of Open Access Journals (Sweden)

    José Marcelo Soriano Viana

    2009-01-01

    Full Text Available The prediction of gains from selection allows the comparison of breeding methods and selection strategies, although these estimates may be biased. The objective of this study was to investigate the extent of such bias in predicting genetic gain. For this, we simulated 10 cycles of a hypothetical breeding program that involved seven traits, three population classes, three experimental conditions and two breeding methods (mass and half-sib selection. Each combination of trait, population, heritability, method and cycle was repeated 10 times. The predicted gains were biased, even when the genetic parameters were estimated without error. Gain from selection in both genders is twice the gain from selection in a single gender only in the absence of dominance. The use of genotypic variance or broad sense heritability in the predictions represented an additional source of bias. Predictions based on additive variance and narrow sense heritability were equivalent, as were predictions based on genotypic variance and broad sense heritability. The predictions based on mass and family selection were suitable for comparing selection strategies, whereas those based on selection within progenies showed the largest bias and lower association with the realized gain.

  17. Comprehensive Cloning of Patient-derived 9022-bp Amplicons of Hepatitis C Virus

    Science.gov (United States)

    Lu, Yang; Xu, Yanjuan; Di Bisceglie, Adrian M.; Fan, Xiaofeng

    2013-01-01

    The instability of recombinant clones accommodating large or full-length viral genomes is frequently a technical challenge in RNA virus research. In an attempt to establish a rapid plasmid-based reverse genetics system that utilizes long RT-PCR technique (LRP), similar difficulty was encountered in the cloning of 9022-bp LRP amplicon. All HCV genotype 1a strains used for LRP cloning showed a remarkable difference in terms of cloning stability. Subsequent analysis revealed the predictive value of phylogenetic positions in determining the cloning stability. Putative E. coli promoters on the HCV genome might be responsible for such cloning difference. An exhaustive exploration, testing nearly one hundred cloning protocols, did not reveal a general approach that can achieve stable cloning for all HCV 1a strains. The selection of appropriate strains, guided by phylogenetic analysis, appears to be necessary prior to the construction of infectious HCV 1a clones. These observations are not only valuable for potentially establishing an HCV 1a cell culture model but also have general implications for other RNA viruses due to concern about cloning instability. PMID:23602804

  18. Evaluating Quantitative and Qualitative Traits of Promising Potato Clones and Commercial Cultivars Using the GGE Bi-plot and AMMI Models

    Directory of Open Access Journals (Sweden)

    D HassanPanah

    2014-07-01

    Full Text Available To evaluate quantitative and qualitative characteristics and stability of marketable tuber yield of 13 promising potato clones, along with three commercial cultivars (Agria, Marfona and Lady Rosetta as checks, an experiment was based on a randomized complete block design with four replications was carried out at the Agricultural and Natural Resources Research Station of Ardabil during 2011 and 2012. During the growing period and after harvest, attributes like number of main stem per plant, plant height, tuber number and weight per plant, total and marketable tuber yield, dry matter percentage, baking type, hollow heart, tuber inner ring and discoloration of raw tuber flesh after 24 hours were measured. Combined ANONA for quantitative traits showed that there were significant differences among promising clones as to total and marketable tuber yield, tuber number and weight per plant, plant height, mean tuber weight, number of main stem per plant and dry matter percentage and their interactions with year in total and marketable tuber yield and tuber number and weight per plant. The clones 396151-7, 397008-5, 397015-8, 397008-2 and 994001-4 were found to have higher total and marketable tuber yield, tuber number and weight per plant and mean tuber weight. These clones produced high and mid-uniform tuber, yellow skin color, yellow and white flesh color, oval round and round tuber shape, mid and shallow eyes, with no hollow heart, tuber inner crack and tuber inner ring, mid-late maturity and mid and high dry matter percentage as compared with control and other clones. In this experiment, GGE Bi-plot and AMMI models were found to be proper methods for selection of 397008-2, 397008-5 and 994001-4 as being high marketable and stable yielding clones.

  19. Public perceptions of animal cloning

    DEFF Research Database (Denmark)

    Jelsøe, Erling; Vincentsen, Ulla; Andersen, Ida-Elisabeth

    What was from the outset meant to be a survey testing predefined categories of ethical positions related to new biotechnologies with animal cloning as an example was subsequently developed into a process of broader involvement of groups of citizens in the issue. The survey was conducted at meetings...... in four different cities in Denmark. The participants were introduced to animal cloning and after that they filled out the questionnaire. Finally, the issue was discussed in focus groups. The process as a whole was run in a dialogue oriented way. Through the information they received in combination...... with reflecting on the survey questions the participants were well prepared for discussions in the focus groups. This approach made it possible, on the one hand to get a measure of the citizen's perceptions of the ethical aspects of animal cloning, but also to go deeper into their own thoughts of the issue...

  20. Statistical inference for classification of RRIM clone series using near IR reflectance properties

    Science.gov (United States)

    Ismail, Faridatul Aima; Madzhi, Nina Korlina; Hashim, Hadzli; Abdullah, Noor Ezan; Khairuzzaman, Noor Aishah; Azmi, Azrie Faris Mohd; Sampian, Ahmad Faiz Mohd; Harun, Muhammad Hafiz

    2015-08-01

    RRIM clone is a rubber breeding series produced by RRIM (Rubber Research Institute of Malaysia) through "rubber breeding program" to improve latex yield and producing clones attractive to farmers. The objective of this work is to analyse measurement of optical sensing device on latex of selected clone series. The device using transmitting NIR properties and its reflectance is converted in terms of voltage. The obtained reflectance index value via voltage was analyzed using statistical technique in order to find out the discrimination among the clones. From the statistical results using error plots and one-way ANOVA test, there is an overwhelming evidence showing discrimination of RRIM 2002, RRIM 2007 and RRIM 3001 clone series with p value = 0.000. RRIM 2008 cannot be discriminated with RRIM 2014; however both of these groups are distinct from the other clones.

  1. Impact of Selection Bias on Treatment Effect Size Estimates in Randomized Trials of Oral Health Interventions: A Meta-epidemiological Study.

    Science.gov (United States)

    Saltaji, H; Armijo-Olivo, S; Cummings, G G; Amin, M; da Costa, B R; Flores-Mir, C

    2018-01-01

    Emerging evidence suggests that design flaws of randomized controlled trials can result in over- or underestimation of the treatment effect size (ES). The objective of this study was to examine associations between treatment ES estimates and adequacy of sequence generation, allocation concealment, and baseline comparability among a sample of oral health randomized controlled trials. For our analysis, we selected all meta-analyses that included a minimum of 5 oral health randomized controlled trials and used continuous outcomes. We extracted data, in duplicate, related to items of selection bias (sequence generation, allocation concealment, and baseline comparability) in the Cochrane Risk of Bias tool. Using a 2-level meta-meta-analytic approach with a random effects model to allow for intra- and inter-meta-analysis heterogeneity, we quantified the impact of selection bias on the magnitude of ES estimates. We identified 64 meta-analyses, including 540 randomized controlled trials analyzing 137,957 patients. Sequence generation was judged to be adequate (at low risk of bias) in 32% ( n = 173) of trials, and baseline comparability was judged to be adequate in 77.8% of trials. Allocation concealment was unclear in the majority of trials ( n = 458, 84.8%). We identified significantly larger treatment ES estimates in trials that had inadequate/unknown sequence generation (difference in ES = 0.13; 95% CI: 0.01 to 0.25) and inadequate/unknown allocation concealment (difference in ES = 0.15; 95% CI: 0.02 to 0.27). In contrast, baseline imbalance (difference in ES = 0.01, 95% CI: -0.09 to 0.12) was not associated with inflated or underestimated ES. In conclusion, treatment ES estimates were 0.13 and 0.15 larger in trials with inadequate/unknown sequence generation and inadequate/unknown allocation concealment, respectively. Therefore, authors of systematic reviews using oral health randomized controlled trials should perform sensitivity analyses based on the adequacy of

  2. The topsy-turvy cloning law.

    Science.gov (United States)

    Brassington, Iain; Oultram, Stuart

    2011-03-01

    In debates about human cloning, a distinction is frequently drawn between therapeutic and reproductive uses of the technology. Naturally enough, this distinction influences the way that the law is framed. The general consensus is that therapeutic cloning is less morally problematic than reproductive cloning--one can hold this position while holding that both are morally unacceptable--and the law frequently leaves the way open for some cloning for the sake of research into new therapeutic techniques while banning it for reproductive purposes. We claim that the position adopted by the law has things the wrong way around: if we accept a moral distinction between therapeutic and reproductive cloning, there are actually more reasons to be morally worried about therapeutic cloning than about reproductive cloning. If cloning is the proper object of legal scrutiny, then, we ought to make sure that we are scrutinising the right kind of clone.

  3. Ethical attitudes on human cloning among professionals in Taiwan and the policy implications for regulation.

    Science.gov (United States)

    Yang, Che-Ming; Chung, Chun-Chih; Lu, Meei-Shiow; Lin, Chiou-Fen; Chen, Jiun-Shyan

    2005-01-01

    This research focused on understanding the attitudes toward human cloning in Taiwan among professionals in healthcare, law, and religion. The study was conducted utilizing a structured questionnaire. 220 healthcare professionals from two regional hospitals located in Taipei, 351 religious professionals in the northern Taiwan and 711 legal professionals were selected by to receive questionnaires. The valid response rate is 42.1% The questions were generated by an expert panel and represented major arguments in the human cloning debate. There were a total of six Likert scaled questions in the questionnaire. The responses were coded from 1 to 5 with 1 representing strong opposition to human cloning, 3 representing a neutral attitude; and 5 representing a strong favorable attitude toward human cloning. Healthcare professionals had the highest overall average score of 2.14 and the religious professionals had the lowest average at 1.58. All three categories of respondents' attitude toward cloning ranged from mild opposition to strong opposition to human cloning. The religious professionals were more strongly opposed to cloning. Age, education, and religion significantly influenced attitudes toward cloning. Professionals between fifty-one and sixty years old, those with less education, and Roman Catholic professionals were more strongly opposed to cloning. Religious professionals were more strongly opposed to human cloning than professionals in healthcare or law. Younger professionals as an age group demonstrated less opposition to human cloning. Regulation of human cloning will be influenced by professionals in healthcare, law, and religion, and the regulatory environment chosen now will play a pivotal role in influencing the acceptance of human cloning in the future.

  4. A Brief, Web-based Personalized Feedback Selective Intervention for College Student Marijuana Use: A Randomized Clinical Trial

    OpenAIRE

    Lee, Christine M.; Neighbors, Clayton; Kilmer, Jason R; Larimer, Mary E.

    2010-01-01

    Despite clear need, brief web-based interventions for marijuana using college students have not been evaluated in the literature. The current study was designed to evaluate a brief, web-based personalized feedback intervention for at-risk marijuana users transitioning to college. All entering first-year students were invited to complete a brief questionnaire. Participants meeting criteria completed a baseline assessment (N = 341) and were randomly assigned to web-based personalized feedback o...

  5. A Randomized Comparative Study of Pulsed Radiofrequency Treatment With or Without Selective Nerve Root Block for Chronic Cervical Radicular Pain.

    Science.gov (United States)

    Wang, Fei; Zhou, Qian; Xiao, Lizu; Yang, Juan; Xong, Donglin; Li, Disen; Liu, LiPing; Ancha, Sigdha; Cheng, Jianguo

    2017-06-01

    We demonstrated a combination of pulsed radiofrequency (PRF) and cervical nerve root block (CNRB) via a posterior approach was superior to a transforaminal epidural steroid injection through the anterolateral approach for cervical radicular pain in a previous study. This randomized trial was conducted to determine the comparative efficacy between CNRB, PRF, and CNRB + PRF for cervical radicular pain. A prospective and randomized design was used in this study. Sixty-two patients were randomized into three parallel groups: CNRB, PRF, or CNRB + PRF. Numeric Rating Scale (NRS) was used to measure pain intensity, and global perceived effect (GPE) was scored by the patient on a 7-point scale, ranging from much worse (-3), no change (0), to total improvement (+3). The outcomes were evaluated at 1 week, 1 month, 3 months, and 6 months. Side effects and complications were noted. The NRS was significantly reduced in all three groups 1 week after the treatments (P 0.05). No serious complications were observed in any of the patients. Combining CNRB and PRF appeared to be a safe and efficacious technique for cervical radicular pain. The combination therapy yielded better outcomes than either CNRB or PRF alone. © 2016 World Institute of Pain.

  6. Use of hyaluronan in the selection of sperm for intracytoplasmic sperm injection (ICSI): significant improvement in clinical outcomes--multicenter, double-blinded and randomized controlled trial.

    Science.gov (United States)

    Worrilow, K C; Eid, S; Woodhouse, D; Perloe, M; Smith, S; Witmyer, J; Ivani, K; Khoury, C; Ball, G D; Elliot, T; Lieberman, J

    2013-02-01

    Does the selection of sperm for ICSI based on their ability to bind to hyaluronan improve the clinical pregnancy rates (CPR) (primary end-point), implantation (IR) and pregnancy loss rates (PLR)? In couples where ≤ 65% of sperm bound hyaluronan, the selection of hyaluronan-bound (HB) sperm for ICSI led to a statistically significant reduction in PLR. HB sperm demonstrate enhanced developmental parameters which have been associated with successful fertilization and embryogenesis. Sperm selected for ICSI using a liquid source of hyaluronan achieved an improvement in IR. A pilot study by the primary author demonstrated that the use of HB sperm in ICSI was associated with improved CPR. The current study represents the single largest prospective, multicenter, double-blinded and randomized controlled trial to evaluate the use of hyaluronan in the selection of sperm for ICSI. Using the hyaluronan binding assay, an HB score was determined for the fresh or initial (I-HB) and processed or final semen specimen (F-HB). Patients were classified as >65% or ≤ 65% I-HB and stratified accordingly. Patients with I-HB scores ≤ 65% were randomized into control and HB selection (HYAL) groups whereas patients with I-HB >65% were randomized to non-participatory (NP), control or HYAL groups, in a ratio of 2:1:1. The NP group was included in the >65% study arm to balance the higher prevalence of patients with I-HB scores >65%. In the control group, oocytes received sperm selected via the conventional assessment of motility and morphology. In the HYAL group, HB sperm meeting the same visual criteria were selected for injection. Patient participants and clinical care providers were blinded to group assignment. Eight hundred two couples treated with ICSI in 10 private and hospital-based IVF programs were enrolled in this study. Of the 484 patients stratified to the I-HB > 65% arm, 115 participants were randomized to the control group, 122 participants were randomized to the HYAL group

  7. The prevalence and classification of chronic kidney disease in cats randomly selected within four age groups and in cats recruited for degenerative joint disease studies

    Science.gov (United States)

    Marino, Christina L; Lascelles, B Duncan X; Vaden, Shelly L; Gruen, Margaret E; Marks, Steven L

    2015-01-01

    Chronic kidney disease (CKD) and degenerative joint disease are both considered common in older cats. Information on the co-prevalence of these two diseases is lacking. This retrospective study was designed to determine the prevalence of CKD in two cohorts of cats: cats randomly selected from four evenly distributed age groups (RS group) and cats recruited for degenerative joint disease studies (DJD group), and to evaluate the concurrence of CKD and DJD in these cohorts. The RS group was randomly selected from four age groups from 6 months to 20 years, and the DJD group comprised cats recruited to four previous DJD studies, with the DJD group excluding cats with a blood urea nitrogen and/or serum creatinine concentration >20% (the upper end of normal) for two studies and cats with CKD stages 3 and 4 for the other two studies. The prevalence of CKD in the RS and DJD groups was higher than expected at 50% and 68.8%, respectively. CKD was common in cats between 1 and 15 years of age, with a similar prevalence of CKD stages 1 and 2 across age groups in both the RS and DJD cats, respectively. We found significant concurrence between CKD and DJD in cats of all ages, indicating the need for increased screening for CKD when selecting DJD treatments. Additionally, this study offers the idea of a relationship and causal commonality between CKD and DJD owing to the striking concurrence across age groups and life stages. PMID:24217707

  8. Blood Selenium Concentration and Blood Cystatin C Concentration in a Randomly Selected Population of Healthy Children Environmentally Exposed to Lead and Cadmium.

    Science.gov (United States)

    Gać, Paweł; Pawlas, Natalia; Wylężek, Paweł; Poręba, Rafał; Poręba, Małgorzata; Pawlas, Krystyna

    2017-01-01

    This study aimed at evaluation of a relationship between blood selenium concentration (Se-B) and blood cystatin C concentration (CST) in a randomly selected population of healthy children, environmentally exposed to lead and cadmium. The studies were conducted on 172 randomly selected children (7.98 ± 0.97 years). Among participants, the subgroups were distinguished, manifesting marginally low blood selenium concentration (Se-B 40-59 μg/l), suboptimal blood selenium concentration (Se-B: 60-79 μg/l) or optimal blood selenium concentration (Se-B ≥ 80 μg/l). At the subsequent stage, analogous subgroups of participants were selected separately in groups of children with BMI below median value (BMI selenium concentration and blood cystatin C concentration. On the other hand, in children with low body mass index, a negative non-linear relationship was present between blood selenium concentration and blood cystatin C concentration.

  9. Prevalence and classification of chronic kidney disease in cats randomly selected from four age groups and in cats recruited for degenerative joint disease studies.

    Science.gov (United States)

    Marino, Christina L; Lascelles, B Duncan X; Vaden, Shelly L; Gruen, Margaret E; Marks, Steven L

    2014-06-01

    Chronic kidney disease (CKD) and degenerative joint disease are both considered common in older cats. Information on the co-prevalence of these two diseases is lacking. This retrospective study was designed to determine the prevalence of CKD in two cohorts of cats: cats randomly selected from four evenly distributed age groups (RS group) and cats recruited for degenerative joint disease studies (DJD group), and to evaluate the concurrence of CKD and DJD in these cohorts. The RS group was randomly selected from four age groups from 6 months to 20 years, and the DJD group comprised cats recruited to four previous DJD studies, with the DJD group excluding cats with a blood urea nitrogen and/or serum creatinine concentration >20% (the upper end of normal) for two studies and cats with CKD stages 3 and 4 for the other two studies. The prevalence of CKD in the RS and DJD groups was higher than expected at 50% and 68.8%, respectively. CKD was common in cats between 1 and 15 years of age, with a similar prevalence of CKD stages 1 and 2 across age groups in both the RS and DJD cats, respectively. We found significant concurrence between CKD and DJD in cats of all ages, indicating the need for increased screening for CKD when selecting DJD treatments. Additionally, this study offers the idea of a relationship and causal commonality between CKD and DJD owing to the striking concurrence across age groups and life stages. © ISFM and AAFP 2013.

  10. SNPs selected by information content outperform randomly selected microsatellite loci for delineating genetic identification and introgression in the endangered dark European honeybee (Apis mellifera mellifera).

    Science.gov (United States)

    Muñoz, Irene; Henriques, Dora; Jara, Laura; Johnston, J Spencer; Chávez-Galarza, Julio; De La Rúa, Pilar; Pinto, M Alice

    2017-07-01

    The honeybee (Apis mellifera) has been threatened by multiple factors including pests and pathogens, pesticides and loss of locally adapted gene complexes due to replacement and introgression. In western Europe, the genetic integrity of the native A. m. mellifera (M-lineage) is endangered due to trading and intensive queen breeding with commercial subspecies of eastern European ancestry (C-lineage). Effective conservation actions require reliable molecular tools to identify pure-bred A. m. mellifera colonies. Microsatellites have been preferred for identification of A. m. mellifera stocks across conservation centres. However, owing to high throughput, easy transferability between laboratories and low genotyping error, SNPs promise to become popular. Here, we compared the resolving power of a widely utilized microsatellite set to detect structure and introgression with that of different sets that combine a variable number of SNPs selected for their information content and genomic proximity to the microsatellite loci. Contrary to every SNP data set, microsatellites did not discriminate between the two lineages in the PCA space. Mean introgression proportions were identical across the two marker types, although at the individual level, microsatellites' performance was relatively poor at the upper range of Q-values, a result reflected by their lower precision. Our results suggest that SNPs are more accurate and powerful than microsatellites for identification of A. m. mellifera colonies, especially when they are selected by information content. © 2016 John Wiley & Sons Ltd.

  11. Positional cloning of deafness genes

    NARCIS (Netherlands)

    Kremer, H.; Cremers, F.P.M.

    2009-01-01

    The identification of the majority of the known causative genes involved in nonsyndromic sensorineural hearing loss (NSHL) started with linkage analysis as part of a positional cloning procedure. The human and mouse genome projects in combination with technical developments on genotyping,

  12. Evidence that certain clones of Campylobacter jejuni persist during successive broiler flock rotations

    DEFF Research Database (Denmark)

    Petersen, L.; Wedderkopp, A.

    2001-01-01

    selected. Twelve broiler houses located on 10 farms were included in the study. The C,jejuni isolates collected from the selected houses during the surveillance were typed using fla typing and macrorestriction profiling (MRP), and a subset of the isolates, representing each of the identified clones...... (7 of 13) had fla type 1/1, but MRPs distinguished between isolates from different houses, and fla type 1/1 clones belonged to different serotypes, Seven houses carried persistent clones that covered an interval of at least four broiler flock rotations, or at least one half year. The dominant fla...... with recurrent Campylobacter problems. The MRPs of clones belonging to fla type 1/1 serotype O:2 isolated from persistently infected flocks shared a high percentage of bands compared to the remaining isolates, indicating that some clones that have the ability to cause persistent infections in broiler farms...

  13. Quantum cloning machines and the applications

    Science.gov (United States)

    Fan, Heng; Wang, Yi-Nan; Jing, Li; Yue, Jie-Dong; Shi, Han-Duo; Zhang, Yong-Liang; Mu, Liang-Zhu

    2014-11-01

    No-cloning theorem is fundamental for quantum mechanics and for quantum information science that states an unknown quantum state cannot be cloned perfectly. However, we can try to clone a quantum state approximately with the optimal fidelity, or instead, we can try to clone it perfectly with the largest probability. Thus various quantum cloning machines have been designed for different quantum information protocols. Specifically, quantum cloning machines can be designed to analyze the security of quantum key distribution protocols such as BB84 protocol, six-state protocol, B92 protocol and their generalizations. Some well-known quantum cloning machines include universal quantum cloning machine, phase-covariant cloning machine, the asymmetric quantum cloning machine and the probabilistic quantum cloning machine. In the past years, much progress has been made in studying quantum cloning machines and their applications and implementations, both theoretically and experimentally. In this review, we will give a complete description of those important developments about quantum cloning and some related topics. On the other hand, this review is self-consistent, and in particular, we try to present some detailed formulations so that further study can be taken based on those results.

  14. Quantum cloning machines and the applications

    Energy Technology Data Exchange (ETDEWEB)

    Fan, Heng, E-mail: hfan@iphy.ac.cn [Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); Collaborative Innovation Center of Quantum Matter, Beijing 100190 (China); Wang, Yi-Nan; Jing, Li [School of Physics, Peking University, Beijing 100871 (China); Yue, Jie-Dong [Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); Shi, Han-Duo; Zhang, Yong-Liang; Mu, Liang-Zhu [School of Physics, Peking University, Beijing 100871 (China)

    2014-11-20

    No-cloning theorem is fundamental for quantum mechanics and for quantum information science that states an unknown quantum state cannot be cloned perfectly. However, we can try to clone a quantum state approximately with the optimal fidelity, or instead, we can try to clone it perfectly with the largest probability. Thus various quantum cloning machines have been designed for different quantum information protocols. Specifically, quantum cloning machines can be designed to analyze the security of quantum key distribution protocols such as BB84 protocol, six-state protocol, B92 protocol and their generalizations. Some well-known quantum cloning machines include universal quantum cloning machine, phase-covariant cloning machine, the asymmetric quantum cloning machine and the probabilistic quantum cloning machine. In the past years, much progress has been made in studying quantum cloning machines and their applications and implementations, both theoretically and experimentally. In this review, we will give a complete description of those important developments about quantum cloning and some related topics. On the other hand, this review is self-consistent, and in particular, we try to present some detailed formulations so that further study can be taken based on those results.

  15. MOLECULAR CLONING OF OVINE cDNA LEPTIN GENE

    Directory of Open Access Journals (Sweden)

    CLAUDIA TEREZIA SOCOL

    2008-05-01

    Full Text Available An efficient bacterial transformation system suitable for cloning the coding sequence of the ovine leptin gene in E. coli DH5α host cells using the pGEMT easy vector it is described in this paper. The necessity of producing leptin is based on the fact that the role of this molecule in the animal and human organism is still unknown, leptin not existing as commercial product on the Romanian market. The results obtained in the bacterial transformation, cloning, recombinant clones selection, control of the insertion experiments and DNA computational analysis represent the first steps in further genetic engineering experiments such as production of DNA libraries, DNA sequencing, protein expression, etc., for a further contribution in elucidating the role of leptin in the animal and human organism.

  16. Efficient four fragment cloning for the construction of vectors for targeted gene replacement in filamentous fungi

    National Research Council Canada - National Science Library

    Frandsen, Rasmus J N; Andersson, Jens A; Kristensen, Matilde B; Giese, Henriette

    2008-01-01

    ... markers such as GFP are essential for this process. Construction of vectors for these experiments depends on the directional cloning of two homologous recombination sequences on each side of a selection marker gene...

  17. Cloning, multicopy expression and fed-batch production of Rhodotorula araucariae epoxide hydrolase in yarrowia lipolytica

    CSIR Research Space (South Africa)

    Ramduth, D

    2008-05-01

    Full Text Available cloned and functionally expressed in Y. lipolytica, under the control of a growth inducible hp4d promoter. The transformation experiments yielded only two positive multicopy transformants, which were assessed in flask cultures. The selected transformant...

  18. Effects of Cottonwood Leaf Beetle (Coleoptera: Chrysomelidae) Larval Defoliation, Clone, and Season on Populus Foliar Phagostimulants

    Science.gov (United States)

    David R. Coyle; Joel D. McMillin; Richard B. Hall; Elwood R. Hart

    2003-01-01

    Abstract: The cottonwood leaf beetle, Chrysomela scripta F., is a serious defoliator of plantation Populus in the United States. Current control methods include biorational and synthetic chemicals as well as selecting Populus clones resistant or tolerant to C. scripta...

  19. Energy Values of Nine Populus Clones

    Science.gov (United States)

    Terry F. Strong

    1980-01-01

    Compares calorific values for components of nine Populus clones. The components include stem wood, stem bark, and branches. Also compares calorific values for clones of balsam poplar and black cottonwood parentages.

  20. Human reproductive cloning: a conflict of liberties.

    Science.gov (United States)

    Havstad, Joyce C

    2010-02-01

    Proponents of human reproductive cloning do not dispute that cloning may lead to violations of clones' right to self-determination, or that these violations could cause psychological harms. But they proceed with their endorsement of human reproductive cloning by dismissing these psychological harms, mainly in two ways. The first tactic is to point out that to commit the genetic fallacy is indeed a mistake; the second is to invoke Parfit's non-identity problem. The argument of this paper is that neither approach succeeds in removing our moral responsibility to consider and to prevent psychological harms to cloned individuals. In fact, the same commitment to personal liberty that generates the right to reproduce by means of cloning also creates the need to limit that right appropriately. Discussion of human reproductive cloning ought to involve a careful and balanced consideration of both the relevant aspects of personal liberty - the parents' right to reproductive freedom and the cloned child's right to self-determination.

  1. The preservation of genetic resources of the vine requires cohabitation between institutional clonal selection, mass selection and private clonal selection

    Directory of Open Access Journals (Sweden)

    Roby Jean-Philippe

    2014-01-01

    Full Text Available Clonal selection allows control of virus diseases and selection of genotypes on agronomic, viticultural or enological criteria. Clonal selection has the major drawback that it impoverishes genetic diversity and exposes growers to environmental instability of clones (genotype X environment interaction. Clonal selection has become the almost unique way of propagating plant material for vineyards, hence threatening the genetic diversity of the grapevine. For major grapevine varieties, some genetic diversity is maintained in institutional collections. However, this way of conservation is insufficiently developed, it is expensive and remains fragile. A cost effective way to preserve intra-varietal diversity is to maintain a limited proportion of mass selection in vine propagation. Private clonal selection can also contribute, in a more limited way, in maintaining genetic resources. Another approach to carry out conservation and selection of grapevine is the methodology followed in Portugal. This strategy is exemplified with the conservation/selection of an ancient Portuguese variety. The work begins with the “ex situ” conservation of a representative sample of the intravarietal diversity of the variety, which, in practice, corresponds to a large field trial with hundreds of clones under an experimental design suitable for reducing random variation of quantitative traits. From evaluating those traits (yield and must quality traits, the intravarietal diversity is quantified and the range of the predicted genotypic effects for each of those traits is analyzed. Different mass selections (polyclonal selections are carried out for distribution and planting of new vineyards. These different mass selections provide high economic gains and also the preservation of diversity in a complementary manner to that which started the work on-farm conservation.

  2. Acute changes of hip joint range of motion using selected clinical stretching procedures: A randomized crossover study.

    Science.gov (United States)

    Hammer, Adam M; Hammer, Roger L; Lomond, Karen V; O'Connor, Paul

    2017-09-01

    Hip adductor flexibility and strength is an important component of athletic performance and many activities of daily living. Little research has been done on the acute effects of a single session of stretching on hip abduction range of motion (ROM). The aim of this study was to compare 3 clinical stretching procedures against passive static stretching and control on ROM and peak isometric maximal voluntary contraction (MVC). Using a randomized crossover study design, a total of 40 participants (20 male and 20 female) who had reduced hip adductor muscle length attended a familiarization session and 5 testing sessions on non-consecutive days. Following the warm-up and pre-intervention measures of ROM and MVC, participants were randomly assigned 1 of 3 clinical stretching procedures (modified lunge, multidirectional, and joint mobilization) or a static stretch or control condition. Post-intervention measures of ROM and MVC were taken immediately following completion of the assigned condition. An ANOVA using a repeated measure design with the change score was conducted. All interventions resulted in small but statistically significant (p stretching was greater than control (p = 0.031). These data suggest that a single session of stretching has only a minimal effect on acute changes of hip abduction ROM. Although hip abduction is a frontal plane motion, to effectively increase the extensibility of the structures that limit abduction, integrating multi-planar stretches may be indicated. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Selepressin, a novel selective vasopressin V1A agonist, is an effective substitute for norepinephrine in a phase IIa randomized, placebo-controlled trial in septic shock patients

    DEFF Research Database (Denmark)

    Russell, James A; Vincent, Jean-Louis; Kjølbye, Anne Louise

    2017-01-01

    BACKGROUND: Vasopressin is widely used for vasopressor support in septic shock patients, but experimental evidence suggests that selective V1A agonists are superior. The initial pharmacodynamic effects, pharmacokinetics, and safety of selepressin, a novel V1A-selective vasopressin analogue......, was examined in a phase IIa trial in septic shock patients. METHODS: This was a randomized, double-blind, placebo-controlled multicenter trial in 53 patients in early septic shock (aged ≥18 years, fluid resuscitation, requiring vasopressor support) who received selepressin 1.25 ng/kg/minute (n = 10), 2.5 ng...... for selepressin 2.5 ng/kg/minute and placebo. Two patients were infused at 3.75 ng/kg/minute, one of whom had the study drug infusion discontinued for possible safety reasons, with subsequent discontinuation of this dose group. CONCLUSIONS: In septic shock patients, selepressin 2.5 ng/kg/minute was able...

  4. Early routine versus late selective surfactant in preterm neonates with respiratory distress syndrome on nasal continuous positive airway pressure: a randomized controlled trial.

    Science.gov (United States)

    Kandraju, Hemasree; Murki, Srinivas; Subramanian, Sreeram; Gaddam, Pramod; Deorari, Ashok; Kumar, Praveen

    2013-01-01

    Preterm neonates with respiratory distress syndrome (RDS) benefit from early application of nasal continuous positive airway pressure (nCPAP). However, it is not clear whether surfactant should be administered early as a routine to all such infants or later in a selective manner. It was the aim of this study to compare the efficacy of early routine versus late selective surfactant treatment in reducing the need for mechanical ventilation (MV) during the first week of life among moderate-sized preterm infants with RDS being supported by nCPAP. Infants born at 28(0/7) to 33(6/7) weeks of gestation with RDS and on nCPAP were randomly assigned within the first 2 h of life to early routine surfactant administration by the InSurE technique (early surfactant group) or to late selective administration of surfactant (late surfactant group). The primary outcome was need for MV in the first 7 days of life. Among 153 infants randomized to early (n = 74) or late surfactant (n = 79) groups, the need for MV was significantly lower in the early surfactant group (16.2 vs. 31.6%; relative risk 0.41, 95% confidence interval 0.19-0.91). The incidence of pneumothorax (1.9 vs. 2.3%) and the need for supplemental O2 at 28 days (2.7 vs. 8.9%) were similar in the two groups. Early routine surfactant administration within 2 h of life as compared to late selective administration significantly reduced the need for MV in the first week of life among preterm infants with RDS on nCPAP. Copyright © 2012 S. Karger AG, Basel.

  5. Does Multimodal Analgesia with Acetaminophen, Nonsteroidal Antiinflammatory Drugs, or Selective Cyclooxygenase-2 Inhibitors and Patient-controlled Analgesia Morphine Offer Advantages over Morphine Alone?: Meta-analyses of Randomized Trials

    National Research Council Canada - National Science Library

    Elia, Nadia; Lysakowski, Christopher; Tramèr, Martin R

    2005-01-01

    The authors analyzed data from 52 randomized placebo-controlled trials (4,893 adults) testing acetaminophen, nonsteroidal antiinflammatory drugs, or selective cyclooxygenase-2 inhibitors given in conjunction with morphine after surgery...

  6. Effective and efficient model clone detection

    DEFF Research Database (Denmark)

    Störrle, Harald

    2015-01-01

    automatically (“MDD-style”) or hand-crafted following the blueprint defined by the model (“MBSD-style”). Unfortunately, however, model clones are much less well studied than code clones. In this paper, we present a clone detection algorithm for UML domain models. Our approach covers a much greater variety...

  7. "Open mesh" or "strictly selected population" recruitment? The experience of the randomized controlled MeMeMe trial

    Directory of Open Access Journals (Sweden)

    Cortellini M

    2017-07-01

    Full Text Available Mauro Cortellini, Franco Berrino, Patrizia Pasanisi Department of Preventive & Predictive Medicine, Foundation IRCCS National Cancer Institute of Milan, Milan, Italy Abstract: Among randomized controlled trials (RCTs, trials for primary prevention require large samples and long follow-up to obtain a high-quality outcome; therefore the recruitment process and the drop-out rates largely dictate the adequacy of the results. We are conducting a Phase III trial on persons with metabolic syndrome to test the hypothesis that comprehensive lifestyle changes and/or metformin treatment prevents age-related chronic diseases (the MeMeMe trial, EudraCT number: 2012-005427-32, also registered on ClinicalTrials.gov [NCT02960711]. Here, we briefly analyze and discuss the reasons which may lead to participants dropping out from trials. In our experience, participants may back out of a trial for different reasons. Drug-induced side effects are certainly the most compelling reason. But what are the other reasons, relating to the participants’ perception of the progress of the trial which led them to withdraw after randomization? What about the time-dependent drop-out rate in primary prevention trials? The primary outcome of this analysis is the point of drop-out from trial, defined as the time from the randomization date to the withdrawal date. Survival functions were non-parametrically estimated using the product-limit estimator. The curves were statistically compared using the log-rank test (P=0.64, not significant. Researchers involved in primary prevention RCTs seem to have to deal with the paradox of the proverbial “short blanket syndrome”. Recruiting only highly motivated candidates might be useful for the smooth progress of the trial but it may lead to a very low enrollment rate. On the other hand, what about enrolling all the eligible subjects without considering their motivation? This might boost the enrollment rate, but it can lead to biased

  8. Cloning of the repertoire of individual Plasmodium falciparum var genes using transformation associated recombination (TAR.

    Directory of Open Access Journals (Sweden)

    Annette Gaida

    Full Text Available One of the major virulence factors of the malaria causing parasite is the Plasmodium falciparum encoded erythrocyte membrane protein 1 (PfEMP1. It is translocated to It the membrane of infected erythrocytes and expressed from approximately 60 var genes in a mutually exclusive manner. Switching of var genes allows the parasite to alter functional and antigenic properties of infected erythrocytes, to escape the immune defense and to establish chronic infections. We have developed an efficient method for isolating VAR genes from telomeric and other genome locations by adapting transformation-associated recombination (TAR cloning, which can then be analyzed and sequenced. For this purpose, three plasmids each containing a homologous sequence representing the upstream regions of the group A, B, and C var genes and a sequence homologous to the conserved acidic terminal segment (ATS of var genes were generated. Co-transfection with P. falciparum strain ITG2F6 genomic DNA in yeast cells yielded 200 TAR clones. The relative frequencies of clones from each group were not biased. Clones were screened by PCR, as well as Southern blotting, which revealed clones missed by PCR due to sequence mismatches with the primers. Selected clones were transformed into E. coli and further analyzed by RFLP and end sequencing. Physical analysis of 36 clones revealed 27 distinct types potentially representing 50% of the var gene repertoire. Three clones were selected for sequencing and assembled into single var gene containing contigs. This study demonstrates that it is possible to rapidly obtain the repertoire of var genes from P. falciparum within a single set of cloning experiments. This technique can be applied to individual isolates which will provide a detailed picture of the diversity of var genes in the field. This is a powerful tool to overcome the obstacles with cloning and assembly of multi-gene families by simultaneously cloning each member.

  9. Cloning of the repertoire of individual Plasmodium falciparum var genes using transformation associated recombination (TAR).

    Science.gov (United States)

    Gaida, Annette; Becker, Marion M; Schmid, Christoph D; Bühlmann, Tobias; Louis, Edward J; Beck, Hans-Peter

    2011-03-07

    One of the major virulence factors of the malaria causing parasite is the Plasmodium falciparum encoded erythrocyte membrane protein 1 (PfEMP1). It is translocated to It the membrane of infected erythrocytes and expressed from approximately 60 var genes in a mutually exclusive manner. Switching of var genes allows the parasite to alter functional and antigenic properties of infected erythrocytes, to escape the immune defense and to establish chronic infections. We have developed an efficient method for isolating VAR genes from telomeric and other genome locations by adapting transformation-associated recombination (TAR) cloning, which can then be analyzed and sequenced. For this purpose, three plasmids each containing a homologous sequence representing the upstream regions of the group A, B, and C var genes and a sequence homologous to the conserved acidic terminal segment (ATS) of var genes were generated. Co-transfection with P. falciparum strain ITG2F6 genomic DNA in yeast cells yielded 200 TAR clones. The relative frequencies of clones from each group were not biased. Clones were screened by PCR, as well as Southern blotting, which revealed clones missed by PCR due to sequence mismatches with the primers. Selected clones were transformed into E. coli and further analyzed by RFLP and end sequencing. Physical analysis of 36 clones revealed 27 distinct types potentially representing 50% of the var gene repertoire. Three clones were selected for sequencing and assembled into single var gene containing contigs. This study demonstrates that it is possible to rapidly obtain the repertoire of var genes from P. falciparum within a single set of cloning experiments. This technique can be applied to individual isolates which will provide a detailed picture of the diversity of var genes in the field. This is a powerful tool to overcome the obstacles with cloning and assembly of multi-gene families by simultaneously cloning each member.

  10. A single-copy galK promoter cloning vector suitable for cloning strong promoters

    DEFF Research Database (Denmark)

    Dandanell, Gert; Court, Donald L.; Hammer, Karin

    1986-01-01

    We report the construction of lambda galK promoter cloning vectors for cloning and characterization of strong promoters. This phage, which contains a unique HindIII cloning site, was applied to the cloning and analysis of transcription initiations of the regulatory region of the deo-operon of...

  11. H-DROP: an SVM based helical domain linker predictor trained with features optimized by combining random forest and stepwise selection.

    Science.gov (United States)

    Ebina, Teppei; Suzuki, Ryosuke; Tsuji, Ryotaro; Kuroda, Yutaka

    2014-08-01

    Domain linker prediction is attracting much interest as it can help identifying novel domains suitable for high throughput proteomics analysis. Here, we report H-DROP, an SVM-based Helical Domain linker pRediction using OPtimal features. H-DROP is, to the best of our knowledge, the first predictor for specifically and effectively identifying helical linkers. This was made possible first because a large training dataset became available from IS-Dom, and second because we selected a small number of optimal features from a huge number of potential ones. The training helical linker dataset, which included 261 helical linkers, was constructed by detecting helical residues at the boundary regions of two independent structural domains listed in our previously reported IS-Dom dataset. 45 optimal feature candidates were selected from 3,000 features by random forest, which were further reduced to 26 optimal features by stepwise selection. The prediction sensitivity and precision of H-DROP were 35.2 and 38.8%, respectively. These values were over 10.7% higher than those of control methods including our previously developed DROP, which is a coil linker predictor, and PPRODO, which is trained with un-differentiated domain boundary sequences. Overall, these results indicated that helical linkers can be predicted from sequence information alone by using a strictly curated training data set for helical linkers and carefully selected set of optimal features. H-DROP is available at http://domserv.lab.tuat.ac.jp.

  12. Exploring the metal phytoremediation potential of three Populus alba L. clones using an in vitro screening.

    Science.gov (United States)

    Di Lonardo, Sara; Capuana, Maurizio; Arnetoli, Miluscia; Gabbrielli, Roberto; Gonnelli, Cristina

    2011-01-01

    This work was planned for providing a useful screening tool for the selection of Populus alba clones suitable for phytoremediation techniques. To this aim, we investigated variation in arsenic, cadmium, copper, and zinc tolerance, accumulation and translocation in three poplar clones through an in vitro screening. Poplars have been widely proposed for phytoremediation, as they are adaptable to grow on contaminated areas and able to accumulate metals. The investigation of possible differences among poplar clones in metal tolerance and accumulation deserves to be deeply studied and exploited for the selection of the more suitable tool for phytoremediation purposes. In vitro multiplied microshoots of a commercial and two autochthonous P. alba clones were subcultured on hormone-free WPM medium for 1 month and then transferred for 2 weeks onto media containing different concentrations of the metals investigated. At the end of the treatments, plantlets were sampled, weighed, and mineralised by wet ashing. Metal concentrations were determined by ICP-OES. For the metal concentration used in the experiments, our clones of P. alba showed variation in metal tolerance, metal accumulation and content. The fast-growing commercial clone, even if rarely showing the highest plant metal concentration, displayed the highest metal content, suggesting biomass production as the key factor in evaluating the phytoextraction capacity of P. alba clones for the metals studied. Data demonstrated that in vitro screening of cuttings represents a valuable way of assessing the ability of different poplar clones to take up, tolerate and survive metal stress.

  13. Genetic variability in clones of 'Prata Anã' bananas based on phenotypic and molecular markers

    Directory of Open Access Journals (Sweden)

    Francisco Ermelindo Rodrigues

    2012-01-01

    Full Text Available The objective of this study was to examine the molecular and phenotypic variability of 'Prata Anã' banana clones cultivated in northern Minas Gerais State. For the phenotypic and molecular characterization, the clones were collected from five properties. The morphological characterization of 20 clones was accomplished through a qualitative evaluation of 74 descriptors. For the molecular evaluations, 45 clones were collected, and 14 Random Amplified Polymorphic DNA primers were used. Among the 74 morphological descriptors evaluated in the 20 'Prata Anã' banana tree clones, 53 descriptors presented in the same homogeneous class for all clones. The presence of anthocyanin in the pseudostem (ANT and the shape (BUS and flexion (FLX of the bunch clearly differentiated the 'Prata Anã' banana clones from the commercial cultivar. A total of 176 bands were produced from the molecular analysis using the 14 RAPD primers; there were 116 monomorphic and 60 polymorphic bands, with an average polymorphism percentage of 52.2%. The amplification using the OPP 14 primer resulted in the greatest percentage of polymorphic bands at 88%. The dendrogram indicated that each of the 45 'Prata Anã' clones that were evaluated using RAPD markers clustered with the commercial 'Prata Anã' cultivar.

  14. Combining ability of elite clones of Eucalyptus grandis and Eucalyptus urophylla with Eucalyptus globulus

    Directory of Open Access Journals (Sweden)

    Odair Bison

    2007-03-01

    Full Text Available In Brazil, eucalyptus breeding programs for cellulose production has used two species, Eucalyptus grandis and Eucalyptus urophylla. Nevertheless, it would be useful to introgress alleles from other species to improve wood quality and volume. The objective of this research was to evaluate the hybrid potential of elite clones of E. grandis and E. urophylla from the Aracruz Celulose Company S. A. with Eucalyptus globulus clones. To do so, six elite clones were crossed with ten E. globulus clones in a half-diallel mating design. The resulting hybrid combinations as well as the four check clones were evaluated in randomized complete block experiments with single plant plots and 40 replicates from September to October 2001 at three Brazilian sites, Aracruz and São Mateus in the Espírito Santo state and Caravelas in Bahia State. Two years later the circumference at breast height (CBH and the wood density (WD were measured. The means were submitted to diallel analysis according to the Griffing method (1956, adapted by Geraldi and Miranda Filho (1988. Although the number of clones involved was small, the crossings of elite clones of E. grandis and E. urophylla with clones of E. globulus were promising, especially for wood quality gains.

  15. A selective neurokinin-1 receptor antagonist in chronic PTSD: a randomized, double-blind, placebo-controlled, proof-of-concept trial.

    Science.gov (United States)

    Mathew, Sanjay J; Vythilingam, Meena; Murrough, James W; Zarate, Carlos A; Feder, Adriana; Luckenbaugh, David A; Kinkead, Becky; Parides, Michael K; Trist, David G; Bani, Massimo S; Bettica, Paolo U; Ratti, Emiliangelo M; Charney, Dennis S

    2011-03-01

    The substance P-neurokinin-1 receptor (SP-NK(1)R) system has been extensively studied in experimental models of stress, fear, and reward. Elevated cerebrospinal fluid (CSF) SP levels were reported previously in combat-related PTSD. No medication specifically targeting this system has been tested in PTSD. This proof-of-concept randomized, double-blind, placebo-controlled trial evaluated the selective NK(1)R antagonist GR205171 in predominately civilian PTSD. Following a 2-week placebo lead-in, 39 outpatients with chronic PTSD and a Clinician-Administered PTSD Scale (CAPS) score ≥50 were randomized to a fixed dose of GR205171 (N=20) or placebo (N=19) for 8weeks. The primary endpoint was mean change from baseline to endpoint in the total CAPS score. Response rate (≥50% reduction in baseline CAPS) and safety/tolerability were secondary endpoints. CSF SP concentrations were measured in a subgroup of patients prior to randomization. There was significant improvement in the mean CAPS total score across all patients over time, but no significant difference was found between GR205171 and placebo. Likewise, there was no significant effect of drug on the proportion of responders [40% GR205171 versus 21% placebo (p=0.30)]. An exploratory analysis showed that GR205171 treatment was associated with significant improvement compared to placebo on the CAPS hyperarousal symptom cluster. GR205171 was well-tolerated, with no discontinuations due to adverse events. CSF SP concentrations were positively correlated with baseline CAPS severity. The selective NK(1)R antagonist GR205171 had fewer adverse effects but was not significantly superior to placebo in the short-term treatment of chronic PTSD. (ClinicalTrials.gov Identifier: NCT 00211861, NCT 00383786). Published by Elsevier B.V.

  16. Age-related Cataract in a Randomized Trial of Selenium and Vitamin E in Men: The SELECT Eye Endpoints (SEE) Study

    Science.gov (United States)

    Christen, William G.; Glynn, Robert J.; Gaziano, J. Michael; Darke, Amy K.; Crowley, John J.; Goodman, Phyllis J.; Lippman, Scott M.; Lad, Thomas E.; Bearden, James D.; Goodman, Gary E.; Minasian, Lori M.; Thompson, Ian M.; Blanke, Charles D.; Klein, Eric A.

    2014-01-01

    Importance Observational studies suggest a role for dietary nutrients such as vitamin E and selenium in cataract prevention. However, the results of randomized trials of vitamin E supplements and cataract have been disappointing, and are not yet available for selenium. Objective To test whether long-term supplementation with selenium and vitamin E affects the incidence of cataract in a large cohort of men. Design, Setting, and Participants The SELECT Eye Endpoints (SEE) study was an ancillary study of the SWOG-coordinated Selenium and Vitamin E Cancer Prevention Trial (SELECT), a randomized, placebo-controlled, four arm trial of selenium and vitamin E conducted among 35,533 men aged 50 years and older for African Americans and 55 and older for all other men, at 427 participating sites in the US, Canada, and Puerto Rico. A total of 11,267 SELECT participants from 128 SELECT sites participated in the SEE ancillary study. Intervention Individual supplements of selenium (200 µg/d from L-selenomethionine) and vitamin E (400 IU/d of all rac-α-tocopheryl acetate). Main Outcome Measures Incident cataract, defined as a lens opacity, age-related in origin, responsible for a reduction in best-corrected visual acuity to 20/30 or worse based on self-report confirmed by medical record review, and cataract extraction, defined as the surgical removal of an incident cataract. Results During a mean (SD) of 5.6 (1.2) years of treatment and follow-up, 389 cases of cataract were documented. There were 185 cataracts in the selenium group and 204 in the no selenium group (hazard ratio [HR], 0.91; 95 percent confidence interval [CI], 0.75 to 1.11; P=.37). For vitamin E, there were 197 cases in the treated group and 192 in the placebo group (HR, 1.02; CI, 0.84 to 1.25; P=.81). Similar results were observed for cataract extraction. Conclusions and Relevance These randomized trial data from a large cohort of apparently healthy men indicate that long-term daily supplementation with selenium

  17. El envejecimiento de los clones

    OpenAIRE

    Trippi, Victorio S.

    2007-01-01

    El envejecimiento de los clones se observa en plantas que muestran crecimiento definido por un determinismo genético, cuando se multiplican con tejidos que evolucionan hacia el crecimiento reproductivo. Las plantas fuertemente influenciadas por el ambiente, pueden mostrar fenómenos de senescencia cuando la condición de ambiente determina el crecimiento reproductivo. Los cambios asociados con la edad resultan de alteraciones del citoplasma como un tipo de diferenciación cel...

  18. Cellular evidence for selfish spermatogonial selection in aged human testes.

    Science.gov (United States)

    Maher, G J; Goriely, A; Wilkie, A O M

    2014-05-01

    Owing to a recent trend for delayed paternity, the genomic integrity of spermatozoa of older men has become a focus of increased interest. Older fathers are at higher risk for their children to be born with several monogenic conditions collectively termed paternal age effect (PAE) disorders, which include achondroplasia, Apert syndrome and Costello syndrome. These disorders are caused by specific mutations originating almost exclusively from the male germline, in genes encoding components of the tyrosine kinase receptor/RAS/MAPK signalling pathway. These particular mutations, occurring randomly during mitotic divisions of spermatogonial stem cells (SSCs), are predicted to confer a selective/growth advantage on the mutant SSC. This selective advantage leads to a clonal expansion of the mutant cells over time, which generates mutant spermatozoa at levels significantly above the background mutation rate. This phenomenon, termed selfish spermatogonial selection, is likely to occur in all men. In rare cases, probably because of additional mutational events, selfish spermatogonial selection may lead to spermatocytic seminoma. The studies that initially predicted the clonal nature of selfish spermatogonial selection were based on DNA analysis, rather than the visualization of mutant clones in intact testes. In a recent study that aimed to identify these clones directly, we stained serial sections of fixed testes for expression of melanoma antigen family A4 (MAGEA4), a marker of spermatogonia. A subset of seminiferous tubules with an appearance and distribution compatible with the predicted mutant clones were identified. In these tubules, termed 'immunopositive tubules', there is an increased density of spermatogonia positive for markers related to selfish selection (FGFR3) and SSC self-renewal (phosphorylated AKT). Here we detail the properties of the immunopositive tubules and how they relate to the predicted mutant clones, as well as discussing the utility of

  19. Therapeutic and reproductive cloning: a critique.

    Science.gov (United States)

    Bowring, Finn

    2004-01-01

    This article is a critical examination of the science and ethics of human cloning. It summarises the key scientific milestones in the development of nuclear transplantation, explains the importance of cloning to research into the medical potential of embryonic stem cells, and discusses the well-worn distinction between 'therapeutic' and 'reproductive' cloning. Suggesting that this distinction will be impossible to police, it goes on to consider the ethics of full human cloning. It is concluded that it represents an unacceptable form of parental despotism, and that the genetic engineering and cloning of future human beings will fracture the foundations of modern humanism.

  20. Cloning expeditions: risky but rewarding.

    Science.gov (United States)

    Lodish, Harvey

    2013-12-01

    In the 1980s, a good part of my laboratory was using the then-new recombinant DNA techniques to clone and characterize many important cell surface membrane proteins: GLUT1 (the red cell glucose transporter) and then GLUT2 and GLUT4, the red cell anion exchange protein (Band 3), asialoglycoprotein receptor subunits, sucrase-isomaltase, the erythropoietin receptor, and two of the subunits of the transforming growth factor β (TGF-β) receptor. These cloned genes opened many new fields of basic research, including membrane insertion and trafficking of transmembrane proteins, signal transduction by many members of the cytokine and TGF-β families of receptors, and the cellular physiology of glucose and anion transport. They also led to many insights into the molecular biology of several cancers, hematopoietic disorders, and diabetes. This work was done by an exceptional group of postdocs and students who took exceptionally large risks in developing and using novel cloning technologies. Unsurprisingly, all have gone on to become leaders in the fields of molecular cell biology and molecular medicine.

  1. Cloning Expeditions: Risky but Rewarding

    Science.gov (United States)

    2013-01-01

    In the 1980s, a good part of my laboratory was using the then-new recombinant DNA techniques to clone and characterize many important cell surface membrane proteins: GLUT1 (the red cell glucose transporter) and then GLUT2 and GLUT4, the red cell anion exchange protein (Band 3), asialoglycoprotein receptor subunits, sucrase-isomaltase, the erythropoietin receptor, and two of the subunits of the transforming growth factor β (TGF-β) receptor. These cloned genes opened many new fields of basic research, including membrane insertion and trafficking of transmembrane proteins, signal transduction by many members of the cytokine and TGF-β families of receptors, and the cellular physiology of glucose and anion transport. They also led to many insights into the molecular biology of several cancers, hematopoietic disorders, and diabetes. This work was done by an exceptional group of postdocs and students who took exceptionally large risks in developing and using novel cloning technologies. Unsurprisingly, all have gone on to become leaders in the fields of molecular cell biology and molecular medicine. PMID:24061478

  2. Food pantry selection solutions: a randomized controlled trial in client-choice food pantries to nudge clients to targeted foods.

    Science.gov (United States)

    Wilson, Norbert L W; Just, David R; Swigert, Jeffery; Wansink, Brian

    2017-06-01

    Food pantries and food banks are interested in cost-effective methods to encourage the selection of targeted foods without restricting choices. Thus, this study evaluates the effectiveness of nudges toward targeted foods. In October/November 2014, we manipulated the display of a targeted product in a New York State food pantry. We evaluated the binary choice of the targeted good when we placed it in the front or the back of the category line (placement order) and when we presented the product in its original box or unboxed (packaging). The average uptake proportion for the back treatment was 0.231, 95% CI = 0.179, 0.29, n = 205, and for the front treatment, the proportion was 0.337, 95% CI = 0.272, 0.406, n = 238 with an odds ratio of 1.688, 95% CI = 1.088, 2.523. The average uptake for the unboxed treatment was 0.224, 95% CI = 0.174, 0.280, n = 255, and for the boxed intervention, the proportion was 0.356, 95% CI = 0.288, 0.429, n = 188 with an odds ratio of 1.923, 95% CI = 1.237, 2.991. Nudges increased uptake of the targeted food. The findings also hold when we control for a potential confounder. Low cost and unobtrusive nudges can be effective tools for food pantry organizers to encourage the selection of targeted foods. NCT02403882.

  3. EcmPred: Prediction of extracellular matrix proteins based on random forest with maximum relevance minimum redundancy feature selection

    KAUST Repository

    Kandaswamy, Krishna Kumar Umar

    2013-01-01

    The extracellular matrix (ECM) is a major component of tissues of multicellular organisms. It consists of secreted macromolecules, mainly polysaccharides and glycoproteins. Malfunctions of ECM proteins lead to severe disorders such as marfan syndrome, osteogenesis imperfecta, numerous chondrodysplasias, and skin diseases. In this work, we report a random forest approach, EcmPred, for the prediction of ECM proteins from protein sequences. EcmPred was trained on a dataset containing 300 ECM and 300 non-ECM and tested on a dataset containing 145 ECM and 4187 non-ECM proteins. EcmPred achieved 83% accuracy on the training and 77% on the test dataset. EcmPred predicted 15 out of 20 experimentally verified ECM proteins. By scanning the entire human proteome, we predicted novel ECM proteins validated with gene ontology and InterPro. The dataset and standalone version of the EcmPred software is available at http://www.inb.uni-luebeck.de/tools-demos/Extracellular_matrix_proteins/EcmPred. © 2012 Elsevier Ltd.

  4. Randomized Controlled Trial of Acupuncture for Women with Fibromyalgia: Group Acupuncture with Traditional Chinese Medicine Diagnosis-Based Point Selection.

    Science.gov (United States)

    Mist, Scott D; Jones, Kim Dupree

    2018-02-13

    Group acupuncture is a growing and cost-effective method for delivering acupuncture in the United States and is the practice model in China. However, group acupuncture has not been tested in a research setting. To test the treatment effect of group acupuncture vs group education in persons with fibromyalgia. Random allocation two-group study with repeated measures. Group clinic in an academic health center in Portland, Oregon. Women with confirmed diagnosis of fibromyalgia (American College of Radiology 1990 criteria) and moderate to severe pain levels. Twenty treatments of a manualized acupuncture treatment based on Traditional Chinese Medicine diagnosis or group education over 10 weeks (both 900 minutes total). Weekly Revised Fibromyalgia Impact Questionnaire (FIQR) and Global Fatigue Index at baseline, five weeks, and 10 weeks and a four-week follow-up were assessed. Thirty women were recruited, with 78% reporting symptoms for longer than 10 years. The mean attendance was 810 minutes for acupuncture and 861 minutes for education. FIQR total, FIQR pain, and Global Fatigue Index all had clinically and statistically significant improvement in the group receiving acupuncture at end of treatment and four weeks post-treatment but not in participants receiving group education between groups. Compared with education, group acupuncture improved global symptom impact, pain, and fatigue. Furthermore, it was a safe and well-tolerated treatment option, improving a broader proportion of patients than current pharmaceutical options.

  5. Randomized trial of switching from prescribed non-selective non-steroidal anti-inflammatory drugs to prescribed celecoxib

    DEFF Research Database (Denmark)

    Macdonald, Thomas M; Hawkey, Chris J; Ford, Ian

    2017-01-01

    infarction or other biomarker positive acute coronary syndrome, non-fatal stroke or CV death analysed using a Cox model with a pre-specified non-inferiority limit of 1.4 for the hazard ratio (HR). RESULTS: In total, 7297 participants were randomized. During a median 3-year follow-up, fewer subjects than......-years with celecoxib and 1.10 per 100 patient-years with nsNSAIDs (HR = 1.04; 95% confidence interval, 0.81-1.33; P = 0.75). Pre-specified non-inferiority was achieved in the ITT analysis. The upper bound of the 95% confidence limit for the absolute increase in OT risk associated with celecoxib treatment was two......NSAIDs. There was no advantage of a strategy of switching prescribed nsNSAIDs to prescribed celecoxib. This study excluded an increased risk of the primary endpoint of more than two events per 1000 patient-years associated with switching to prescribed celecoxib....

  6. Suicide in Nepal: a modified psychological autopsy investigation from randomly selected police cases between 2013 and 2015.

    Science.gov (United States)

    Hagaman, Ashley K; Khadka, S; Lohani, S; Kohrt, B

    2017-12-01

    Yearly, 600,000 people complete suicide in low- and middle-income countries, accounting for 75% of the world's burden of suicide mortality. The highest regional rates are in South and East Asia. Nepal has one of the highest suicide rates in the world; however, few investigations exploring patterns surrounding both male and female suicides exist. This study used psychological autopsies to identify common factors, precipitating events, and warning signs in a diverse sample. Randomly sampled from 302 police case reports over 24 months, psychological autopsies were conducted for 39 completed suicide cases in one urban and one rural region of Nepal. In the total police sample (n = 302), 57.0% of deaths were male. Over 40% of deaths were 25 years or younger, including 65% of rural and 50.8% of female suicide deaths. We estimate the crude urban and rural suicide rates to be 16.1 and 22.8 per 100,000, respectively. Within our psychological autopsy sample, 38.5% met criteria for depression and only 23.1% informants believed that the deceased had thoughts of self-harm or suicide before death. Important warning signs include recent geographic migration, alcohol abuse, and family history of suicide. Suicide prevention strategies in Nepal should account for the lack of awareness about suicide risk among family members and early age of suicide completion, especially in rural and female populations. Given the low rates of ideation disclosure to friends and family, educating the general public about other signs of suicide may help prevention efforts in Nepal.

  7. Recruitment strategies should not be randomly selected: empirically improving recruitment success and diversity in developmental psychology research

    Science.gov (United States)

    Sugden, Nicole A.; Moulson, Margaret C.

    2015-01-01

    Psychological and developmental research have been critiqued for the lack of diversity of research samples. Because differences in culture, race, and ethnicity can influence participant behavior, limited diversity limits the generalizability of the findings. These differences may also impact how participants behave in response to recruitment attempts, which suggests that recruitment itself may be leveraged to increase sample diversity. The goal of the current study was to determine what factors, within a recruitment interaction, could be leveraged to increase success and diversity when recruiting families with children for developmental research. Study 1 found three factors influenced success: (1) recruitment was more successful when other potential participants were also interested (i.e., recruiters were busy), (2) recruiters of particular races were more successful than recruiters of other races, and (3) differences in success were related to what the recruiter said to engage the potential participant (i.e., the script). The latter two factors interacted, suggesting some recruiters were using less optimal scripts. To improve success rates, study 2 randomly assigned scripts to recruiters and encouraged them to recruit more vigorously during busy periods. Study 2 found that two factors influenced success: (1) some scripts were more successful than others and (2) we were more successful at recruiting non-White potential participants than White participants. These two interacted, with some scripts being more successful with White and other scripts being more successful with non-White families. This intervention significantly increased recruitment success rate by 8.1% and the overall number of families recruited by 15.3%. These findings reveal that empirically evaluating and tailoring recruitment efforts based on the most successful strategies is effective in boosting diversity through increased participation of children from non-White families. PMID:25972829

  8. Recruitment strategies should not be randomly selected: empirically improving recruitment success and diversity in developmental psychology research.

    Science.gov (United States)

    Sugden, Nicole A; Moulson, Margaret C

    2015-01-01

    Psychological and developmental research have been critiqued for the lack of diversity of research samples. Because differences in culture, race, and ethnicity can influence participant behavior, limited diversity limits the generalizability of the findings. These differences may also impact how participants behave in response to recruitment attempts, which suggests that recruitment itself may be leveraged to increase sample diversity. The goal of the current study was to determine what factors, within a recruitment interaction, could be leveraged to increase success and diversity when recruiting families with children for developmental research. Study 1 found three factors influenced success: (1) recruitment was more successful when other potential participants were also interested (i.e., recruiters were busy), (2) recruiters of particular races were more successful than recruiters of other races, and (3) differences in success were related to what the recruiter said to engage the potential participant (i.e., the script). The latter two factors interacted, suggesting some recruiters were using less optimal scripts. To improve success rates, study 2 randomly assigned scripts to recruiters and encouraged them to recruit more vigorously during busy periods. Study 2 found that two factors influenced success: (1) some scripts were more successful than others and (2) we were more successful at recruiting non-White potential participants than White participants. These two interacted, with some scripts being more successful with White and other scripts being more successful with non-White families. This intervention significantly increased recruitment success rate by 8.1% and the overall number of families recruited by 15.3%. These findings reveal that empirically evaluating and tailoring recruitment efforts based on the most successful strategies is effective in boosting diversity through increased participation of children from non-White families.

  9. Recruitment strategies shouldn’t be randomly selected: Empirically improving recruitment success and diversity in developmental psychology research

    Directory of Open Access Journals (Sweden)

    Nicole Andrea Sugden

    2015-04-01

    Full Text Available Psychological and developmental research have been critiqued for the lack of diversity of research samples. Because differences in culture, race, and ethnicity can influence participant behavior, limited diversity limits the generalizability of the findings. These differences may also impact how participants behave in response to recruitment attempts, which suggests that recruitment itself may be leveraged to increase sample diversity. The goal of the current study was to determine what factors, within a recruitment interaction, could be leveraged to increase success and diversity when recruiting families with children for developmental research. Study 1 found three factors influenced success: 1 recruitment was more successful when other potential participants were also interested (i.e., recruiters were busy, 2 recruiters of particular races were more successful than recruiters of other races, and 3 differences in success were related to what the recruiter said to engage the potential participant (i.e., the script. The latter two factors interacted, suggesting some recruiters were using less optimal scripts. To improve success rates, study 2 randomly assigned scripts to recruiters and encouraged them to recruit more vigorously during busy periods. Study 2 found that two factors influenced success: 1 some scripts were more successful than others and 2 we were more successful at recruiting non-White potential participants than White participants. These two interacted, with some scripts being more successful with White and other scripts being more successful with non-White families. This intervention significantly increased recruitment success rate by 8.1% and the overall number of families recruited by 15.3%. These findings reveal that empirically evaluating and tailoring recruitment efforts based on the most successful strategies is effective in boosting diversity through increased participation of children from non-White families.

  10. Selection of single blastocysts for fresh transfer via standard morphology assessment alone and with array CGH for good prognosis IVF patients: results from a randomized pilot study

    Science.gov (United States)

    2012-01-01

    Background Single embryo transfer (SET) remains underutilized as a strategy to reduce multiple gestation risk in IVF, and its overall lower pregnancy rate underscores the need for improved techniques to select one embryo for fresh transfer. This study explored use of comprehensive chromosomal screening by array CGH (aCGH) to provide this advantage and improve pregnancy rate from SET. Methods First-time IVF patients with a good prognosis (age IVF program to select single blastocysts for fresh SET in good prognosis patients. The observed aneuploidy rate (44.9%) among biopsied blastocysts highlights the inherent imprecision of SET when conventional morphology is used alone. Embryos randomized to the aCGH group implanted with greater efficiency, resulted in clinical pregnancy more often, and yielded a lower miscarriage rate than those selected without aCGH. Additional studies are needed to verify our pilot data and confirm a role for on-site, rapid aCGH for IVF patients contemplating fresh SET. PMID:22551456

  11. Quality of life and standard of living in a randomly selected group of psychiatrically disabled people in Sweden 2 years after a psychiatry reform.

    Science.gov (United States)

    Carlsson, I; Frederiksen, S-O; Gottfries, C-G

    2002-07-01

    In Sweden, a psychiatry reform, aimed at improving the living conditions of the psychiatrically disabled, came into force in 1995. The aim of the present study was to evaluate the impact of the reform by investigating quality of life and standard of living 2 years later in a randomly selected group of people with longstanding psychiatric disability. Self-ratings and interviews were conducted in a study group and a control group. The study group consisted of 19 women and 18 men (mean age 46.1 years) diagnosed with neurosis, schizophrenia or affective disorder. The control group consisted of 19 women and 17 men (mean age 48.7 years). Self-rated quality of life was significantly poorer in the study group (P standard of living in either group but a significant negative correlation in the control group (P standard of living.

  12. Effect of a Counseling Session Bolstered by Text Messaging on Self-Selected Health Behaviors in College Students: A Preliminary Randomized Controlled Trial.

    Science.gov (United States)

    Sandrick, Janice; Tracy, Doreen; Eliasson, Arn; Roth, Ashley; Bartel, Jeffrey; Simko, Melanie; Bowman, Tracy; Harouse-Bell, Karen; Kashani, Mariam; Vernalis, Marina

    2017-05-17

    The college experience is often the first time when young adults live independently and make their own lifestyle choices. These choices affect dietary behaviors, exercise habits, techniques to deal with stress, and decisions on sleep time, all of which direct the trajectory of future health. There is a need for effective strategies that will encourage healthy lifestyle choices in young adults attending college. This preliminary randomized controlled trial tested the effect of coaching and text messages (short message service, SMS) on self-selected health behaviors in the domains of diet, exercise, stress, and sleep. A second analysis measured the ripple effect of the intervention on health behaviors not specifically selected as a goal by participants. Full-time students aged 18-30 years were recruited by word of mouth and campuswide advertisements (flyers, posters, mailings, university website) at a small university in western Pennsylvania from January to May 2015. Exclusions included pregnancy, eating disorders, chronic medical diagnoses, and prescription medications other than birth control. Of 60 participants, 30 were randomized to receive a single face-to-face meeting with a health coach to review results of behavioral questionnaires and to set a health behavior goal for the 8-week study period. The face-to-face meeting was followed by SMS text messages designed to encourage achievement of the behavioral goal. A total of 30 control subjects underwent the same health and behavioral assessments at intake and program end but did not receive coaching or SMS text messages. The texting app showed that 87.31% (2187/2505) of messages were viewed by intervention participants. Furthermore, 28 of the 30 intervention participants and all 30 control participants provided outcome data. Among intervention participants, 22 of 30 (73%) showed improvement in health behavior goal attainment, with the whole group (n=30) showing a mean improvement of 88% (95% CI 39-136). Mean

  13. The effects of Nordic Walking training on selected upper-body muscle groups in female-office workers: A randomized trial.

    Science.gov (United States)

    Kocur, Piotr; Pospieszna, Barbara; Choszczewski, Daniel; Michalowski, Lukasz; Wiernicka, Marzena; Lewandowski, Jacek

    2017-01-01

    Regular Nordic Walking training could improve fitness and reduce tenderness in selected muscle groups in office workers. An assessment of the effects of a 12-week Nordic Walking training program on the perceived pain threshold (PPT) and the flexibility of selected upper-body muscle groups in postmenopausal female office workers. 39 office workers were selected at random for the treatment group (NWg, n = 20) and the control group (Cg, n = 19). The persons from the NW group completed a 12-week Nordic Walking training program (3 times a week/1 hour). PPTs measurements in selected muscles and functional tests evaluating upper-body flexibility (Back Scratch - BS) were carried out twice in every participant of the study: before and after the training program. A significant increase in PPT (kg/cm2) was observed in the following muscles in the NW group only: upper trapezius (from 1,32 kg/cm2 to 1,99 kg/cm2), mid trapezius (from 2,92 kg/cm2 to 3,30 kg/cm2), latissimus dorsi (from 1,66 kg/cm2 to 2,21 kg/cm2) and infraspinatus (from 1,63 kg/cm2 to 2,93 kg/cm2). Moreover, a significant improvement in the BS test was noted in the NW group compared with the control group (from -1,16±5,7 cm to 2,18±5,1 cm in the NW group vs from -2,52±6,1 to -2,92±6,2 in the control group). A 12-week Nordic Walking training routine improves shoulder mobility and reduces tenderness in the following muscles: trapezius pars descendens and middle trapezius, infraspinatus and latissimus dorsi, in female office workers.

  14. Zeta Sperm Selection Improves Pregnancy Rate and Alters Sex Ratio in Male Factor Infertility Patients: A Double-Blind, Randomized Clinical Trial

    Directory of Open Access Journals (Sweden)

    Nasr Esfahani Mohammad Hossein

    2016-07-01

    Full Text Available Background Selection of sperm for intra-cytoplasmic sperm injection (ICSI is usually considered as the ultimate technique to alleviate male-factor infertility. In routine ICSI, selection is based on morphology and viability which does not necessarily preclude the chance injection of DNA-damaged or apoptotic sperm into the oocyte. Sperm with high negative surface electrical charge, named “Zeta potential”, are mature and more likely to have intact chromatin. In addition, X-bearing spermatozoa carry more negative charge. Therefore, we aimed to compare the clinical outcomes of Zeta procedure with routine sperm selection in infertile men candidate for ICSI. Materials and Methods From a total of 203 ICSI cycles studied, 101 cycles were allocated to density gradient centrifugation (DGC/Zeta group and the remaining 102 were included in the DGC group in this prospective study. Clinical outcomes were com- pared between the two groups. The ratios of Xand Y bearing sperm were assessed by fluorescence in situ hybridization (FISH and quantitative polymerase chain reaction (qPCR methods in 17 independent semen samples. Results In the present double-blind randomized clinical trial, a significant increase in top quality embryos and pregnancy rate were observed in DGC/Zeta group compared to DGC group. Moreover, sex ratio (XY/XX at birth significantly was lower in the DGC/Zeta group compared to DGC group despite similar ratio of X/Y bearings sper- matozoa following Zeta selection. Conclusion Zeta method not only improves the percentage of top embryo quality and pregnancy outcome but also alters the sex ratio compared to the conventional DGC method, despite no significant change in the ratio of Xand Ybearing sperm population (Registration number: IRCT201108047223N1.

  15. A comparison of the effects of random and selective mass extinctions on erosion of evolutionary history in communities of digital organisms.

    Directory of Open Access Journals (Sweden)

    Gabriel Yedid

    Full Text Available The effect of mass extinctions on phylogenetic diversity and branching history of clades remains poorly understood in paleobiology. We examined the phylogenies of communities of digital organisms undergoing open-ended evolution as we subjected them to instantaneous "pulse" extinctions, choosing survivors at random, and to prolonged "press" extinctions involving a period of low resource availability. We measured age of the phylogenetic root and tree stemminess, and evaluated how branching history of the phylogenetic trees was affected by the extinction treatments. We found that strong random (pulse and strong selective extinction (press both left clear long-term signatures in root age distribution and tree stemminess, and eroded deep branching history to a greater degree than did weak extinction and control treatments. The widely-used Pybus-Harvey gamma statistic showed a clear short-term response to extinction and recovery, but differences between treatments diminished over time and did not show a long-term signature. The characteristics of post-extinction phylogenies were often affected as much by the recovery interval as by the extinction episode itself.

  16. A theory for the origin of a self-replicating chemical system. I - Natural selection of the autogen from short, random oligomers

    Science.gov (United States)

    White, D. H.

    1980-01-01

    A general theory is presented for the origin of a self-replicating chemical system, termed an autogen, which is capable of both crude replication and translation (protein synthesis). The theory requires the availability of free energy and monomers to the system, a significant background low-yield synthesis of kinetically stable oligopeptides and oligonucleotides, the localization of the oligomers, crude oligonucleotide selectivity of amino acids during oligopeptide synthesis, crude oligonucleotide replication, and two short peptide families which catalyze replication and translation, to produce a localized group of at least one copy each of two protogenes and two protoenzymes. The model posits a process of random oligomerization, followed by the random nucleation of functional components and the rapid autocatalytic growth of the functioning autogen to macroscopic amounts, to account for the origin of the first self-replicating system. Such a process contains steps of such high probability and short time periods that it is suggested that the emergence of an autogen in a laboratory experiment of reasonable time scale may be possible.

  17. A Biobrick Library for Cloning Custom Eukaryotic Plasmids

    OpenAIRE

    Marco Constante; Raik Grünberg; Mark Isalan

    2011-01-01

    Researchers often require customised variations of plasmids that are not commercially available. Here we demonstrate the applicability and versatility of standard synthetic biological parts (biobricks) to build custom plasmids. For this purpose we have built a collection of 52 parts that include multiple cloning sites (MCS) and common protein tags, protein reporters and selection markers, amongst others. Importantly, most of the parts are designed in a format to allow fusions that maintain th...

  18. Effects of Video Game Training on Measures of Selective Attention and Working Memory in Older Adults: Results from a Randomized Controlled Trial

    Science.gov (United States)

    Ballesteros, Soledad; Mayas, Julia; Prieto, Antonio; Ruiz-Marquez, Eloísa; Toril, Pilar; Reales, José M.

    2017-01-01

    Video game training with older adults potentially enhances aspects of cognition that decline with aging and could therefore offer a promising training approach. Although, previous published studies suggest that training can produce transfer, many of them have certain shortcomings. This randomized controlled trial (RCT; Clinicaltrials.gov ID: NCT02796508) tried to overcome some of these limitations by incorporating an active control group and the assessment of motivation and expectations. Seventy-five older volunteers were randomly assigned to the experimental group trained for 16 sessions with non-action video games from Lumosity, a commercial platform (http://www.lumosity.com/) or to an active control group trained for the same number of sessions with simulation strategy games. The final sample included 55 older adults (30 in the experimental group and 25 in the active control group). Participants were tested individually before and after training to assess working memory (WM) and selective attention and also reported their perceived improvement, motivation and engagement. The results showed improved performance across the training sessions. The main results were: (1) the experimental group did not show greater improvements in measures of selective attention and working memory than the active control group (the opposite occurred in the oddball task); (2) a marginal training effect was observed for the N-back task, but not for the Stroop task while both groups improved in the Corsi Blocks task. Based on these results, one can conclude that training with non-action games provide modest benefits for untrained tasks. The effect is not specific for that kind of training as a similar effect was observed for strategy video games. Groups did not differ in motivation, engagement or expectations. PMID:29163136

  19. Effects of Video Game Training on Measures of Selective Attention and Working Memory in Older Adults: Results from a Randomized Controlled Trial.

    Science.gov (United States)

    Ballesteros, Soledad; Mayas, Julia; Prieto, Antonio; Ruiz-Marquez, Eloísa; Toril, Pilar; Reales, José M

    2017-01-01

    Video game training with older adults potentially enhances aspects of cognition that decline with aging and could therefore offer a promising training approach. Although, previous published studies suggest that training can produce transfer, many of them have certain shortcomings. This randomized controlled trial (RCT; Clinicaltrials.gov ID: NCT02796508) tried to overcome some of these limitations by incorporating an active control group and the assessment of motivation and expectations. Seventy-five older volunteers were randomly assigned to the experimental group trained for 16 sessions with non-action video games from Lumosity, a commercial platform (http://www.lumosity.com/) or to an active control group trained for the same number of sessions with simulation strategy games. The final sample included 55 older adults (30 in the experimental group and 25 in the active control group). Participants were tested individually before and after training to assess working memory (WM) and selective attention and also reported their perceived improvement, motivation and engagement. The results showed improved performance across the training sessions. The main results were: (1) the experimental group did not show greater improvements in measures of selective attention and working memory than the active control group (the opposite occurred in the oddball task); (2) a marginal training effect was observed for the N-back task, but not for the Stroop task while both groups improved in the Corsi Blocks task. Based on these results, one can conclude that training with non-action games provide modest benefits for untrained tasks. The effect is not specific for that kind of training as a similar effect was observed for strategy video games. Groups did not differ in motivation, engagement or expectations.

  20. Effects of Video Game Training on Measures of Selective Attention and Working Memory in Older Adults: Results from a Randomized Controlled Trial

    Directory of Open Access Journals (Sweden)

    Soledad Ballesteros

    2017-11-01

    Full Text Available Video game training with older adults potentially enhances aspects of cognition that decline with aging and could therefore offer a promising training approach. Although, previous published studies suggest that training can produce transfer, many of them have certain shortcomings. This randomized controlled trial (RCT; Clinicaltrials.gov ID: NCT02796508 tried to overcome some of these limitations by incorporating an active control group and the assessment of motivation and expectations. Seventy-five older volunteers were randomly assigned to the experimental group trained for 16 sessions with non-action video games from Lumosity, a commercial platform (http://www.lumosity.com/ or to an active control group trained for the same number of sessions with simulation strategy games. The final sample included 55 older adults (30 in the experimental group and 25 in the active control group. Participants were tested individually before and after training to assess working memory (WM and selective attention and also reported their perceived improvement, motivation and engagement. The results showed improved performance across the training sessions. The main results were: (1 the experimental group did not show greater improvements in measures of selective attention and working memory than the active control group (the opposite occurred in the oddball task; (2 a marginal training effect was observed for the N-back task, but not for the Stroop task while both groups improved in the Corsi Blocks task. Based on these results, one can conclude that training with non-action games provide modest benefits for untrained tasks. The effect is not specific for that kind of training as a similar effect was observed for strategy video games. Groups did not differ in motivation, engagement or expectations.

  1. Genetic evaluation and selection response for growth in meat-type quail through random regression models using B-spline functions and Legendre polynomials.

    Science.gov (United States)

    Mota, L F M; Martins, P G M A; Littiere, T O; Abreu, L R A; Silva, M A; Bonafé, C M

    2017-08-14

    The objective was to estimate (co)variance functions using random regression models (RRM) with Legendre polynomials, B-spline function and multi-trait models aimed at evaluating genetic parameters of growth traits in meat-type quail. A database containing the complete pedigree information of 7000 meat-type quail was utilized. The models included the fixed effects of contemporary group and generation. Direct additive genetic and permanent environmental effects, considered as random, were modeled using B-spline functions considering quadratic and cubic polynomials for each individual segment, and Legendre polynomials for age. Residual variances were grouped in four age classes. Direct additive genetic and permanent environmental effects were modeled using 2 to 4 segments and were modeled by Legendre polynomial with orders of fit ranging from 2 to 4. The model with quadratic B-spline adjustment, using four segments for direct additive genetic and permanent environmental effects, was the most appropriate and parsimonious to describe the covariance structure of the data. The RRM using Legendre polynomials presented an underestimation of the residual variance. Lesser heritability estimates were observed for multi-trait models in comparison with RRM for the evaluated ages. In general, the genetic correlations between measures of BW from hatching to 35 days of age decreased as the range between the evaluated ages increased. Genetic trend for BW was positive and significant along the selection generations. The genetic response to selection for BW in the evaluated ages presented greater values for RRM compared with multi-trait models. In summary, RRM using B-spline functions with four residual variance classes and segments were the best fit for genetic evaluation of growth traits in meat-type quail. In conclusion, RRM should be considered in genetic evaluation of breeding programs.

  2. Impacts of Water Deficiency on Life History of Sitobion avenae Clones From Semi-arid and Moist Areas.

    Science.gov (United States)

    Dai, Peng; Liu, Deguang; Shi, Xiaoqin

    2015-10-01

    The climate warming trend appears to be evident with an increasing frequency of drought events in Shaanxi Province of China, which may have contributed to an increase in outbreaks of the English grain aphid, Sitobion avenae (Fabricius). To explore the potential effects of water-deficit stress on aphid outbreak risks, clones of S. avenae were collected from semi-arid and moist areas of Shaanxi. The life histories of collected clones were then compared on wheat under well-watered and moderately water-stressed conditions in the laboratory. Our results demonstrated that semi-arid area clones of S. avenae had longer developmental times, shorter reproductive times, lower fecundities, and lower net reproductive rates compared with moist area clones. Age-specific reproductive rates of moist area clones tended to be higher than those of semi-arid area clones. Significant differences between semi-arid and moist area clones were found for the survival functions when tested under water-stressed conditions, and semi-arid area clones tended to have a lower survival rate than moist area clones throughout their lives. "Population origin" (i.e., semi-arid and moist area clones) and "clone" together explained 62.74-96.56% of the total variance of tested life-history traits, suggesting the genetic basis for differentiation of clones from both areas. Significant differences in correlations, and selection differentials and gradients of life-history traits were also found between clones from both areas, providing further evidence of genetic basis for the life-history differentiation between them. Divergence between clones from both areas and its implications for S. avenae outbreaks are discussed. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  3. Crecimiento y producción en tres clones de Gypsophila paniculata L.. cultivadas bajo idénticas condiciones de invernadero Production and growth of three gypsophila paniculata clones cultured under identical greenhouse conditions

    Directory of Open Access Journals (Sweden)

    Arenas Blanco Gustavo

    1992-06-01

    tuvieron
    la fase reproductiva más larga y viceversa, pero, en todos los casos,la duración total en el, invernadero de producción fué
    de 227 días. La producción de ramos/planta varío entre
    clones (1.80, 1.72 y 1.46 para los clones T1, T2 y T3, respectivamente. Estos valores difieren de los registrados por la empresa donde se realizó el ensayo (1 .2 ramos/
    planta. Las flores fueron de excelente calidad y no se presentó la coloración lila de los pétalos, se asume que esta
    caracteristica aparece como respuesta a un efecto ambiental desconocido.
    There clones of Gypsophila paniculata c.v. perfecta were compared in the present research, with the aim of selecting the most efficient and productive propagation material for ou r tropical condition and to determine the genetical or environmental origin of the purple color that sometimes is present during flower development. A Randomized Complete Block (RCB design was selected, with three replicates,
    undercommercial growing conditions in an export cutflower industry located in Madrid (Cundinamarca. Highly homogeneous cuttings, original from Balborts, Raham
    Meristem and Cor van Duyn were used; these were obtained from mother plants grown in there production farms located in
    the Sabana of Bogotá (300 cuttings per farm. Forty five days after planting, 522 cuttings were rooted using the comercial
    methodology and then planted under commercial greenhouse. The first harvest of flowers in each treatment was programmed according the flower development, continuing until the end of the harvest cycle. The cut flowers were
    arranged in bunches of 300 grams each. The variables related to plant growth, production and flower quality were
    registered. In the process of rooting, the experimental
    results show differences between clones; the once coming from Cor van Duyn (T3 were more vigorous. In the initial samples, the variables associated with growth (height,
    stem

  4. Mathematical design of prokaryotic clone-based microarrays

    Directory of Open Access Journals (Sweden)

    Quirijns Elisabeth J

    2005-09-01

    Full Text Available Abstract Background Clone-based microarrays, on which each spot represents a random genomic fragment, are a good alternative to open reading frame-based microarrays, especially for microorganisms for which the complete genome sequence is not available. Since the generation of a genomic DNA library is a random process, it is beforehand uncertain which genes are represented. Nevertheless, the genome coverage of such an array, which depends on different variables like the insert size and the number of clones in the library, can be predicted by mathematical approaches. When applying the classical formulas that determine the probability that a certain sequence is represented in a DNA library at the nucleotide level, massive amounts of clones would be necessary to obtain a proper coverage of the genome. Results This paper describes the development of two complementary equations for determining the genome coverage at the gene level. The first equation predicts the fraction of genes that is represented on the array in a detectable way and cover at least a set part (the minimal insert coverage of the genomic fragment by which these genes are represented. The higher this minimal insert coverage, the larger the chance that changes in expression of a specific gene can be detected and attributed to that gene. The second equation predicts the fraction of genes that is represented in spots on the array that only represent genes from a single transcription unit, which information can be interpreted in a quantitative way. Conclusion Validation of these equations shows that they form reliable tools supporting optimal design of prokaryotic clone-based microarrays.

  5. Towards Clone Detection in UML Domain Models

    DEFF Research Database (Denmark)

    Störrle, Harald

    2013-01-01

    Code clones (i.e., duplicate fragments of code) have been studied for long, and there is strong evidence that they are a major source of software faults. Anecdotal evidence suggests that this phenomenon occurs similarly in models, suggesting that model clones are as detrimental to model quality...... as they are to code quality. However, programming language code and visual models have significant differences that make it difficult to directly transfer notions and algorithms developed in the code clone arena to model clones. In this article, we develop and propose a definition of the notion of “model clone” based...... on the thorough analysis of practical scenarios. We propose a formal definition of model clones, specify a clone detection algorithm for UML domain models, and implement it prototypically. We investigate different similarity heuristics to be used in the algorithm, and report the performance of our approach. While...

  6. The method for breeding and genetic assessment of Scotch pine clones at forest seed orchards

    Directory of Open Access Journals (Sweden)

    B. V. Raevsky

    2016-10-01

    Full Text Available Fast height growth selection usually considered as the basic type of Scotch pine breeding strategy. Due to this fact height growth of pine clones usually is taken as the first key feature. In the view of good seed production there is only one indicator that could be adopted as having summarized effect reflecting the real contribution of a clone to the whole seed orchard yield. This is an average number of full seeds per tree (ramet. This trait is the second most important one after the height growth ability feature. The way of two-trait breeding program with the aforesaid features seemed to be the most suitable for Scotch pine. Main theses of 4-stages complex assessment procedure have been formulated concerning Scotch pine vegetative progenies grown at seed orchards. It was stated that this system of breeding and genetic assessment is based on correlations found for habitus and reproductive features of Scotch pine clones along with the height growth ability of their seed progenies. In the first stage pine clones meeting the criteria (≥ X + 0.5σx regarding height growth are to be selected. In the second stage, clones with hard tapering stem and crown formed by long and thick branches have to be discarded. At this stage, such feature as «mean diameter of three thickest limbs at the height of 1.5–2.0 m» became the key factor. Its mean value for selected clones must not be by 1–2 % higher than for general clone set. In the third stage a complex of reproductive features for clones that have passed the previous stages are taken into account. The trait «average number of full seeds per ramet» is the key feature in this stage according to the criteria (≥ X . The fourth stage implies that progeny trials with open-pollinated progenies ought to be laid down to calculate the general and specific combining ability. It has been concluded that high intensive selection of clones grown at the I-stage seed orchards promotes a substantial genetic gain

  7. EFFECT OF AGE AND CLONE ON THE QUALITY OF Eucalyptus spp WOOD AIMING BIOENERGY PRODUCTION

    Directory of Open Access Journals (Sweden)

    Thiago de Paula Protásio

    2014-06-01

    Full Text Available http://dx.doi.org/10.5902/1980509814587The aim of this work was to evaluate the effect of age and clone on the quality of Eucalyptus spp wood aiming the production of charcoal and bioenergy. Four Eucalyptus spp clones at the ages of 57 and 69 months were evaluated. Four trees per clone in each age were evaluated. The average basic density, the basic density at the DBH, higher heating value and contents of lignin, total extractives, ashes, holocellulose an elemental chemica analylsis (C, H, N, S and O were evaluated. In the evaluation of the assay, and entirely randomized design in the factorial scheme 4 x 2 was used. Besides, a multivariate analysis of main components was made. In general, it was observed effect of age on wood quality. Ash, hydrogen and nitrogen contents tended to diminish with increases in age for all the clones evaluated. However, oxygen content presented an increase with the increase in age of the clones. Lignin content presented significant increase with age increase, being the contrary observed for holocellulose content. The clones at the age of 69 months presented the highest contents of lignin, but the same did not happen for basic density of wood. The clones I144 and I220 had the highest average values for this characteristic, what may be advantageous for charcoal production. 

  8. Telomeres and the ethics of human cloning.

    Science.gov (United States)

    Allhoff, Fritz

    2004-01-01

    In search of a potential problem with cloning, I investigate the phenomenon of telomere shortening which is caused by cell replication; clones created from somatic cells will have shortened telomeres and therefore reach a state of senescence more rapidly. While genetic intervention might fix this problem at some point in the future, I ask whether, absent technological advances, this biological phenomenon undermines the moral permissibility of cloning.

  9. A randomized controlled trial investigating the use of a predictive nomogram for the selection of the FSH starting dose in IVF/ICSI cycles.

    Science.gov (United States)

    Allegra, Adolfo; Marino, Angelo; Volpes, Aldo; Coffaro, Francesco; Scaglione, Piero; Gullo, Salvatore; La Marca, Antonio

    2017-04-01

    The number of oocytes retrieved is a relevant intermediate outcome in women undergoing IVF/intracytoplasmic sperm injection (ICSI). This trial compared the efficiency of the selection of the FSH starting dose according to a nomogram based on multiple biomarkers (age, day 3 FSH, anti-Müllerian hormone) versus an age-based strategy. The primary outcome measure was the proportion of women with an optimal number of retrieved oocytes defined as 8-14. At their first IVF/ICSI cycle, 191 patients underwent a long gonadotrophin-releasing hormone agonist protocol and were randomized to receive a starting dose of recombinant (human) FSH, based on their age (150 IU if ≤35 years, 225 IU if >35 years) or based on the nomogram. Optimal response was observed in 58/92 patients (63%) in the nomogram group and in 42/99 (42%) in the control group (+21%, 95% CI = 0.07 to 0.35, P = 0.0037). No significant differences were found in the clinical pregnancy rate or the number of embryos cryopreserved per patient. The study showed that the FSH starting dose selected according to ovarian reserve is associated with an increase in the proportion of patients with an optimal response: large trials are recommended to investigate any possible effect on the live-birth rate. Copyright © 2017 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

  10. AN APPROACH FOR CLONE DETECTION IN DOCUMENTATION REUSE

    OpenAIRE

    D. V. Lutsiv; D. V. Koznov; H. A. Basit; E. L. Ouh; M. N. Smirnov; K. Y. Romanovsky

    2014-01-01

    The paper focuses on the searching method for repetitions in DocBook/DRL or plain text documents. An algorithm has been designed based on software clone detection. The algorithm supports filtering results: clones are rejected if clone length in the group is less than 5 symbols, intersection of clone groups is eliminated, meaningfulness clones are removed, the groups containing clones consisting only of XML are eliminated. Remaining search is supported: found clones are extracted from the docu...

  11. Human cloning: Eastern Mediterranean Region perspective.

    Science.gov (United States)

    Abdur Rab, M; Khayat, M H

    2006-01-01

    Recent advances in genomics and biotechnology have ushered in a new era in health development. Therapeutic cloning possesses enormous potential for revolutionizing medical and therapeutic techniques. Cloning technology, however, is perceived as having the potential for reproductive cloning, which raises serious ethical and moral concerns. It is important that the Islamic countries come to a consensus on this vital issue. Developing science and technology for better health is a religious and moral obligation. There is an urgent need for Muslim scholars to discuss the issue of stem cell research and cloning rationally; such dialogue will not only consider the scientific merits but also the moral, ethical and legal implications.

  12. Metabolomic phenotyping of a cloned pig model

    Directory of Open Access Journals (Sweden)

    Callesen Henrik

    2011-08-01

    Full Text Available Abstract Background Pigs are widely used as models for human physiological changes in intervention studies, because of the close resemblance between human and porcine physiology and the high degree of experimental control when using an animal model. Cloned animals have, in principle, identical genotypes and possibly also phenotypes and this offer an extra level of experimental control which could possibly make them a desirable tool for intervention studies. Therefore, in the present study, we address how phenotype and phenotypic variation is affected by cloning, through comparison of cloned pigs and normal outbred pigs. Results The metabolic phenotype of cloned pigs (n = 5 was for the first time elucidated by nuclear magnetic resonance (NMR-based metabolomic analysis of multiple bio-fluids including plasma, bile and urine. The metabolic phenotype of the cloned pigs was compared with normal outbred pigs (n = 6 by multivariate data analysis, which revealed differences in the metabolic phenotypes. Plasma lactate was higher for cloned vs control pigs, while multiple metabolites were altered in the bile. However a lower inter-individual variability for cloned pigs compared with control pigs could not be established. Conclusions From the present study we conclude that cloned and normal outbred pigs are phenotypically different. However, it cannot be concluded that the use of cloned animals will reduce the inter-individual variation in intervention studies, though this is based on a limited number of animals.

  13. Metabolomic phenotyping of a cloned pig model

    Science.gov (United States)

    2011-01-01

    Background Pigs are widely used as models for human physiological changes in intervention studies, because of the close resemblance between human and porcine physiology and the high degree of experimental control when using an animal model. Cloned animals have, in principle, identical genotypes and possibly also phenotypes and this offer an extra level of experimental control which could possibly make them a desirable tool for intervention studies. Therefore, in the present study, we address how phenotype and phenotypic variation is affected by cloning, through comparison of cloned pigs and normal outbred pigs. Results The metabolic phenotype of cloned pigs (n = 5) was for the first time elucidated by nuclear magnetic resonance (NMR)-based metabolomic analysis of multiple bio-fluids including plasma, bile and urine. The metabolic phenotype of the cloned pigs was compared with normal outbred pigs (n = 6) by multivariate data analysis, which revealed differences in the metabolic phenotypes. Plasma lactate was higher for cloned vs control pigs, while multiple metabolites were altered in the bile. However a lower inter-individual variability for cloned pigs compared with control pigs could not be established. Conclusions From the present study we conclude that cloned and normal outbred pigs are phenotypically different. However, it cannot be concluded that the use of cloned animals will reduce the inter-individual variation in intervention studies, though this is based on a limited number of animals. PMID:21859467

  14. Species-specific challenges in dog cloning.

    Science.gov (United States)

    Kim, G A; Oh, H J; Park, J E; Kim, M J; Park, E J; Jo, Y K; Jang, G; Kim, M K; Kim, H J; Lee, B C

    2012-12-01

    Somatic cell nuclear transfer (SCNT) is now an established procedure used in cloning of several species. SCNT in dogs involves multiple steps including the removal of the nuclear material, injection of a donor cell, fusion, activation of the reconstructed oocytes and finally transfer to a synchronized female recipient. There are therefore many factors that contribute to cloning efficiency. By performing a retrospective analysis of 2005-2012 published papers regarding dog cloning, we define the optimum procedure and summarize the specific feature for dog cloning. © 2012 Blackwell Verlag GmbH.

  15. Quantum cloning disturbed by thermal Davies environment

    Science.gov (United States)

    Dajka, Jerzy; Łuczka, Jerzy

    2016-06-01

    A network of quantum gates designed to implement universal quantum cloning machine is studied. We analyze how thermal environment coupled to auxiliary qubits, `blank paper' and `toner' required at the preparation stage of copying, modifies an output fidelity of the cloner. Thermal environment is described in terms of the Markovian Davies theory. We show that such a cloning machine is not universal any more but its output is independent of at least a part of parameters of the environment. As a case study, we consider cloning of states in a six-state cryptography's protocol. We also briefly discuss cloning of arbitrary input states.

  16. Human cloning and our sense of self.

    Science.gov (United States)

    Brock, Dan W

    2002-04-12

    This Viewpoint formulates and responds to three lines of argument concerning human reproductive cloning's potential to undermine our sense of self or identity. First, cloning would undermine our sense of individuality or uniqueness. But it could only undermine our genetic uniqueness, not our full individuality. Second, cloning would undermine the value or worth of human beings. But it would not make individuals replaceable or of any less moral worth. Third, a clone's freedom or autonomy to construct his or her own life would be undermined by the presence of an earlier twin. But only a mistaken belief in genetic determinism supports this feared loss of freedom.

  17. Prevalence of at-risk genotypes for genotoxic effects decreases with age in a randomly selected population in Flanders: a cross sectional study

    Directory of Open Access Journals (Sweden)

    van Delft Joost HM

    2011-10-01

    Full Text Available Abstract Background We hypothesized that in Flanders (Belgium, the prevalence of at-risk genotypes for genotoxic effects decreases with age due to morbidity and mortality resulting from chronic diseases. Rather than polymorphisms in single genes, the interaction of multiple genetic polymorphisms in low penetrance genes involved in genotoxic effects might be of relevance. Methods Genotyping was performed on 399 randomly selected adults (aged 50-65 and on 442 randomly selected adolescents. Based on their involvement in processes relevant to genotoxicity, 28 low penetrance polymorphisms affecting the phenotype in 19 genes were selected (xenobiotic metabolism, oxidative stress defense and DNA repair, respectively 13, 6 and 9 polymorphisms. Polymorphisms which, based on available literature, could not clearly be categorized a priori as leading to an 'increased risk' or a 'protective effect' were excluded. Results The mean number of risk alleles for all investigated polymorphisms was found to be lower in the 'elderly' (17.0 ± 2.9 than the 'adolescent' (17.6 ± 3.1 subpopulation (P = 0.002. These results were not affected by gender nor smoking. The prevalence of a high (> 17 = median number of risk alleles was less frequent in the 'elderly' (40.6% than the 'adolescent' (51.4% subpopulation (P = 0.002. In particular for phase II enzymes, the mean number of risk alleles was lower in the 'elderly' (4.3 ± 1.6 than the 'adolescent' age group (4.8 ± 1.9 P 4 = median number of risk alleles was less frequent in the 'elderly' (41.3% than the adolescent subpopulation (56.3%, P 8 = median number of risk alleles for DNA repair enzyme-coding genes was lower in the 'elderly' (37,3% than the 'adolescent' subpopulation (45.6%, P = 0.017. Conclusions These observations are consistent with the hypothesis that, in Flanders, the prevalence of at-risk alleles in genes involved in genotoxic effects decreases with age, suggesting that persons carrying a higher number of

  18. A high-throughput, restriction-free cloning and screening strategy based on ccdB-gene replacement.

    Science.gov (United States)

    Lund, Bjarte Aarmo; Leiros, Hanna-Kirsti Schrøder; Bjerga, Gro Elin Kjæreng

    2014-03-10

    In high-throughput demanding fields, such as biotechnology and structural biology, molecular cloning is an essential tool in obtaining high yields of recombinant protein. Here, we address recently developed restriction-free methods in cloning, and present a more cost-efficient protocol that has been optimized to improve both cloning and clone screening. In our case study, three homologous β-lactamase genes were successfully cloned using these restriction-free protocols. To clone the genes, we chose a gene replacement strategy, where the recombinant genes contained overhangs that targeted a region of the expression vector including a cytotoxin-encoding ccdB-gene. We provide further evidence that gene replacement can be applied with high-throughput cloning protocols. Targeting a replacement of the ccdB-gene was found to be very successful for counterselection using these protocols. This eliminated the need for treatment with the restriction enzyme DpnI that has so far been the preferred clone selection approach. We thus present an optimized cloning protocol using a restriction-free ccdB-gene replacement strategy, which allows for parallel cloning at a high-throughput level.

  19. Avaliação de clones de bananeira do subgrupo Cavendish (Musa acuminata, AAA em Cruz das Almas-BA Evaluation of banana Cavendish clones in Cruz das Almas City, Bahia State, Brazil

    Directory of Open Access Journals (Sweden)

    Sebastião de Oliveira e Silva

    2004-12-01

    Full Text Available Foram avaliados em Cruz das Almas-BA, em dois ciclos, 69 clones Cavendish coletados em São Paulo, Minas Gerais, Bahia e Santa Catarina, sendo 49 do tipo Nanicão e 20 do tipo Grande Naine. Os clones foram estabelecidos em área experimental da Embrapa Mandioca e Fruticultura utilizando-se um delineamento em blocos ao acaso com cinco repetições e cinco plantas por parcela. Foram utilizados a irrigação por microaspersão, o espaçamento de 3,0 m x 2,0 m e um sistema de condução com três plantas/touceira. Os requerimentos agronômicos foram aplicados conforme preconizados para o cultivo. Na avaliação dos clones, foram consideradas as seguintes variáveis: altura da planta em centímetros (AP; número de dias do plantio à colheita (ND; peso do cacho em quilogramas (PC; número de frutos por cacho (NF; e comprimento do fruto em centímetros (CF. Pelos resultados obtidos, verificou-se uma variabilidade média em todas as variáveis avaliadas. Por apresentarem caracteres superiores, foram selecionados cinco clones de Grande Naine (G.N. Taperão, G.N.Rossete, G.N. Willians, G.N. Magário, G.N. SC-074 e quatro de Nanicão (N. IAC Abóbada Verde, N. Rossete, N. SC-0008 e N. SC-063.Sixty-nine clones of Cavendish type bananas (49 Nanicão and 20 Grande Naine collected in the States of São Paulo, Minas Gerais, Bahia and Santa Catarina were evaluated. The clones were established in an experimental area at the Cassava and Fruit Crops Research Center - EMBRAPA, using micro-aspersion irrigation, in plants spaced at 3.0 m x 2.0 m, and conducted with three plants/bushes. Random blocks were used with five replications and five plants per plot. All cultural requirements for the crop were carried out. For the clone evaluations, the following variables were considered: plant height in centimeters (PH; number of days from planting to yield (ND; weight of bunch in kilograms (WB; number of fruits per bunch (FB and length of fruit in centimeters (LF. The

  20. Genetic molecular diversity, production and resistance to witches’ broom in cacao clones

    Directory of Open Access Journals (Sweden)

    José Luis Pires

    2013-06-01

    Full Text Available The 32 cacao clones selected as being resistant following the witches’ broom epidemic and for having distinct productivitywere characterized according to their genetic diversity and were submitted to a new selection. These plants were assessed for eightyears at the Oceania Farm (FO in Itagibá, Bahia, Brazil. The 13 microsatellite primers generated an average of 11.7 amplicons perlocus, and based on them it was demonstrated that the 32 clones distribute themselves in groups apart from the nine clones used ascontrols. The 32 materials displayed significant differences in relation to the characters assessed in the field. Two criteria were formedfrom the classification of the most productive and resistant plants, and then used to select plants within the clusters. The selected plantsdisplayed potential for the cacao improvement program, that they have a high production and high resistance to witches’ broom.

  1. Ensemble of random forests One vs. Rest classifiers for MCI and AD prediction using ANOVA cortical and subcortical feature selection and partial least squares.

    Science.gov (United States)

    Ramírez, J; Górriz, J M; Ortiz, A; Martínez-Murcia, F J; Segovia, F; Salas-Gonzalez, D; Castillo-Barnes, D; Illán, I A; Puntonet, C G

    2017-12-11

    Alzheimer's disease (AD) is the most common cause of dementia in the elderly and affects approximately 30 million individuals worldwide. Mild cognitive impairment (MCI) is very frequently a prodromal phase of AD, and existing studies have suggested that people with MCI tend to progress to AD at a rate of about 10-15% per year. However, the ability of clinicians and machine learning systems to predict AD based on MRI biomarkers at an early stage is still a challenging problem that can have a great impact in improving treatments. The proposed system, developed by the SiPBA-UGR team for this challenge, is based on feature standardization, ANOVA feature selection, partial least squares feature dimension reduction and an ensemble of One vs. Rest random forest classifiers. With the aim of improving its performance when discriminating healthy controls (HC) from MCI, a second binary classification level was introduced that reconsiders the HC and MCI predictions of the first level. The system was trained and evaluated on an ADNI datasets that consist of T1-weighted MRI morphological measurements from HC, stable MCI, converter MCI and AD subjects. The proposed system yields a 56.25% classification score on the test subset which consists of 160 real subjects. The classifier yielded the best performance when compared to: (i) One vs. One (OvO), One vs. Rest (OvR) and error correcting output codes (ECOC) as strategies for reducing the multiclass classification task to multiple binary classification problems, (ii) support vector machines, gradient boosting classifier and random forest as base binary classifiers, and (iii) bagging ensemble learning. A robust method has been proposed for the international challenge on MCI prediction based on MRI data. The system yielded the second best performance during the competition with an accuracy rate of 56.25% when evaluated on the real subjects of the test set. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Future and applications of cloning.

    Science.gov (United States)

    Trounson, Alan O

    2006-01-01

    The birth of viable offspring from somatic cell nuclear transfer (SCNT) in mammals caused a major re-examination of the understanding of the commitment of cells to specific tissue lineages during differentiation. The questions of whether cells undergo dedifferentiation or transdifferentiation during the development of offspring and how these changes are controlled is a source of ongoing debate that is yet to be resolved. Irrespective of the outcome of this debate, it is clear that cloning using SCNT has a place and purpose in the future of research and animal breeding. The future uses of SCNT could include the production of transgenic mice, the production of transgenic livestock and assisting with the re-establishment of endangered species. Human medicine also would benefit from future use of SCNT because it would allow the production of patient-specific embryonic stem cells.

  3. Initiating genomic selection in tetraploid potato

    DEFF Research Database (Denmark)

    Sverrisdóttir, Elsa; Janss, Luc; Byrne, Stephen

    Breeding for more space and resource efficient crops is important to feed the world’s increasing population. Potatoes produce approximately twice the amount of calories per hectare compared to cereals. The traditional “mate and phenotype” breeding approach is costly and time-consuming; however......, the completion of the genome sequence of potato has enabled the application of genomics-assisted breeding technologies. Genomic selection using genome-wide molecular markers is becoming increasingly applicable to crops as the genotyping costs continue to reduce and it is thus an attractive breeding alternative....... We have used genotyping-by-sequencing to genotype 762 individuals. The individuals were randomly selected from a population of 5,000 individuals derived from a poly-parental cross generated from 18 tetraploid cultivars and breeding clones (MASPot population). Phenotypic data have been established...

  4. The ethics of human reproductive cloning.

    Science.gov (United States)

    Strong, Carson

    2005-03-01

    This article addresses the question of whether human reproductive cloning could be ethically justifiable in at least some cases involving infertile couples who would choose cloning as a way to have a genetically related child. At present, the risk of congenital anomalies constitutes a compelling argument against human reproductive cloning. The article explores whether reproductive cloning could be ethically justifiable if, at some future time, cloning becomes possible without an elevated risk of anomalies. It is argued that freedom to use cloning is a form of procreative freedom and, as such, deserves respect. All of the objections that have been raised against human reproductive cloning fall under three main categories: those that appeal to the interests of the child, those based on consequences for society, and those arising from teleological views. Objections that appeal to the child's interests are, in turn, of two main kinds: consequentialist and deontological. All of these types of objections are examined, and it is found that each involves serious problems that prevent it from being a reasonable objection in the context of the infertility cases considered. It is concluded that human reproductive cloning would be ethically justifiable in at least some cases involving infertile couples, provided that it could be performed without an elevated risk of anomalies.

  5. What's so bad about human cloning?

    Science.gov (United States)

    Breitowitz, Yitzchok

    2002-12-01

    There appears to be a consensus in the general community that reproductive cloning is an immoral technology that should be banned. It may, however, be argued, at least from the perspective of the Jewish tradition, that reproductive cloning has many positive benefits. It is thus essential that one carefully weigh the costs and the benefits before deciding on a definitive course of action.

  6. Computerized adaptive testing with item cloning

    NARCIS (Netherlands)

    Glas, Cornelis A.W.; van der Linden, Willem J.

    2003-01-01

    To increase the number of items available for adaptive testing and reduce the cost of item writing, the use of techniques of item cloning has been proposed. An important consequence of item cloning is possible variability between the item parameters. To deal with this variability, a multilevel item

  7. Recombination-assisted megaprimer (RAM) cloning

    Science.gov (United States)

    Mathieu, Jacques; Alvarez, Emilia; Alvarez, Pedro J.J.

    2014-01-01

    No molecular cloning technique is considered universally reliable, and many suffer from being too laborious, complex, or expensive. Restriction-free cloning is among the simplest, most rapid, and cost-effective methods, but does not always provide successful results. We modified this method to enhance its success rate through the use of exponential amplification coupled with homologous end-joining. This new method, recombination-assisted megaprimer (RAM) cloning, significantly extends the application of restriction-free cloning, and allows efficient vector construction with much less time and effort when restriction-free cloning fails to provide satisfactory results. The following modifications were made to the protocol:•Limited number of PCR cycles for both megaprimer synthesis and the cloning reaction to reduce error propagation.•Elimination of phosphorylation and ligation steps previously reported for cloning methods that used exponential amplification, through the inclusion of a reverse primer in the cloning reaction with a 20 base pair region of homology to the forward primer.•The inclusion of 1 M betaine to enhance both reaction specificity and yield. PMID:26150930

  8. Challenges in regulating farm animal cloning

    DEFF Research Database (Denmark)

    Gunning, Jennifer; Hartlev, Mette; Gamborg, Christian

    Report from the project Cloning in Public: A specific support action within the 6th framework programme, priority 5: Food quality and safety......Report from the project Cloning in Public: A specific support action within the 6th framework programme, priority 5: Food quality and safety...

  9. Cloning of endangered mammalian species: any progress?

    Science.gov (United States)

    Loi, Pasqualino; Galli, Cesare; Ptak, Grazyna

    2007-05-01

    Attempts through somatic cell nuclear transfer to expand wild populations that have shrunk to critical numbers is a logical extension of the successful cloning of mammals. However, although the first mammal was cloned 10 years ago, nuclear reprogramming remains phenomenological, with abnormal gene expression and epigenetic deregulation being associated with the cloning process. In addition, although cloning of wild animals using host oocytes from different species has been successful, little is known about the implication of partial or total mitochondrial DNA heteroplasmy in cloned embryos, fetuses and offspring. Finally, there is a need for suitable foster mothers for inter-intra specific cloned embryos. Considering these issues, the limited success achieved in cloning endangered animals is not surprising. However, optimism comes from the rapid gain in the understanding of the molecular clues underlying nuclear reprogramming. If it is possible to achieve a controlled reversal of the differentiated state of a cell then it is probable that other issues that impair the cloning of endangered animals, such as the inter-intra species oocyte or womb donor, will be overcome in the medium term.

  10. Cloning of partial putative gonadotropin hormone receptor ...

    Indian Academy of Sciences (India)

    Equus asinus. –. 71·0. –. Macaca fascicularis. –. 83·9. –. Gallus gallus. –. 74·2. –. Canis familiaris. –. –. 74·2. Drosophila melanogaster. –. 61·3. –. Figure 2. Structure of the cloned insert. (a) Diagrammatic representation of the cloned DNA fragment; arrangement of the PCR products are illustrated with primers. Letters 'F' and.

  11. Cloning and superluminal signaling£

    Indian Academy of Sciences (India)

    is possible, we can then have (usable) superluminal signaling [8]. The basic principle behind no exact cloning is the principle of no-signaling (i.e., no superluminal signaling). Allowing no-signaling, Gisin [7] has reproduced the 1. 2 optimal universal symmetric cloning machine of Buzek and Hillery [2] for qubits. We shall ...

  12. Metabolomic phenotyping of af cloned pig model

    DEFF Research Database (Denmark)

    Clausen, Morten Rahr; Christensen, Kirstine Lykke; Hedemann, Mette Skou

    2011-01-01

    outbred pigs. Results The metabolic phenotype of cloned pigs (n = 5) was for the first time elucidated by nuclear magnetic resonance (NMR)-based metabolomic analysis of multiple bio-fluids including plasma, bile and urine. The metabolic phenotype of the cloned pigs was compared with normal outbred pigs (n...

  13. [Human cloning in Muslim and Arab law].

    Science.gov (United States)

    Aldeeb Abu-Sahlieh, Sami A

    2009-01-01

    Cloning is a modern medical procedure that Muslim religious authorities treat en resorting to the general principles established by classical Muslim law based on the Koran and the Sunnah of Muhhamad as the messenger of God. In this regard, human beings are not capable of deciding what is or what is not lawful without resorting to divine norms. Cloning clashes with several principles. Firstly, the principle of the respect for life in relation to surpernumeraries, but Muslim authors are not in unanimous agreement on the determination of the moment at which life begins. Secondly, is the respect of progeny: cloning could only take place between a married couple. But even if these two principles are respected, cloning poses two major problems: the diversity of species expounded by the Koran and the Sunnah and a lack of interest. Which explains the quasi-unanimous opposition of Muslim writings regarding cloning.

  14. "Goodbye Dolly?" The ethics of human cloning.

    Science.gov (United States)

    Harris, J

    1997-01-01

    The ethical implications of human clones have been much alluded to, but have seldom been examined with any rigour. This paper examines the possible uses and abuses of human cloning and draws out the principal ethical dimensions, both of what might be done and its meaning. The paper examines some of the major public and official responses to cloning by authorities such as President Clinton, the World Health Organisation, the European parliament, UNESCO, and others and reveals their inadequacies as foundations for a coherent public policy on human cloning. The paper ends by defending a conception of reproductive rights of "procreative autonomy" which shows human cloning to be not inconsistent with human rights and dignity. PMID:9451604

  15. Clonal tests of new cottonwood selections from the southeast

    Science.gov (United States)

    Jonathan Paul Jeffreys; Samuel B. Land; Emily B. Schultz; Andrew J. Londo

    2006-01-01

    One hundred “new” clones and 20 “check” clones were established with unrooted cuttings during March-April 2003 in a second-stage clonal trial in Missouri and Georgia. The new clones had been selected for 2-year superiority in Melampsora leaf rust resistance, height growth, and diameter growth during first-stage rooted cutting trials. All 120 clones were vegetatively...

  16. JUVENILE-MATURE GENETIC CORRELATIONS IN Pinus taeda CLONES PROPAGATED VIA SOMATIC EMBRYOGENESIS

    Directory of Open Access Journals (Sweden)

    Poliana Coqueiro Dias

    2016-04-01

    Full Text Available ABSTRACT This study aimed to estimate the genetic correlation among selection ages (juvenile - adult and efficiency of early selection for the height, diameter, and volume traits of individuals from Pinus taeda families propagated via somatic embryogenesis. This study was carried out by genetic-statistical analysis, estimation procedure of variance (Reml, and prediction components of breeding values (Blup, using the Selegen-Reml/Blup software. Genetic correlations among juvenile ages and rotation age were performed by applying the linear model developed by Lambeth (1980. In accordance with results of the established model, the early selection can be performed in clones of Pinus taeda with high selection efficiency. Ages from 4 to 6 years old are enough to select Pinus taeda clones propagated via somatic embryogenesis for harvesting at 8 and 12 years old; and 6 to 10 years old are enough to select them for harvesting at 20 years old. On the basis of the genetic correlations estimates from the environments, the clones' selection of Pinus taeda propagated via somatic embryogenesis should be developed specifically for each environment. The clones' selection can be performed considering the diameter due to the high correlation between volume and diameter.

  17. Rock magnetic evidence of non-random raw material selection criteria in Cerro Toledo Obsidian Artifacts from Valles Caldera, New Mexico

    Science.gov (United States)

    Gregovich, A.; Feinberg, J. M.; Steffen, A.; Sternberg, R. S.

    2014-12-01

    Stone tools are one of the most enduring forms of ancient human behavior available to anthropologists. The geologic materials that comprise stone tools are a reflection of the rocks that were available locally or through trade, as are the intended use of the tools and the knapping technology needed to produce them. Investigation of the rock magnetic and geochemical characteristics of the artifacts and the geological source materials provides a baseline to explore these past behaviors. This study uses rock magnetic properties to explore the raw material selection criteria involved in the production of obsidian tools in the region around Valles Caldera in northern New Mexico. Obsidian is locally abundant and was traded by tribes across the central United States. Here we compare the rock magnetic properties of a sample of obsidian projectile points (N =25) that have been geochemically sourced to the Cerro Toledo obsidian flow with geological samples collected from four sites within the same flow (N =135). This collection of archaeological artifacts, albeit small, contains representatives of at least 8 different point styles that were used over 6000 years from the Archaic into the Late Prehistoric. Bulk rock hysteresis parameters (Mr, Ms, Bc, and Bcr) and low-field susceptibility (Χ) measurements show that the projectile points generally contain a lower concentration of magnetic minerals than the geologic samples. For example, the artifacts' median Ms value is 2.9 x 10-3 Am2kg-1, while that of the geological samples is 6.5 x 10-3 Am2kg-1. The concentration of magnetic minerals in obsidian is a proxy for the concentration of microlites in general, and this relationship suggests that although obsidian was locally abundant, toolmakers employed non-random selection criteria resulting in generally lower concentrations of microlites in their obsidian tools.

  18. Radiofrequency catheter selection based on cavotricuspid angiography compared with a control group with an externally cooled-tip catheter: a randomized pilot study.

    Science.gov (United States)

    Da Costa, Antoine; Romeyer-Bouchard, Cécile; Jamon, Yann; Bisch, Laurence; Isaaz, Karl

    2009-05-01

    Radiofrequency ablation (RFA) of cavotricuspid isthmus (CTI)-dependent atrial flutter (AFL) can be performed using either externally cooled-tip RFA catheters or large-tip (8 mm) catheters. However, experimental and clinical studies suggest that the efficacy of both catheters may vary with CTI anatomy and catheters orientation. The aim of this prospective study was to evaluate: a RFA catheter selection based on CTI angiography compared with a control group with an externally cooled-tip catheter together with the risk of an expensive crossover catheter in both groups. Over a period of 16 months, 119 patients were included and randomized. When comparing the angiographic group (n = 56) and the externally cooled-tip RFA catheter group (n = 63), the duration of application time with a median of 7 min (interquartile range 4.5-11) versus a median of 10 min (interquartile range 6-20; P = 0.008) and the duration of X-ray exposure with a median of 7 min (interquartile range 4-10) versus a median of 10 min (interquartile range 5-15; P = 0.025) were significantly lower in the angiographic group versus externally cooled-tip catheter group. Furthermore, the number of catheters crossover was significantly higher in the angiographic group versus externally cooled-tip catheter group I (27% vs 7%; P = 0.007). This study shows that a strategy with a catheter selection based on a CTI angiographic evaluation is superior to an empirical use of an externally cooled-tip catheter during CTI RFA. Thus, angiographic isthmus evaluation predicts the effectiveness of a RFA catheter and the risk of an expensive catheter crossover.

  19. Comparative Evolutionary Histories of the Fungal Chitinase Gene Family Reveal Non-Random Size Expansions and Contractions due to Adaptive Natural Selection

    Directory of Open Access Journals (Sweden)

    Jan Stenlid

    2008-01-01

    Full Text Available Gene duplication and loss play an important role in the evolution of novel functions and for shaping an organism’s gene content. Recently, it was suggested that stress-related genes frequently are exposed to duplications and losses, while growth-related genes show selection against change in copy number. The fungal chitinase gene family constitutes an interesting case study of gene duplication and loss, as their biological roles include growth and development as well as more stress-responsive functions. We used genome sequence data to analyze the size of the chitinase gene family in different fungal taxa, which range from 1 in Batrachochytrium dendrobatidis and Schizosaccharomyces pombe to 20 in Hypocrea jecorina and Emericella nidulans, and to infer their phylogenetic relationships. Novel chitinase subgroups are identified and their phylogenetic relationships with previously known chitinases are discussed. We also employ a stochastic birth and death model to show that the fungal chitinase gene family indeed evolves non-randomly, and we identify six fungal lineages where larger-than-expected expansions (Pezizomycotina, H. jecorina, Gibberella zeae, Uncinocarpus reesii, E. nidulans and Rhizopus oryzae, and two contractions (Coccidioides immitis and S. pombe potentially indicate the action of adaptive natural selection. The results indicate that antagonistic fungal-fungal interactions are an important process for soil borne ascomycetes, but not for fungal species that are pathogenic in humans. Unicellular growth is correlated with a reduction of chitinase gene copy numbers which emphasizes the requirement of the combined action of several chitinases for filamentous growth.

  20. Préférences alimentaires de Sahlbergella singularis Hagl. (Hemiptera: Miridae vis-à-vis de quelques clones de cacaoyers (Theobroma cacao L.

    Directory of Open Access Journals (Sweden)

    Amang, J.

    2005-01-01

    Full Text Available Feeding Preferences of Sahlbergella singularis Hagl. (Hemiptera: Miridae to some Cocoa (Theobroma cacao L. Clones. The selection of cocoa clones, resistant to Sahlbergella singularis Hagl. was done in the laboratory according to the standardized method of indoor microtests based on the study of mirid feeding preferences. Fourteen cocoa clones were involved. The Sca6 clone was the control. An index (i which expresses the ratio of the number of stings on the clone to that obtained on the control was calculated for each cultivar. Which has enabled to quantify the levels of attractiveness of cocoa clones to S. singularis and to classify these clones in three groups: less attractive clones (i< 1, non different (i= 1 and more attractive (i> 1. The results obtained showed that the mean numbers of feeding stings on the control (tr ranged from 5.49 to 5.62 (5.49≤ tr≤ 5.62 and that obtained on the other clones (tc from 5.29 to 6.18 (5.29≤ tc ≤ 6.18. The Na33 clone had the highest stings mean number (6.18 and IFC 100 the lowest one (5.29. The High Amazonian clone Na33 was the most attractive and the clones ICS100, IFC100, (exotic trinitario, Sca12 (catongo and Na32 (High Amazonian were less attractive. On the other hand the clones IFC1363, IFC1362, IFC1374 (catongo, UPA337, T60/887, ICS1 and IMC60 (High Amazonians and ICS95 (exotic trinitario were non different. The reactivity seemed not depending on the origin of the clone. Save the High Amazonian clone Na33 which was the most attractive there were among non different and less attractive clones as well exotic trinitario, catongo as High Amazonians.

  1. Adaptability of promissory clones of national cocoa (Theobroma cacao L. in the Arosemena Tola Canton from Equator

    Directory of Open Access Journals (Sweden)

    Guillermo Armando Pérez Garcia

    2017-07-01

    Full Text Available The research was conducted in order to evaluate the adaptability of three promissory clones of National cocoa proposed by the Autonomous Equatorian Institute of Agricultural Research to the ecological conditions of the Arosemena Tola canton, belonging to the Napo province, Equator. To carry out to this objective a random blocks design was made, where the treatments consisted on the promissory clones, EET-95, EET-96 and EET-103 compared with the clone CCN-51 used as control. Morphological and agronomic indicators were determined. The promissory clones have characteristic of adaptability to the conditions study, in particular the clone EET-103, with high index of seeds, similar values of fruit index and yield that the control, but with higher quality and lower content of heavy metals in the seeds.

  2. Chemical Profiles of Wood Components of Poplar Clones for Their Energy Utilization

    Directory of Open Access Journals (Sweden)

    Danica Kačíková

    2012-12-01

    Full Text Available Selected and tested poplar clones are very suitable biomass resources for various applications such as biofuels, the pulp and paper industry as well as chemicals production. In this study, we determined the content of lignin, cellulose, holocellulose, and extractives, syringyl to guaiacyl (S/G ratio in lignin, and also calculated higher heating values (HHV among eight examined clones of Populus grown on three different experimental sites. The highest lignin content for all the examined sites was determined in ‘I-214’ and ‘Baka 5’ clones, whereas the highest content of extractives was found in ‘Villafranca’ and ‘Baka 5’ clones. The highest S/G ratio for all the examined sites was determined in ‘Villafranca’ and ‘Agathe F’ clones. The chemical profiles of main wood components, extractives, and the S/G ratio in lignin were also influenced by both the experimental site and the clone × site interaction. Higher heating values, derived from calculations based on the contents of lignin and extractives (or lignin only, were in close agreement with the previously published data. The highest heating values were found for ‘Baka 5’ and ‘I-214’ clones. The optimal method of poplar biomass utilization can be chosen on basis of the lignocellulosics chemical composition and the S/G ratio in lignin.

  3. Production of Cloned Pigs with Targeted Attenuation of Gene Expression

    Science.gov (United States)

    Bordignon, Vilceu; El-Beirouthi, Nayla; Gasperin, Bernardo G.; Albornoz, Marcelo S.; Martinez-Diaz, Mario A.; Schneider, Carine; Laurin, Denyse; Zadworny, David; Agellon, Luis B.

    2013-01-01

    The objective of this study was to demonstrate that RNA interference (RNAi) and somatic cell nuclear transfer (SCNT) technologies can be used to attenuate the expression of specific genes in tissues of swine, a large animal species. Apolipoprotein E (apoE), a secreted glycoprotein known for its major role in lipid and lipoprotein metabolism and transport, was selected as the target gene for this study. Three synthetic small interfering RNAs (siRNA) targeting the porcine apoE mRNA were tested in porcine granulosa cells in primary culture and reduced apoE mRNA abundance ranging from 45–82% compared to control cells. The most effective sequence was selected for cloning into a short hairpin RNA (shRNA) expression vector under the control of RNA polymerase III (U6) promoter. Stably transfected fetal porcine fibroblast cells were generated and used to produce embryos with in vitro matured porcine oocytes, which were then transferred into the uterus of surrogate gilts. Seven live and one stillborn piglet were born from three gilts that became pregnant. Integration of the shRNA expression vector into the genome of clone piglets was confirmed by PCR and expression of the GFP transgene linked to the expression vector. Analysis showed that apoE protein levels in the liver and plasma of the clone pigs bearing the shRNA expression vector targeting the apoE mRNA was significantly reduced compared to control pigs cloned from non-transfected fibroblasts of the same cell line. These results demonstrate the feasibility of applying RNAi and SCNT technologies for introducing stable genetic modifications in somatic cells for eventual attenuation of gene expression in vivo in large animal species. PMID:23737990

  4. Unruptured intracranial aneurysms: their illusive natural history and why subgroup statistics cannot provide normative criteria for clinical decisions or selection criteria for a randomized trial.

    Science.gov (United States)

    Raymond, J; Roy, D; Weill, A; Guilbert, F; Nguyen, T; Molyneux, A J; Fox, A J; Johnston, S C; Cognard, C; Pierot, L; Meder, J-F; Rouleau, Isabelle

    2008-10-01

    There is currently no evidence that treatment of unruptured aneurysms is beneficial. Confronted with the uncertainty, many clinicians are attracted by an individual calculus of risks using numbers extracted from subgroup statistics of observational studies or natural history data. The so-called natural history of unruptured aneurysms refers to a purely man-made ratio of events divided by the number of untreated patients identified by imaging, a ratio heavily influenced by referral patterns and arbitrary clinical decisions. Available studies lacked prespecified hypotheses, exposing all analyses to sampling error and bias, and sample sizes were too small to provide reliable subgroup statistics. Far from being "natural kinds" of aneurysms, subgroups were post-hoc creations. Resulting data-driven statistics can only be exploratory, the error too uncontrollable to serve for clinical decisions. A randomized trial is in order, but selection according to fixed size criteria is ill-advised, given the imprecision of imaging, the influence of other factors such as location, previous history, multiplicity of lesions, risks of treatment, age and the danger of arbitrarily excluding from a long trial a large segment of the population with aneurysms for whom the research question is most pertinent.

  5. Production potential of 36 poplar clones grown at medium length rotation in Denmark

    DEFF Research Database (Denmark)

    Nielsen, Ulrik Brauner; Madsen, Palle; Hansen, Jon Kehlet

    2014-01-01

    group's potential for use in Northern Europe and comparable growth conditions. Based on two trials with randomized block designs, 36 clones from 4 species and 5 groups of species hybrids, measurements of height and diameter were used for estimating biomass production for rotation lengths of 5 and 13...

  6. Cloning systems for Rhodococcus and related bacteria

    Science.gov (United States)

    Finnerty, W.R.; Singer, M.E.

    1990-08-28

    A plasmid transformation system for Rhodococcus was developed using an Escherichia coli-Rhodococcus shuttle plasmid. Rhodococcus sp. H13-A contains three cryptic indigenous plasmids, designated pMVS100, pMVS200 and pMVS300, of 75, 19.5 and 13.4 kilobases (Kb), respectively. A 3.8 Kb restriction fragment of pMVS300 was cloned into pIJ30, a 6.3 Kb pBR322 derivative, containing the E. coli origin of replication (ori) and ampicillin resistance determinant (bla) as well as a Streptomyces gene for thiostrepton resistance, tsr. The resulting 10.1 Kb recombinant plasmid, designated pMVS301, was isolated from E. coli DH1 (pMVS301) and transformed into Rhodococcus sp. AS-50, a derivative of strain H13-A, by polyethylene glycol-assisted transformation of Rhodococcus protoplasts and selection for thiostrepton-resistant transformants. This strain was deposited with the ATCC on Feb. 1, 1988 and assigned ATCC 53719. The plasmid contains the Rhodococcus origin of replication. The plasmid and derivatives thereof can therefore be used to introduce nucleic acid sequences to and from Rhodococcus for subsequent expression and translation into protein. The isolated origin of replication can also be used in the construction of new vectors. 2 figs.

  7. Cloning systems for Rhodococcus and related bacteria

    Science.gov (United States)

    Finnerty, William R.; Singer, Mary E.

    1990-01-01

    A plasmid transformation system for Rhodococcus was developed using an Escherichia coli-Rhodococcus shuttle plasmid. Rhodococcus sp. H13-A contains three cryptic indigenous plasmids, designated pMVS100, pMVS200 and pMVS300, of 75, 19.5 and 13.4 kilobases (Kb), respectively. A 3.8 Kb restriction fragment of pMVS300 was cloned into pIJ30, a 6.3 Kb pBR322 derivative, containing the E. coli origin of replication (ori) and ampicillin resistance determinant (bla) as well as a Streptomyces gene for thiostrepton resistance, tsr. The resulting 10.1 Kb recombinant plasmid, designated pMVS301, was isolated from E. coli DH1 (pMVS301) and transformed into Rhodococcus sp. AS-50, a derivative of strain H13-A, by polyethylene glycol-assisted transformation of Rhodococcus protoplasts and selection for thiostrepton-resistant transformants. This strain was deposited with the ATCC on Feb. 1, 1988 and assigned ATCC 53719. The plasmid contains the Rhodococcus origin of replication. The plasmid and derivatives thereof can therefore be used to introduce nucleic acid sequences to and from Rhodococcus for subsequent expression and translation into protein. The isolated origin of replication can also be used in the construction of new vectors.

  8. Rapid Characterization of S. mansoni Expression Library Clones of Potential Interest

    Directory of Open Access Journals (Sweden)

    Herminia Yohko KANAMURA

    1997-11-01

    Full Text Available A S. mansoni adult worm cDNA expression library was screened with sera from baboons in a early phase after infection. The clones that were positive with the early infection sera were examined for reactivity with pre-infection sera and heterologous infection sera. In order to discriminate a positive antibody reaction from the reactivity due to residual anti-E. coli antibodies, an unrelated cDNA clone was plated with the positive clone. The unrelated clone provided the negative background and the contrast necessary to discern a positive antibody reaction. In this way, we were able to eliminate selected clones that were positive with the pre-infection sera or heterologous infection sera. This characterization of the expression library clones enabled us to quickly target only clones with the desired pattern of antibody reactivity for sequencing, subcloning, and expressingUma biblioteca de expressão de cDNA de verme adulto de S. mansoni foi selecionada utilizando-se soros de macacos babuínos em fase inicial da infecção. Os clones que reagiram positivamente com os soros de infecção recente foram examinados quanto à reatividade contra soros normais e soros de infecção heteróloga. Com a finalidade de se conseguir melhor discriminação entre reatividade positiva com o anticorpo específico e aquela devido aos anticorpos anti-E. coli residuais, um clone de cDNA não relacionado ao S. mansoni foi plaqueado em mistura com o clone positivo. O plano de fundo negativo proporcionado pelo clone não relacionado forneceu o contraste necessário para discriminar a reação positiva específica. Esta metodologia de caracterização dos clones de expressão permite alcançar rapidamente os clones que apresentam o perfil de reatividade desejada, para posterior sequenciamento, subclonagem e expressão

  9. Homologous recombination-mediated cloning and manipulation of genomic DNA regions using Gateway and recombineering systems.

    Science.gov (United States)

    Rozwadowski, Kevin; Yang, Wen; Kagale, Sateesh

    2008-11-17

    Employing genomic DNA clones to characterise gene attributes has several advantages over the use of cDNA clones, including the presence of native transcription and translation regulatory sequences as well as a representation of the complete repertoire of potential splice variants encoded by the gene. However, working with genomic DNA clones has traditionally been tedious due to their large size relative to cDNA clones and the presence, absence or position of particular restriction enzyme sites that may complicate conventional in vitro cloning procedures. To enable efficient cloning and manipulation of genomic DNA fragments for the purposes of gene expression and reporter-gene studies we have combined aspects of the Gateway system and a bacteriophage-based homologous recombination (i.e. recombineering) system. To apply the method for characterising plant genes we developed novel Gateway and plant transformation vectors that are of small size and incorporate selectable markers which enable efficient identification of recombinant clones. We demonstrate that the genomic coding region of a gene can be directly cloned into a Gateway Entry vector by recombineering enabling its subsequent transfer to Gateway Expression vectors. We also demonstrate how the coding and regulatory regions of a gene can be directly cloned into a plant transformation vector by recombineering. This construct was then rapidly converted into a novel Gateway Expression vector incorporating cognate 5' and 3' regulatory regions by using recombineering to replace the intervening coding region with the Gateway Destination cassette. Such expression vectors can be applied to characterise gene regulatory regions through development of reporter-gene fusions, using the Gateway Entry clones of GUS and GFP described here, or for ectopic expression of a coding region cloned into a Gateway Entry vector. We exemplify the utility of this approach with the Arabidopsis PAP85 gene and demonstrate that the expression

  10. Immortality of cancers: a consequence of inherent karyotypic variations and selections for autonomy.

    Science.gov (United States)

    Duesberg, Peter; McCormack, Amanda

    2013-03-01

    Immortality is a common characteristic of cancers, but its origin and purpose are still unclear. Here we advance a karyotypic theory of immortality based on the theory that carcinogenesis is a form of speciation. Accordingly, cancers are generated from normal cells by random karyotypic rearrangements and selection for cancer-specific reproductive autonomy. Since such rearrangements unbalance long-established mitosis genes, cancer karyotypes vary spontaneously but are stabilized perpetually by clonal selections for autonomy. To test this theory we have analyzed neoplastic clones, presumably immortalized by transfection with overexpressed telomerase or with SV40 tumor virus, for the predicted clonal yet flexible karyotypes. The following results were obtained: (1) All immortal tumorigenic lines from cells transfected with overexpressed telomerase had clonal and flexible karyotypes; (2) Searching for the origin of such karyotypes, we found spontaneously increasing, random aneuploidy in human fibroblasts early after transfection with overexpressed telomerase; (3) Late after transfection, new immortal tumorigenic clones with new clonal and flexible karyotypes were found; (4) Testing immortality of one clone during 848 unselected generations showed the chromosome number was stable, but the copy numbers of 36% of chromosomes drifted ± 1; (5) Independent immortal tumorigenic clones with individual, flexible karyotypes arose after individual latencies; (6) Immortal tumorigenic clones with new flexible karyotypes also arose late from cells of a telomerase-deficient mouse rendered aneuploid by SV40 virus. Because immortality and tumorigenicity: (1) correlated exactly with individual clonal but flexible karyotypes; (2) originated simultaneously with such karyotypes; and (3) arose in the absence of telomerase, we conclude that clonal and flexible karyotypes generate the immortality of cancers.

  11. Early prevention of antisocial personality: long-term follow-up of two randomized controlled trials comparing indicated and selective approaches.

    Science.gov (United States)

    Scott, Stephen; Briskman, Jackie; O'Connor, Thomas G

    2014-06-01

    Antisocial personality is a common adult problem that imposes a major public health burden, but for which there is no effective treatment. Affected individuals exhibit persistent antisocial behavior and pervasive antisocial character traits, such as irritability, manipulativeness, and lack of remorse. Prevention of antisocial personality in childhood has been advocated, but evidence for effective interventions is lacking. The authors conducted two follow-up studies of randomized trials of group parent training. One involved 120 clinic-referred 3- to 7-year-olds with severe antisocial behavior for whom treatment was indicated, 93 of whom were reassessed between ages 10 and 17. The other involved 109 high-risk 4- to 6-year-olds with elevated antisocial behavior who were selectively screened from the community, 90 of whom were reassessed between ages 9 and 13. The primary psychiatric outcome measures were the two elements of antisocial personality, namely, antisocial behavior (assessed by a diagnostic interview) and antisocial character traits (assessed by a questionnaire). Also assessed were reading achievement (an important domain of youth functioning at work) and parent-adolescent relationship quality. In the indicated sample, both elements of antisocial personality were improved in the early intervention group at long-term follow-up compared with the control group (antisocial behavior: odds ratio of oppositional defiant disorder=0.20, 95% CI=0.06, 0.69; antisocial character traits: B=-4.41, 95% CI=-1.12, -8.64). Additionally, reading ability improved (B=9.18, 95% CI=0.58, 18.0). Parental expressed emotion was warmer (B=0.86, 95% CI=0.20, 1.41) and supervision was closer (B=-0.43, 95% CI=-0.11, -0.75), but direct observation of parenting showed no differences. Teacher-rated and self-rated antisocial behavior were unchanged. In contrast, in the selective high-risk sample, early intervention was not associated with improved long-term outcomes. Early intervention with

  12. Selection of single blastocysts for fresh transfer via standard morphology assessment alone and with array CGH for good prognosis IVF patients: results from a randomized pilot study

    Directory of Open Access Journals (Sweden)

    Yang Zhihong

    2012-05-01

    Full Text Available Abstract Background Single embryo transfer (SET remains underutilized as a strategy to reduce multiple gestation risk in IVF, and its overall lower pregnancy rate underscores the need for improved techniques to select one embryo for fresh transfer. This study explored use of comprehensive chromosomal screening by array CGH (aCGH to provide this advantage and improve pregnancy rate from SET. Methods First-time IVF patients with a good prognosis (age Results For patients in Group A (n = 55, 425 blastocysts were biopsied and analyzed via aCGH (7.7 blastocysts/patient. Aneuploidy was detected in 191/425 (44.9% of blastocysts in this group. For patients in Group B (n = 48, 389 blastocysts were microscopically examined (8.1 blastocysts/patient. Clinical pregnancy rate was significantly higher in the morphology + aCGH group compared to the morphology-only group (70.9 and 45.8%, respectively; p = 0.017; ongoing pregnancy rate for Groups A and B were 69.1 vs. 41.7%, respectively (p = 0.009. There were no twin pregnancies. Conclusion Although aCGH followed by frozen embryo transfer has been used to screen at risk embryos (e.g., known parental chromosomal translocation or history of recurrent pregnancy loss, this is the first description of aCGH fully integrated with a clinical IVF program to select single blastocysts for fresh SET in good prognosis patients. The observed aneuploidy rate (44.9% among biopsied blastocysts highlights the inherent imprecision of SET when conventional morphology is used alone. Embryos randomized to the aCGH group implanted with greater efficiency, resulted in clinical pregnancy more often, and yielded a lower miscarriage rate than those selected without aCGH. Additional studies are needed to verify our pilot data and confirm a role for on-site, rapid aCGH for IVF patients contemplating fresh SET.

  13. Comparison of growth, biomass and nutrient distribution in five promising clones of Populus deltoides under an agrisilviculture system.

    Science.gov (United States)

    Swamy, S L; Mishra, Alka; Puri, S

    2006-01-01

    Variations in growth, above- and below-ground biomass and nutrient distribution were examined in five clones (G3, G48, 65/27, D121 and S7C1) of Populus deltoides grown under agrisilviculture system in sub-humid tropics of Central India. The monoclonal blocks were planted at 4x5 m in a randomized block design with three replications. Diameter at breast height (dbh) and tree height were consistently higher in clone 65/27 and lowest in clone S7C1. Mean annual increments (MAI) in dbh and height were 1.6 and 1.3 times higher in clone 65/27 compared to clone S7C1. Total biomass varied from 48.5 to 62.2 Mg ha(-1) in six-year-old clones. In rank order, the total biomass of clones was: 65/27>D121>G48>G3>S7C1. Stem wood accounted 60.4-68.9% to total biomass followed by coarse roots (12.2-18.9%), branches (12.3-15%), leaves (3.02-6.9%) and fine roots (1.5-2.7%). Root-shoot ratio ranged from 0.2 to 0.35. It was highest in clone G48 and lowest in clone S7C1. In six-year-old clones, total N ranged from 184.3 to 266.3 kg ha(-1), P from 16.8 to 31.1 kg ha(-1) and K from 81.9 to 128.7 kg ha(-1). Total N and P were highest in clone 65/27, while K in clone G48. Nutrients were lowest in clone S7C1. In general, maximum nutrients (N, P and K) were allocated to above-ground components (leaves>stem>branches) than below-ground components. Available N, P and K in the soil improved significantly after six years of planting. It was higher in 0-20 cm and decreased with soil depth. At 0-20 cm soil depth, N increased from 14.9% to 24.1%, P from 17.2% to 23.3% and K from 3.1% to 5.1% under different clones. The yield of both soybean and wheat reduced under poplar clones. Yield losses in soybean ranged from 10.1% to 33% and wheat from 15% to 30.3% under different clones. The management strategies for reducing tree-crop competition and nutrient export from the site under P. deltoides based agrisilviculture system for achieving sustainable production are discussed.

  14. Quality of Wood and Charcoal from Eucalyptus Clones for Ironmaster Use

    Directory of Open Access Journals (Sweden)

    Bárbara Luísa Corradi Pereira

    2012-01-01

    Full Text Available Considering the wide variety of species and clones of Eucalyptus cultivated in Brazil, it is necessary to search for new information on wood properties, so that the selection of genetically superior material may be successful. The present study aimed to determine the properties of wood and charcoal from different clones of Eucalyptus spp. Six clones at the age of 7.5 years were evaluated and the samples were from a clonal, located in the city of Lassance, Minas Gerais, Brazil. Basic density, chemical composition, and higher heating value were determined. Carbonizations in a laboratory kiln were done and the levels of volatile matter, ash, and fixed carbon, higher heating value, and bulk density of the charcoal produced were determined. Evaluated genetic materials showed differences in their properties. According to research results, several properties of wood should be considered together for the selection of clones for charcoal production. However, basic density and chemical composition of wood, especially high contents of lignin and low contents of extractives, are the properties that had more influence on charcoal yield and its quality. Concerning charcoal production for steelmaking, clone 6 stood out and, conversely, clone 4 showed inferior properties to those of others.

  15. Field performance and biomass production of 12 willow and poplar clones in short-rotation coppice in southern Quebec (Canada)

    Energy Technology Data Exchange (ETDEWEB)

    Labrecque, Michel; Teodorescu, Traian I. [Montreal Botanical Garden, Inst. de Recherche en Biologie Vegetale, Montreal, QC (Canada)

    2005-07-01

    Twelve clones of fast growing trees (willow and poplar) were planted in 1999 under short-rotation intensive culture (SRIC) on an abandoned farmland in southern Quebec. The plantation was established at a density of 18,000 trees per hectare from stem cuttings and no fertilizer and irrigation were applied. Tree performances were measured at regular intervals during four growing seasons. The aims of the experiment were to compare the growth, insect and disease resistance of these clones in order to select those that have good potential for use as commercial biomass energy crops in northern regions of North America. The follow up of the growing performance has shown statistically significant differences between the clones. Poplar clones registered the highest above ground biomass yield after 4 growing seasons (from 66.48 to 72.20 tDM ha{sup -1}). The best willow biomass productivity was obtained from clones SX64 (67.58 tDM ha{sup -1}) and clone SX61 (62.34 tDM ha{sup -1}). Only one willow clone S301 (Salix interior x S. eriocephala) was sensitive to leaf rust (Melampsora spp.) and clones SVQ (S. viminalis) and SV1 (S. dasyclados) were more prone to insect attacks. The results proved that some clones of S. miyabeana and S. sachalinensis were more productive and more resistant to insect and disease damage than S. viminalis which has been widely planted in SRIC in southern Quebec for many years. (Author)

  16. Potential complications when developing gene deletion clones in Xylella fastidiosa.

    Science.gov (United States)

    Johnson, Kameka L; Cursino, Luciana; Athinuwat, Dusit; Burr, Thomas J; Mowery, Patricia

    2015-04-16

    The Gram-negative xylem-limited bacterium, Xylella fastidiosa, is an important plant pathogen that infects a number of high value crops. The Temecula 1 strain infects grapevines and induces Pierce's disease, which causes symptoms such as scorching on leaves, cluster collapse, and eventual plant death. In order to understand the pathogenesis of X. fastidiosa, researchers routinely perform gene deletion studies and select mutants via antibiotic markers. Site-directed pilJ mutant of X. fastidiosa were generated and selected on antibiotic media. Mutant cultures were assessed by PCR to determine if they were composed of purely transformant cells or included mixtures of non-transformants cells. Then pure pilJ mutant and wildtype cells were mixed in PD2 medium and following incubation and exposure to kanamycin were assessed by PCR for presence of mutant and wildtype populations. We have discovered that when creating clones of targeted mutants of X. fastidiosa Temecula 1 with selection on antibiotic plates, X. fastidiosa lacking the gene deletion often persist in association with targeted mutant cells. We believe this phenomenon is due to spontaneous antibiotic resistance and/or X. fastidiosa characteristically forming aggregates that can be comprised of transformed and non-transformed cells. A combined population was confirmed by PCR, which showed that targeted mutant clones were mixed with non-transformed cells. After repeated transfer and storage the non-transformed cells became the dominant clone present. We have discovered that special precautions are warranted when developing a targeted gene mutation in X. fastidiosa because colonies that arise following transformation and selection are often comprised of transformed and non-transformed cells. Following transfer and storage the cells can consist primarily of the non-transformed strain. As a result, careful monitoring of targeted mutant strains must be performed to avoid mixed populations and confounding results.

  17. Combustion quality of poplar and willow clones grown as SRC at four sites in Brandenburg, Germany

    DEFF Research Database (Denmark)

    Liu, Na; Ugilt Larsen, Søren; Jørgensen, Uffe

    2017-01-01

    , the concentrations were no higher in willow than in the poplar clones. Shoot diameter significantly affected fuel quality with thin shoots generally having higher ash mass fraction and element concentrations than thicker shoots. In conclusion, fuel quality of SRC biomass may be improved by selecting appropriate......The fuel quality was assessed for nine poplar clones (AF2, Androscoggin, Max1, Max3, Max4, Monviso, Muhle-Larsen, NE42, Weser6) and one willow clone (Inger) grown as short rotation coppice (SRC) on four sites in the Brandenburg area in Germany. Fuel quality was analysed in 3-year old shoots...... in terms of dry matter (DM) mass fraction, total ash mass fraction and concentration of 14 ash-related elements (Al, Ca, Cd, Cl, Cu, Fe, K, Mg, Mn, Na, P, S, Si, Zn). Clone significantly affected DM and ash mass fraction and concentration of 11 of the 14 elements, site affected concentration of 7 elements...

  18. Human embryo cloning prohibited in Hong Kong.

    Science.gov (United States)

    Liu, Athena

    2005-12-01

    Since the birth of Dolly (the cloned sheep) in 1997, debates have arisen on the ethical and legal questions of cloning-for-biomedical-research (more commonly termed "therapeutic cloning") and of reproductive cloning using human gametes. Hong Kong enacted the Human Reproductive Technology Ordinance (Cap 561) in 2000. Section 15(1)(e) of this Ordinance prohibits the "replacing of the nucleus of a cell of an embryo with a nucleus taken from any other cell," i.e., nucleus substitution. Section 15(1)(f) prohibits the cloning of any embryo. The scope of the latter, therefore, is arguably the widest, prohibiting all cloning techniques such as cell nucleus replacement, embryo splitting, parthenogenesis, and cloning using stem cell lines. Although the Human Reproductive Technology Ordinance is not yet fully operative, this article examines how these prohibitions may adversely impact on basic research and the vision of the Hong Kong scientific community. It concludes that in light of recent scientific developments, it is time to review if the law offers a coherent set of policies in this area.

  19. Growth and nutrition of eucalyptus clones seedlings inoculated with mycorrhizal fungi

    Directory of Open Access Journals (Sweden)

    Francisco de Sousa Lima

    2014-06-01

    Full Text Available Eucalyptus is one of the most planted forest species, in Brazil, due to its rapid growth and high economic yield. Arbuscular mycorrhizal fungi improve the seedlings nutritional and phytosanitary status, besides increasing their resistance to biotic and abiotic stress. This study aimed to evaluate the effect of inoculation with arbuscular mycorrhizal fungi species on the growth and nutrition of different eucalyptus clones seedlings. The experiment was conducted under greenhouse conditions, in a randomized blocks design and a 5x5 factorial scheme (five fungal species and five eucalyptus clones, with five replications. In general, the mycorrhizal symbiosis significantly increased the growth and nutrition of eucalyptus seedlings, when compared to the non-inoculated seedlings. The most efficient interaction occured between the 2361 clone and the Entrophospora infrequens fungus, with increases of 107.3% and 120.6%, for the shoot and root dry biomass yield, and 107.7%, 94.1% and 103.3%, respectively for the accumulation of N, P and K in the seedlings shoots. All the fungal species studied showed a high absolute compatibility index with eucalyptus clones. The Glomus manihots and E. infrequens fungi presented a higher functional compatibility index with the clones tested. The 5204 clone showed 75% of compatibility with the fungi evaluated.

  20. Serial cloning of pigs by somatic cell nuclear transfer: restoration of phenotypic normality during serial cloning.

    Science.gov (United States)

    Cho, Seong-Keun; Kim, Jae-Hwan; Park, Jong-Yi; Choi, Yun-Jung; Bang, Jae-Il; Hwang, Kyu-Chan; Cho, Eun-Jeong; Sohn, Sea-Hwan; Uhm, Sang Jun; Koo, Deog-Bon; Lee, Kyung-Kwang; Kim, Teoan; Kim, Jin-Hoi

    2007-12-01

    Somatic cell nuclear transfer (scNT) is a useful way to create cloned animals. However, scNT clones exhibit high levels of phenotypic instability. This instability may be due to epigenetic reprogramming and/or genomic damage in the donor cells. To test this, we produced transgenic pig fibroblasts harboring the truncated human thrombopoietin (hTPO) gene and used them as donor cells in scNT to produce first-generation (G1) cloned piglets. In this study, 2,818 scNT embryos were transferred to 11 recipients and five G1 piglets were obtained. Among them, a clone had a dimorphic facial appearance with severe hypertelorism and a broad prominent nasal bridge. The other clones looked normal. Second-generation (G2) scNT piglets were then produced using ear cells from a G1 piglet that had an abnormal nose phenotype. We reasoned that, if the phenotypic abnormality of the G1 clone was not present in the G2 and third-generation (G3) clones, or was absent in the G2 clones but reappeared in the G3 clones, the phenotypic instability of the G1 clone could be attributed to faulty epigenetic reprogramming rather than to inherent/accidental genomic damage to the donor cells. Blastocyst rates, cell numbers in blastocyst, pregnancy rates, term placenta weight and ponderal index, and birth weight between G1 and G2 clones did not differ, but were significantly (P clones and could not find any significant differences in the methylation patterns between G1 and G2 clones. Indeed, we failed to detect the phenotypic abnormality in the G2 and G3 clones. Thus, the phenotypic abnormality of the G1 clone is likely to be due to epigenetic dysregulation. Additional observations then suggested that expression of the hTPO gene in the transgenic clones did not appear to be the cause of the phenotypic abnormality in the G1 clones and that the abnormality was acquired by only a few of the G1 clone's cells during its gestational development. 2007 Wiley-Liss, Inc

  1. ON-F ARM TESTING OF SELECTED CASSAVA CLONES

    African Journals Online (AJOL)

    la concentration on sucre, la resistance aux maladies, les rendements des raciness, et le contenu en matiere seche. Mots Clés: .... differences were also detected across sites for. TABLE 1. Soil properties across seven sites used in the evaluation of the cassava varieties. Sites Soil nutrient .... Advanced Training in Agriculture.

  2. Generic-reference and generic-generic bioequivalence of forty-two, randomly-selected, on-market generic products of fourteen immediate-release oral drugs.

    Science.gov (United States)

    Hammami, Muhammad M; De Padua, Sophia J S; Hussein, Rajaa; Al Gaai, Eman; Khodr, Nesrine A; Al-Swayeh, Reem; Alvi, Syed N; Binhashim, Nada

    2017-12-08

    The extents of generic-reference and generic-generic average bioequivalence and intra-subject variation of on-market drug products have not been prospectively studied on a large scale. We assessed bioequivalence of 42 generic products of 14 immediate-release oral drugs with the highest number of generic products on the Saudi market. We conducted 14 four-sequence, randomized, crossover studies on the reference and three randomly-selected generic products of amlodipine, amoxicillin, atenolol, cephalexin, ciprofloxacin, clarithromycin, diclofenac, ibuprofen, fluconazole, metformin, metronidazole, paracetamol, omeprazole, and ranitidine. Geometric mean ratios of maximum concentration (Cmax) and area-under-the-concentration-time-curve, to last measured concentration (AUCT), extrapolated to infinity (AUCI), or truncated to Cmax time of reference product (AUCReftmax) were calculated using non-compartmental method and their 90% confidence intervals (CI) were compared to the 80.00%-125.00% bioequivalence range. Percentages of individual ratios falling outside the ±25% range were also determined. Mean (SD) age and body-mass-index of 700 healthy volunteers (28-80/study) were 32.2 (6.2) years and 24.4 (3.2) kg/m2, respectively. In 42 generic-reference comparisons, 100% of AUCT and AUCI CIs showed bioequivalence, 9.5% of Cmax CIs barely failed to show bioequivalence, and 66.7% of AUCReftmax CIs failed to show bioequivalence/showed bioinequivalence. Adjusting for 6 comparisons, 2.4% of AUCT and AUCI CIs and 21.4% of Cmax CIs failed to show bioequivalence. In 42 generic-generic comparisons, 2.4% of AUCT, AUCI, and Cmax CIs failed to show bioequivalence, and 66.7% of AUCReftmax CIs failed to show bioequivalence/showed bioinequivalence. Adjusting for 6 comparisons, 2.4% of AUCT and AUCI CIs and 14.3% of Cmax CIs failed to show bioequivalence. Average geometric mean ratio deviation from 100% was ≤3.2 and ≤5.4 percentage points for AUCI and Cmax, respectively, in both generic

  3. Efficacy of aerobic exercise and a prudent diet for improving selected lipids and lipoproteins in adults: a meta-analysis of randomized controlled trials

    Directory of Open Access Journals (Sweden)

    Roberts Susan

    2011-06-01

    Full Text Available Abstract Background Studies addressing the effects of aerobic exercise and a prudent diet on lipid and lipoprotein concentrations in adults have reached conflicting conclusions. The purpose of this study was to determine the effects of aerobic exercise combined with a prudent diet on lipid and lipoprotein concentrations in adults. Methods Studies were located by searching nine electronic databases, cross-referencing, and expert review. Two independent reviewers selected studies that met the following criteria: (1 randomized controlled trials, (2 aerobic exercise combined with diet recommendations (saturated/trans fat intake less than 10% of total calories and cholesterol less than 300 mg/day and/or fiber intake ≥25 g/day in women and ≥35 grams per day in men, (3 intervention ≥4 weeks, (4 humans ≥18 years of age, (5 published studies, including dissertations and Master's theses, (6 studies published in any language, (7 studies published between January 1, 1955 and May 1, 2009, (8 assessment of one or more of the following lipid and lipoprotein concentrations: total cholesterol (TC, high-density lipoprotein cholesterol (HDL-C, ratio of TC to HDL-C, non-HDL-C, low-density lipoprotein cholesterol (LDL-C and triglycerides (TG. Two reviewers independently extracted all data. Random-effects models that account for heterogeneity and 95% confidence intervals were used to pool findings. Results Of the 1,401 citations reviewed, six studies representing 16 groups (8 intervention, 8 control and up to 559 men and women (282 intervention, 277 control met the criteria for analysis. Statistically significant intervention minus control reductions were found for TC (-15.5 mg/dl, 95% CI, -20.3 to -10.7, TC:HDL-C (-0.4 mg/dl, 95% CI, -0.7 to -0.2, LDL-C (-9.2 mg/dl, 95% CI, -12.7 to -5.8 and TG (-10.6 mg/dl, 95% CI, -17.2 to -4.0 but not HDL-C (-0.5 mg/dl, 95% CI, -4.0 to 3.1. Changes were equivalent to reductions of 7.5%, 6.6%, 7.2% and 18.2% respectively

  4. Simplified cryopreservation of porcine cloned blastocysts

    DEFF Research Database (Denmark)

    Du, Yutao; Zhang, Yunhai; Li, Juan

    2007-01-01

    )â€"handmade cloning (HMC)â€"to establish a simplified and efficient cryopreservation system for porcine cloned embryos. In Experiment 1, zonae pellucidae of oocytes were partially digested with pronase, followed by centrifugation to polarize lipid particles. Ninety percent (173/192) oocytes were successfully......). Our results prove that porcine embryos produced from delipated oocytes by PA or HMC can be cryopreserved effectively by ultrarapid vitrification. Further experiments are required to assess the in vivo developmental competence of the cloned-vitrified embryos  ...

  5. LONGITUDINAL RESIDUAL AND TANGENTIAL STRAIN (LRS and LRT IN SIX Eucalyptus spp. CLONES

    Directory of Open Access Journals (Sweden)

    Paulo Fernando Trugilho

    2006-09-01

    Full Text Available The species of Eucalyptus genus present high levels of growth stress. These stresses are mechanical efforts generated during the tree growth to help maintaining the balance of the cup, in response to environmental (light, wind and inclination of the land and silvicultural agents (pruning, thinning and planting density. The growth stresses are responsible for the cracks of tops, in logs and boards, and for the warp after the breaking down. This research evaluated the level of growth stress, measured by the longitudinal residual and tangential strain (DRL and DRT, around the circumference of the trunks of alive trees of six clones of Eucalyptus spp., at the age of 10.5 years, and verified the effect of the planting parcel. The clones belong to VMM-AGRO, and they are coming from a clonal test area implanted in the Bom Sucesso farm, located in Vazante-MG. For evaluating the experiment, the model adopted was the completely randomized one disposed in factorial outline with two factors (clone and portion in three repetitions. The results indicated that the average LRS was 0.093 mm and that the average LRT was 0.025 mm. It was verified that, for LRS, the clone effects and planting parcel were significant, while the interaction effect was not significant. For LRT the parcel and interaction effect were significant, while clone effect was not significant. Clones 44, 58 and 47 presented the smallest levels and better distributions of LRS, while, the clones 27, 44 and 58 presented the highest LRS levels. The clones 44 and 58 presented the best distribution and the smallest level of growth stress and may be considered potentially apt for producing sawn wood or solid wood.

  6. Melhoramento genético da cana-de-açúcar: avaliação de clones provenientes de hibridações efetuadas em 1965 Sugarcane breeding: performance of iac sugarcane clones originated from hybridation

    Directory of Open Access Journals (Sweden)

    Raphael Alvarez

    1987-01-01

    Full Text Available Objetivando estudar dezoito clones de cana-de-açúcar provenientes de hibridações efetuadas em Ubatuba, SP, em 1965, tendo como padrão as variedades comerciais NA56-79 e CB41-76, efetuou-se um experimento em latossolo roxo na Usina Santa Lydia, em Ribeirão Preto, SP. No ensaio, plantado em março de 1973, utilizou-se o delineamento em blocos casualizados com quatro repetições, sendo a análise estatística feita com a média das três colheitas (cana-planta, soca e ressoca. Avaliou-se a produção agrícola, teor de açúcar provável e produtividade de açúcar provável. O clone IAC65-55 apresentou produtividade de açúcar significativamente superior ao padrão CB41-76, enquanto os clones IAC65-220, IAC65-257, IAC65-255, IAC65-155 e IAC65-113 não diferiram significativamente dele. Nenhum desses clones diferiu da variedade NA56-79 em produtividade de açúcar. Em função dessas características, associadas à resistência ao "carvão", os clones IAC65-55, IAC65-257, IAC65-113, IAC65-155 e IAC65-255 poderão constituir alternativas para o cultivo na região de Ribeirão Preto.A group of 18 of the best sugarcane clones obtained from hybridation in 1965, at the Experimental Station of Ubatuba, Instituto Agronômico, were evaluated in one experiment carried out in Santa Lydia mill, Ribeirão Preto, State of São Paulo, Brazil. In 1973, it was started a field trial using as controls the commercial varieties NA56-79, and CB41-76. The experiment design was a randomized complete block with four replications. The cane yield (t/ha, sugar content (kg/t cane, and sugar yield (t/ha were expressed as the average of three harvests: cane plant (18 months, first ratoon (12 months after and second ratoon (12 months after. According to these characteristics the clones IAC65-55, IAC65-257, IAC65-113, IAC65-155 and IAC65-255 were selected, and constitute alternatives of new varieties for the sugarcane cropping in the region of Ribeirão Preto.

  7. A biobrick library for cloning custom eukaryotic plasmids.

    Science.gov (United States)

    Constante, Marco; Grünberg, Raik; Isalan, Mark

    2011-01-01

    Researchers often require customised variations of plasmids that are not commercially available. Here we demonstrate the applicability and versatility of standard synthetic biological parts (biobricks) to build custom plasmids. For this purpose we have built a collection of 52 parts that include multiple cloning sites (MCS) and common protein tags, protein reporters and selection markers, amongst others. Importantly, most of the parts are designed in a format to allow fusions that maintain the reading frame. We illustrate the collection by building several model contructs, including concatemers of protein binding-site motifs, and a variety of plasmids for eukaryotic stable cloning and chromosomal insertion. For example, in 3 biobrick iterations, we make a cerulean-reporter plasmid for cloning fluorescent protein fusions. Furthermore, we use the collection to implement a recombinase-mediated DNA insertion (RMDI), allowing chromosomal site-directed exchange of genes. By making one recipient stable cell line, many standardised cell lines can subsequently be generated, by fluorescent fusion-gene exchange. We propose that this biobrick collection may be distributed peer-to-peer as a stand-alone library, in addition to its distribution through the Registry of Standard Biological Parts (http://partsregistry.org/).

  8. A biobrick library for cloning custom eukaryotic plasmids.

    Directory of Open Access Journals (Sweden)

    Marco Constante

    Full Text Available Researchers often require customised variations of plasmids that are not commercially available. Here we demonstrate the applicability and versatility of standard synthetic biological parts (biobricks to build custom plasmids. For this purpose we have built a collection of 52 parts that include multiple cloning sites (MCS and common protein tags, protein reporters and selection markers, amongst others. Importantly, most of the parts are designed in a format to allow fusions that maintain the reading frame. We illustrate the collection by building several model contructs, including concatemers of protein binding-site motifs, and a variety of plasmids for eukaryotic stable cloning and chromosomal insertion. For example, in 3 biobrick iterations, we make a cerulean-reporter plasmid for cloning fluorescent protein fusions. Furthermore, we use the collection to implement a recombinase-mediated DNA insertion (RMDI, allowing chromosomal site-directed exchange of genes. By making one recipient stable cell line, many standardised cell lines can subsequently be generated, by fluorescent fusion-gene exchange. We propose that this biobrick collection may be distributed peer-to-peer as a stand-alone library, in addition to its distribution through the Registry of Standard Biological Parts (http://partsregistry.org/.

  9. Sequence based prediction of DNA-binding proteins based on hybrid feature selection using random forest and Gaussian naïve Bayes.

    Directory of Open Access Journals (Sweden)

    Wangchao Lou

    Full Text Available Developing an efficient method for determination of the DNA-binding proteins, due to their vital roles in gene regulation, is becoming highly desired since it would be invaluable to advance our understanding of protein functions. In this study, we proposed a new method for the prediction of the DNA-binding proteins, by performing the feature rank using random forest and the wrapper-based feature selection using forward best-first search strategy. The features comprise information from primary sequence, predicted secondary structure, predicted relative solvent accessibility, and position specific scoring matrix. The proposed method, called DBPPred, used Gaussian naïve Bayes as the underlying classifier since it outperformed five other classifiers, including decision tree, logistic regression, k-nearest neighbor, support vector machine with polynomial kernel, and support vector machine with radial basis function. As a result, the proposed DBPPred yields the highest average accuracy of 0.791 and average MCC of 0.583 according to the five-fold cross validation with ten runs on the training benchmark dataset PDB594. Subsequently, blind tests on the independent dataset PDB186 by the proposed model trained on the entire PDB594 dataset and by other five existing methods (including iDNA-Prot, DNA-Prot, DNAbinder, DNABIND and DBD-Threader were performed, resulting in that the proposed DBPPred yielded the highest accuracy of 0.769, MCC of 0.538, and AUC of 0.790. The independent tests performed by the proposed DBPPred on completely a large non-DNA binding protein dataset and two RNA binding protein datasets also showed improved or comparable quality when compared with the relevant prediction methods. Moreover, we observed that majority of the selected features by the proposed method are statistically significantly different between the mean feature values of the DNA-binding and the non DNA-binding proteins. All of the experimental results indicate that

  10. The CAP study, evaluation of integrated universal and selective prevention strategies for youth alcohol misuse: study protocol of a cluster randomized controlled trial

    Directory of Open Access Journals (Sweden)

    Newton Nicola C

    2012-08-01

    Full Text Available Abstract Background Alcohol misuse amongst young people is a serious concern. The need for effective prevention is clear, yet there appear to be few evidenced-based programs that prevent alcohol misuse and none that target both high and low-risk youth. The CAP study addresses this gap by evaluating the efficacy of an integrated approach to alcohol misuse prevention, which combines the effective universal internet-based Climate Schools program with the effective selective personality-targeted Preventure program. This article describes the development and protocol of the CAP study which aims to prevent alcohol misuse and related harms in Australian adolescents. Methods/Design A cluster randomized controlled trial (RCT is being conducted with Year 8 students aged 13 to 14-years-old from 27 secondary schools in New South Wales and Victoria, Australia. Blocked randomisation was used to assign schools to one of four groups; Climate Schools only, Preventure only, CAP (Climate Schools and Preventure, or Control (alcohol, drug and health education as usual. The primary outcomes of the trial will be the uptake and harmful use of alcohol and alcohol related harms. Secondary outcomes will include alcohol and cannabis related knowledge, cannabis related harms, intentions to use, and mental health symptomatology. All participants will complete assessments on five occasions; baseline; immediately post intervention, and at 12, 24 and 36 months post baseline. Discussion This study protocol presents the design and current implementation of a cluster RCT to evaluate the efficacy of the CAP study; an integrated universal and selective approach to prevent alcohol use and related harms among adolescents. Compared to students who receive the stand-alone universal Climate Schools program or alcohol and drug education as usual (Controls, we expect the students who receive the CAP intervention to have significantly less uptake of alcohol use, a reduction in average

  11. Impact of amoxicillin therapy on resistance selection in patients with community-acquired lower respiratory tract infections: a randomized, placebo-controlled study.

    Science.gov (United States)

    Malhotra-Kumar, Surbhi; Van Heirstraeten, Liesbet; Coenen, Samuel; Lammens, Christine; Adriaenssens, Niels; Kowalczyk, Anna; Godycki-Cwirko, Maciek; Bielicka, Zuzana; Hupkova, Helena; Lannering, Christina; Mölstad, Sigvard; Fernandez-Vandellos, Patricia; Torres, Antoni; Parizel, Maxim; Ieven, Margareta; Butler, Chris C; Verheij, Theo; Little, Paul; Goossens, Herman

    2016-11-01

    To determine the effect of amoxicillin treatment on resistance selection in patients with community-acquired lower respiratory tract infections in a randomized, placebo-controlled trial. Patients were prescribed amoxicillin 1 g, three times daily (n = 52) or placebo (n = 50) for 7 days. Oropharyngeal swabs obtained before, within 48 h post-treatment and at 28-35 days were assessed for proportions of amoxicillin-resistant (ARS; amoxicillin MIC ≥2 mg/L) and -non-susceptible (ANS; MIC ≥0.5 mg/L) streptococci. Alterations in amoxicillin MICs and in penicillin-binding-proteins were also investigated. ITT and PP analyses were conducted. ARS and ANS proportions increased 11- and 2.5-fold, respectively, within 48 h post-amoxicillin treatment compared with placebo [ARS mean increase (MI) 9.46, 95% CI 5.57-13.35; ANS MI 39.87, 95% CI 30.96-48.78; P  0.1588). ARS/ANS were grouped by pbp mutations. Group 1 strains exhibited significantly lower amoxicillin resistance (mean MIC 2.8 mg/L, 95% CI 2.6-3.1) than group 2 (mean MIC 9.3 mg/L, 95% CI 8.1-10.5; P amoxicillin is modest and short-lived, probably due to 'fitness costs' engendered by high-level resistance-conferring mutations. This evidence further supports European guidelines that recommend amoxicillin when an antibiotic is indicated for community-acquired lower respiratory tract infections. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy.

  12. Acne RA-1,2, a novel UV-selective face cream for patients with acne: Efficacy and tolerability results of a randomized, placebo-controlled clinical study.

    Science.gov (United States)

    Cestone, Enza; Michelotti, Angela; Zanoletti, Valentina; Zanardi, Andrea; Mantegazza, Raffaella; Dossena, Maurizia

    2017-06-01

    General skincare measures such as the use of moisturisers and products containing adequate photoprotection are important components of acne patients' management to complement the pharmacological regimen. Acne RA-1,2 is a novel dermato-cosmetic product which contains selective photofilters and active ingredients against the multifactorial pathophysiology of acne. To evaluate the tolerability of Acne RA-1,2 and its effect on the clinical signs of acne. This double-blind, placebo-controlled study randomized 40 adult patients with 10-25 comedones per half face to once-daily application of Acne RA-1,2 or placebo for 8 weeks. Evaluations after 4 and 8 weeks included the number of comedones, transepidermal water loss (TEWL), sebum production, and tolerability. In the Acne RA-1,2 group, there was a significant 35% decrease in the mean number of comedones from 26 at baseline to 17 at Week 8 (P<.001), a 7% significant reduction in TEWL (9.32 to 8.66 g/h/m(2) ; P<.001), and a 24% significant reduction in sebum production (154.8 to 117.6 μg/cm(2) ; P<.001). The reductions in TEWL and sebum production were significantly greater than those in the placebo group at Weeks 4 and 8 (P<0.05). There were no adverse events. Acne RA-1,2 was well tolerated and effective at reducing comedones and sebum production and improving epidermal barrier function. These results suggest that Acne RA-1,2 is useful against acne-prone facial skin, particularly as it targets sebum production, which topical pharmacological acne therapies do not address. © 2017 Wiley Periodicals, Inc.

  13. An assessment of the quality of care for children in eighteen randomly selected district and sub-district hospitals in Bangladesh

    Directory of Open Access Journals (Sweden)

    Hoque Dewan ME

    2012-12-01

    Full Text Available Abstract Background Quality hospital care is important in ensuring that the needs of severely ill children are met to avert child mortality. However, the quality of hospital care for children in developing countries has often been found poor. As the first step of a country road map for improving hospital care for children, we assessed the baseline situation with respect to the quality of care provided to children under-five years age in district and sub-district level hospitals in Bangladesh. Methods Using adapted World Health Organization (WHO hospital assessment tools and standards, an assessment of 18 randomly selected district (n=6 and sub-district (n=12 hospitals was undertaken. Teams of trained assessors used direct case observation, record review, interviews, and Management Information System (MIS data to assess the quality of clinical case management and monitoring; infrastructure, processes and hospital administration; essential hospital and laboratory supports, drugs and equipment. Results Findings demonstrate that the overall quality of care provided in these hospitals was poor. No hospital had a functioning triage system to prioritise those children most in need of immediate care. Laboratory supports and essential equipment were deficient. Only one hospital had all of the essential drugs for paediatric care. Less than a third of hospitals had a back-up power supply, and just under half had functioning arrangements for safe-drinking water. Clinical case management was found to be sub-optimal for prevalent illnesses, as was the quality of neonatal care. Conclusion Action is needed to improve the quality of paediatric care in hospital settings in Bangladesh, with a particular need to invest in improving newborn care.

  14. Human cloning and the myth of disenchantment

    National Research Council Canada - National Science Library

    Laurențiu, Staicu

    2012-01-01

    This study has a twofold objective: firstly, it aims to examine the main types of argument that have been formulated against human cloning, to identify their presuppositions and to evaluate their strength...

  15. Cloning and molecular characterization of glyceraldehyde-3 ...

    African Journals Online (AJOL)

    Cloning and molecular characterization of glyceraldehyde-3-phosphate dehydrogenase gene from thermotolerant mushroom, Lentinus polychrous. ... sequence of the L. polychrous GAPDH-encoded protein shared significant sequence identity with other GAPDH proteins from basidiomycetes. Phylogenetic analysis ...

  16. DNA microarrays : a molecular cloning manual

    National Research Council Canada - National Science Library

    Sambrook, Joseph; Bowtell, David

    2002-01-01

    .... This manual, designed to extend and to complement the information in the best-selling Molecular Cloning, is a synthesis of the expertise and experience of more than 30 contributors all innovators in a fast moving field...

  17. Cloning and characterization of new bioluminescent proteins

    Science.gov (United States)

    Szent-Gyorgyi, Christopher; Ballou, Byron T.; Dagnal, Erich; Bryan, Bruce

    1999-07-01

    Over the past two years Prolume has undertaken a comprehensive program to clone luciferases and associated 'green fluorescent proteins' (GFPs) from marine animals that use coelenterazine as the luciferin. To data we have cloned several bioluminescent proteins, including two novel copepod luciferases and two anthozoan GFPs. These four proteins have sequences that differ greatly form previously cloned analogous proteins; the sequence diversity apparently is due to independent evolutionary origins and unusual evolutionary constraints. Thus coelenterazine-based bioluminescent systems may also manifest a variety of useful properties. We discuss form this taxonomic perspective the initial biochemical and spectral characterization of our cloned proteins. Emphasis is placed on the anthozoan luciferase-GFP systems, whose efficient resonance energy transfer has elicited much current interest.

  18. Meat and Milk Compositions of Bovine Clones

    National Research Council Canada - National Science Library

    X. Cindy Tian; Chikara Kubota; Kunihito Sakashita; Yoshiaki Izaike; Ryoichi Okano; Norio Tabara; Carol Curchoe; Lavina Jacob; Yuqin Zhang; Sadie Smith; Charles Bormann; Jie Xu; Masumi Sato; Sheila Andrew; Xiangzhong Yang; R. Michael Roberts

    2005-01-01

    ...? Here, we provide data on >100 parameters that compare the composition of meat and milk from beef and dairy cattle derived from cloning to those of genetic- and breed-matched control animals from conventional reproduction...

  19. Endangered wolves cloned from adult somatic cells.

    Science.gov (United States)

    Kim, Min Kyu; Jang, Goo; Oh, Hyun Ju; Yuda, Fibrianto; Kim, Hye Jin; Hwang, Woo Suk; Hossein, Mohammad Shamim; Kim, Joung Joo; Shin, Nam Shik; Kang, Sung Keun; Lee, Byeong Chun

    2007-01-01

    Over the world, canine species, including the gray wolf, have been gradually endangered or extinct. Many efforts have been made to recover and conserve these canids. The aim of this study was to produce the endangered gray wolf with somatic cell nuclear transfer (SCNT) for conservation. Adult ear fibroblasts from a female gray wolf (Canis lupus) were isolated and cultured in vitro as donor cells. Because of limitations in obtaining gray wolf matured oocytes, in vivo matured canine oocytes obtained by flushing the oviducts from the isthmus to the infundibulum were used. After removing the cumulus cells, the oocyte was enucleated, microinjected, fused with a donor cell, and activated. The reconstructed cloned wolf embryos were transferred into the oviducts of the naturally synchronized surrogate mothers. Two pregnancies were detected by ultrasonography at 23 days of gestation in recipient dogs. In each surrogate dog, two fetal sacs were confirmed by early pregnancy diagnosis at 23 days, but only two cloned wolves were delivered. The first cloned wolf was delivered by cesarean section on October 18, 2005, 60 days after embryo transfer. The second cloned wolf was delivered on October 26, 2005, at 61 days postembryo transfer. Microsatellite analysis was performed with genomic DNA from the donor wolf, the two cloned wolves, and the two surrogate female recipients to confirm the genetic identity of the cloned wolves. Analysis of 19 microsatellite loci confirmed that the cloned wolves were genetically identical to the donor wolf. In conclusion, we demonstrated live birth of two cloned gray wolves by nuclear transfer of wolf somatic cells into enucleated canine oocyte, indicating that SCNT is a practical approach for conserving endangered canids.

  20. Reproductive cloning combined with genetic modification.

    Science.gov (United States)

    Strong, C

    2005-11-01

    Although there is widespread opposition to reproductive cloning, some have argued that its use by infertile couples to have genetically related children would be ethically justifiable. Others have suggested that lesbian or gay couples might wish to use cloning to have genetically related children. Most of the main objections to human reproductive cloning are based on the child's lack of unique nuclear DNA. In the future, it may be possible safely to create children using cloning combined with genetic modifications, so that they have unique nuclear DNA. The genetic modifications could be aimed at giving such children genetic characteristics of both members of the couple concerned. Thus, cloning combined with genetic modification could be appealing to infertile, lesbian, or gay couples who seek genetically related children who have genetic characteristics of both members. In such scenarios, the various objections to human reproductive cloning that are based on the lack of genetic uniqueness would no longer be applicable. The author argues that it would be ethically justifiable for such couples to create children in this manner, assuming these techniques could be used safely.

  1. Potato improvement for tropical conditions: II. Selection indices and efficiency of indirect selection

    Directory of Open Access Journals (Sweden)

    Eduardo de Souza Lambert

    2006-01-01

    Full Text Available This study evaluated the efficiency of selection indices that can contribute to potato clone selection underfavorable and stressful conditions as well as the possibility of indirect selection for heat tolerance. Among the selectionindices, the arithmetic and geometric means and index 4 were the most appropriate. The susceptibility index and percentageof yield reduction indicate only specifically adapted clones. Indirect selection for heat tolerance is not suitable in view of thelow correlation coefficient among clone means in the environments. Selection based on the overall environment mean is morefit to select broadly adapted genotypes. In general, clones that performed best under stress conditions and presented heattolerance were specifically adapted, in spite of low performance means under favorable conditions. Well-adapted genotypes toboth stress and favorable conditions can however be selected.

  2. Birth of viable puppies derived from breeding cloned female dogs with a cloned male.

    Science.gov (United States)

    Park, J E; Hong, S G; Kang, J T; Oh, H J; Kim, M K; Kim, M J; Kim, H J; Kim, D Y; Jang, G; Lee, B C

    2009-09-15

    Since the establishment of production of viable cloned dogs by somatic cell nucleus transfer, great concern has been given to the reproductive abilities of these animals (Canis familiaris). Therefore, we investigated reproductive activity of cloned dogs by (1) performing sperm analysis using computer-assisted sperm analysis and early embryonic development, (2) assessing reproductive cycling by measuring serum progesterone (P4) levels and performing vaginal cytology, and (3) breeding cloned dogs using artificial insemination. Results showed that most parameters of sperm motility in a cloned male dog were within the reference range, and in vivo-matured oocytes from a noncloned female were successfully fertilized by spermatozoa from a cloned male dog and develop normally to the 8-cell stage. Three cloned female dogs displayed normal patterns of P4 levels and morphologic changes of the vaginal epithelium. Two cloned female dogs became pregnant using semen from a cloned male dog and successfully delivered 10 puppies by natural labor. In conclusion, these data demonstrated that both cloned male and female dogs are fertile, and their puppies are currently alive and healthy with normal growth patterns.

  3. Effectiveness of a selective intervention program targeting personality risk factors for alcohol misuse among young adolescents: results of a cluster randomized controlled trial

    NARCIS (Netherlands)

    Lammers, J.; Goossens, F.; Conrod, P.; Engels, R.; Wiers, R.W.; Kleinjan, M.

    2015-01-01

    Aim: The effectiveness of Preventure was tested on drinking behaviour of young adolescents in secondary education in the Netherlands. Design: A cluster randomized controlled trial was carried out, with participants assigned randomly to a two-session coping skills intervention or a control

  4. In vivo cloning of up to 16 kb plasmids in E. coli is as simple as PCR.

    Directory of Open Access Journals (Sweden)

    Faqing Huang

    Full Text Available The precise assembly of defined DNA sequences into plasmids is an essential task in bioscience research. While a number of molecular cloning techniques have been developed, many methods require specialized expensive reagents or laborious experimental procedure. Not surprisingly, conventional cloning techniques based on restriction digestion and ligation are still commonly used in routine DNA cloning. Here, we describe a simple, fast, and economical cloning method based on RecA- and RecET-independent in vivo recombination of DNA fragments with overlapping ends using E. coli. All DNA fragments were prepared by a 2-consecutive PCR procedure with Q5 DNA polymerase and used directly for transformation resulting in 95% cloning accuracy and zero background from parental template plasmids. Quantitative relationships were established between cloning efficiency and three factors-the length of overlapping nucleotides, the number of DNA fragments, and the size of target plasmids-which can provide general guidance for selecting in vivo cloning parameters. The method may be used to accurately assemble up to 5 DNA fragments with 25 nt overlapping ends into relatively small plasmids, and 3 DNA fragments into plasmids up to 16 kb in size. The whole cloning procedure may be completed within 2 days by a researcher with little training in cloning. The combination of high accuracy and zero background eliminates the need for screening a large number of colonies. The method requires no enzymes other than Q5 DNA polymerase, has no sequence restriction, is highly reliable, and represents one of the simplest, fastest, and cheapest cloning techniques available. Our method is particularly suitable for common cloning tasks in the lab where the primary goal is to quickly generate a plasmid with a pre-defined sequence at low costs.

  5. In vivo cloning of up to 16 kb plasmids in E. coli is as simple as PCR.

    Science.gov (United States)

    Huang, Faqing; Spangler, Joseph Rankin; Huang, Allen Yang

    2017-01-01

    The precise assembly of defined DNA sequences into plasmids is an essential task in bioscience research. While a number of molecular cloning techniques have been developed, many methods require specialized expensive reagents or laborious experimental procedure. Not surprisingly, conventional cloning techniques based on restriction digestion and ligation are still commonly used in routine DNA cloning. Here, we describe a simple, fast, and economical cloning method based on RecA- and RecET-independent in vivo recombination of DNA fragments with overlapping ends using E. coli. All DNA fragments were prepared by a 2-consecutive PCR procedure with Q5 DNA polymerase and used directly for transformation resulting in 95% cloning accuracy and zero background from parental template plasmids. Quantitative relationships were established between cloning efficiency and three factors-the length of overlapping nucleotides, the number of DNA fragments, and the size of target plasmids-which can provide general guidance for selecting in vivo cloning parameters. The method may be used to accurately assemble up to 5 DNA fragments with 25 nt overlapping ends into relatively small plasmids, and 3 DNA fragments into plasmids up to 16 kb in size. The whole cloning procedure may be completed within 2 days by a researcher with little training in cloning. The combination of high accuracy and zero background eliminates the need for screening a large number of colonies. The method requires no enzymes other than Q5 DNA polymerase, has no sequence restriction, is highly reliable, and represents one of the simplest, fastest, and cheapest cloning techniques available. Our method is particularly suitable for common cloning tasks in the lab where the primary goal is to quickly generate a plasmid with a pre-defined sequence at low costs.

  6. Public perceptions of farm animal cloning in Europe

    DEFF Research Database (Denmark)

    Lassen, Jesper

    This report presents a picture of European opinion on farm animal cloning. In the report, both agricultural and biomedical applications of farm animal cloning are considered. With the arrival of Dolly, animal cloning became an integral part of the biotech debate, but this debate did not isolate...... animal cloning as a single issue....

  7. Cloning: Past, Present, and the Exciting Future. Breakthroughs in Bioscience.

    Science.gov (United States)

    Di Berardino, Marie A.

    This document explores the history of cloning by focusing on Dolly the Sheep, one of the first large animal clonings. The disadvantages and advantages of transgenic clones are discussed as well as the future implications of cloning from the perspective of human health. (Contains 10 resources.) (YDS)

  8. Development of an R4 dual-site (R4DS) gateway cloning system enabling the efficient simultaneous cloning of two desired sets of promoters and open reading frames in a binary vector for plant research.

    Science.gov (United States)

    Aboulela, Mostafa; Tanaka, Yuji; Nishimura, Kohji; Mano, Shoji; Nishimura, Mikio; Ishiguro, Sumie; Kimura, Tetsuya; Nakagawa, Tsuyoshi

    2017-01-01

    Vast numbers of proteins work cooperatively to exert their functions in various cells. In order to understand the functions and molecular mechanisms of these proteins in plants, analyses of transgenic plants that concomitantly express two protein-coding genes are often required. We developed a novel Gateway cloning technology-compatible binary vector system, the R4 dual-site (R4DS) Gateway cloning system, which enables the easy and efficient cloning of two desired sets of promoters and open reading frames (ORFs) into a binary vector using promoter and ORF entry clones. In this system, C-terminal fusions with 17 kinds of tags including visible reporters and epitope tags are available for each ORF, and selection by four kinds of resistance markers is possible. We verified that the R4DS Gateway cloning system functioned well in Arabidopsis thaliana by observing the expression and localization patterns of fluorescent proteins fused with organelle-targeting signals and driven by stomatal-lineage specific promoters. We also confirmed that the two cloning sites in the R4DS Gateway cloning system were equivalent and independently regulated. The results obtained indicate that the R4DS Gateway cloning system facilitates detailed comparisons of the expression patterns of two promoters as well as co-localization and interaction analyses of two proteins in specific cells in plants.

  9. Stable MSAP markers for the distinction of Vitis vinifera cv Pinot noir clones.

    Science.gov (United States)

    Ocaña, Juan; Walter, Bernard; Schellenbaum, Paul

    2013-11-01

    Grapevine is one of the most economically important fruit crops. Molecular markers have been used to study grapevine diversity. For instance, simple sequence repeats are a powerful tool for identification of grapevine cultivars, while amplified fragment length polymorphisms have shown their usefulness in intra-varietal diversity studies. Other techniques such as sequence-specific amplified polymorphism are based on the presence of mobile elements in the genome, but their detection lies upon their activity. Relevant attention has been drawn toward epigenetic sources of variation. In this study, a set of Vitis vinifera cv Pinot noir clones were analyzed using the methylation-sensitive amplified polymorphism technique with isoschizomers MspI and HpaII. Nine out of fourteen selective primer combinations were informative and generated two types of polymorphic fragments which were categorized as "stable" and "unstable." In total, 23 stable fragments were detected and they discriminated 92.5 % of the studied clones. Detected stable polymorphisms were either common to several clones, restricted to a few clones or unique to a single clone. The identification of these stable epigenetic markers will be useful in clonal diversity studies. We highlight the relevance of stable epigenetic variation in V. vinifera clones and analyze at which level these markers could be applicable for the development of forthright techniques for clonal distinction.

  10. Construction of adenovirus vectors encoding the lumican gene by gateway recombinant cloning technology.

    Science.gov (United States)

    Wang, Gui-Fang; Qi, Bing; Tu, Lei-Lei; Liu, Lian; Yu, Guo-Cheng; Zhong, Jing-Xiang

    2016-01-01

    To construct adenovirus vectors of lumican gene by gateway recombinant cloning technology to further understand the role of lumican gene in myopia. Gateway recombinant cloning technology was used to construct adenovirus vectors. The wild-type (wt) and mutant (mut) forms of the lumican gene were synthesized and amplified by polymerase chain reaction (PCR). The lumican cDNA fragments were purified and ligated into the adenovirus shuttle vector pDown-multiple cloning site (MCS)-/internal ribozyme entry site (IRES)/enhanced green fluorescent protein (EGFP). Then the desired DNA fragments were integrated into the destination vector pAV.Des1d yielding the final expression constructs pAV.Ex1d-cytomegalovirus (CMV)>wt-lumican/IRES/EGFP and pAV.Ex1d-CMV>mut-lumican/IRES /EGFP, respectively. The adenovirus plasmids pAV.Ex1d-CMV>wt-lumican/IRES/EGFP and pAV.Ex1d-CMV>mut-lumican/IRES/EGFP were successfully constructed by gateway recombinant cloning technology. Positive clones identified by PCR and sequencing were selected and packaged into recombinant adenovirus in HEK293 cells. We construct adenovirus vectors containing the lumican gene by gateway recombinant cloning technology, which provides a basis for investigating the role of lumican gene in the pathogenesis of high myopia.

  11. Variability of anatomical-physiological traits in black locust clones - Robinia pseudoacacia L

    Directory of Open Access Journals (Sweden)

    Orlović Saša S.

    2004-01-01

    Full Text Available Variability within R. pseudoacacia species represents an important factor in selection of fast-growing genotypes. Therefore, it is important to identify superior individuals according to their anatomical and physiological traits. This paper presents the results of a study of genotype variability of the main leaf anatomical (frequency, length and width of stomata, leaflet thickness among veins, leaflet thickness on the main vein, mesophyll thickness, length and width of vascular bundle of main vein and physiological (leaf area, photosynthetic pigments content and content of N P, K, Ca, Na parameters among five clones of Robinia pseudoacacia L. Significant interclonal variations were observed in the investigated parameters. Clone R-56 had the highest N, P, and K concentrations, the largest mesophyll volume and the highest pigment concentration. We concluded that the clone R-56, although without a remarkable leaf area, possesses the ability for high photosynthetic production. The results are going to be used in further work on selection.

  12. Genetic heterogeneity of induced pluripotent stem cells: results from 24 clones derived from a single C57BL/6 mouse.

    Directory of Open Access Journals (Sweden)

    Cheng Li

    Full Text Available Induced pluripotent stem cells (iPSCs have tremendous potential as a tool for disease modeling, drug testing, and other applications. Since the generation of iPSCs "captures" the genetic history of the individual cell that was reprogrammed, iPSC clones (even those derived from the same individual would be expected to demonstrate genetic heterogeneity. To assess the degree of genetic heterogeneity, and to determine whether some cells are more genetically "fit" for reprogramming, we performed exome sequencing on 24 mouse iPSC clones derived from skin fibroblasts obtained from two different sites of the same 8-week-old C57BL/6J male mouse. While no differences in the coding regions were detected in the two parental fibroblast pools, each clone had a unique genetic signature with a wide range of heterogeneity observed among the individual clones: a total of 383 iPSC variants were validated for the 24 clones (mean 16.0/clone, range 0-45. Since these variants were all present in the vast majority of the cells in each clone (variant allele frequencies of 40-60% for heterozygous variants, they most likely preexisted in the individual cells that were reprogrammed, rather than being acquired during reprogramming or cell passaging. We then tested whether this genetic heterogeneity had functional consequences for hematopoietic development by generating hematopoietic progenitors in vitro and enumerating colony forming units (CFUs. While there was a range of hematopoietic potentials among the 24 clones, only one clone failed to differentiate into hematopoietic cells; however, it was able to form a teratoma, proving its pluripotent nature. Further, no specific association was found between the mutational spectrum and the hematopoietic potential of each iPSC clone. These data clearly highlight the genetic heterogeneity present within individual fibroblasts that is captured by iPSC generation, and suggest that most of the changes are random, and functionally

  13. Genetic heterogeneity of induced pluripotent stem cells: results from 24 clones derived from a single C57BL/6 mouse.

    Science.gov (United States)

    Li, Cheng; Klco, Jeffery M; Helton, Nichole M; George, Daniel R; Mudd, Jacqueline L; Miller, Christopher A; Lu, Charles; Fulton, Robert; O'Laughlin, Michelle; Fronick, Catrina; Wilson, Richard K; Ley, Timothy J

    2015-01-01

    Induced pluripotent stem cells (iPSCs) have tremendous potential as a tool for disease modeling, drug testing, and other applications. Since the generation of iPSCs "captures" the genetic history of the individual cell that was reprogrammed, iPSC clones (even those derived from the same individual) would be expected to demonstrate genetic heterogeneity. To assess the degree of genetic heterogeneity, and to determine whether some cells are more genetically "fit" for reprogramming, we performed exome sequencing on 24 mouse iPSC clones derived from skin fibroblasts obtained from two different sites of the same 8-week-old C57BL/6J male mouse. While no differences in the coding regions were detected in the two parental fibroblast pools, each clone had a unique genetic signature with a wide range of heterogeneity observed among the individual clones: a total of 383 iPSC variants were validated for the 24 clones (mean 16.0/clone, range 0-45). Since these variants were all present in the vast majority of the cells in each clone (variant allele frequencies of 40-60% for heterozygous variants), they most likely preexisted in the individual cells that were reprogrammed, rather than being acquired during reprogramming or cell passaging. We then tested whether this genetic heterogeneity had functional consequences for hematopoietic development by generating hematopoietic progenitors in vitro and enumerating colony forming units (CFUs). While there was a range of hematopoietic potentials among the 24 clones, only one clone failed to differentiate into hematopoietic cells; however, it was able to form a teratoma, proving its pluripotent nature. Further, no specific association was found between the mutational spectrum and the hematopoietic potential of each iPSC clone. These data clearly highlight the genetic heterogeneity present within individual fibroblasts that is captured by iPSC generation, and suggest that most of the changes are random, and functionally benign.

  14. Evaluation of phenotypic stability of cassava clones by AMMI analysis in northwestern Paraná state

    Directory of Open Access Journals (Sweden)

    Marcus Vinícius Kvitschal

    2006-01-01

    Full Text Available High yield stability and adaptability of storage root are highly desirable attributes of cassava clones. Theobjective of this study was therefore to evaluate the effect of the genotype x environment interaction (G x E and the stability ofcassava clones developed at IAC. A subset of eight cassava genotypes was chosen in trials of storage root yield, arranged ina randomized complete block design with four replications, in two counties (Araruna and Maringá, in the northwesternregion of Paraná State, over five growing seasons (1997-2001. The G x E interaction was evaluated by joint varianceanalysis and stability and adaptability by AMMI analysis. The G x E interaction was significant (P<0.05 for storage rootyield. Results indicated AMMI analysis as an efficient tool for the evaluation of phenotypic adaptability and stability of cassavaclones and IAC 190 as the most promising clone.

  15. Discovery of Functional Toxin/Antitoxin Systems in Bacteria by Shotgun Cloning

    Energy Technology Data Exchange (ETDEWEB)

    Sberro, Hila; Leavitt, Azita; Kiro, Ruth; Koh, Eugene; Peleg, Yoav; Qimron, Udi; Sorek, Rotem

    2013-04-01

    Toxin-antitoxin (TA) modules, composed of a toxic protein and a counteracting antitoxin, play important roles in bacterial physiology. We examined the experimental insertion of 1.5 million genes from 388 microbial genomes into an Escherichia coli host using over 8.5 million random clones. This revealed hundreds of genes (toxins) that could only be cloned when the neighboring gene (antitoxin) was present on the same clone. Clustering of these genes revealed TA families widespread in bacterial genomes, some of which deviate from the classical characteristics previously described for such modules. Introduction of these genes into E. coli validated that the toxin toxicity is mitigated by the antitoxin. Infection experiments with T7 phage showed that two of the new modules can provide resistance against phage. Moreover, our experiments revealed an 'anti-defense' protein in phage T7 that neutralizes phage resistance. Our results expose active fronts in the arms race between bacteria and phage.

  16. Survival and growth of eucalypts clones seedlings in response to organic fertilizer application

    Directory of Open Access Journals (Sweden)

    Sula Janaína de Oliveira Fernandes

    2011-12-01

    Full Text Available This work aimed to evaluate the effect of Fert-Bokashi® on survival and seedlings growth of two Eucalyptus urophylla clones propagated by minicutting technique. The experiment was conducted over a period of 28 days using a randomized block design and three replicates in an 6 x 2 factorial arrangement, with six Fert-Bokashi® concentrations (0.0%, 0.1%, 0.3%, 0.5%, 0.7% and 0.9% and two clones. Seedlings survival, height growth and shoot, root and total dry matter were evaluated. Experimental results demonstrated no significant effect of Fert- Bokashi® on survival and seedlings growth of two Eucalyptus urophylla clones.

  17. [Identification of APEC genes expressed in vivo by selective capture of transcribed sequences].

    Science.gov (United States)

    Chen, Xiang; Gao, Song; Wang, Xiao-quan; Jiao, Xin-an; Liu, Xiu-fan

    2007-06-01

    Direct screening of bacterial genes expressed during infection in the host is limited, because isolation of bacterial transcripts from host tissues necessitates separation from the abundance of host RNA. Selective capture of transcribed sequences (SCOTS) allows the selective capture of bacterial cDNA derived from infected tissues using hybridization to biotinylated bacterial genomic DNA. Avian pathogenic E. coli strain E037 (serogroup O78) was used in a chicken infection model to identify bacterial genes that are expressed in infected tissues. Three-week-old white leghorn specific-pathogen-free chickens were inoculated into the right thoracic air sac with a 0.1 mL suspension containing 10(7) CFU of APEC strain E037. Total RNA was isolated from infected tissues (pericardium and air sacs) 6 or 24h postinfection and converted to cDNAs. By using the cDNA selection method of selective capture of transcribed sequences and enrichment for the isolation of pathogen-specific (non-pathogenic E. coli K-12 strain ) transcripts, pathogen-specific cDNAs were identified. Randomly chosen cDNA clones derived from transcripts in the air sacs or pericardium were selected and sequenced. The clones, termed aec, contained numerous APEC-specific sequences. Among the distinct 31 aec clones, pathogen-specific clones contained sequences homologous to known and novel putative bacterial virulence gene products involved in adherence, iron transport, lipopolysaccharide (LPS) synthesis, plasmid replication and conjugation, putative phage encoded products, and gene products of unknown function. Overall, the current study provided a means to identify novel pathogen-specific genes expressed in vivo and insight regarding the global gene expression of a pathogenic E. coli strain in a natural animal host during the infectious process.

  18. A Multi-Center, Randomized, Controlled, Pivotal Study to Assess the Safety and Efficacy of a Selective Cytopheretic Device in Patients with Acute Kidney Injury.

    Directory of Open Access Journals (Sweden)

    James A Tumlin

    Full Text Available Acute kidney injury (AKI is a highly morbid condition in critically ill patients that is associated with high mortality. Previous clinical studies have demonstrated the safety and efficacy of the Selective Cytopheretic Device (SCD in the treatment of AKI requiring continuous renal replacement therapy in the intensive care unit (ICU.A randomized, controlled trial of 134 ICU patients with AKI, 69 received continuous renal replacement therapy (CRRT alone and 65 received SCD therapy.No significant difference in 60-day mortality was observed between the treated (27/69; 39% and control patients (21/59; 36%, with six patients lost to follow up in the intention to treat (ITT analysis. Of the 19 SCD subjects (CRRT+SCD and 31 control subjects (CRRT alone who maintained a post-filter ionized calcium (iCa level in the protocol's recommended range (≤ 0.4 mmol/L for greater or equal to 90% of the therapy time, 60-day mortality was 16% (3/19 in the SCD group compared to 41% (11/27 in the CRRT alone group (p = 0.11. Dialysis dependency showed a borderline statistically significant difference between the SCD treated versus control CRRT alone patients maintained for ≥ 90% of the treatment in the protocol's recommended (r iCa target range of ≤ 0.4 mmol/L with values of, 0% (0/16 and 25% (4/16, respectively (P = 0.10. When the riCa treated and control subgroups were compared for a composite index of 60 day mortality and dialysis dependency, the percentage of SCD treated subjects was 16% versus 58% in the control subjects (p<0.01. The incidence of serious adverse events did not differ between the treated (45/69; 65% and control groups (40/65; 63%; p = 0·86.SCD therapy may improve mortality and reduce dialysis dependency in a tightly controlled regional hypocalcaemic environment in the perfusion circuit.ClinicalTrials.gov NCT01400893 http://clinicaltrials.gov/ct2/show/NCT01400893.

  19. A prospective randomized multicenter trial of amnioreduction versus selective fetoscopic laser photocoagulation for the treatment of severe twin–twin transfusion syndrome

    Science.gov (United States)

    Crombleholme, Timothy M.; Shera, David; Lee, Hanmin; Johnson, Mark; D’Alton, Mary; Porter, Flint; Chyu, Jacquelyn; Silver, Richard; Abuhamad, Alfred; Saade, George; Shields, Laurence; Kauffman, David; Stone, Joanne; Albanese, Craig T.; Bahado-Singh, Ray; Ball, Robert H.; Bilaniuk, Larissa; Coleman, Beverly; Farmer, Diana; Feldstein, Vickie; Harrison, Michael R.; Hedrick, Holly; Livingston, Jeffrey; Lorenz, Robert P.; Miller, David A.; Norton, Mary E.; Polzin, William J.; Robinson, Julian N.; Rychik, Jack; Sandberg, Per L.; Seri, Istvan; Simon, Erin; Simpson, Lynn L.; Yedigarova, Larisa; Wilson, R. Douglas; Young, Bruce

    2009-01-01

    Objective To examine the effect of selective fetoscopic laser photocoagulation (SFLP) versus serial amnioreduction (AR) on perinatal mortality in severe twin-twin transfusion syndrome (TTTS). Study Design 5-year multicenter prospective randomized controlled trial. The primary outcome variable was 30-day postnatal survival of donors and recipients. Results There is no statistically significant difference in 30-day postnatal survival between SFLP or AR treatment for donors at 55% (11/20) vs 55% (11/20) (p=1, OR=1, 95%CI=0.242 to 4.14) or recipients at 30% (6/20) vs 45% (9/20) (p=0.51, OR=1.88, 95%CI=0.44 to 8.64). There is no difference in 30-day survival of one or both twins on a per pregnancy basis between AR at 75% (15/20) and SFLP at 65% (13/20) (p=0.73, OR=1.62, 95%CI=0.34 to 8.09). Overall survival (newborns divided by the number of fetuses treated) is not statistically significant for AR at 60% (24/40) vs SFLP 45% (18/40) (p=0.18, OR=2.01, 95%CI=0.76 to 5.44). There is a statistically significant increase in fetal recipient mortality in the SFLP arm at 70% (14/20) versus the AR arm at 35% (7/20) (p=0.25, OR=5.31, 95%CI=1.19 to 27.6). This is offset by increased recipient neonatal mortality of 30% (6/20) in the AR arm. Echocardiographic abnormality in recipient twin Cardiovascular Profile Score is the most significant predictor of recipient mortality (p=0.055, OR=3.025/point) by logistic regression analysis. Conclusions The outcome of the trial does not conclusively determine whether AR or SFLP is a superior treatment modality. TTTS cardiomyopathy appears to be an important factor in recipient survival in TTTS. PMID:17904975

  20. A randomized control trial to evaluate the effect of adjuvant selective laser trabeculoplasty versus medication alone in primary open-angle glaucoma: preliminary results

    Directory of Open Access Journals (Sweden)

    Lee JWY

    2014-09-01

    Full Text Available Jacky WY Lee,1,2 Catherine WS Chan,2 Mandy OM Wong,3 Jonathan CH Chan,3 Qing Li,2 Jimmy SM Lai2 1The Department of Ophthalmology, Caritas Medical Centre, 2The Department of Ophthalmology, The University of Hong Kong, 3The Department of Ophthalmology, Queen Mary Hospital, Hong Kong Background: The objective of this study was to investigate the effects of adjuvant selective laser trabeculoplasty (SLT versus medication alone on intraocular pressure (IOP control, medication use, and quality of life in patients with primary open-angle glaucoma.Methods: This prospective, randomized control study recruited 41 consecutive primary open-angle glaucoma subjects with medically-controlled IOP ≤21 mmHg. The SLT group (n=22 received a single 360-degree SLT treatment. The medication-only group (n=19 continued with their usual treatment regimen. In both groups, medication was titrated to maintain a target IOP defined as a 25% reduction from baseline IOP without medication, or <18 mmHg, whichever was lower. Outcomes, which were measured at baseline and at 6 months, included the Glaucoma Quality of Life-15 (GQL-15 and Comparison of Ophthalmic Medications for Tolerability (COMTOL survey scores, IOP, and the number of antiglaucoma medicines. Results: The baseline IOP was 15.8±2.7 mmHg and 14.5±2.5 mmHg in the SLT and medication-only groups, respectively (P=0.04. Both groups had a comparable number of baseline medication (P=0.2, GQL-15 (P=0.3 and COMTOL scores (P=0.7. At 6 months, the SLT group had a lower IOP (P=0.03 and required fewer medications compared with both baseline (P<0.0001 and with the medication-only group (P=0.02. There was no statistically significant difference in the 6-month GQL-15 or COMTOL score as compared to baseline (P≥0.4 or between the two treatment groups (P≥0.2.Conclusion: A single session of adjuvant SLT provided further reductions in IOP and medication without substantial changes in quality of life or medication tolerability at 6

  1. Phenomenon of Cloning and specificity of its usage

    OpenAIRE

    Yusubova, Zyliya; Zeremskaya, Yuliya Aleksandrovna

    2017-01-01

    Cloning is studied by different branches of science. Medicine is interested in cloning because of its ability to transplant special tissues and organs, genetics - with the purpose of studying heredity and succession, sociology deals with moral and ethic aspects of the phenomenon. The paper is devoted to the study of cloning, its special features and usage in different spheres of social life. The article represents main types of cloning, specificity of vegetative and animal cloning and problem...

  2. Protocol: Streamline cloning of genes into binary vectors in Agrobacterium via the Gateway® TOPO vector system

    Directory of Open Access Journals (Sweden)

    Xu Ruqiang

    2008-01-01

    Full Text Available Abstract Background In plant functional genomic studies, gene cloning into binary vectors for plant transformation is a routine procedure. Traditionally, gene cloning has relied on restriction enzyme digestion and ligation. In recent years, however, Gateway® cloning technology (Invitrogen Co. has developed a fast and reliable alternative cloning methodology which uses a phage recombination strategy. While many Gateway- compatible vectors are available, we frequently encounter problems in which antibiotic resistance genes for bacterial selection are the same between recombinant vectors. Under these conditions, it is difficult, if not sometimes impossible, to use antibiotic resistance in selecting the desired transformants. We have, therefore, developed a practical procedure to solve this problem. Results An integrated protocol for cloning genes of interest from PCR to Agrobacterium transformants via the Gateway® System was developed. The protocol takes advantage of unique characteristics of the replication origins of plasmids used and eliminates the necessity for restriction enzyme digestion in plasmid selections. Conclusion The protocol presented here is a streamlined procedure for fast and reliable cloning of genes of interest from PCR to Agrobacterium via the Gateway® System. This protocol overcomes a key problem in which two recombinant vectors carry the same antibiotic selection marker. In addition, the protocol could be adapted for high-throughput applications.

  3. Cloning mice and men: prohibiting the use of iPS cells for human reproductive cloning.

    Science.gov (United States)

    Lo, Bernard; Parham, Lindsay; Alvarez-Buylla, Arturo; Cedars, Marcelle; Conklin, Bruce; Fisher, Susan; Gates, Elena; Giudice, Linda; Halme, Dina Gould; Hershon, William; Kriegstein, Arnold; Kwok, Pui-Yan; Wagner, Richard

    2010-01-08

    The use of iPSCs and tetraploid complementation for human reproductive cloning would raise profound ethical objections. Professional standards and laws that ban human reproductive cloning by somatic cell nuclear transfer should be revised to also forbid it by other methods, such as iPSCs via tetraploid complementation. Copyright 2010 Elsevier Inc. All rights reserved.

  4. Update on the First Cloned Dog and Outlook for Canine Cloning.

    Science.gov (United States)

    Jang, Goo; Lee, ByeongChun

    2015-10-01

    As man's best friend, dogs have an important position in human society. Ten years ago, we reported the first cloned dog, and his birth has raised various scientific issues, such as those related to health, reproduction, and life span. He has developed without any unique health issues. In this article, we summarize and present perspectives on canine cloning.

  5. Effects of Video Game Training on Measures of Selective Attention and Working Memory in Older Adults: Results from a Randomized Controlled Trial

    National Research Council Canada - National Science Library

    Reales, Jos? M; Mayas, Julia; Ruiz-Marquez, Elo?Sa; Ballesteros, Soledad; Prieto, Antonio; Toril, Pilar

    2017-01-01

    .... Seventy-five older volunteers were randomly assigned to the experimental group trained for 16 sessions with non-action video games from Lumosity, a commercial platform (http://www.lumosity.com...

  6. Contributions of weather variables for specific adaptation of rubber tree (Hevea brasiliensis Muell.- Arg clones

    Directory of Open Access Journals (Sweden)

    Priyadarshan P.M.

    2003-01-01

    Full Text Available The specific adaptation of 15 rubber tree (Hevea brasiliensis clones was assessed by analyzing yield during a normal year (1997-98 and a year (1998-99 in which the yield was exceptional. Differences in yield in response to changes in weather conditions over the years were evident with clones RRII 203, RRIM 703, PB 5/51 and PB 235 which all exhibited a negative trend with increasing wind velocity during 1997-98, these clones also exhibited a negative correlation with minimum temperature during 1998-99. The prominent yield differences across the years made selection based on both yield and stability inevitable through computing weather variables and environmental index as covariant. To determine the contribution of variable(s to genotype-environment (GE interactions, the GE interaction was partitioned into heterogeneity and residual GE interaction. Heterogeneity only for environmental index was highly significant (p = 0.01, meaning that stability or instability of clones was due to a linear effect of the environmental index. The non-significant values of heterogeneity for the weather variables revealed that none of these factors individually was sufficient to explain heterogeneity. A QBASIC computer program called STABLE was used to select simultaneously for yield and stability. Clones PB 235, RRII 118, RRII 203, RRIM 703 and RRIM 600 were stable over the years investigated.

  7. Cell cloning-on-the-spot by using an attachable silicone cylinder.

    Science.gov (United States)

    Park, Hong Bum; Son, Wonseok; Chae, Dong Han; Lee, Jisu; Kim, Il-Woung; Yang, Woomi; Sung, Jae Kyu; Lim, Kyu; Lee, Jun Hee; Kim, Kyung-Hee; Park, Jong-Il

    2016-06-10

    Cell cloning is a laboratory routine to isolate and keep particular properties of cultured cells. Transfected or other genetically modified cells can be selected by the traditional microbiological cloning. In addition, common laboratory cell lines are prone to genotypic drift during their continual culture, so that supplementary cloning steps are often required to maintain correct lineage phenotypes. Here, we designed a silicone-made attachable cloning cylinder, which facilitated an easy and bona fide cloning of interested cells. This silicone cylinder was easy to make, showed competent stickiness to laboratory plastics including culture dishes, and hence enabled secure isolation and culture for days of selected single cells, especially, on the spots of preceding cell-plating dishes under microscopic examination of visible cellular phenotypes. We tested the silicone cylinder in the monoclonal subcloning from a heterogeneous population of a breast cancer cell line, MDA-MB-231, and readily established independent MDA-MB-231 subclones showing different sublineage phenotypes. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Benefits and problems with cloning animals.

    Science.gov (United States)

    Smith, L C; Bordignon, V; Babkine, M; Fecteau, G; Keefer, C

    2000-01-01

    Animal cloning is becoming a useful technique for producing transgenic farm animals and is likely to be used to produce clones from valuable adults. Other applications will also undoubtedly be discovered in the near future, such as for preserving endangered breeds and species. Although cloning promises great advantages for commerce and research alike, its outcome is not always certain due to high pregnancy losses and high morbidity and mortality during the neonatal period. Research into the mechanisms involved in the reprogramming of the nucleus is being conducted throughout the world in an attempt to better understand the molecular and cellular mechanisms involved in correcting these problems. Although the cause of these anomalies remains mostly unknown, similar phenotypes have been observed in calves derived through in vitro fertilization, suggesting that culture conditions are involved in these phenomena. In the meantime, veterinarians and theriogenologists have an important role to play in improving the efficiency of cloning by finding treatments to assure normal gestation to term and to develop preventative and curative care for cloned neonates. Images Figure 1. PMID:11143925

  9. Elephant grass clones for silage production

    Directory of Open Access Journals (Sweden)

    Rerisson José Cipriano dos Santos

    2013-02-01

    Full Text Available Ensiling warm-season grasses often requires wilting due to their high moisture content, and the presence of low-soluble sugars in these grasses usually demands the use of additives during the ensiling process. This study evaluated the bromatological composition of the fodder and silage from five Pennisetum sp. clones (IPA HV 241, IPA/UFRPE Taiwan A-146 2.114, IPA/UFRPE Taiwan A-146 2.37, Elephant B, and Mott. The contents of 20 Polyvinyl chloride (PVC silos, which were opened after 90 days of storage, were used for the bromatological analysis and the evaluation of the pH, nitrogen, ammonia, buffer capacity, soluble carbohydrates, and fermentation coefficients. The effluent losses, gases and dry matter recovery were also calculated. Although differences were observed among the clones (p < 0.05 for the concentrations of dry matter, insoluble nitrogen in acid detergents, insoluble nitrogen in neutral detergents, soluble carbohydrates, fermentation coefficients, and in vitro digestibility in the forage before ensiling, no differences were observed for most of these variables after ensiling. All of the clones were efficient in the fermentation process. The IPA/UFRPE TAIWAN A-146 2.37 clone, however, presented a higher dry matter concentration and the best fermentation coefficient, resulting in a better silage quality, compared to the other clones.

  10. Phage display used for gene cloning of human recombinant antibody against the erythrocyte surface antigen, rhesus D

    DEFF Research Database (Denmark)

    Dziegiel, M; Nielsen, L K; Andersen, P S

    1995-01-01

    A novel phage display system has been developed for PCR amplification and cloning of the Fab fragments of human immunoglobulin genes. Using this system, we have cloned an antibody from a mouse-human hybridoma cell line directed against the erythrocyte antigen rhesus D. Intact erythrocytes were used...... for absorption of the Fab phages. Soluble Fab fragments produced from the cloned material showed identical performance to the parental antibody in agglutination assays. Gel filtration confirmed that the Fab fragment consists of a kappa-Fd heterodimer. The successful use of intact cells for selection of specific...

  11. Cloning and characterization of Rhodotorula glutinis thymine hydroxylase.

    Science.gov (United States)

    Neidigh, Jonathan W; Darwanto, Agus; Williams, Adides A; Wall, Nathan R; Sowers, Lawrence C

    2009-05-01

    Thymine hydroxylase (TH) is a member of the alpha-ketoglutarate-dependent nonheme iron dioxygenase family that includes a series of DNA repair proteins including alkB. Substantial interest in this family of enzymes derives from their capacity to modify DNA bases and precursors by oxidation. Previously, a sequence has been published for cloned Rhodotorula glutinis TH. However, the minimal reported activity of this enzyme, coupled with inconsistencies with previously published mass spectrometry data, compelled us to reexamine TH. The sequence reported here differs from the previously reported sequence at two amino acid positions and is consistent with previously reported mass spectrometry data. The cloned enzyme characterized in this report displayed substantial activity, indicating that the sequence differences are critical for activity. The substrate selectivity of TH against a series of pyrimidine analogues is consistent with that reported for the wild-type enzyme and, in part, explains the mode of selection of uracil analogues. A preliminary model of the active site has been constructed for the purposes of comparing TH with other members of this family. TH and alkB share in common the capacity to oxidize N-methyl groups. However, TH has the added capacity to oxidize the 5-methyl group of thymine, a property that is potentially important for enzymes that could act on DNA and modify DNA-protein interactions.

  12. Growth dynamics of rubber tree clones in northwestern Minas Gerais, Brazil

    Directory of Open Access Journals (Sweden)

    Maria Isabela da Costa Terra

    2016-06-01

    Full Text Available ABSTRACT: This study aimed to evaluate the growth of rubber tree clones ( Hevea brasiliensis (Willd.exA.Juss. Müll. Arg. in the Northwest region of Minas Gerais, Brazil. Randomized blocks, constituted of three treatments (rubber tree clones and four repetitions