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Sample records for allelic odds ratio

  1. A note on the use of the generalized odds ratio in meta-analysis of association studies involving bi- and tri-allelic polymorphisms

    PubMed Central

    2011-01-01

    Background The generalized odds ratio (GOR) was recently suggested as a genetic model-free measure for association studies. However, its properties were not extensively investigated. We used Monte Carlo simulations to investigate type-I error rates, power and bias in both effect size and between-study variance estimates of meta-analyses using the GOR as a summary effect, and compared these results to those obtained by usual approaches of model specification. We further applied the GOR in a real meta-analysis of three genome-wide association studies in Alzheimer's disease. Findings For bi-allelic polymorphisms, the GOR performs virtually identical to a standard multiplicative model of analysis (e.g. per-allele odds ratio) for variants acting multiplicatively, but augments slightly the power to detect variants with a dominant mode of action, while reducing the probability to detect recessive variants. Although there were differences among the GOR and usual approaches in terms of bias and type-I error rates, both simulation- and real data-based results provided little indication that these differences will be substantial in practice for meta-analyses involving bi-allelic polymorphisms. However, the use of the GOR may be slightly more powerful for the synthesis of data from tri-allelic variants, particularly when susceptibility alleles are less common in the populations (≤10%). This gain in power may depend on knowledge of the direction of the effects. Conclusions For the synthesis of data from bi-allelic variants, the GOR may be regarded as a multiplicative-like model of analysis. The use of the GOR may be slightly more powerful in the tri-allelic case, particularly when susceptibility alleles are less common in the populations. PMID:21645382

  2. A comparison of marginal odds ratio estimators.

    PubMed

    Loux, Travis M; Drake, Christiana; Smith-Gagen, Julie

    2017-02-01

    Uses of the propensity score to obtain estimates of causal effect have been investigated thoroughly under assumptions of linearity and additivity of exposure effect. When the outcome variable is binary relationships such as collapsibility, valid for the linear model, do not always hold. This article examines uses of the propensity score when both exposure and outcome are binary variables and the parameter of interest is the marginal odds ratio. We review stratification and matching by the propensity score when calculating the Mantel-Haenszel estimator and show that it is consistent for neither the marginal nor conditional odds ratio. We also investigate a marginal odds ratio estimator based on doubly robust estimators and summarize its performance relative to other recently proposed estimators under various conditions, including low exposure prevalence and model misspecification. Finally, we apply all estimators to a case study estimating the effect of Medicare plan type on the quality of care received by African-American breast cancer patients.

  3. Prevalence odds ratio versus prevalence ratio: choice comes with consequences.

    PubMed

    Tamhane, Ashutosh R; Westfall, Andrew O; Burkholder, Greer A; Cutter, Gary R

    2016-12-30

    Odds ratio, risk ratio, and prevalence ratio are some of the measures of association which are often reported in research studies quantifying the relationship between an independent variable and the outcome of interest. There has been much debate on the issue of which measure is appropriate to report depending on the study design. However, the literature on selecting a particular category of the outcome to be modeled and/or change in reference group for categorical independent variables and the effect on statistical significance, although known, is scantly discussed nor published with examples. In this article, we provide an example of a cross-sectional study wherein prevalence ratio was chosen over (Prevalence) odds ratio and demonstrate the analytic implications of the choice of category to be modeled and choice of reference level for independent variables. Copyright © 2016 John Wiley & Sons, Ltd.

  4. [Odds Ratio: review about the meaning of an epidemiological measure].

    PubMed

    Aguiar, Pedro; Nunes, Baltazar

    2013-01-01

    Introdução: É importante rever a validade do Odds Ratio como medida de associação e efeito, assim como, qual o viés introduzido pelo Odds Ratio quando este representa uma razão de riscos ou uma razão de prevalências em situação de doença mais frequente.Material e Métodos: Simulámos numa coorte de 200 indivíduos com 100 expostos e 100 não expostos a um fator de risco, um cenário de doença rara e outro de doença mais frequente, com razão de riscos igual em ambos os cenários. Determinaram-se o Odds Ratio e o Risco Relativo pelo método clássico (padrão) e respectivamente por regressão logística e regressão de Poisson. Introduziu-se de seguida uma variável de confundimento e determinaram-se o Odds Ratio e o Risco Relativo pelo método de Mantel-Hanszel (análise estratificada padrão) e respectivamente por regressão logística e regressão de Poisson. As análises estatísticas foram efectuadas em SPSS V20.Resultados: Para a doença rara, o Odds Ratio aproximou-se do Risco Relativo. Quando a doença foi mais frequente, o Odds Ratio sobrestimou o Risco Relativo. Nesta situação, e com a presença de uma variável de confundimento, o Risco Relativo ajustado por regressão de Poisson permitiu obter estimativas mais válidas da razão de riscos que o Odds Ratio ajustado por regressão logística. Os intervalos de confiança do Risco Relativo estimado por regressão de Poisson foram sempre mais largos que os determinados por análise de Mantel-Hanszel.Conclusões: O Odds Ratio e a regressão logística múltipla são procedimentos válidos em estudos caso-controlo e em estudosprospetivos e transversais de natureza exploratória. O Odds Ratio não deve ser interpretado como uma razão de riscos ou razão de prevalências se o resultado de saúde não é raro. A análise de regressão múltipla de Poisson deve ser considerada como alternativa válida à regressão logística múltipla, especialmente em estudos de uma exposição específica.

  5. Odds ratios for mediation analysis for a dichotomous outcome.

    PubMed

    Vanderweele, Tyler J; Vansteelandt, Stijn

    2010-12-15

    For dichotomous outcomes, the authors discuss when the standard approaches to mediation analysis used in epidemiology and the social sciences are valid, and they provide alternative mediation analysis techniques when the standard approaches will not work. They extend definitions of controlled direct effects and natural direct and indirect effects from the risk difference scale to the odds ratio scale. A simple technique to estimate direct and indirect effect odds ratios by combining logistic and linear regressions is described that applies when the outcome is rare and the mediator continuous. Further discussion is given as to how this mediation analysis technique can be extended to settings in which data come from a case-control study design. For the standard mediation analysis techniques used in the epidemiologic and social science literatures to be valid, an assumption of no interaction between the effects of the exposure and the mediator on the outcome is needed. The approach presented here, however, will apply even when there are interactions between the effect of the exposure and the mediator on the outcome.

  6. Odds ratio analysis in women with endometrial cancer

    PubMed Central

    Żak, Ewa; Pięta, Beata

    2016-01-01

    Introduction Despite the progress in diagnosis and treatment of malignant tumours, the effects of treatment are insufficient. Reduction of the risk of cervical, ovarian, and endometrial cancer is possible by introducing preventative actions. Aim of the study The aim of the thesis is the analysis of selected risk factors that may affect the increase or decrease in the odds ratio of developing endometrial cancer. Material and methods The study was conducted among patients of the Gynaecology and Obstetrics Hospital of Poznań University of Medical Sciences in the years 2011-2013. The research included a total of 548 female respondents aged between 40 and 84 years. Women responded to questions assessing elements of lifestyle such as consumption of alcohol, smoking, and eating certain groups of foods. Results The respondents consuming fruits and vegetables several times a week have a reduced risk of odds ratio and the OR is 0.85; 95% CI: 0.18-4.09, compared to the women who rarely consume vegetables and fruits. Consumption of whole-wheat bread several times a week reduces the risk of developing the cancer, OR = 0.59; 95% CI: 0.14-2.47, compared to women not consuming wholegrain bread at all. Respondents who consumed red meat, such as veal, pork, and lamb in the amount of 101-200 g per day have an increased risk of developing the disease: OR = 2.16; 95% CI: 1.09-4.28, compared to women not consuming red meat at all. Conclusions A diet rich in fruit and vegetables, onions, garlic, whole grains, and beans should be introduced in order to reduce the risk of endometrial cancer. The consumption of red meat and white pasta should be reduced or even eliminated. PMID:27095953

  7. [Razón de posibilidades: a proposed translation of the term odds ratio].

    PubMed

    Tapia, J A; Nieto, F J

    1993-01-01

    In English, odds ratio is a basic epidemiological measure approximating the relative risk. Odds ratio has been translated into Spanish in several ways, which has produced great terminological confusion. On the other hand, the English word odds is often used in epidemiology or statistics English textbooks, alone or as part of other expressions, but always keeping a definite mathematical meaning, which calls for a similarly definite term in Spanish. We discuss several translations of odds ratio found in the literature and propose the Spanish word "posibilidades" as a translation of odds and "razón de posibilidades" as a translation of odds ratio.

  8. Quantifying RNA allelic ratios by microfluidic multiplex PCR and sequencing.

    PubMed

    Zhang, Rui; Li, Xin; Ramaswami, Gokul; Smith, Kevin S; Turecki, Gustavo; Montgomery, Stephen B; Li, Jin Billy

    2014-01-01

    We developed a targeted RNA sequencing method that couples microfluidics-based multiplex PCR and deep sequencing (mmPCR-seq) to uniformly and simultaneously amplify up to 960 loci in 48 samples independently of their gene expression levels and to accurately and cost-effectively measure allelic ratios even for low-quantity or low-quality RNA samples. We applied mmPCR-seq to RNA editing and allele-specific expression studies. mmPCR-seq complements RNA-seq for studying allelic variations in the transcriptome.

  9. Isomer residual ratio of odd-odd isotope {sup 180}Ta in supernova nucleosynthsis

    SciTech Connect

    Hayakawa, Takehito; Kajino, Toshitaka; Chiba, Satoshi; Mathews, Grant

    2010-06-01

    The nucleosynthesis of {sup 180}Ta has remained an unsolved problem and as its origin many nucleosynthesis mechanisms have been proposed. This isotope has the unique feature that the naturally occurring abundance of {sup 180}Ta is actually a meta-stable isomer (half-life of >=10{sup 15} yr), while the ground state is a 1{sup +} unstable state which beta-decays with a half-life of only 8.15 hr. We have made a new time-dependent calculation of {sup 180}Ta meta-stable isomer residual ratio after supernova neutrino-induced reactions. This residual isomer ratio is crucial for understanding the production and survival of this naturally occurring rare isotope. We have constructed a new model under temperature evolution after type II supernova explosion. We include the explicit linking between the isomer and all known excited states and found that the residual ratio is insensitive to astrophysical parameters such as neutrino energy spectrum, explosion energy, decay time constant. We find that the explicit time evolution of the synthesis of {sup 180}Ta avoids the overproduction relative to {sup 138}La for a neutrino process neutrino temperature of 4 MeV.

  10. At Odds: Concerns Raised by Using Odds Ratios for Continuous or Common Dichotomous Outcomes in Research on Physical Activity and Obesity.

    PubMed

    Lovasi, Gina S; Underhill, Lindsay J; Jack, Darby; Richards, Catherine; Weiss, Christopher; Rundle, Andrew

    2012-01-01

    PURPOSE: Research on obesity and the built environment has often featured logistic regression and the corresponding parameter, the odds ratio. Use of odds ratios for common outcomes such obesity may unnecessarily hinder the validity, interpretation, and communication of research findings. METHODS: We identified three key issues raised by the use of odds ratios, illustrating them with data on walkability and body mass index from a study of 13,102 New York City residents. RESULTS: First, dichotomization of continuous measures such as body mass index discards theoretically relevant information, reduces statistical power, and amplifies measurement error. Second, odds ratios are systematically higher (further from the null) than prevalence ratios; this inflation is trivial for rare outcomes, but substantial for common outcomes like obesity. Third, odds ratios can lead to incorrect conclusions during tests of interactions. The odds ratio in a particular subgroup might higher simply because the outcome is more common (and the odds ratio inflated) compared with other subgroups. CONCLUSION: Our recommendations are to take full advantage of continuous outcome data when feasible and to use prevalence ratios in place of odds ratios for common dichotomous outcomes. When odds ratios must be used, authors should document outcome prevalence across exposure groups.

  11. Understanding relative risk, odds ratio, and related terms: as simple as it can get.

    PubMed

    Andrade, Chittaranjan

    2015-07-01

    Risk, and related measures of effect size (for categorical outcomes) such as relative risks and odds ratios, are frequently presented in research articles. Not all readers know how these statistics are derived and interpreted, nor are all readers aware of their strengths and limitations. This article examines several measures, including absolute risk, attributable risk, attributable risk percent, population attributable risk percent, relative risk, odds, odds ratio, and others. The concept and method of calculation are explained for each of these in simple terms and with the help of examples. The interpretation of each is presented in plain English rather than in technical language. Clinically useful notes are provided, wherever necessary.

  12. How Much More Likely? The Implications of Odds Ratios for Probabilities

    ERIC Educational Resources Information Center

    Liberman, Akiva M.

    2005-01-01

    Binary outcome data are common in research and evaluation. They are often analyzed using logistic regression, and results of these analyses are often reported in the form of odds ratios (ORs). However, ORs are not directly interpretable in the metric commonly used in policy-relevant discussions, which concerns probabilities. ORs are unfamiliar to…

  13. An Odds Ratio Approach for Detecting DDF under the Nested Logit Modeling Framework

    ERIC Educational Resources Information Center

    Terzi, Ragip; Suh, Youngsuk

    2015-01-01

    An odds ratio approach (ORA) under the framework of a nested logit model was proposed for evaluating differential distractor functioning (DDF) in multiple-choice items and was compared with an existing ORA developed under the nominal response model. The performances of the two ORAs for detecting DDF were investigated through an extensive…

  14. Exact Confidence Intervals for the Relative Risk and the Odds Ratio

    PubMed Central

    Wang, Weizhen; Shan, Guogen

    2015-01-01

    Summary For comparison of proportions there are three commonly used measurements: the difference, the relative risk and the odds ratio. Significant effort has been spent on exact confidence intervals for the difference. In this paper, we focus on the relative risk and the odds ratio when data are collected from a matched-pairs design or a two-arm independent binomial experiment. Exact one-sided and two-sided confidence intervals are proposed for each configuration of two measurements and two types of data. The one-sided intervals are constructed using an inductive order, they are the smallest under the order, and are admissible under the set inclusion criterion. The two-sided intervals are the intersection of two one-sided intervals. R codes are developed to implement the intervals. Supplementary materials for this article are available online. PMID:26228945

  15. Odds ratios and confidence intervals: a review for the pediatric oncology clinician.

    PubMed

    Laing, Catherine M; Rankin, James A

    2011-01-01

    Professional registered nurses (RNs) are active participants in seeking and interpreting research evidence. To facilitate knowledge transfer for RNs at the bedside, it behooves researchers to present their findings in a format that facilitates understanding. There is also an expectation that clinicians are capable of interpreting results in a meaningful way. It is important to be able to understand and interpret research reports where statistical methods are used as part of providing the safest and best care for patients. The purpose of this article is to describe the basic concepts of odds ratios and confidence intervals used in research. These statistical measures are used frequently in quantitative research and are often the principle measure of association that is reported. The more comfortable pediatric oncology clinicians are with the interpretation of odds ratios and confidence intervals, the better equipped they will be to bring relevant research results from the "bench" to the bedside.

  16. Odds Ratio Product of Sleep EEG as a Continuous Measure of Sleep State

    PubMed Central

    Younes, Magdy; Ostrowski, Michele; Soiferman, Marc; Younes, Henry; Younes, Mark; Raneri, Jill; Hanly, Patrick

    2015-01-01

    Study Objectives: To develop and validate an algorithm that provides a continuous estimate of sleep depth from the electroencephalogram (EEG). Design: Retrospective analysis of polysomnograms. Setting: Research laboratory. Participants: 114 patients who underwent clinical polysomnography in sleep centers at the University of Manitoba (n = 58) and the University of Calgary (n = 56). Interventions: None. Measurements and Results: Power spectrum of EEG was determined in 3-second epochs and divided into delta, theta, alpha-sigma, and beta frequency bands. The range of powers in each band was divided into 10 aliquots. EEG patterns were assigned a 4-digit number that reflects the relative power in the 4 frequency ranges (10,000 possible patterns). Probability of each pattern occurring in 30-s epochs staged awake was determined, resulting in a continuous probability value from 0% to 100%. This was divided by 40 (% of epochs staged awake) producing the odds ratio product (ORP), with a range of 0–2.5. In validation testing, average ORP decreased progressively as EEG progressed from wakefulness (2.19 ± 0.29) to stage N3 (0.13 ± 0.05). ORP < 1.0 predicted sleep and ORP > 2.0 predicted wakefulness in > 95% of 30-s epochs. Epochs with intermediate ORP occurred in unstable sleep with a high arousal index (> 70/h) and were subject to much interrater scoring variability. There was an excellent correlation (r2 = 0.98) between ORP in current 30-s epochs and the likelihood of arousal or awakening occurring in the next 30-s epoch. Conclusions: Our results support the use of the odds ratio product (ORP) as a continuous measure of sleep depth. Citation: Younes M, Ostrowski M, Soiferman M, Younes H, Younes M, Raneri J, Hanly P. Odds ratio product of sleep EEG as a continuous measure of sleep state. SLEEP 2015;38(4):641–654. PMID:25348125

  17. A method to compute multiplicity corrected confidence intervals for odds ratios and other relative effect estimates.

    PubMed

    Efird, Jimmy Thomas; Nielsen, Susan Searles

    2008-12-01

    Epidemiological studies commonly test multiple null hypotheses. In some situations it may be appropriate to account for multiplicity using statistical methodology rather than simply interpreting results with greater caution as the number of comparisons increases. Given the one-to-one relationship that exists between confidence intervals and hypothesis tests, we derive a method based upon the Hochberg step-up procedure to obtain multiplicity corrected confidence intervals (CI) for odds ratios (OR) and by analogy for other relative effect estimates. In contrast to previously published methods that explicitly assume knowledge of P values, this method only requires that relative effect estimates and corresponding CI be known for each comparison to obtain multiplicity corrected CI.

  18. Likelihood ratio and posterior odds in forensic genetics: Two sides of the same coin.

    PubMed

    Caliebe, Amke; Walsh, Susan; Liu, Fan; Kayser, Manfred; Krawczak, Michael

    2017-05-01

    It has become widely accepted in forensics that, owing to a lack of sensible priors, the evidential value of matching DNA profiles in trace donor identification or kinship analysis is most sensibly communicated in the form of a likelihood ratio (LR). This restraint does not abate the fact that the posterior odds (PO) would be the preferred basis for returning a verdict. A completely different situation holds for Forensic DNA Phenotyping (FDP), which is aimed at predicting externally visible characteristics (EVCs) of a trace donor from DNA left behind at the crime scene. FDP is intended to provide leads to the police investigation helping them to find unknown trace donors that are unidentifiable by DNA profiling. The statistical models underlying FDP typically yield posterior odds (PO) for an individual possessing a certain EVC. This apparent discrepancy has led to confusion as to when LR or PO is the appropriate outcome of forensic DNA analysis to be communicated to the investigating authorities. We thus set out to clarify the distinction between LR and PO in the context of forensic DNA profiling and FDP from a statistical point of view. In so doing, we also addressed the influence of population affiliation on LR and PO. In contrast to the well-known population dependency of the LR in DNA profiling, the PO as obtained in FDP may be widely population-independent. The actual degree of independence, however, is a matter of (i) how much of the causality of the respective EVC is captured by the genetic markers used for FDP and (ii) by the extent to which non-genetic such as environmental causal factors of the same EVC are distributed equally throughout populations. The fact that an LR should be communicated in cases of DNA profiling whereas the PO are suitable for FDP does not conflict with theory, but rather reflects the immanent differences between these two forensic applications of DNA information.

  19. Beta-binomial model for meta-analysis of odds ratios.

    PubMed

    Bakbergenuly, Ilyas; Kulinskaya, Elena

    2017-01-25

    In meta-analysis of odds ratios (ORs), heterogeneity between the studies is usually modelled via the additive random effects model (REM). An alternative, multiplicative REM for ORs uses overdispersion. The multiplicative factor in this overdispersion model (ODM) can be interpreted as an intra-class correlation (ICC) parameter. This model naturally arises when the probabilities of an event in one or both arms of a comparative study are themselves beta-distributed, resulting in beta-binomial distributions. We propose two new estimators of the ICC for meta-analysis in this setting. One is based on the inverted Breslow-Day test, and the other on the improved gamma approximation by Kulinskaya and Dollinger (2015, p. 26) to the distribution of Cochran's Q. The performance of these and several other estimators of ICC on bias and coverage is studied by simulation. Additionally, the Mantel-Haenszel approach to estimation of ORs is extended to the beta-binomial model, and we study performance of various ICC estimators when used in the Mantel-Haenszel or the inverse-variance method to combine ORs in meta-analysis. The results of the simulations show that the improved gamma-based estimator of ICC is superior for small sample sizes, and the Breslow-Day-based estimator is the best for n⩾100. The Mantel-Haenszel-based estimator of OR is very biased and is not recommended. The inverse-variance approach is also somewhat biased for ORs≠1, but this bias is not very large in practical settings. Developed methods and R programs, provided in the Web Appendix, make the beta-binomial model a feasible alternative to the standard REM for meta-analysis of ORs. © 2017 The Authors. Statistics in Medicine Published by John Wiley & Sons Ltd.

  20. Estimation of conditional and marginal odds ratios using the prognostic score.

    PubMed

    Hajage, David; De Rycke, Yann; Chauvet, Guillaume; Tubach, Florence

    2017-02-20

    Introduced by Hansen in 2008, the prognostic score (PGS) has been presented as 'the prognostic analogue of the propensity score' (PPS). PPS-based methods are intended to estimate marginal effects. Most previous studies evaluated the performance of existing PGS-based methods (adjustment, stratification and matching using the PGS) in situations in which the theoretical conditional and marginal effects are equal (i.e., collapsible situations). To support the use of PGS framework as an alternative to the PPS framework, applied researchers must have reliable information about the type of treatment effect estimated by each method. We propose four new PGS-based methods, each developed to estimate a specific type of treatment effect. We evaluated the ability of existing and new PGS-based methods to estimate the conditional treatment effect (CTE), the (marginal) average treatment effect on the whole population (ATE), and the (marginal) average treatment effect on the treated population (ATT), when the odds ratio (a non-collapsible estimator) is the measure of interest. The performance of PGS-based methods was assessed by Monte Carlo simulations and compared with PPS-based methods and multivariate regression analysis. Existing PGS-based methods did not allow for estimating the ATE and showed unacceptable performance when the proportion of exposed subjects was large. When estimating marginal effects, PPS-based methods were too conservative, whereas the new PGS-based methods performed better with low prevalence of exposure, and had coverages closer to the nominal value. When estimating CTE, the new PGS-based methods performed as well as traditional multivariate regression. Copyright © 2016 John Wiley & Sons, Ltd.

  1. The Overall Odds Ratio as an Intuitive Effect Size Index for Multiple Logistic Regression: Examination of Further Refinements

    ERIC Educational Resources Information Center

    Le, Huy; Marcus, Justin

    2012-01-01

    This study used Monte Carlo simulation to examine the properties of the overall odds ratio (OOR), which was recently introduced as an index for overall effect size in multiple logistic regression. It was found that the OOR was relatively independent of study base rate and performed better than most commonly used R-square analogs in indexing model…

  2. Body mass index, cigarette smoking, and alcohol consumption and cancers of the oral cavity, pharynx, and larynx: modeling odds ratios in pooled case-control data.

    PubMed

    Lubin, Jay H; Gaudet, Mia M; Olshan, Andrew F; Kelsey, Karl; Boffetta, Paolo; Brennan, Paul; Castellsague, Xavier; Chen, Chu; Curado, Maria Paula; Dal Maso, Luigino; Daudt, Alexander W; Fabianova, Eleonora; Fernandez, Leticia; Wünsch-Filho, Victor; Franceschi, Silvia; Herrero, Rolando; Koifman, Sergio; La Vecchia, Carlo; Lazarus, Philip; Levi, Fabio; Lissowska, Jolanta; Mates, Ioan Nicolae; Matos, Elena; McClean, Michael; Menezes, Ana; Morgenstern, Hal; Muscat, Joshua; Eluf Neto, Jose; Purdue, Mark P; Rudnai, Peter; Schwartz, Stephen M; Shangina, Oxana; Sturgis, Erich M; Szeszenia-Dabrowska, Neonilia; Talamini, Renato; Wei, Qingyi; Winn, Deborah; Zhang, Zuo-Feng; Hashibe, Mia; Hayes, Richard B

    2010-06-15

    Odds ratios for head and neck cancer increase with greater cigarette and alcohol use and lower body mass index (BMI; weight (kg)/height(2) (m(2))). Using data from the International Head and Neck Cancer Epidemiology Consortium, the authors conducted a formal analysis of BMI as a modifier of smoking- and alcohol-related effects. Analysis of never and current smokers included 6,333 cases, while analysis of never drinkers and consumers of < or =10 drinks/day included 8,452 cases. There were 8,000 or more controls, depending on the analysis. Odds ratios for all sites increased with lower BMI, greater smoking, and greater drinking. In polytomous regression, odds ratios for BMI (P = 0.65), smoking (P = 0.52), and drinking (P = 0.73) were homogeneous for oral cavity and pharyngeal cancers. Odds ratios for BMI and drinking were greater for oral cavity/pharyngeal cancer (P < 0.01), while smoking odds ratios were greater for laryngeal cancer (P < 0.01). Lower BMI enhanced smoking- and drinking-related odds ratios for oral cavity/pharyngeal cancer (P < 0.01), while BMI did not modify smoking and drinking odds ratios for laryngeal cancer. The increased odds ratios for all sites with low BMI may suggest related carcinogenic mechanisms; however, BMI modification of smoking and drinking odds ratios for cancer of the oral cavity/pharynx but not larynx cancer suggests additional factors specific to oral cavity/pharynx cancer.

  3. Np.OR: an S-Plus function for pointwise nonparametric estimation of odds-ratios of continuous predictors.

    PubMed

    Saez, Marc; Cadarso-Suárez, Carmen; Figueiras, Adolfo

    2003-06-01

    Calculating odds ratios (OR) and corresponding confidence intervals (CI) for exposures that have been measured using a continuous scale, presents important limitations in the traditional practice of epidemiology. Our objective is to describe an S-Plus function, that we called np.OR, that allows the computation of the pointwise estimates of the ORs as well as their corresponding CIs of continuous predictors introduced nonlinearly in a generalised model. The function can also be generalised to compute the pointwise estimates of categorical predictors that were introduced nonlinearly. To illustrate usage of the program we analyse the relationship between ambient temperature and total mortality in Barcelona for the period 1991-1995, while controlling for observed and unobserved confounders.

  4. The association in a two-way contingency table through log odds ratio analysis: the case of Sarno river pollution.

    PubMed

    Camminatiello, Ida; D'Ambra, Antonello; Sarnacchiaro, Pasquale

    2014-01-01

    In this paper we are proposing a general framework for the analysis of the complete set of log Odds Ratios (ORs) generated by a two-way contingency table. Starting from the RC (M) association model and hypothesizing a Poisson distribution for the counts of the two-way contingency table we are obtaining the weighted Log Ratio Analysis that we are extending to the study of log ORs. Particularly we are obtaining an indirect representation of the log ORs and some synthesis measures. Then for studying the matrix of log ORs we are performing a generalized Singular Value Decomposition that allows us to obtain a direct representation of log ORs. We also expect to get summary measures of association too. We have considered the matrix of complete set of ORs, because, it is linked to the two-way contingency table in terms of variance and it allows us to represent all the ORs on a factorial plan. Finally, a two-way contingency table, which crosses pollution of the Sarno river and sampling points, is to be analyzed to illustrate the proposed framework.

  5. Correlating observed odds ratios from lung cancer case-control studies to SNP functional scores predicted by bioinformatic tools

    PubMed Central

    Zhu, Yong; Hoffman, Aaron; Wu, Xifeng; Zhang, Heping; Zhang, Yawei; Leaderer, Derek; Zheng, Tongzhang

    2008-01-01

    Bioinformatic tools are widely utilized to predict functional single nucleotide polymorphisms (SNPs) for genotyping in molecular epidemiological studies. However, the extent to which these approaches are mirrored by epidemiological findings has not been fully explored. In this study, we first surveyed SNPs examined in case-control studies of lung cancer, the most extensively-studied cancer type. We then computed SNP functional scores using four popular bioinformatics tools: SIFT, PolyPhen, SNPs3D, and PMut, and determined their predictive potential using the odds ratios (ORs) reported. Spearman’s correlation coefficient (r) for the association with SNP score from SIFT, PolyPhen, SNPs3D, and PMut, and the summary ORs were r = −0.36 (p = 0.007), r = 0.25 (p = 0.068), r = −0.20 (p = 0.205), and r = −0.12 (p = 0.370) respectively. By creating a combined score using information from all four tools we were able to achieve a correlation coefficient of r = 0.51 (p < 0.001). These results indicate that scores of predicted functionality could explain a certain fraction of the lung cancer risk detected in genetic association studies and more accurate predictions may be obtained by combining information from a variety of tools. Our findings suggest that bioinformatic tools are useful in predicting SNP functionality and may facilitate future genetic epidemiological studies. PMID:18191955

  6. [Odds ratio between sociocultural factors, body dissatisfaction, and body mass index in university students of Hidalgo, Mexico].

    PubMed

    Zaragoza Cortes, Jessica; Saucedo-Molina, Teresita de Jesús; Fernández Cortés, Trinidad Lorena

    2011-03-01

    After to identify risky factors involved in the prediction and prevention of eating disorders (ED), in a sample of university males and females students from an urban setting in Hidalgo. Mexico; the main purpose of this paper was to reaffirm the following assumptions: 1) Dissatisfaction with body shape is closely related to both, the influence of sociocultural factors as Body Mass Index (BMI); 2) The participating women reported more dissatisfaction with body shape, indicating greater influence of sociocultural factors than men.Transversal, descriptive and association field research was carried out in a sample of 490 students (57% females. 43% males), from 16 to 30 years old (X(-) = 19.63, SD = +/- 2.11). Multidimensional self-reported questionnaire were applied. BMI was obtained by measuring each subject's weight and height. Regarding the impact association measures obtained by Odds Ratio, there were significant association (p < 0.05) between high BMI and body image dissatisfaction. Also, statistically significant associations (p < 0.05) were found between body dissatisfaction and sociocultural factors (distress because of body image, influence of advertising, and influence of verbal messages), and between BMI and these latter, where men showed a higher risk. Findings suggest that body dissatisfaction in women, and BMI, specifically overweight in men, act like key agents of the impact of sociocultural factors in the researched sample.

  7. Non-parametric estimation of the odds ratios for continuous exposures using generalized additive models with an unknown link function.

    PubMed

    Cadarso-Suárez, Carmen; Roca-Pardiñas, Javier; Figueiras, Adolfo; González-Manteiga, Wenceslao

    2005-04-30

    The generalized additive, model (GAM) is a powerful and widely used tool that allows researchers to fit, non-parametrically, the effect of continuous predictors on a transformation of the mean response variable. Such a transformation is given by a so-called link function, and in GAMs this link function is assumed to be known. Nevertheless, if an incorrect choice is made for the link, the resulting GAM is misspecified and the results obtained may be misleading. In this paper, we propose a modified version of the local scoring algorithm that allows for the non-parametric estimation of the link function, by using local linear kernel smoothers. To better understand the effect that each covariate produces on the outcome, results are expressed in terms of the non-parametric odds ratio (OR) curves. Bootstrap techniques were used to correct the bias in the OR estimation and to construct point-wise confidence intervals. A simulation study was carried out to assess the behaviour of the resulting estimates. The proposed methodology was illustrated using data from the AIDS Register of Galicia (NW Spain), with a view to assessing the effect of the CD4 lymphocyte count on the probability of being AIDS-diagnosed via Tuberculosis (TB). This application shows how the link's flexibility makes it possible to obtain OR curve estimates that are less sensitive to the presence of outliers and unusual values that are often present in the extremes of the covariate distributions.

  8. Somatic Mutation Allelic Ratio Test Using ddPCR (SMART-ddPCR): An Accurate Method for Assessment of Preferential Allelic Imbalance in Tumor DNA

    PubMed Central

    de Smith, Adam J.; Walsh, Kyle M.; Hansen, Helen M.; Endicott, Alyson A.; Wiencke, John K.; Metayer, Catherine; Wiemels, Joseph L.

    2015-01-01

    The extent to which heritable genetic variants can affect tumor development has yet to be fully elucidated. Tumor selection of single nucleotide polymorphism (SNP) risk alleles, a phenomenon called preferential allelic imbalance (PAI), has been demonstrated in some cancer types. We developed a novel application of digital PCR termed Somatic Mutation Allelic Ratio Test using Droplet Digital PCR (SMART-ddPCR) for accurate assessment of tumor PAI, and have applied this method to test the hypothesis that heritable SNPs associated with childhood acute lymphoblastic leukemia (ALL) may demonstrate tumor PAI. These SNPs are located at CDKN2A (rs3731217) and IKZF1 (rs4132601), genes frequently lost in ALL, and at CEBPE (rs2239633), ARID5B (rs7089424), PIP4K2A (rs10764338), and GATA3 (rs3824662), genes located on chromosomes gained in high-hyperdiploid ALL. We established thresholds of AI using constitutional DNA from SNP heterozygotes, and subsequently measured allelic copy number in tumor DNA from 19–142 heterozygote samples per SNP locus. We did not find significant tumor PAI at these loci, though CDKN2A and IKZF1 SNPs showed a trend towards preferential selection of the risk allele (p = 0.17 and p = 0.23, respectively). Using a genomic copy number control ddPCR assay, we investigated somatic copy number alterations (SCNA) underlying AI at CDKN2A and IKZF1, revealing a complex range of alterations including homozygous and hemizygous deletions and copy-neutral loss of heterozygosity, with varying degrees of clonality. Copy number estimates from ddPCR showed high agreement with those from multiplex ligation-dependent probe amplification (MLPA) assays. We demonstrate that SMART-ddPCR is a highly accurate method for investigation of tumor PAI and for assessment of the somatic alterations underlying AI. Furthermore, analysis of publicly available data from The Cancer Genome Atlas identified 16 recurrent SCNA loci that contain heritable cancer risk SNPs associated with a

  9. Binary Logistic Regression Analysis for Detecting Differential Item Functioning: Effectiveness of R[superscript 2] and Delta Log Odds Ratio Effect Size Measures

    ERIC Educational Resources Information Center

    Hidalgo, Mª Dolores; Gómez-Benito, Juana; Zumbo, Bruno D.

    2014-01-01

    The authors analyze the effectiveness of the R[superscript 2] and delta log odds ratio effect size measures when using logistic regression analysis to detect differential item functioning (DIF) in dichotomous items. A simulation study was carried out, and the Type I error rate and power estimates under conditions in which only statistical testing…

  10. The Effects of Small Sample Size on Identifying Polytomous DIF Using the Liu-Agresti Estimator of the Cumulative Common Odds Ratio

    ERIC Educational Resources Information Center

    Carvajal, Jorge; Skorupski, William P.

    2010-01-01

    This study is an evaluation of the behavior of the Liu-Agresti estimator of the cumulative common odds ratio when identifying differential item functioning (DIF) with polytomously scored test items using small samples. The Liu-Agresti estimator has been proposed by Penfield and Algina as a promising approach for the study of polytomous DIF but no…

  11. Odd + Odd = Odd: Is It Possible?

    ERIC Educational Resources Information Center

    Sinitsky, Ilya; Zazkis, Rina; Leikin, Roza

    2011-01-01

    In this article, the authors explore the reasons why some mathematical functions are referred to as odd, and others as even. They start by recalling the definitions of both functions. Simply stated, the value of an even function is the same for a number and its opposite, whereas the value of an odd function changes for the opposite number when the…

  12. Pooling dietary data using questionnaires with open-ended and predefined responses: implications for comparing mean intake or estimating odds ratios.

    PubMed

    Swartz, Michael D; Forman, Michele R; Mahabir, Somdat; Etzel, Carol J

    2010-03-15

    In the current era of diet-gene analyses, large sample sizes are required to uncover the etiology of complex diseases. As such, consortia form and often combine available data. Food frequency questionnaires, which commonly use 2 different types of responses about the frequency of intake (predefined responses and open-ended responses), may be pooled to achieve the desired sample size. The common practice is to categorize open-ended responses into the predefined response categories. A problem arises when the predefined categories are noncontiguous: possible open-ended responses may fall in gaps between the predefined categories. Using simulated data modeled from frequency of intake among 1,664 controls in a lung cancer case-control study at The University of Texas M. D. Anderson Cancer Center (Houston, Texas, 2000-2005), the authors describe the effect of different categories of open-ended responses that fall in between noncontiguous, predefined response sets on estimates of the mean difference in intake and the odds ratios. A significant inflation of false positives appears when comparing mean differences of intake, while the bias in estimating odds ratios may be acceptably small. Therefore, if pooling data cannot be restricted to the same type of response, inferences should focus on odds ratio estimation to minimize bias.

  13. Positive Selection of Deleterious Alleles through Interaction with a Sex-Ratio Suppressor Gene in African Buffalo: A Plausible New Mechanism for a High Frequency Anomaly

    PubMed Central

    van Hooft, Pim; Greyling, Ben J.; Getz, Wayne M.; van Helden, Paul D.; Zwaan, Bas J.; Bastos, Armanda D. S.

    2014-01-01

    Although generally rare, deleterious alleles can become common through genetic drift, hitchhiking or reductions in selective constraints. Here we present a possible new mechanism that explains the attainment of high frequencies of deleterious alleles in the African buffalo (Syncerus caffer) population of Kruger National Park, through positive selection of these alleles that is ultimately driven by a sex-ratio suppressor. We have previously shown that one in four Kruger buffalo has a Y-chromosome profile that, despite being associated with low body condition, appears to impart a relative reproductive advantage, and which is stably maintained through a sex-ratio suppressor. Apparently, this sex-ratio suppressor prevents fertility reduction that generally accompanies sex-ratio distortion. We hypothesize that this body-condition-associated reproductive advantage increases the fitness of alleles that negatively affect male body condition, causing genome-wide positive selection of these alleles. To investigate this we genotyped 459 buffalo using 17 autosomal microsatellites. By correlating heterozygosity with body condition (heterozygosity-fitness correlations), we found that most microsatellites were associated with one of two gene types: one with elevated frequencies of deleterious alleles that have a negative effect on body condition, irrespective of sex; the other with elevated frequencies of sexually antagonistic alleles that are negative for male body condition but positive for female body condition. Positive selection and a direct association with a Y-chromosomal sex-ratio suppressor are indicated, respectively, by allele clines and by relatively high numbers of homozygous deleterious alleles among sex-ratio suppressor carriers. This study, which employs novel statistical techniques to analyse heterozygosity-fitness correlations, is the first to demonstrate the abundance of sexually-antagonistic genes in a natural mammal population. It also has important

  14. Positive selection of deleterious alleles through interaction with a sex-ratio suppressor gene in African Buffalo: a plausible new mechanism for a high frequency anomaly.

    PubMed

    van Hooft, Pim; Greyling, Ben J; Getz, Wayne M; van Helden, Paul D; Zwaan, Bas J; Bastos, Armanda D S

    2014-01-01

    Although generally rare, deleterious alleles can become common through genetic drift, hitchhiking or reductions in selective constraints. Here we present a possible new mechanism that explains the attainment of high frequencies of deleterious alleles in the African buffalo (Syncerus caffer) population of Kruger National Park, through positive selection of these alleles that is ultimately driven by a sex-ratio suppressor. We have previously shown that one in four Kruger buffalo has a Y-chromosome profile that, despite being associated with low body condition, appears to impart a relative reproductive advantage, and which is stably maintained through a sex-ratio suppressor. Apparently, this sex-ratio suppressor prevents fertility reduction that generally accompanies sex-ratio distortion. We hypothesize that this body-condition-associated reproductive advantage increases the fitness of alleles that negatively affect male body condition, causing genome-wide positive selection of these alleles. To investigate this we genotyped 459 buffalo using 17 autosomal microsatellites. By correlating heterozygosity with body condition (heterozygosity-fitness correlations), we found that most microsatellites were associated with one of two gene types: one with elevated frequencies of deleterious alleles that have a negative effect on body condition, irrespective of sex; the other with elevated frequencies of sexually antagonistic alleles that are negative for male body condition but positive for female body condition. Positive selection and a direct association with a Y-chromosomal sex-ratio suppressor are indicated, respectively, by allele clines and by relatively high numbers of homozygous deleterious alleles among sex-ratio suppressor carriers. This study, which employs novel statistical techniques to analyse heterozygosity-fitness correlations, is the first to demonstrate the abundance of sexually-antagonistic genes in a natural mammal population. It also has important

  15. Enhanced Ratio of Signals Enables Digital Mutation Scanning for Rare Allele Detection

    PubMed Central

    Castellanos-Rizaldos, Elena; Paweletz, Cloud; Song, Chen; Oxnard, Geoffrey R.; Mamon, Harvey; Jänne, Pasi A.; Makrigiorgos, G. Mike

    2016-01-01

    The use of droplet digital PCR (ddPCR) for low-level DNA mutation detection in cancer, prenatal diagnosis, and infectious diseases is growing rapidly. However, although ddPCR has been implemented successfully for detection of rare mutations at pre-determined positions, no ddPCR adaptation for mutation scanning exists. Yet, frequently, clinically relevant mutations reside on multiple sequence positions in tumor suppressor genes or complex hotspot mutations in oncogenes. Here, we describe a combination of coamplification at lower denaturation temperature PCR (COLD-PCR) with ddPCR that enables digital mutation scanning within approximately 50-bp sections of a target amplicon. Two FAM/HEX-labeled hydrolysis probes matching the wild-type sequence are used during ddPCR. The ratio of FAM/HEX-positive droplets is constant when wild-type amplicons are amplified but deviates when mutations anywhere under the FAM or HEX probes are present. To enhance the change in FAM/HEX ratio, we employed COLD-PCR cycling conditions that enrich mutation-containing amplicons anywhere on the sequence. We validated COLD-ddPCR on multiple mutations in TP53 and in EGFR using serial mutation dilutions and cell-free circulating DNA samples, and demonstrate detection down to approximately 0.2% to 1.2% mutation abundance. COLD-ddPCR enables a simple, rapid, and robust two-fluorophore detection method for the identification of multiple mutations during ddPCR and potentially can identify unknown DNA variants present in the target sequence. PMID:25772705

  16. A case-control study of cholecystectomy and right-side colon cancer: the influence of alternative data sources and differential interview participation proportions on odds ratio estimates.

    PubMed

    Vernick, L J; Kuller, L H

    1982-07-01

    One hundred fifty patients with right-side colon cancer (i.e., patients with adenocarcinoma of the cecum or ascending colon) were compared to 150 matched left-side colon cancer controls (i.e., patients with adenocarcinoma of the descending or sigmoid colon) and to 123 neighborhood controls, Pittsburgh, Pennsylvania, Standard Metropolitan Statistical Area, 1975-1978. The gastrointestinal surgical history was ascertained for all study subjects so that the presence or absence of a history of cholecystectomy could be noted. Cholecystectomy history was obtained through telephone interviews and whenever possible subsequently validated from operative and pathology reports at time of cholecystectomy. Cholecystectomy history for the colon cancer patients was also abstracted from hospital records at time of colon cancer diagnosis with an attempt to confirm the gallbladder's status through operative reports, cholecystograms, and physical examinations. Hospital records and interviews for the colon cancer patients appeared to provide accurate exposure history. Point estimates of the odds ratios and confidence intervals for intra- and inter-data source comparisons (i.e., hospital records, interviews, and hospital records and interviews combined) were comparable with similar measures of effect. Consistent odds ratio estimates appeared in both left-side colon cancer controls (1.9) and neighborhood controls (1.89). The authors suggest that changes in bile acid metabolism following cholecystectomy may be associated an increased risk of right-side colon cancer.

  17. An efficient test based on the inferential model for the non-inferiority of odds ratio in matched-pairs design.

    PubMed

    Wang, Zhining; Jin, Hua; Lu, Hezhi; Jin, Yaolan

    2017-01-01

    Non-inferiority of one treatment to another based on odds ratio for the matched-pair design is a common issue in the medical research. Liu et al. derived two asymptotic tests, delta method and score test, which can be applicable for large samples but may tend to be liberal for small sample sizes. Jin et al. proposed an IM-based method that can control the type I risk well but may be somewhat conservative. In this paper, we extend the IM-based method to RIM-based test using the randomized plausibility function. We prove that our new proposed method is not only valid but also efficient. Simulation studies confirm that the RIM-based test is better than other methods. A numerical example illustrates the proposed method.

  18. Oppositional Defiant Disorder (ODD)

    MedlinePlus

    ... manage a child with ODD. Doctors, counselors and child development experts can help. Treatment of ODD involves therapy, ... exhibit oppositional behavior at certain stages of a child's development. Signs of ODD generally begin during preschool years. ...

  19. Sibling assessment based on likelihood ratio and total number of shared alleles using 21 short tandem repeat loci included in the GlobalFiler™ kit.

    PubMed

    Inoue, Hiroyuki; Manabe, Sho; Fujii, Koji; Iwashima, Yasuki; Miyama, Saori; Tanaka, Ayako; Saitoh, Hisako; Iwase, Hirotaro; Tamaki, Keiji; Sekiguchi, Kazumasa

    2016-03-01

    Sibling assessment using the 15 autosomal short tandem repeat (STR) loci included in the Identifiler® kit can be difficult when comparing an unidentified party to an alleged sibling. Therefore, we investigated the likelihood ratio (LR) and the total number of shared alleles (TNSA) for sibship determination using the 21 autosomal STR loci included in the GlobalFiler™ kit. We computationally generated the genotypes of 10,000 sibling pairs and 10,000 unrelated pairs based on previously reported allele frequencies of the 15 Identifiler loci and the remaining 6 GlobalFiler loci. The LR and the TNSA were then calculated in each pair using the 15 and 21 loci. Next, these calculations were applied to 22 actual sibling pairs. LR values ⩾ 10,000 were observed in 48% of the sibling pairs using the 15 loci and in 80% of the sibling pairs using the 21 loci. The TNSA distribution between siblings and unrelated pairs was more divergent in GlobalFiler than in Identifiler. TNSA values ⩾ 20 were found only in true siblings in Identifiler, while TNSA values ⩾24 in GlobalFiler. In Identifiler, all pairs with TNSA ⩾ 24 had LR values ⩾ 10,000 and the same was true in GlobalFiler for TNSA ⩾29. Therefore, increasing the number of loci is very efficient for sibship determination. The LR is most reliable for determining sibship. However, TNSA values may be useful for the preliminary method of LR values because LR value demonstrated a significantly positive correlation with TNSA value in both Identifiler and GlobalFiler.

  20. Odd-odd deformed proton emitters.

    PubMed

    Ferreira, L S; Maglione, E

    2001-02-26

    Proton decay from odd-odd deformed nuclei is a long-standing unsolved problem. We present for the first time an exact solution using single particle Nilsson resonances. The lifetime is found to depend strongly on the single particle level occupied by the unpaired neutron, allowing a clear assignment of its Nilsson level. The emitters 112Cs, 140Ho, 150Lu, and 150Lu(m) are considered. The agreement with the experimental data is very good with deformations 0.1

  1. Ratio

    NASA Astrophysics Data System (ADS)

    Webster, Nathan A. S.; Pownceby, Mark I.; Madsen, Ian C.; Studer, Andrew J.; Manuel, James R.; Kimpton, Justin A.

    2014-12-01

    Effects of basicity, B (CaO:SiO2 ratio) on the thermal range, concentration, and formation mechanisms of silico-ferrite of calcium and aluminum (SFCA) and SFCA-I iron ore sinter bonding phases have been investigated using an in situ synchrotron X-ray diffraction-based methodology with subsequent Rietveld refinement-based quantitative phase analysis. SFCA and SFCA-I phases are the key bonding materials in iron ore sinter, and improved understanding of the effects of processing parameters such as basicity on their formation and decomposition may assist in improving efficiency of industrial iron ore sintering operations. Increasing basicity significantly increased the thermal range of SFCA-I, from 1363 K to 1533 K (1090 °C to 1260 °C) for a mixture with B = 2.48, to ~1339 K to 1535 K (1066 °C to 1262 °C) for a mixture with B = 3.96, and to ~1323 K to 1593 K (1050 °C to 1320 °C) at B = 4.94. Increasing basicity also increased the amount of SFCA-I formed, from 18 wt pct for the mixture with B = 2.48 to 25 wt pct for the B = 4.94 mixture. Higher basicity of the starting sinter mixture will, therefore, increase the amount of SFCA-I, considered to be more desirable of the two phases. Basicity did not appear to significantly influence the formation mechanism of SFCA-I. It did, however, affect the formation mechanism of SFCA, with the decomposition of SFCA-I coinciding with the formation of a significant amount of additional SFCA in the B = 2.48 and 3.96 mixtures but only a minor amount in the highest basicity mixture. In situ neutron diffraction enabled characterization of the behavior of magnetite after melting of SFCA produced a magnetite plus melt phase assemblage.

  2. Structure of odd-odd 136La at high spin

    NASA Astrophysics Data System (ADS)

    Bhattacharjee, Tumpa; Chanda, Somen; Bhattacharyya, Sarmishtha; Basu, Swapan Kumar; Bhowmik, R. K.; Muralithar, S.; Singh, R. P.; Pattabiraman, N. S.; Ghugre, S. S.; Datta Pramanik, U.; Bhattacharya, S.

    2005-04-01

    The high spin states in the N=79 odd-odd 136La nucleus have been investigated by in-beam γ-spectroscopic techniques following the 130Te( 11B, 5 n) 136La reaction at E=52 MeV using an array, consisting of eight Compton-suppressed clover germanium detectors. Thirty nine new γ rays have been assigned to 136La on the basis of γ ray singles and γγ-coincidence data. The level scheme of 136La has been extended above the known 115 ms isomer upto an excitation energy of 4.6 MeV and spin 18 ℏ. Thirty one new levels have been proposed and spin-parity assignments for most of the newly proposed levels have been made on the basis of the deduced asymmetry ratios and polarisation information for the de-exciting transitions. The observed positive parity yrast band has been compared with the theoretical calculation, done within the framework of particle rotor coupling model (PRM) where the two odd quasi-particles are coupled to an axially symmetric core. The level structure has been discussed in the light of the known systematics of the neighbouring N=79 isotonic nuclei.

  3. Against All Odds

    ERIC Educational Resources Information Center

    Manzo, Kathleen Kennedy

    2005-01-01

    More than a decade ago, no one held out much hope for the poor, immigrant children at Kennedy Middle School. Nobody thinks that now. This article presents how Kennedy Middle School transformed and beat all the odds to be a "school to watch." In many ways, Kennedy Middle School has become a model of middle-grades improvement. Test scores,…

  4. Odd Shape Out

    ERIC Educational Resources Information Center

    Cady, Jo Ann; Wells, Pamela

    2016-01-01

    The Odd Shape Out task was an open-ended problem that engaged students in comparing shapes based on their properties. Four teachers submitted the work of 116 students from across the country. This article compares various student's responses to the task. The problem allowed for differentiation, as shown by the many different ways that students…

  5. Relationship between HLA-DRB1 allele polymorphisms and familial aggregations of hepatocellular carcinoma

    PubMed Central

    Ma, S.; Wu, J.; Wu, J.; Wei, Y.; Zhang, L.; Ning, Q.; Hu, D.

    2016-01-01

    Objective We explored the relationship between HLA-DRB1 allele polymorphisms and familial aggregation of hepatocellular carcinoma (fhcc). Methods Polymerase chain reaction sequence-specific primers were used to determine HLA-DRB1 genotypes for 130 members of families with 2 or more liver cancer patients and for 130 members of families without any diagnosed cancers. The genotype profiles were then compared to explore the relationship between HLA-DRB1 gene polymorphism and fhcc. Result Of 11 selected alleles, the frequencies of DRB1*11 and DRB1*12 were significantly lower in the fhcc group than in no-cancer group (p < 0.05; odds ratio: 0.286; 95% confidence interval: 0.091 to 0.901; and odds ratio: 0.493; 95% confidence interval: 0.292 to 0.893). Differences in the frequencies of the other 9 alleles were not statistically significant in the two groups (p > 0.05). Conclusions Our research suggests that if genetic factors play a role in fhcc, the deficiency in the DRB1*11 and DRB1*12 alleles might be the risk factor at work in Guangxi Zhuang Autonomous Region, P.R.C. PMID:26966407

  6. Tilted axis rotation in odd-odd {sup 164}Tm

    SciTech Connect

    Reviol, W.; Riedinger, L.L.; Wang, X.Z.; Zhang, J.Y.

    1996-12-31

    Ten band structures are observed in {sup 164}Tm, among them sets of parallel and anti-parallel couplings of the proton and neutron spins. The Tilted Axis Cranking scheme is applied for the first time to an odd-odd nucleus in a prominent region of nuclear deformation.

  7. Associations of High-Grade Glioma With Glioma Risk Alleles and Histories of Allergy and Smoking

    PubMed Central

    Lachance, Daniel H.; Yang, Ping; Johnson, Derek R.; Decker, Paul A.; Kollmeyer, Thomas M.; McCoy, Lucie S.; Rice, Terri; Xiao, Yuanyuan; Ali-Osman, Francis; Wang, Frances; Stoddard, Shawn M.; Sprau, Debra J.; Kosel, Matthew L.; Wiencke, John K.; Wiemels, Joseph L.; Patoka, Joseph S.; Davis, Faith; McCarthy, Bridget; Rynearson, Amanda L.; Worra, Joel B.; Fridley, Brooke L.; O’Neill, Brian Patrick; Buckner, Jan C.; Il’yasova, Dora; Jenkins, Robert B.; Wrensch, Margaret R.

    2011-01-01

    Glioma risk has consistently been inversely associated with allergy history but not with smoking history despite putative biologic plausibility. Data from 855 high-grade glioma cases and 1,160 controls from 4 geographic regions of the United States during 1997–2008 were analyzed for interactions between allergy and smoking histories and inherited variants in 5 established glioma risk regions: 5p15.3 (TERT), 8q24.21 (CCDC26/MLZE), 9p21.3 (CDKN2B), 11q23.3 (PHLDB1/DDX6), and 20q13.3 (RTEL1). The inverse relation between allergy and glioma was stronger among those who did not (odds ratioallergy-glioma = 0.40, 95% confidence interval: 0.28, 0.58) versus those who did (odds ratioallergy-glioma = 0.76, 95% confidence interval: 0.59, 0.97; Pinteraction = 0.02) carry the 9p21.3 risk allele. However, the inverse association with allergy was stronger among those who carried (odds ratioallergy-glioma = 0.44, 95% confidence interval: 0.29, 0.68) versus those who did not carry (odds ratioallergy-glioma = 0.68, 95% confidence interval: 0.54, 0.86) the 20q13.3 glioma risk allele, but this interaction was not statistically significant (P = 0.14). No relation was observed between glioma risk and smoking (odds ratio = 0.92, 95% confidence interval: 0.77, 1.10; P = 0.37), and there were no interactions for glioma risk of smoking history with any of the risk alleles. The authors’ observations are consistent with a recent report that the inherited glioma risk variants in chromosome regions 9p21.3 and 20q13.3 may modify the inverse association of allergy and glioma. PMID:21742680

  8. ODD Symptom Network during Preschool.

    PubMed

    Smith, Tess E; Lee, Christine A; Martel, Michelle M; Axelrad, Marni E

    2016-08-15

    Several different conceptualizations of Oppositional Defiant Disorder (ODD) symptoms have been proposed, including one undivided set of symptoms (DSM-IV-TR; APA 2000); two domains of symptoms subdivided into affective and behavioral; and three domains of symptoms subdivided as angry/irritable, argumentative/defiant, and spiteful. The current study utilizes a novel approach to examining the division of ODD symptoms through use of network analysis. Participants were 109 preschoolers (64 male) between the ages of three and six (M = 4.34 years, SD = 1.08) and their parents and teachers/caregivers, who provided ratings of ODD symptoms. Results are consistent with one-, two-, and three- cluster solutions of ODD, but perhaps provide most support for the three-cluster solution. In addition, results support the idea that negative affect, particularly anger, forms the core of the ODD symptom network during preschool. These results suggest the importance of targeting anger in preschool interventions for ODD.

  9. CYP2C9*2 allele increases risk for hypoglycemia in POR*1/*1 type 2 diabetic patients treated with sulfonylureas.

    PubMed

    Ragia, G; Tavridou, A; Elens, L; Van Schaik, R H N; Manolopoulos, V G

    2014-01-01

    It is previously shown that carriers of the defective allele CYP2C9*3 that leads to impaired sulfonylurea metabolism are at increased sulfonylurea-induced hypoglycemia risk due to diminished drug metabolism, whereas no effect of CYP2C9*2 allele was found. Recently, a polymorphism in P450 oxidoreductase (POR) gene, assigned as POR*28 allele, was associated with increased CYP2C9 activity. The aim of this study was to assess i) the effect of POR*28 allele on sulfonylurea-induced hypoglycemia risk and ii) the association of CYP2C9*2 allele with hypoglycemia risk in non-carriers of POR*28 allele. The study group consisted of 176 patients with diagnosed type 2 diabetes mellitus (T2DM) treated with sulfonylureas, of whom 92 patients had experienced at least one drug-associated hypoglycemic event (cases), while 84 had never experienced a hypoglycemic event (controls). POR*28 allele was detected by use of real-time TaqMan PCR. POR*28 allele was not associated with sulfonyl-urea-induced hypoglycemia. In POR*1/*1 patients, CYP2C9*1/*2 genotype was more common in cases than in controls (32.7 vs. 14.3%, p=0.041). In a model adjusted for age, BMI, duration of T2DM and renal function, and POR*1/*1 entered as a selection variable, CYP2C9*2 allele increased the hypoglycemia risk in response to sulfonylurea (odds ratio: 3.218, p=0.031). In conclusion, our results suggest that POR*28 allele is masking the association of CYP2C9*2 allele with sulfonyl-urea-induced hypoglycemia. Therefore, POR*28 allele is an important source of CYP2C9 activity variability and combined with CYP2C9 gene poly-morphisms may explain individual variability in the effect of sulfonylureas.

  10. Modeling level structures of odd-odd deformed nuclei

    SciTech Connect

    Hoff, R.W.; Kern, J.; Piepenbring, R.; Boisson, J.P.

    1985-01-15

    A technique for modeling quasiparticle excitation energies and rotational parameters in odd-odd deformed nuclei has been applied to actinide species where new experimental data have been obtained by use of neutron-capture gamma-ray spectroscopy. The input parameters required for the calculation were derived from empirical data on single-particle excitations in neighboring odd-mass nuclei. Calculated configuration-specific values for the Gallagher-Moszkowski splittings were used. Calculated and experimental level structures for /sup 238/Np, /sup 244/Am, and /sup 250/Bk are compared, as well as those for several nuclei in the rare-earch region. The agreement for the actinide species is excellent, with bandhead energies deviating 22 keV and rotational parameters 5%, on the average. Corresponding average deviations for five rare-earth nuclei are 47 keV and 7%. Several applications of this modeling technique are discussed.

  11. Modeling level structures of odd-odd deformed nuclei

    SciTech Connect

    Hoff, R.W.; Kern, J.; Piepenbring, R.; Boisson, J.P.

    1984-09-07

    A technique for modeling quasiparticle excitation energies and rotational parameters in odd-odd deformed nuclei has been applied to actinide species where new experimental data have been obtained by use of neutron-capture gamma-ray spectroscopy. The input parameters required for the calculation were derived from empirical data on single-particle excitations in neighboring odd-mass nuclei. Calculated configuration-specific values for the Gallagher-Moszkowski splittings were used. Calculated and experimental level structures for /sup 238/Np, /sup 244/Am, and /sup 250/Bk are compared, as well as those for several nuclei in the rare-earth region. The agreement for the actinide species is excellent, with bandhead energies deviating 22 keV and rotational parameters 5%, on the average. Corresponding average deviations for five rare-earth nuclei are 47 keV and 7%. Several applications of this modeling technique are discussed. 18 refs., 5 figs., 4 tabs.

  12. Nonadiabatic effects in odd-odd deformed proton emitters

    SciTech Connect

    Patial, M.; Jain, A. K.; Arumugam, P.; Maglione, E.; Ferreira, L. S.

    2011-11-30

    We present for the first time, the nonadiabatic quasiparticle approach to study proton emission from odd-odd deformed nuclei. Coriolis effects are incorporated in both the parent and daughter wavefunctions and hence our formalism allows us to study their complete role on the decay widths. First results obtained for the nucleus {sup 112}Cs suggest a weak dependance on Coriolis effect. However, we are able to reproduce the experimental half-lives without assuming the exact Nilsson orbital from which the decay proceeds.

  13. Association of BoLA-DRB3.2 Alleles with BLV Infection Profiles (Persistent Lymphocytosis/Lymphosarcoma) and Lymphocyte Subsets in Iranian Holstein Cattle.

    PubMed

    Nikbakht Brujeni, Gholamreza; Ghorbanpour, Reyhaneh; Esmailnejad, Atefeh

    2016-04-01

    Major histocompatibility complex (MHC) is the best-characterized genetic region associated with resistance and susceptibility to a wide range of diseases. In cattle, the most important example of the relationship between the MHC and infectious diseases has been established by the resistance to Bovine leukemia virus (BLV) infection. The association of the bovine MHC class II BoLA-DRB3.2 alleles with BLV infection profiles was examined. BoLA-DRB3.2 allelic diversity was determined in 190 Iranian Holstein cattle using direct sequencing method. Association of the DRB3.2 alleles with BLV infection profiles was found as the odds ratio. Effects of the alleles on lymphocyte subsets were also evaluated by multivariate regression analysis and GLM procedures. The studied cattle were categorized into three groups: BLV seronegative, BLV seropositive with persistent lymphocytosis (PL), and BLV seropositive with lymphosarcoma (LS). The PL profile was significantly associated with the BoLA-DRB3.2*0101, *1101 and *4201 alleles, although the *3202 allele mediating resistance to PL was observed. Significant association was found between the BoLA-DRB3.2*1802, *3202, and *0901 alleles and susceptibility to LS, while the *0101 and *1101 alleles were associated with resistance to LS. BoLA-DRB3.2 alleles also showed a significant correlation with CD4, CD8, CD21 cells and CD4/CD8 ratio. Allelic differences influence the immune response to BLV infection and developing the disease profile. These differences also have important consequences for tumor resistance.

  14. On Quantizable Odd Lie Bialgebras

    NASA Astrophysics Data System (ADS)

    Khoroshkin, Anton; Merkulov, Sergei; Willwacher, Thomas

    2016-09-01

    Motivated by the obstruction to the deformation quantization of Poisson structures in infinite dimensions, we introduce the notion of a quantizable odd Lie bialgebra. The main result of the paper is a construction of the highly non-trivial minimal resolution of the properad governing such Lie bialgebras, and its link with the theory of so-called quantizable Poisson structures.

  15. Reflection asymmetry in odd-A and odd-odd actinium nuclei

    SciTech Connect

    Ahmad, I.

    1993-09-01

    Theoretical calculations and measurements indicate that octupole correlations are at a maximum in the ground states of the odd-proton nuclei Ac and Pa. It has been expected that odd-odd nuclei should have even larger amount of octupole-octupole correlations. We have recently made measurements on the structure of {sup 224}Ac. Although spin and parity assignments could not be made, two bands starting at 354.1 and 360.0 keV have properties characteristic of reflection asymmetric shape. These two bands have very similar rotational constants and also similar alpha decay rates, which suggest similarity between the wavefunctions of these bands. These signatures provide evidence for octupole correlations in these nuclides.

  16. Theoretical description of fine structure in the α decay of heavy odd-odd nuclei

    NASA Astrophysics Data System (ADS)

    Ni, Dongdong; Ren, Zhongzhou

    2013-02-01

    The newly developed multichannel cluster model (MCCM), based on the coupled-channel Schrödinger equation with outgoing wave boundary conditions, is extended to study the α-decay fine structure in heavy odd-odd nuclei. Calculations are performed for the α transitions to favored rotational bands where the unpaired nucleons remain unchanged. The simple WKB barrier penetration formula is also used to evaluate the branching ratios for various daughter states. It is found that the WKB formula seems to overestimate the branching ratios for the second and third members of the favored rotational band, while the MCCM gives a precise description of them without any adjustable parameters. Moreover, the experimental total α-decay half-lives are well reproduced within the MCCM.

  17. Excited states of the 150Pm odd-odd nucleus

    NASA Astrophysics Data System (ADS)

    Bucurescu, D.; Drăgulescu, E.; Pascu, S.; Wirth, H.-F.; Filipescu, D.; Căta-Danil, G.; Căta-Danil, I.; Deleanu, D.; Eppinger, K.; Faestermann, T.; Ghiţă, D. G.; Glodariu, T.; Hertenberger, R.; Ivaşcu, M.; Krücken, R.; Mărginean, N.; Mărginean, R.; Mihai, C.; Negret, A.; Sava, T.; Stroe, L.; Wimmer, K.; Zamfir, N. V.

    2012-01-01

    The knowledge of excited states in the odd-odd 150Pm, completely unknown until recently, is important both for understanding double β decay of 150Nd and for nuclear structure studies in mass regions with a quantum phase transition. A large number of excited states have been determined for the first time in this nucleus by measuring spectra of the 152Sm(d,α) direct reaction at 25 MeV with the Munich Q3D spectrograph and by γ-ray spectroscopy with the (p,nγ) reaction at 7.1 MeV at the Bucharest tandem accelerator. Some of these levels correspond to peaks recently observed with the (3He,t) reaction at 140 MeV/u.

  18. Association of BLV infection profiles with alleles of the BoLA-DRB3.2 gene.

    PubMed

    Juliarena, M A; Poli, M; Sala, L; Ceriani, C; Gutierrez, S; Dolcini, G; Rodríguez, E M; Mariño, B; Rodríguez-Dubra, C; Esteban, E N

    2008-08-01

    Bovine leukaemia virus (BLV) causes lymphosarcoma and persistent lymphocytosis (PL). Some MHC class II gene polymorphisms have been associated with resistance and susceptibility to the development of lymphosarcoma and PL, as well as with a reduced number of circulating BLV-infected lymphocytes. Previously, 230 BLV-infected Holstein cattle were classified into two infection profiles characterized by low and high proviral loads (LPL and HPL respectively). Here, the influence of the polymorphism at the BoLA-DRB3.2* gene of these animals was examined. After genotyping, the association between the BoLA-DRB3.2* alleles and the BLV infection profile was determined as the odds ratio (OR). Two subtypes of allele *11 were identified (ISAG*0901 and *0902). Allele ISAG*0902 showed a stronger association with the LPL profile (OR = 8.24; P < 0.0001) than allele *11 itself (OR = 5.82; P < 0.0001). Allele ISAG*1701 (*12) also showed significant association with the LPL profile (OR = 3.46; P < 0.0055). Only one allele, ISAG*1501 or 03 (*16), showed significant association with HPL (OR = 0.36; P < 0.0005). The DRB3.2* alleles were assigned to three categories: resistant (R), susceptible (S) and neutral (N). Based on their DRB3 genotypes, cattle were classified as homozygous or heterozygous. The RR and RN genotypes were associated with the LPL profile, while the SS and NS genotypes were associated with the HPL profile. The RS genotype could not be associated with any particular profile. Our results show that allele ISAG*0902 appears to be the best BLV resistance marker in Holstein cattle.

  19. Is serotonin transporter polymorphism (5-HTTLPR) allele status a predictor for obsessive-compulsive disorder? A meta-analysis.

    PubMed

    Mak, Lauren; Streiner, David L; Steiner, Meir

    2015-06-01

    The serotonin transporter polymorphism has been implicated in obsessive-compulsive disorder (OCD). However, molecular genetic association studies have yielded inconsistent results. Variation may be due to lack of OCD subtype classification. The goal of this systematic review is to investigate the association of the S-allele of the serotonin transporter polymorphism with OCD and OCD subtypes. A total of 69 studies were initially found through a systematic search of the literature but only 13 with sufficient information to compute odds ratios were suitable for review. A total of 1991 participants with OCD and their 5-HTTLPR allele status were examined. The primary outcome measures were allele frequency and OCD diagnosis. A full meta-analysis was completed comparing the L- and S-alleles using a random effects model in RevMan 5.2.1. Further, a secondary meta-analysis stratified by sex and late-onset was conducted for S- versus L-allele frequency. In the primary meta-analysis, OCD was not associated with the S-allele of the 5-HTTLPR polymorphism (Z = 0.07, p = 0.94). Moreover, late-onset OCD was not associated with the S-allele (Z = 1.45, p = 0.15). However, when stratified by sex, there is an emerging sex-specific relationship. There was a trending association between the S-allele and OCD status in females (Z = 1.62, p = 0.10) but not in males (Z = 0.69, p = 0.49). The findings provide further support for the need of subtype classification of this heterogeneous disorder. Future studies should clearly examine sex differences and OCD age-of-onset. In particular, emphasis should be placed on the effect of female reproductive milestones on OCD onset and symptom exacerbation.

  20. Levels in doubly odd 138Pr

    NASA Astrophysics Data System (ADS)

    Gangopadhyay, G.; Bhowal, Samit; Bhowmik, R. K.; Datta Pramanik, U.; Ghosh, P.; Goswami, A.; Petrache, C.; Mukherjee, A.; Muralithar, S.; Raut, Rajarshi; Saha Sarkar, M.; Singh, A. K.; Singh, R. P.; Bhattacharya, S.

    2005-05-01

    The band structures of the doubly odd 138Pr nucleus have been investigated using the 128Te(14N, 4n)138Pr reaction at a beam energy of 55-65 MeV. Altogether six distinct structures have been established, of which the lower part of the yrast band and two side bands were known from earlier works. The observed level properties of the members of the yrast band have been compared with theoretical calculations performed within the Particle Rotor Model (PRM) with axially symmetric core. The experimental branching ratios and B(M1)/B(E2) values when compared with the theoretical results of the PRM, suggest an oblate core.

  1. Population-based analysis of Alzheimer’s disease risk alleles implicates genetic interactions

    PubMed Central

    Ebbert, Mark T. W.; Ridge, Perry G.; Wilson, Andrew R.; Sharp, Aaron R.; Bailey, Matthew; Norton, Maria C.; Tschanz, JoAnn T.; Munger, Ronald G.; Corcoran, Christopher D.; Kauwe, John S. K.

    2013-01-01

    Background Reported odds ratios and population attributable fractions (PAF) for late-onset Alzheimer’s disease (LOAD) risk loci (BIN1, ABCA7, CR1, MS4A4E, CD2AP, PICALM, MS4A6A, CD33, and CLU) come from clinically ascertained samples. Little is known about the combined PAF for these LOAD risk alleles and the utility of these combined markers for case-control prediction. Here we evaluate these loci in a large population-based sample to estimate PAF and explore the effects of additive and non-additive interactions on LOAD status prediction performance. Methods 2,419 samples from the Cache County Memory Study were genotyped for APOE and nine LOAD risk loci from AlzGene.org. We used logistic regression and ROC analysis to assess the LOAD status prediction performance of these loci using additive and non-additive models, and compared ORs and PAFs between AlzGene.org and Cache County. Results Odds ratios were comparable between Cache County and AlzGene.org when identical SNPs were genotyped. PAFs from AlzGene.org ranged from 2.25–37%; those from Cache County ranged from 0.05–20%. Including non-APOE alleles significantly improved LOAD status prediction performance (AUC = 0.80) over APOE alone (AUC = 0.78) when not constrained to an additive relationship (p < 0.03). We identified potential allelic interactions (p-values uncorrected): CD33-MS4A4E (Synergy Factor = 5.31; p < 0.003) and CLU-MS4A4E (SF = 3.81; p < 0.016). Conclusions While non-additive interactions between loci significantly improve diagnostic ability, the improvement does not reach the desired sensitivity or specificity for clinical use. Nevertheless, these results suggest that understanding gene-gene interactions may be important in resolving Alzheimer’s disease etiology. PMID:23954108

  2. Worldwide ethnic distribution of the G protein beta3 subunit 825T allele and its association with obesity in Caucasian, Chinese, and Black African individuals.

    PubMed

    Siffert, W; Forster, P; Jöckel, K H; Mvere, D A; Brinkmann, B; Naber, C; Crookes, R; Du P Heyns, A; Epplen, J T; Fridey, J; Freedman, B I; Müller, N; Stolke, D; Sharma, A M; Al Moutaery, K; Grosse-Wilde, H; Buerbaum, B; Ehrlich, T; Ahmad, H R; Horsthemke, B; Du Toit, E D; Tiilikainen, A; Ge, J; Wang, Y; Rosskopf, D

    1999-09-01

    Recently, it was demonstrated that one allele (825T) of the gene encoding the G protein beta3 subunit (GNB3) is associated with hypertension in Germans. This study investigates a possible association with obesity in young male Germans, Chinese, and black South Africans with low, intermediate, and high 825T allele frequencies, respectively. In each of these three distinct cohorts, the 825T allele frequency was increased significantly in overweight (body mass index [BMI] > or =25 kg/m2) and obese individuals (BMI >27 kg/m2) compared to those with normal weight. The 825T allele frequencies in these three BMI groups were, respectively, 29.5, 39.3, and 47.7% in Germans, 46.8, 53.9, and 58.6% in Chinese, and 83.1, 87.7, and 90.9% in South Africans. In each of these three distinct groups, the 825T allele was significantly associated with obesity with odds ratios between 2 and 3. More urban than rural black Africans were overweight despite similar 825T allele frequencies in both populations, which underscores the role of both genetic and environmental factors. BP values in young male whites increased significantly with increasing BMI values but were independent of the C825T polymorphism, suggesting that hypertension associated with the 825T allele could be a consequence of obesity. Genotyping of 5254 individuals from 55 native population samples from Africa, the Americas, Europe, Asia, Australia, and New Guinea demonstrated highest 825T allele frequencies in black Africans (82%) and intermediate values in east Asians (47%). It is anticipated that high frequencies of the 825T allele in Africans and Asians may contribute to an obesity and hypertension epidemic if Westernization of lifestyles continues.

  3. Dual role of vitamin D-binding protein 1F allele in chronic obstructive pulmonary disease susceptibility: a meta-analysis.

    PubMed

    Xiao, M; Wang, T; Zhu, T; Wen, F

    2015-04-17

    Vitamin D-binding protein (DBP), a highly polymorphic serum protein, encoded by GC gene, is important in the development of chronic obstructive pulmonary disease (COPD). This meta-analysis was performed to assess the association between GC polymorphisms (1F, 1S, and 2 alleles) and COPD susceptibility. Published case-control studies were retrieved from the Pubmed, Embase, and China National Knowledge Infrastructure databases. After data extraction, pooled odds ratios (ORs) with 95% confidence intervals (CIs) were calculated. Seven case-control studies were included. Pooled effect size showed that GC polymorphisms were not significantly associated with COPD susceptibility. According to ethnicity, the 1F allele was significantly correlated with COPD susceptibility in Asians (1F vs 1S, OR: 1.52, 95%CI: 1.16-2.00 and 1F vs 2, OR: 1.87, 95%CI: 1.42-2.44), indicating that individuals with the 1F allele have an increased risk of COPD compared to those with the 1S or 2 allele. However, the 1F allele was associated with a lower, insignificant risk of COPD than the 1S and 2 alleles in Caucasians (1F vs 1S, OR: 0.83, 95%CI: 0.64-1.08 and 1F vs 2, OR: 0.73, 95%CI: 0.54-0.98). Moreover, no significant association was found for the 1S and 2 alleles in Asians (OR: 1.23, 95%CI: 0.90- 1.69) and Caucasians (OR: 0.89, 95%CI: 0.70-1.13). After excluding each study, the pooled results were robust and no publication bias was observed. We found that the GC 1F allele confers a risk of COPD in Asians, whereas the 1F allele may protect against COPD in Caucasians.

  4. Use of prior odds for missing persons identifications

    PubMed Central

    2011-01-01

    Identification of missing persons from mass disasters is based on evaluation of a number of variables and observations regarding the combination of features derived from these variables. DNA typing now is playing a more prominent role in the identification of human remains, and particularly so for highly decomposed and fragmented remains. The strength of genetic associations, by either direct or kinship analyses, is often quantified by calculating a likelihood ratio. The likelihood ratio can be multiplied by prior odds based on nongenetic evidence to calculate the posterior odds, that is, by applying Bayes' Theorem, to arrive at a probability of identity. For the identification of human remains, the path creating the set and intersection of variables that contribute to the prior odds needs to be appreciated and well defined. Other than considering the total number of missing persons, the forensic DNA community has been silent on specifying the elements of prior odds computations. The variables include the number of missing individuals, eyewitness accounts, anthropological features, demographics and other identifying characteristics. The assumptions, supporting data and reasoning that are used to establish a prior probability that will be combined with the genetic data need to be considered and justified. Otherwise, data may be unintentionally or intentionally manipulated to achieve a probability of identity that cannot be supported and can thus misrepresent the uncertainty with associations. The forensic DNA community needs to develop guidelines for objectively computing prior odds. PMID:21707977

  5. Odds of observing the multiverse

    SciTech Connect

    Dahlen, A.

    2010-03-15

    Eternal inflation predicts that our observable universe lies within a bubble (or pocket universe) embedded in a volume of inflating space. The interior of the bubble undergoes inflation and standard cosmology, while the bubble walls expand outward and collide with other neighboring bubbles. The collisions provide either an opportunity to make a direct observation of the multiverse or, if they produce unacceptable anisotropy, a threat to inflationary theory. The probability of an observer in our bubble detecting the effects of collisions has an absolute upper bound set by the odds of being in the part of our bubble that lies in the forward light cone of a collision; in the case of collisions with bubbles of identical vacua, this bound is given by the bubble nucleation rate times (H{sub O}/H{sub I}){sup 2}, where H{sub O} is the Hubble scale outside the bubbles and H{sub I} is the scale of the second round of inflation that occurs inside our bubble. Similar results were obtained by Freigovel et al. using a different method for the case of collisions with bubbles of much larger cosmological constant; here, it is shown to hold in the case of collisions with identical bubbles as well.

  6. General parity-odd CMB bispectrum estimation

    SciTech Connect

    Shiraishi, Maresuke; Liguori, Michele; Fergusson, James R. E-mail: michele.liguori@pd.infn.it

    2014-05-01

    We develop a methodology for estimating parity-odd bispectra in the cosmic microwave background (CMB). This is achieved through the extension of the original separable modal methodology to parity-odd bispectrum domains (ℓ{sub 1}+ℓ{sub 2}+ℓ{sub 3} = odd). Through numerical tests of the parity-odd modal decomposition with some theoretical bispectrum templates, we verify that the parity-odd modal methodology can successfully reproduce the CMB bispectrum, without numerical instabilities. We also present simulated non-Gaussian maps produced by modal-decomposed parity-odd bispectra, and show the consistency with the exact results. Our new methodology is applicable to all types of parity-odd temperature and polarization bispectra.

  7. Natalizumab-related anaphylactoid reactions in MS patients are associated with HLA class II alleles

    PubMed Central

    de la Hera, Belén; Urcelay, Elena; Brassat, David; Chan, Andrew; Vidal-Jordana, Angela; Salmen, Anke; Villar, Luisa Maria; Álvarez-Cermeño, José Carlos; Izquierdo, Guillermo; Fernández, Oscar; Oliver, Begoña; Saiz, Albert; Ara, Jose Ramón; Vigo, Ana G.; Arroyo, Rafael; Meca, Virginia; Malhotra, Sunny; Fissolo, Nicolás; Horga, Alejandro; Montalban, Xavier

    2014-01-01

    Objectives: We aimed to investigate potential associations between human leukocyte antigen (HLA) class I and class II alleles and the development of anaphylactic/anaphylactoid reactions in patients with multiple sclerosis (MS) treated with natalizumab. Methods: HLA class I and II genotyping was performed in patients with MS who experienced anaphylactic/anaphylactoid reactions and in patients who did not develop infusion-related allergic reactions following natalizumab administration. Results: A total of 119 patients with MS from 3 different cohorts were included in the study: 54 with natalizumab-related anaphylactic/anaphylactoid reactions and 65 without allergic reactions. HLA-DRB1*13 and HLA-DRB1*14 alleles were significantly increased in patients who developed anaphylactic/anaphylactoid reactions (pM-H = 3 × 10−7; odds ratio [OR]M-H = 8.96, 95% confidence interval [CI] = 3.40–23.64), with a positive predictive value (PPV) of 82%. In contrast, the HLA-DRB1*15 allele was significantly more represented in patients who did not develop anaphylactic/anaphylactoid reactions to natalizumab (pM-H = 6 × 10−4; ORM-H = 0.2, 95% CI = 0.08–0.50), with a PPV of 81%. Conclusions: HLA-DRB1 genotyping before natalizumab treatment may help neurologists to identify patients with MS at risk for developing serious systemic hypersensitivity reactions associated with natalizumab administration. PMID:25520955

  8. Observed parity-odd CMB temperature bispectrum

    SciTech Connect

    Shiraishi, Maresuke; Liguori, Michele; Fergusson, James R. E-mail: michele.liguori@pd.infn.it

    2015-01-01

    Parity-odd non-Gaussianities create a variety of temperature bispectra in the cosmic microwave background (CMB), defined in the domain: ℓ{sub 1} + ℓ{sub 2} + ℓ{sub 3} = odd. These models are yet unconstrained in the literature, that so far focused exclusively on the more common parity-even scenarios. In this work, we provide the first experimental constraints on parity-odd bispectrum signals in WMAP 9-year temperature data, using a separable modal parity-odd estimator. Comparing theoretical bispectrum templates to the observed bispectrum, we place constraints on the so-called nonlineality parameters of parity-odd tensor non-Gaussianities predicted by several Early Universe models. Our technique also generates a model-independent, smoothed reconstruction of the bispectrum of the data for parity-odd configurations.

  9. Association of HLA-DRB1 alleles with susceptibility to mixed connective tissue disease in Polish patients.

    PubMed

    Paradowska-Gorycka, A; Stypińska, B; Olesińska, M; Felis-Giemza, A; Mańczak, M; Czuszynska, Z; Zdrojewski, Z; Wojciechowicz, J; Jurkowska, M

    2015-11-09

    Mixed connective tissue disease (MCTD) is a systemic autoimmune disease, originally defined as a connective tissue inflammatory syndrome with overlapping features of systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), polymyositis/dermatomyositis (PM/DM) and systemic sclerosis (SSc), characterized by the presence of antibodies against components of the U1 small nuclear ribonucleoprotein (U1snRNP). The aim of the study was to assess the frequency of (high-resolution-typed) DRB1 alleles in a cohort of Polish patients with MCTD (n = 103). Identification of the variants potentially associated with risk and protection was carried out by comparison with the DKMS Polish Bone Marrow Donor Registry (41306 alleles). DRB1*15:01 (odds ratio (OR): 6.06; 95% confidence interval (CI) 4.55-8.06), DRB1*04 (OR: 3.69; 95% CI 2.69-5.01) and *09:01 (OR: 8.12; 95% CI 2.15-21.75) were identified as risk alleles for MCTD, while HLA-DRB1*07:01 allele was found to be protective (OR: 0.50; 95% CI 0.28-0.83). The carrier frequency of the DRB1*01 was higher in MCTD patients compared with controls, although the differences were not statistically significant. Our results confirm the modulating influence of HLA-DRB1 genotypes on development of connective tissue diseases such as MCTD.

  10. Association of HLA-DRB1 alleles with susceptibility to mixed connective tissue disease in Polish patients.

    PubMed

    Paradowska-Gorycka, A; Stypińska, B; Olesińska, M; Felis-Giemza, A; Mańczak, M; Czuszynska, Z; Zdrojewski, Z; Wojciechowicz, J; Jurkowska, M

    2016-01-01

    Mixed connective tissue disease (MCTD) is a systemic autoimmune disease, originally defined as a connective tissue inflammatory syndrome with overlapping features of systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), polymyositis/dermatomyositis (PM/DM) and systemic sclerosis (SSc), characterized by the presence of antibodies against components of the U1 small nuclear ribonucleoprotein (U1snRNP). The aim of the study was to assess the frequency of (high-resolution-typed) DRB1 alleles in a cohort of Polish patients with MCTD (n = 103). Identification of the variants potentially associated with risk and protection was carried out by comparison with the DKMS Polish Bone Marrow Donor Registry (41306 alleles). DRB1*15:01 (odds ratio (OR): 6.06; 95% confidence interval (CI) 4.55-8.06), DRB1*04 (OR: 3.69; 95% CI 2.69-5.01) and *09:01 (OR: 8.12; 95% CI 2.15-21.75) were identified as risk alleles for MCTD, while HLA-DRB1*07:01 allele was found to be protective (OR: 0.50; 95% CI 0.28-0.83). The carrier frequency of the DRB1*01 was higher in MCTD patients compared with controls, although the differences were not statistically significant. Our results confirm the modulating influence of HLA-DRB1 genotypes on development of connective tissue diseases such as MCTD.

  11. Deleterious alleles in the human genome are on average younger than neutral alleles of the same frequency.

    PubMed

    Kiezun, Adam; Pulit, Sara L; Francioli, Laurent C; van Dijk, Freerk; Swertz, Morris; Boomsma, Dorret I; van Duijn, Cornelia M; Slagboom, P Eline; van Ommen, G J B; Wijmenga, Cisca; de Bakker, Paul I W; Sunyaev, Shamil R

    2013-01-01

    Large-scale population sequencing studies provide a complete picture of human genetic variation within the studied populations. A key challenge is to identify, among the myriad alleles, those variants that have an effect on molecular function, phenotypes, and reproductive fitness. Most non-neutral variation consists of deleterious alleles segregating at low population frequency due to incessant mutation. To date, studies characterizing selection against deleterious alleles have been based on allele frequency (testing for a relative excess of rare alleles) or ratio of polymorphism to divergence (testing for a relative increase in the number of polymorphic alleles). Here, starting from Maruyama's theoretical prediction (Maruyama T (1974), Am J Hum Genet USA 6:669-673) that a (slightly) deleterious allele is, on average, younger than a neutral allele segregating at the same frequency, we devised an approach to characterize selection based on allelic age. Unlike existing methods, it compares sets of neutral and deleterious sequence variants at the same allele frequency. When applied to human sequence data from the Genome of the Netherlands Project, our approach distinguishes low-frequency coding non-synonymous variants from synonymous and non-coding variants at the same allele frequency and discriminates between sets of variants independently predicted to be benign or damaging for protein structure and function. The results confirm the abundance of slightly deleterious coding variation in humans.

  12. Association of chronic fatigue syndrome with human leucocyte antigen class II alleles

    PubMed Central

    Smith, J; Fritz, E L; Kerr, J R; Cleare, A J; Wessely, S; Mattey, D L

    2005-01-01

    Background: A genetic component to the development of chronic fatigue syndrome (CFS) has been proposed, and a possible association between human leucocyte antigen (HLA) class II antigens and chronic fatigue immune dysfunction has been shown in some, but not all, studies. Aims: To investigate the role of HLA class II antigens in CFS. Methods: Forty nine patients with CFS were genotyped for the HLA-DRB1, HLA-DQA1, and HLA-DQB1 alleles and the frequency of these alleles was compared with a control group comprising 102 normal individuals from the UK. All patients and controls were from the same region of England and, apart from two patients, were white. Results: Analysis by 2 × 2 contingency tables revealed an increased frequency of HLA-DQA1*01 alleles in patients with CFS (51.0% v 35%; odds ratio (OR), 1.93; p  =  0.008). HLA-DQB1*06 was also increased in the patients with CFS (30.2% v 20.0%; OR, 1.73, p  =  0.052). Only the association between HLA-DQA1*01 and CFS was significant in logistic regression models containing HLA-DQA1*01 and HLA-DRQB1*06, and this was independent of HLA-DRB1 alleles. There was a decreased expression of HLA-DRB1*11 in CFS, although this association disappeared after correction for multiple comparisons. Conclusions: CFS may be associated with HLA-DQA1*01, although a role for other genes in linkage disequilibrium cannot be ruled out. PMID:16049290

  13. The Arg160Trp allele of melanocortin-1 receptor gene might protect against vitiligo.

    PubMed

    Széll, Márta; Baltás, Eszter; Bodai, László; Bata-Csörgo, Zsuzsanna; Nagy, Nikoletta; Dallos, Attila; Pourfarzi, Reza; Simics, Eniko; Kondorosi, Ildikó; Szalai, Zsuzsanna; Tóth, Gábor K; Hunyadi, János; Dobozy, Attila; Kemény, Lajos

    2008-01-01

    Melanocortin-1 receptor (MC1R) and agouti signaling protein (ASIP) play pivotal roles in the regulation of human pigmentation. We aimed to study whether single nucleotide polymorphisms (SNPs) of the MC1R and ASIP genes contribute to the pathogenesis of the polygenic pigment skin disorder, vitiligo. The PCR-amplified, full-length MC1R gene was studied with sequence analysis, and the 3' untranslated region (3' UTR) SNP of ASIP was detected using restriction fragment length polymorphism. The allele frequency of the ASIP SNP did not show any difference between the skin type, hair color and eye color-matched 97 vitiligo patients and the 59 healthy control individuals. As one of the MC1R polymorphisms showed significantly higher incidence among fair-skinned individuals (Fitzpatrick I+II, n=140) than among dark-skinned individuals (Fitzpatrick III+IV, n=90), both vitiligo patients and controls were divided into two groups and the frequency of the MC1R alleles was studied separately in fair-skinned and dark-skinned subgroups of diseased and healthy groups. C478T, one of the MC1R SNPs studied in 108 fair-skinned vitiligo patients and in 70 fair-skinned healthy control individuals, showed a significant difference (P=0.0262, odds ratio [95% confidence interval]=3.6 [0.0046-0.1003]) in allele frequency between the two groups: the allele frequency was higher in the control group, suggesting protection against vitiligo. Computer prediction of antigenicity has revealed that the Arg160Trp amino acid change caused by this SNP results in a decrease in antigenicity of the affected peptide epitope.

  14. Structure evolution and phase transition in odd-mass nuclei

    NASA Astrophysics Data System (ADS)

    Bucurescu, D.; Zamfir, N. V.

    2017-01-01

    The evolution of level structures due to the unique parity orbitals g9 /2, h11 /2, and i13 /2 in odd-mass nuclei from Zn to Am is studied within a unified framework, by correlations between ratios of excitation energies in both odd-mass nuclei and their even-even core nuclei. These plots reveal regularities that can be understood in terms of the particle-plus-rotor model, as evolutions along its three limiting coupling schemes: weak coupling, decoupling, and strong coupling, and transitions between them. Peculiar transitions between the decoupling and strong coupling schemes are found in both i13 /2 structures of neutron-odd nuclei and h11 /2 structures of proton-odd nuclei, at neutron numbers around 90 and 70, respectively. These are correlated with the critical shape phase transitions from vibrator to rotor from the even-even nuclei in the same regions and are characterized as critical phase transitions too. This behavior is corroborated with a nonmonotonic behavior of the differential variation of the two-neutron separation energies in the same nuclear regions.

  15. Topology Explains Why Automobile Sunshades Fold Oddly

    ERIC Educational Resources Information Center

    Feist, Curtis; Naimi, Ramin

    2009-01-01

    Automobile sunshades always fold into an "odd" number of loops. The explanation why involves elementary topology (braid theory and linking number, both explained in detail here with definitions and examples), and an elementary fact from algebra about symmetric group.

  16. Intrinsic excitations in doubly odd nuclei

    SciTech Connect

    Sood, P.C.

    1985-01-15

    A procedure is outlined for predicting the bandhead energies of the two-particle (intrinsic) states of odd-odd deformed nuclei based on a quantitative evaluation of the zero range n-p residual interaction energy. We present our results for 250Bk, where many such levels are experimentally known, and for 236Np and 246Am, where the information is very scarce and that too uncertain, to illustrate the effectiveness of this approach.

  17. The variant allele of the rs188140481 polymorphism confers a moderate increase in the risk of prostate cancer in Polish men.

    PubMed

    Antczak, Andrzej; Wokołorczyk, Dominika; Kluźniak, Wojciech; Kashyap, Aniruddh; Jakubowska, Anna; Gronwald, Jacek; Huzarski, Tomasz; Byrski, Tomasz; Dębniak, Tadeusz; Masojć, Bartłomiej; Górski, Bohdan; Gromowski, Tomasz; Gołąb, Adam; Sikorski, Andrzej; Słojewski, Marcin; Gliniewicz, Bartłomiej; Borkowski, Tomasz; Borkowski, Andrzej; Przybyła, Jacek; Sosnowski, Marek; Małkiewicz, Bartosz; Zdrojowy, Romuald; Sikorska-Radek, Paulina; Matych, Józef; Wilkosz, Jacek; Różański, Waldemar; Kiś, Jacek; Bar, Krzysztof; Janiszewska, Hanna; Stawicka, Małgorzata; Milecki, Piotr; Lubiński, Jan; Narod, Steven A; Cybulski, Cezary

    2015-03-01

    A number of single nucleotide polymorphisms (SNPs) in the human genome have been associated with increased risk of prostate cancer. Recently, a single SNP in the region of chromosome 8q24 (rs188140481) has been associated with a three-fold increased risk of prostate cancer in Europe and North America. To establish whether rs188140481 is associated with the risk of prostate cancer in Poland, we genotyped 3467 men with prostate cancer and 1958 controls. The A allele of rs188140481 was detected in 44 of 3467 (1.3%) men with prostate cancer and in seven of 1958 (0.4%) controls (odds ratio=3.6; 95% confidence interval 1.6-7.9; P=0.0006). The allele was present in eight of 390 (2.1%) men with familial prostate cancer (odds ratio=5.8; 95% confidence interval 2.1-16.2; P=0.001). A positive family history of cancers at sites other than the prostate was observed in 27% of men who carried the rs188140481 risk allele and in 44% of noncarriers (P=0.04). No cancer at a site other than the prostate was more common in first-degree or second-degree relatives of carriers of the rs188140481 risk allele than relatives of noncarriers. The rs188140481 polymorphism in the 8q24 region confers a moderate increase in the risk of prostate cancer in Polish men. The SNP does not appear to be associated with susceptibility to cancers of other types.

  18. Extremal charged rotating black holes in odd dimensions

    SciTech Connect

    Allahverdizadeh, Masoud; Kunz, Jutta; Navarro-Lerida, Francisco

    2010-07-15

    Employing higher order perturbation theory, we obtain charged rotating black holes in odd dimensions, where the Einstein-Maxwell Lagrangian may be supplemented with a Chern-Simons term. Starting from the Myers-Perry solutions, we use the electric charge as the perturbative parameter and focus on extremal black holes with equal-magnitude angular momenta. For Einstein-Maxwell-Chern-Simons theory with arbitrary Chern-Simons coupling constant, we perform the perturbations up to 3rd order for any odd dimension. We discuss the physical properties of these black holes and study their dependence on the charge. In particular, we show that the gyromagnetic ratio g of Einstein-Maxwell black holes differs from the lowest order perturbative value D-2, and that the first correction term to g/(D-2) is universal.

  19. Allelic polymorphism in IL-1 beta and IL-1 receptor antagonist (IL-1Ra) genes in inflammatory bowel disease.

    PubMed Central

    Bioque, G; Crusius, J B; Koutroubakis, I; Bouma, G; Kostense, P J; Meuwissen, S G; Peña, A S

    1995-01-01

    Recent reports have shown that allele 2 of the IL-1 receptor antagonist (IL-1Ra) gene is over-represented in ulcerative colitis (UC). Healthy individuals carrying allele 2 of this gene have increased production of IL-1Ra protein. Since the final outcome of the biological effects of IL-1 beta may depend on the relative proportion of these two cytokines, we have studied if a TaqI polymorphism in the IL-1 beta gene, which is relevant to IL-1 beta protein production, may be involved in the genetic susceptibility to UC and Crohn's disease (CD), in association with the established IL-1Ra gene polymorphism. Polymorphisms in the closely linked genes for IL-1 beta and IL-1Ra were typed in 100 unrelated Dutch patients with UC, 79 with CD, and 71 healthy controls. The polymorphic regions in exon 5 of the IL-1 beta gene and in intron 2 of the IL-1Ra gene, were studied by polymerase chain reaction (PCR)-based methods. The IL-1 beta allele frequencies in UC and CD patients did not differ from those in healthy controls. In order to study if the IL-1 beta gene polymorphism might participate synergistically with the IL-1Ra gene polymorphism in susceptibility to UC and CD, individuals were distributed into carriers and non-carriers of allele 2 of the genes encoding IL-1 beta and IL-1Ra, in each of the patient groups and controls. Results indicated a significant association of this pair of genes, estimated by the odds ratio (OR) after performing Fisher's exact test, in the UC group (P = 0.023, OR = 2.81), as well as in the CD group (P = 0.01, OR = 3.79). Thus, non-carriers of IL-1 beta allele 2 were more often present in the subgroup of patients carrying the IL-1Ra allele 2. By contrast, no association of these alleles was detected in the group of healthy controls (P = 1.00, OR = 0.92). These results suggest that the IL-1 beta/IL-1Ra allelic cluster may participate in defining the biological basis of predisposition to chronic inflammatory bowel diseases. PMID:7586694

  20. MicroRNA-3148 Modulates Allelic Expression of Toll-Like Receptor 7 Variant Associated with Systemic Lupus Erythematosus

    PubMed Central

    Sakurai, Daisuke; Kaufman, Kenneth M.; Edberg, Jeffrey C.; Kimberly, Robert P.; Kamen, Diane L.; Gilkeson, Gary S.; Jacob, Chaim O.; Scofield, R. Hal; Langefeld, Carl D.; Kelly, Jennifer A.; Ramsey-Goldman, Rosalind; Petri, Michelle A.; Reveille, John D.; Vilá, Luis M.; Alarcón, Graciela S.; Vyse, Timothy J.; Pons-Estel, Bernardo A.; Freedman, Barry I.; Gaffney, Patrick M.; Sivils, Kathy Moser; James, Judith A.; Gregersen, Peter K.; Anaya, Juan-Manuel; Niewold, Timothy B.; Merrill, Joan T.; Criswell, Lindsey A.; Stevens, Anne M.; Boackle, Susan A.; Cantor, Rita M.; Chen, Weiling; Grossman, Jeniffer M.; Hahn, Bevra H.; Harley, John B.; Alarcόn-Riquelme, Marta E.; Brown, Elizabeth E.; Tsao, Betty P.

    2013-01-01

    We previously reported that the G allele of rs3853839 at 3′untranslated region (UTR) of Toll-like receptor 7 (TLR7) was associated with elevated transcript expression and increased risk for systemic lupus erythematosus (SLE) in 9,274 Eastern Asians [P = 6.5×10−10, odds ratio (OR) (95%CI) = 1.27 (1.17–1.36)]. Here, we conducted trans-ancestral fine-mapping in 13,339 subjects including European Americans, African Americans, and Amerindian/Hispanics and confirmed rs3853839 as the only variant within the TLR7-TLR8 region exhibiting consistent and independent association with SLE (P meta = 7.5×10−11, OR = 1.24 [1.18–1.34]). The risk G allele was associated with significantly increased levels of TLR7 mRNA and protein in peripheral blood mononuclear cells (PBMCs) and elevated luciferase activity of reporter gene in transfected cells. TLR7 3′UTR sequence bearing the non-risk C allele of rs3853839 matches a predicted binding site of microRNA-3148 (miR-3148), suggesting that this microRNA may regulate TLR7 expression. Indeed, miR-3148 levels were inversely correlated with TLR7 transcript levels in PBMCs from SLE patients and controls (R2 = 0.255, P = 0.001). Overexpression of miR-3148 in HEK-293 cells led to significant dose-dependent decrease in luciferase activity for construct driven by TLR7 3′UTR segment bearing the C allele (P = 0.0003). Compared with the G-allele construct, the C-allele construct showed greater than two-fold reduction of luciferase activity in the presence of miR-3148. Reduced modulation by miR-3148 conferred slower degradation of the risk G-allele containing TLR7 transcripts, resulting in elevated levels of gene products. These data establish rs3853839 of TLR7 as a shared risk variant of SLE in 22,613 subjects of Asian, EA, AA, and Amerindian/Hispanic ancestries (Pmeta = 2.0×10−19, OR = 1.25 [1.20–1.32]), which confers allelic effect on transcript turnover via differential binding to the

  1. MicroRNA-3148 modulates allelic expression of toll-like receptor 7 variant associated with systemic lupus erythematosus.

    PubMed

    Deng, Yun; Zhao, Jian; Sakurai, Daisuke; Kaufman, Kenneth M; Edberg, Jeffrey C; Kimberly, Robert P; Kamen, Diane L; Gilkeson, Gary S; Jacob, Chaim O; Scofield, R Hal; Langefeld, Carl D; Kelly, Jennifer A; Ramsey-Goldman, Rosalind; Petri, Michelle A; Reveille, John D; Vilá, Luis M; Alarcón, Graciela S; Vyse, Timothy J; Pons-Estel, Bernardo A; Freedman, Barry I; Gaffney, Patrick M; Sivils, Kathy Moser; James, Judith A; Gregersen, Peter K; Anaya, Juan-Manuel; Niewold, Timothy B; Merrill, Joan T; Criswell, Lindsey A; Stevens, Anne M; Boackle, Susan A; Cantor, Rita M; Chen, Weiling; Grossman, Jeniffer M; Hahn, Bevra H; Harley, John B; Alarcόn-Riquelme, Marta E; Brown, Elizabeth E; Tsao, Betty P

    2013-01-01

    We previously reported that the G allele of rs3853839 at 3'untranslated region (UTR) of Toll-like receptor 7 (TLR7) was associated with elevated transcript expression and increased risk for systemic lupus erythematosus (SLE) in 9,274 Eastern Asians [P = 6.5×10(-10), odds ratio (OR) (95%CI) = 1.27 (1.17-1.36)]. Here, we conducted trans-ancestral fine-mapping in 13,339 subjects including European Americans, African Americans, and Amerindian/Hispanics and confirmed rs3853839 as the only variant within the TLR7-TLR8 region exhibiting consistent and independent association with SLE (Pmeta = 7.5×10(-11), OR = 1.24 [1.18-1.34]). The risk G allele was associated with significantly increased levels of TLR7 mRNA and protein in peripheral blood mononuclear cells (PBMCs) and elevated luciferase activity of reporter gene in transfected cells. TLR7 3'UTR sequence bearing the non-risk C allele of rs3853839 matches a predicted binding site of microRNA-3148 (miR-3148), suggesting that this microRNA may regulate TLR7 expression. Indeed, miR-3148 levels were inversely correlated with TLR7 transcript levels in PBMCs from SLE patients and controls (R(2) = 0.255, P = 0.001). Overexpression of miR-3148 in HEK-293 cells led to significant dose-dependent decrease in luciferase activity for construct driven by TLR7 3'UTR segment bearing the C allele (P = 0.0003). Compared with the G-allele construct, the C-allele construct showed greater than two-fold reduction of luciferase activity in the presence of miR-3148. Reduced modulation by miR-3148 conferred slower degradation of the risk G-allele containing TLR7 transcripts, resulting in elevated levels of gene products. These data establish rs3853839 of TLR7 as a shared risk variant of SLE in 22,613 subjects of Asian, EA, AA, and Amerindian/Hispanic ancestries (Pmeta  = 2.0×10(-19), OR = 1.25 [1.20-1.32]), which confers allelic effect on transcript turnover via differential binding to the epigenetic factor

  2. Odd-frequency Superconductivity in Driven Systems

    NASA Astrophysics Data System (ADS)

    Triola, Christopher; Balatsky, Alexander

    We show that Berezinskii's classification of the symmetries of Cooper pair amplitudes in terms of parity under transformations that invert spin, space, time, and orbital degrees of freedom holds for driven systems even in the absence of translation invariance. We then discuss the conditions under which pair amplitudes which are odd in frequency can emerge in driven systems. Considering a model Hamiltonian for a superconductor coupled to an external driving potential, we investigate the influence of the drive on the anomalous Green's function, density of states, and spectral function. We find that the anomalous Green's function develops odd in frequency component in the presence of an external drive. Furthermore we investigate how these odd-frequency terms are related to satellite features in the density of states and spectral function. Supported by US DOE BES E 304.

  3. Odd-frequency superconductivity in driven systems

    NASA Astrophysics Data System (ADS)

    Triola, Christopher; Balatsky, Alexander V.

    2016-09-01

    We show that Berezinskii's classification of the symmetries of Cooper pair amplitudes holds for driven systems even in the absence of translation invariance. We then consider a model Hamiltonian for a superconductor coupled to an external driving potential and, treating the drive as a perturbation, we investigate the corrections to the anomalous Green's function, density of states, and spectral function. We find that in the presence of an external drive the anomalous Green's function develops terms that are odd in frequency and that the same mechanism responsible for these odd-frequency terms generates additional features in the density of states and spectral function.

  4. Assignment of SNP allelic configuration in polyploids using competitive allele-specific PCR: application to citrus triploid progeny

    PubMed Central

    Cuenca, José; Aleza, Pablo; Navarro, Luis; Ollitrault, Patrick

    2013-01-01

    Background Polyploidy is a major component of eukaryote evolution. Estimation of allele copy numbers for molecular markers has long been considered a challenge for polyploid species, while this process is essential for most genetic research. With the increasing availability and whole-genome coverage of single nucleotide polymorphism (SNP) markers, it is essential to implement a versatile SNP genotyping method to assign allelic configuration efficiently in polyploids. Scope This work evaluates the usefulness of the KASPar method, based on competitive allele-specific PCR, for the assignment of SNP allelic configuration. Citrus was chosen as a model because of its economic importance, the ongoing worldwide polyploidy manipulation projects for cultivar and rootstock breeding, and the increasing availability of SNP markers. Conclusions Fifteen SNP markers were successfully designed that produced clear allele signals that were in agreement with previous genotyping results at the diploid level. The analysis of DNA mixes between two haploid lines (Clementine and pummelo) at 13 different ratios revealed a very high correlation (average = 0·9796; s.d. = 0·0094) between the allele ratio and two parameters [θ angle = tan−1 (y/x) and y′ = y/(x + y)] derived from the two normalized allele signals (x and y) provided by KASPar. Separated cluster analysis and analysis of variance (ANOVA) from mixed DNA simulating triploid and tetraploid hybrids provided 99·71 % correct allelic configuration. Moreover, triploid populations arising from 2n gametes and interploid crosses were easily genotyped and provided useful genetic information. This work demonstrates that the KASPar SNP genotyping technique is an efficient way to assign heterozygous allelic configurations within polyploid populations. This method is accurate, simple and cost-effective. Moreover, it may be useful for quantitative studies, such as relative allele-specific expression analysis and bulk segregant analysis

  5. Confusion between Odds and Probability, a Pandemic?

    ERIC Educational Resources Information Center

    Fulton, Lawrence V.; Mendez, Francis A.; Bastian, Nathaniel D.; Musal, R. Muzaffer

    2012-01-01

    This manuscript discusses the common confusion between the terms probability and odds. To emphasize the importance and responsibility of being meticulous in the dissemination of information and knowledge, this manuscript reveals five cases of sources of inaccurate statistical language imbedded in the dissemination of information to the general…

  6. PARITY ODD BUBBLES IN HOT QCD.

    SciTech Connect

    KHARZEEV,D.; PISARSKI,R.D.; TYTGAT,M.H.G.

    1998-04-16

    We consider the topological susceptibility for an SU(N) gauge theory in the limit of a large number of colors, N {r_arrow} {infinity}. At nonzero temperature, the behavior of the topological susceptibility depends upon the order of the deconfining phase transition. The most interesting possibility is if the deconfining transition, at T = T{sub d}, is of second order. Then we argue that Witten's relation implies that the topological susceptibility vanishes in a calculable fashion at Td. As noted by Witten, this implies that for sufficiently light quark masses, metastable states which act like regions of nonzero {theta}--parity odd bubbles--can arise at temperatures just below T{sub d}. Experimentally, parity odd bubbles have dramatic signatures: the {eta}{prime} meson, and especially the {eta} meson, become light, and are copiously produced. Further, in parity odd bubbles, processes which are normally forbidden, such as {eta} {r_arrow} {pi}{sup 0}{pi}{sup 0}, are allowed. The most direct way to detect parity violation is by measuring a parity odd global asymmetry for charged pions, which we define.

  7. Odd numbers of photons and teleportation

    NASA Astrophysics Data System (ADS)

    Enk, S. J.

    2003-02-01

    Several teleportation protocols, namely those using entangled coherent states, entangled squeezed states, and the single-photon Einstein-Podolsky-Rosen state, are all shown to be particular instances of a more general scheme that relies on the detection of an odd number of photons.

  8. Experimental level-structure determination in odd-odd actinide nuclei

    SciTech Connect

    Hoff, R.W.

    1985-04-04

    The status of experimental determination of level structure in odd-odd actinide nuclei is reviewed. A technique for modeling quasiparticle excitation energies and rotational parameters in odd-odd deformed nuclei is applied to actinide species where new experimental data have been obtained by use of neutron-capture gamma-ray spectroscopy. The input parameters required for the calculation are derived from empirical data on single-particle excitations in neighboring odd-mass nuclei. Calculated configuration-specific values for the Gallagher-Moszkowski splittings are used. Calculated and experimental level structures for /sup 238/Np, /sup 244/Am, and /sup 250/Bk are compared, as well as those for several nuclei in the rare-earth region. The agreement for the actinide species is excellent, with bandhead energies deviating 22 keV and rotational parameters 5%, on the average. Applications of this modeling technique are discussed.

  9. Human leukocyte antigen class II DQB1*0301, DRB1*1101 alleles and spontaneous clearance of hepatitis C virus infection: A meta-analysis

    PubMed Central

    Hong, Xin; Yu, Rong-Bin; Sun, Nan-Xiong; Wang, Bin; Xu, Yao-Chu; Wu, Guan-Ling

    2005-01-01

    AIM: To assess the associations of human leukocyte antigen (HLA) class II DQB1*0301 and/or DRB1*1101 allele with spontaneous hepatitis C virus (HCV) clearance by meta-analysis of individual dataset from all studies published till date. METHODS: To clarify the impact of HLA class II polymorphisms on viral clearance, we performed a meta-analysis of the published data from 11 studies comparing the frequencies of DQB1*0301 and DRB1*1101 alleles in individuals with spontaneous resolution to those with persistent infection. As we identified the heterogeneity between studies, summary statistical data were calculated based on a random-effect model. RESULTS: Meta-analyses yielded summary estimates-odds ratio (OR) of 2.36 [95%CI (1.62, 3.43), P<0.00001] and 2.02 [95%CI (1.56, 2.62), P<0.00001] for the effects of DQB1*0301 and DRB1*1101 alleles on spontaneous clearance of HCV, respectively. CONCLUSION: These results support the hypothesis that specific HLA class II alleles might influence the susceptibility or resistance to persistent HCV infection. Both DQB1*0301 and DRB1*1101 are protective alleles and present HCV epitopes more effectively to CD4+T lymphocytes than others, and subjects with these two alleles are at a lower risk of developing chronic HCV infection. Large, multi-ethnic confirmatory and well-designed studies are needed to determine the host genetic determinants of HCV infection. PMID:16437632

  10. (abstract) Odd Hydrogen in the Atmospheres of Earth and Mars

    NASA Technical Reports Server (NTRS)

    Nair, Hari; Allen, Mark; Yung, Yuk L.

    1994-01-01

    The Martian atmosphere has many features in common with the terrestrial mesosphere. Both share similar pressure and temperature ranges, and much of the same chemistry operates in each. For example, the radical species H, OH, and H(sub 2)O, which comprise the odd hydrogen family, are of central importance in the catalytic destruction of CO and O(sub 3) in both atmospheres. The inclusion of recent chemical kinetics data, specifically temperature dependent CO(sub 2) absorption cross-sections, into our one dimensional photochemical model of the Martial atmosphere shows that oxidation of CO by odd hydrogen is too efficient. The incorporation of smaller cross sections for CO(sub 2) leads to an enhanced photolysis rate of water vapor, increasing odd hydrogen to the point where the predicted mixing ratio of CO in our model is substantially less than the observed value of 6.5 x 10(sup -4). Interestingly, most photochemical models of the terrestrial mesosphere underestimate the CO and O(sub 3) densities using currently accepted photodissociation and kinetic rate coefficients. This has also been attributed to an overabundance of odd hydrogen in the models. We shall show that agreement between models and observations of CO in the Martian atmosphere as well as of CO and O(sub 3) in the terrestrial mesosphere can be achieved by revising the rate constants for the reactions OH + HO(sub 2) and CO + OH within their published uncertainties. The fact that similar revisions alleviate discrepancies in both the terrestrial and Martian atmospheres warrants a re-evaluation of these key rate constants at the appropriate temperatures and pressures.

  11. Spectroscopic evidence of odd frequency superconducting order

    PubMed Central

    Pal, Avradeep; Ouassou, J. A.; Eschrig, M.; Linder, J.; Blamire, M. G.

    2017-01-01

    Spin filter superconducting S/I/N tunnel junctions (NbN/GdN/TiN) show a robust and pronounced Zero Bias Conductance Peak (ZBCP) at low temperatures, the magnitude of which is several times the normal state conductance of the junction. Such a conductance anomaly is representative of unconventional superconductivity and is interpreted as a direct signature of an odd frequency superconducting order. PMID:28106102

  12. The profile of HLA-DRB1 alleles in Arabs with type 1 diabetes; meta-analyses.

    PubMed

    Hamzeh, A R; Nair, P; Al Ali, M T

    2016-01-01

    Genes from the HLA complex have a major contribution in type 1 diabetes (T1D), which results from an interplay between environmental and genetic factors. The latter can explain some of the geographic variability in T1D occurrence around the world. Of a particular importance in this regard are the HLA-DR, -DP and -DQ loci. Consequently, we aimed at elucidating the collective genetic profiles of various alleles relating to HLA-DRB1 and -DP in T1D patients throughout the Arab World using the tools of meta-analysis. As for HLA-DQA1 and DQB1 alleles; this analysis was completed and published previously (see Introduction). As a result of limited availability of relevant studies of the HLA-DP locus, only HLA-DRB1 alleles were tackled in this paper. Our study showed that significant increases in T1D risk resulted from harboring the alleles DRB1*03:01 and *04:05 (odds ratio 7.76 and 7.52, respectively). DRB1*04:01 and *04:02 were also predisposing for T1D in Arabs. Very strong evidence supported the protective effects of DRB1*10:01, *13:01, *15:02 and *16:01, with low heterogeneity and no publication bias. The results from the series of meta-analyses performed in this study help to complete the global genetic epidemiological map of T1D by providing statistically robust data from the Arab World.

  13. The profile of HLA-DRB1 alleles in Arabs with type 1 diabetes; meta-analyses.

    PubMed

    Hamzeh, A R; Nair, P; Al Ali, M T

    2015-12-02

    Genes from the HLA complex have a major contribution in type 1 diabetes (T1D), which results from an interplay between environmental and genetic factors. The latter can explain some of the geographic variability in T1D occurrence around the world. Of a particular importance in this regard are the HLA-DR, -DP and -DQ loci. Consequently, we aimed at elucidating the collective genetic profiles of various alleles relating to HLA-DRB1 and -DP in T1D patients throughout the Arab World using the tools of meta-analysis. As for HLA-DQA1 and DQB1 alleles; this analysis was completed and published previously (see Introduction). As a result of limited availability of relevant studies of the HLA-DP locus, only HLA-DRB1 alleles were tackled in this paper. Our study showed that significant increases in T1D risk resulted from harboring the alleles DRB1*03:01 and *04:05 (odds ratio 7.76 and 7.52, respectively). DRB1*04:01 and *04:02 were also predisposing for T1D in Arabs. Very strong evidence supported the protective effects of DRB1*10:01, *13:01, *15:02 and *16:01, with low heterogeneity and no publication bias. The results from the series of meta-analyses performed in this study help to complete the global genetic epidemiological map of T1D by providing statistically robust data from the Arab World.

  14. HLA-DRB1*14 is a protective allele for multiple sclerosis in an admixed Colombian population

    PubMed Central

    Cuellar-Giraldo, David; Díaz-Cruz, Camilo; Burbano, Lisseth-Estefania; Guío, Claudia-Marcela; Reyes, Saúl; Cortes, Fabián; Cárdenas-Robledo, Simón; Narváez, Diana M.; Cárdenas, Wilmer; Porras, Alexandra; Lattig, María-Claudia; Groot de Restrepo, Helena

    2015-01-01

    Objective: The aim of this study was to determine ancestry informative markers, mitochondrial DNA haplogroups, and the association between HLA-DRB1 alleles and multiple sclerosis (MS) in a group of patients from Bogotá, Colombia. Methods: In this case-control study, genomic DNA was isolated and purified from blood samples. HLA-DRB1 allele genotyping was done using PCR. Mitochondrial hypervariable region 1 was amplified and haplogroups were determined using HaploGrep software. Genomic ancestry was estimated by genotyping a panel of ancestry informative markers. To test the association of HLA polymorphisms and MS, we ran separate multivariate logistic regression models. Bonferroni correction was used to account for multiple regression tests. Results: A total of 100 patients with MS (mean age 40.4 ± 12 years; 70% females) and 200 healthy controls (mean age 37.6 ± 11 years; 83.5% females) were included in the analysis. Ancestry proportions and haplogroup frequencies did not differ between patients and controls. HLA-DRB1*15 was present in 31% of cases and 13.5% of controls, whereas HLA-DRB1*14 was present in 5% of cases and 15.5% of controls. In the multivariate model, HLA-DRB1*15 was significantly associated with MS (odds ratio [OR] = 3.05, p < 0.001), whereas HLA-DRB1*14 was confirmed as a protective factor in our population (OR = 0.16, p = 0.001). Conclusions: This study provides evidence indicating that HLA-DRB1*15 allele confers susceptibility to MS and HLA-DRB1*14 allele exerts resistance to MS in a highly admixed population. This latter finding could partially explain the low prevalence of MS in Bogotá, Colombia. PMID:26740965

  15. What Is a Recessive Allele?

    ERIC Educational Resources Information Center

    American Biology Teacher, 1991

    1991-01-01

    Presents four misconceptions students have concerning the concepts of recessive and dominant alleles. Discusses the spectrum of dominant-recessive relationships, different levels of analysis between phenotype and genotype, possible causes of dominance, and an example involving wrinkled peas. (MDH)

  16. Stratospheric distributions of odd nitrogen and odd hydrogen in a two-dimensional model

    NASA Technical Reports Server (NTRS)

    Prinn, R. G.; Alyea, F. N.; Cunnold, D. M.

    1975-01-01

    A two-dimensional pole-to-pole chemical model of the stratosphere is developed which extends from 8 to 38 km in altitude. Atmospheric motions are simulated by mean vertical and meridional winds and eddy diffusion coefficients. Seasonally averaged distributions of important odd nitrogen (NO, NO2, and HNO3) and odd hydrogen (H, OH, HO2, H2O2) compounds are computed. Photodissociation of N2O leads to production of odd nitrogen in the stratosphere, and the odd nitrogen is ultimately removed by downward transport into the troposphere and by rain-out (modeled by a rain-out lifetime of 30 days below 8-km altitude). Results are presented for a quasi-steady state in which seasonal cycles repeat themselves. These results show significant latitudinal as well as vertical variations in the predicted species which emphasize the need for at least two dimensions in accurate stratospheric modeling. Computed concentrations are compared with observations when they exist.

  17. Choreography of Ig allelic exclusion.

    PubMed

    Cedar, Howard; Bergman, Yehudit

    2008-06-01

    Allelic exclusion guarantees that each B or T cell only produces a single antigen receptor, and in this way contributes to immune diversity. This process is actually initiated in the early embryo when the immune receptor loci become asynchronously replicating in a stochastic manner with one early and one late allele in each cell. This distinct differential replication timing feature then serves an instructive mark that directs a series of allele-specific epigenetic events in the immune system, including programmed histone modification, nuclear localization and DNA demethylation that ultimately bring about preferred rearrangement on a single allele, and this decision is temporally stabilized by feedback mechanisms that inhibit recombination on the second allele. In principle, these same molecular components are also used for controlling monoallelic expression at other genomic loci, such as those carrying interleukins and olfactory receptor genes that require the choice of one gene out of a large array. Thus, allelic exclusion appears to represent a general epigenetic phenomenon that is modeled on the same basis as X chromosome inactivation.

  18. Odd-parity D states in He.

    NASA Technical Reports Server (NTRS)

    Bhatia, A. K.

    1972-01-01

    The states considered lie below the n = 2 threshold of He(+) and decay radiatively to the lower states. The most general D-state wave function of odd parity of two electrons is examined. The results presented are optimized with respect to four nonlinear parameters for 112 terms. A mass-polarization correction is given for all the states listed. The positions of the D states, including the reduced mass and the mass-polarization corrections, with respect to the ground state of He are reported.

  19. Ovarian cancer susceptibility alleles and risk of ovarian cancer in BRCA1 and BRCA2 mutation carriers.

    PubMed

    Ramus, Susan J; Antoniou, Antonis C; Kuchenbaecker, Karoline B; Soucy, Penny; Beesley, Jonathan; Chen, Xiaoqing; McGuffog, Lesley; Sinilnikova, Olga M; Healey, Sue; Barrowdale, Daniel; Lee, Andrew; Thomassen, Mads; Gerdes, Anne-Marie; Kruse, Torben A; Jensen, Uffe Birk; Skytte, Anne-Bine; Caligo, Maria A; Liljegren, Annelie; Lindblom, Annika; Olsson, Håkan; Kristoffersson, Ulf; Stenmark-Askmalm, Marie; Melin, Beatrice; Domchek, Susan M; Nathanson, Katherine L; Rebbeck, Timothy R; Jakubowska, Anna; Lubinski, Jan; Jaworska, Katarzyna; Durda, Katarzyna; Złowocka, Elżbieta; Gronwald, Jacek; Huzarski, Tomasz; Byrski, Tomasz; Cybulski, Cezary; Toloczko-Grabarek, Aleksandra; Osorio, Ana; Benitez, Javier; Duran, Mercedes; Tejada, Maria-Isabel; Hamann, Ute; Rookus, Matti; van Leeuwen, Flora E; Aalfs, Cora M; Meijers-Heijboer, Hanne E J; van Asperen, Christi J; van Roozendaal, K E P; Hoogerbrugge, Nicoline; Collée, J Margriet; Kriege, Mieke; van der Luijt, Rob B; Peock, Susan; Frost, Debra; Ellis, Steve D; Platte, Radka; Fineberg, Elena; Evans, D Gareth; Lalloo, Fiona; Jacobs, Chris; Eeles, Ros; Adlard, Julian; Davidson, Rosemarie; Eccles, Diana; Cole, Trevor; Cook, Jackie; Paterson, Joan; Douglas, Fiona; Brewer, Carole; Hodgson, Shirley; Morrison, Patrick J; Walker, Lisa; Porteous, Mary E; Kennedy, M John; Pathak, Harsh; Godwin, Andrew K; Stoppa-Lyonnet, Dominique; Caux-Moncoutier, Virginie; de Pauw, Antoine; Gauthier-Villars, Marion; Mazoyer, Sylvie; Léoné, Mélanie; Calender, Alain; Lasset, Christine; Bonadona, Valérie; Hardouin, Agnès; Berthet, Pascaline; Bignon, Yves-Jean; Uhrhammer, Nancy; Faivre, Laurence; Loustalot, Catherine; Buys, Saundra; Daly, Mary; Miron, Alex; Terry, Mary Beth; Chung, Wendy K; John, Esther M; Southey, Melissa; Goldgar, David; Singer, Christian F; Tea, Muy-Kheng; Pfeiler, Georg; Fink-Retter, Anneliese; Hansen, Thomas v O; Ejlertsen, Bent; Johannsson, Oskar Th; Offit, Kenneth; Kirchhoff, Tomas; Gaudet, Mia M; Vijai, Joseph; Robson, Mark; Piedmonte, Marion; Phillips, Kelly-Anne; Van Le, Linda; Hoffman, James S; Ewart Toland, Amanda; Montagna, Marco; Tognazzo, Silvia; Imyanitov, Evgeny; Issacs, Claudine; Janavicius, Ramunas; Lazaro, Conxi; Blanco, Iganacio; Tornero, Eva; Navarro, Matilde; Moysich, Kirsten B; Karlan, Beth Y; Gross, Jenny; Olah, Edith; Vaszko, Tibor; Teo, Soo-Hwang; Ganz, Patricia A; Beattie, Mary S; Dorfling, Cecelia M; van Rensburg, Elizabeth J; Diez, Orland; Kwong, Ava; Schmutzler, Rita K; Wappenschmidt, Barbara; Engel, Christoph; Meindl, Alfons; Ditsch, Nina; Arnold, Norbert; Heidemann, Simone; Niederacher, Dieter; Preisler-Adams, Sabine; Gadzicki, Dorotehea; Varon-Mateeva, Raymonda; Deissler, Helmut; Gehrig, Andrea; Sutter, Christian; Kast, Karin; Fiebig, Britta; Schäfer, Dieter; Caldes, Trinidad; de la Hoya, Miguel; Nevanlinna, Heli; Aittomäki, Kristiina; Plante, Marie; Spurdle, Amanda B; Neuhausen, Susan L; Ding, Yuan Chun; Wang, Xianshu; Lindor, Noralane; Fredericksen, Zachary; Pankratz, V Shane; Peterlongo, Paolo; Manoukian, Siranoush; Peissel, Bernard; Zaffaroni, Daniela; Bonanni, Bernardo; Bernard, Loris; Dolcetti, Riccardo; Papi, Laura; Ottini, Laura; Radice, Paolo; Greene, Mark H; Mai, Phuong L; Andrulis, Irene L; Glendon, Gord; Ozcelik, Hilmi; Pharoah, Paul D P; Gayther, Simon A; Simard, Jacques; Easton, Douglas F; Couch, Fergus J; Chenevix-Trench, Georgia

    2012-04-01

    Germline mutations in BRCA1 and BRCA2 are associated with increased risks of breast and ovarian cancer. A genome-wide association study (GWAS) identified six alleles associated with risk of ovarian cancer for women in the general population. We evaluated four of these loci as potential modifiers of ovarian cancer risk for BRCA1 and BRCA2 mutation carriers. Four single-nucleotide polymorphisms (SNPs), rs10088218 (at 8q24), rs2665390 (at 3q25), rs717852 (at 2q31), and rs9303542 (at 17q21), were genotyped in 12,599 BRCA1 and 7,132 BRCA2 carriers, including 2,678 ovarian cancer cases. Associations were evaluated within a retrospective cohort approach. All four loci were associated with ovarian cancer risk in BRCA2 carriers; rs10088218 per-allele hazard ratio (HR) = 0.81 (95% CI: 0.67-0.98) P-trend = 0.033, rs2665390 HR = 1.48 (95% CI: 1.21-1.83) P-trend = 1.8 × 10(-4), rs717852 HR = 1.25 (95% CI: 1.10-1.42) P-trend = 6.6 × 10(-4), rs9303542 HR = 1.16 (95% CI: 1.02-1.33) P-trend = 0.026. Two loci were associated with ovarian cancer risk in BRCA1 carriers; rs10088218 per-allele HR = 0.89 (95% CI: 0.81-0.99) P-trend = 0.029, rs2665390 HR = 1.25 (95% CI: 1.10-1.42) P-trend = 6.1 × 10(-4). The HR estimates for the remaining loci were consistent with odds ratio estimates for the general population. The identification of multiple loci modifying ovarian cancer risk may be useful for counseling women with BRCA1 and BRCA2 mutations regarding their risk of ovarian cancer.

  20. Enhanced T-odd, P-odd electromagnetic moments in reflection asymmetric nuclei

    SciTech Connect

    Spevak, V.; Auerbach, N.; Flambaum, V.V.

    1997-09-01

    Collective P- and T-odd moments produced by parity and time invariance violating forces in reflection asymmetric nuclei are considered. The enhanced collective Schiff, electric dipole, and octupole moments appear due to the mixing of rotational levels of opposite parity. These moments can exceed single-particle moments by more than 2 orders of magnitude. The enhancement is due to the collective nature of the intrinsic moments and the small energy separation between members of parity doublets. In turn these nuclear moments induce enhanced T- and P-odd effects in atoms and molecules. A simple estimate is given and a detailed theoretical treatment of the collective T-, P-odd electric moments in reflection asymmetric, odd-mass nuclei is presented. In the present work we improve on the simple liquid drop model by evaluating the Strutinsky shell correction and include corrections due to pairing. Calculations are performed for octupole deformed long-lived odd-mass isotopes of Rn, Fr, Ra, Ac, and Pa and the corresponding atoms. Experiments with such atoms may improve substantially the limits on time reversal violation. {copyright} {ital 1997} {ital The American Physical Society}

  1. Quantum Hall effect on odd spheres

    NASA Astrophysics Data System (ADS)

    Coşkun, Ü. H.; Kürkçüoǧlu, S.; Toga, G. C.

    2017-03-01

    We solve the Landau problem for charged particles on odd dimensional spheres S2 k -1 in the background of constant SO (2 k -1 ) gauge fields carrying the irreducible representation (I/2 ,I/2 ,…,I/2 ). We determine the spectrum of the Hamiltonian, the degeneracy of the Landau levels and give the eigenstates in terms of the Wigner D -functions, and for odd values of I , the explicit local form of the wave functions in the lowest Landau level (LLL). The spectrum of the Dirac operator on S2 k -1 in the same gauge field background together with its degeneracies is also determined, and in particular, its number of zero modes is found. We show how the essential differential geometric structure of the Landau problem on the equatorial S2 k -2 is captured by constructing the relevant projective modules. For the Landau problem on S5, we demonstrate an exact correspondence between the union of Hilbert spaces of LLLs, with I ranging from 0 to Imax=2 K or Imax=2 K +1 to the Hilbert spaces of the fuzzy CP 3 or that of winding number ±1 line bundles over CP 3 at level K , respectively.

  2. Sigma decomposition: the CP-odd Lagrangian

    NASA Astrophysics Data System (ADS)

    Hierro, I. M.; Merlo, L.; Rigolin, S.

    2016-04-01

    In Alonso et al., JHEP 12 (2014) 034, the CP-even sector of the effective chiral Lagrangian for a generic composite Higgs model with a symmetric coset has been constructed, up to four momenta. In this paper, the CP-odd couplings are studied within the same context. If only the Standard Model bosonic sources of custodial symmetry breaking are considered, then at most six independent operators form a basis. One of them is the weak- θ term linked to non-perturbative sources of CP violation, while the others describe CP-odd perturbative couplings between the Standard Model gauge bosons and an Higgs-like scalar belonging to the Goldstone boson sector. The procedure is then applied to three distinct exemplifying frameworks: the original SU(5)/SO(5) Georgi-Kaplan model, the minimal custodial-preserving SO(5)/SO(4) model and the minimal SU(3)/(SU(2) × U(1)) model, which intrinsically breaks custodial symmetry. Moreover, the projection of the high-energy electroweak effective theory to the low-energy chiral effective Lagrangian for a dynamical Higgs is performed, uncovering strong relations between the operator coefficients and pinpointing the differences with the elementary Higgs scenario.

  3. Soil clay content underlies prion infection odds

    USGS Publications Warehouse

    David, Walter W.; Walsh, D.P.; Farnsworth, Matthew L.; Winkelman, D.L.; Miller, M.W.

    2011-01-01

    Environmental factors-especially soil properties-have been suggested as potentially important in the transmission of infectious prion diseases. Because binding to montmorillonite (an aluminosilicate clay mineral) or clay-enriched soils had been shown to enhance experimental prion transmissibility, we hypothesized that prion transmission among mule deer might also be enhanced in ranges with relatively high soil clay content. In this study, we report apparent influences of soil clay content on the odds of prion infection in free-ranging deer. Analysis of data from prion-infected deer herds in northern Colorado, USA, revealed that a 1% increase in the clay-sized particle content in soils within the approximate home range of an individual deer increased its odds of infection by up to 8.9%. Our findings suggest that soil clay content and related environmental properties deserve greater attention in assessing risks of prion disease outbreaks and prospects for their control in both natural and production settings. ?? 2011 Macmillan Publishers Limited. All rights reserved.

  4. Meeting report for Odd Pols 2012.

    PubMed

    Roy-Engel, Astrid M; Moss, Thomas; Maraia, Richard J

    2013-08-15

    The Eighth International Biennial Conference on RNA polymerases I and III (the 'Odd Pols') was held June 7-11, 2012 at The Airlie Center in Warrenton Virginia, USA. It was sponsored by the Universite Laval and the Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, and organized by Rich Maraia and Tom Moss. The meeting honored the memory of Pierre Thuriaux (Jan 1, 1950-March 18, 2012) and David Schneider reminisced on the important accomplishments his mentor Masayasu Nomura (1927-2011). The goal of the conference was to bring together the world's experts on RNA polymerase I and RNA polymerase III to highlight and share their latest results and varied experimental approaches. The meeting drew attendees from twelve countries and most contributed through oral and poster presentations. The talks were organized into several sessions subdivided into 10 distinct topics. The keynote speaker, Ian Willis, opened the meeting with his presentation entitled "New Regulators of Signaling to Odd Pols" and the closing presentation was given by Patrick Cramer with his presentation "Conservation of the RNA polymerase I, II and III transcription initiation machineries". Here we present some of the highlights from the meeting using summaries provided by the participants.

  5. Cytochrome P450 CYP2D6 genotypes: association with hair colour, Breslow thickness and melanocyte stimulating hormone receptor alleles in patients with malignant melanoma.

    PubMed

    Strange, R C; Ellison, T; Ichii-Jones, F; Bath, J; Hoban, P; Lear, J T; Smith, A G; Hutchinson, P E; Osborne, J; Bowers, B; Jones, P W; Fryer, A A

    1999-06-01

    We previously identified associations between polymorphism in the cytochrome P450 CYP2D6 gene and outcome in several cancers. We have now examined the hypothesis that homozygosity for the mutant alleles, CYP2D6*4 and CYP2D6*3, is associated with susceptibility and outcome in malignant melanoma. Outcome was assessed by Breslow thickness. We first confirmed previous reports that these mutant alleles are associated with increased susceptibility to malignant melanoma. For example, the frequency of homozygosity for CYP2D6*4 was significantly greater (P = 0.006, chi-squared 1 d.f. = 7.4, odds ratio 2.2, 95% confidence interval 1.2, 3.9) in cases (9.1%) than in control individuals (4.3%). The frequency of homozygosity for the mutant alleles was next examined in the malignant melanoma cases grouped on the basis of characteristics associated with malignant melanoma risk. Homozygosity was significantly more common (P = 0.038) in cases with red/blonde hair than in those with brown/black hair. We found no associations between the CYP2D6 genotype and sex, skin type or eye colour. The possible association of CYP2D6 with outcome was assessed by comparing genotype frequencies in patients with tumours of Breslow thickness < 1.5 mm with those whose tumours were > or = 1.5 mm. In patients with red/blonde, but not brown or black hair, homozygosity for CYP2D6*4 was significantly associated with thicker lesions in a multivariate model (P = 0.036). We further examined the association of CYP2D6*4 homozygosity with red/blonde hair by classifying patients on the basis of homo- or heterozygosity for wild-type or val92met, asp294his or asp84glu melanocyte stimulating hormone receptor (MC1R) alleles. None of the nine patients with brown/black hair with the asp294his allele were homozygotes for CYP2D6*4. By contrast, in the patients with red/blonde hair, three of five cases with asp294his were homozygotes for the mutant CYP2D6 allele. The difference in the frequency of CYP2D6*4 homozygotes in

  6. HLA class II allele polymorphism in an outbreak of chikungunya fever in Middle Andaman, India.

    PubMed

    Chaaithanya, Itta Krishna; Muruganandam, Nagarajan; Anwesh, Maile; Rajesh, Reesu; Ghosal, Sruti R; Kartick, Chinnaiah; Prasad, Kadiyala Nageswara; Muthumani, Karuppiah; Vijayachari, Paluru

    2013-10-01

    A sudden upsurge of fever cases with joint pain was observed in the outpatient department, Community Health Centre, Rangat during July-August 2010 in Rangat Middle Andaman, India. The aetiological agent responsible for the outbreak was identified as chikungunya virus (CHIKV), by using RT-PCR and IgM ELISA. The study investigated the association of polymorphisms in the human leucocyte antigen class II genes with susceptibility or protection against CHIKV. One hundred and one patients with clinical features suggestive of CHIKV infection and 104 healthy subjects were included in the study. DNA was extracted and typed for HLA-DRB1 and DQB1 alleles. Based on the amino acid sequences of HLA-DQB1 retrieved from the IMGT/HLA database, critical amino acid differences in the specific peptide-binding pockets of HLA-DQB1 molecules were investigated. The frequencies of HLA-DRB1 alleles were not significantly different, whereas lower frequency of HLA-DQB1*03:03 was observed in CHIKV patients compared with the control population [P = 0·001, corrected P = 0·024; odds ratio (OR)  = 0, 95% confidence interval (95% CI) 0·0-0·331; Peto's OR = 0·1317, 95% CI 0·0428-0·405). Significantly lower frequency of glutamic acid at position 86 of peptide-binding pocket 1 coding HLA-DQB1 genotypes was observed in CHIKV patients compared with healthy controls (P = 0·004, OR = 0·307, 95% CI 0·125-0·707). Computational binding predictions of CD4 epitopes of CHIKV by NetMHCII revealed that HLA-DQ molecules are known to bind more CHIKV peptides than HLA-DRB1 molecules. The results suggest that HLA-DQB1 alleles and critical amino acid differences in the peptide-binding pockets of HLA-DQB1 alleles might have role in influencing infection and pathogenesis of CHIKV.

  7. Odd-even staggering of heavy cluster spontaneous emission rates

    NASA Astrophysics Data System (ADS)

    Poenaru, D. N.; Greiner, W.; Ivaşcu, M.; Mazilu, D.; Plonski, I. H.

    1986-12-01

    Experimentally observed enhanced14C and24Ne emission rates from even-even parents in comparison with that from even-odd or odd-even nuclei are explained in the framework of the analytical superasymmetric fission model, by taking various prescriptions for the zero point vibration energy of even-even, even-odd, odd-even and odd-odd emitters. Longer half-lives than previously computed are obtained by extrapolating the present prescriptions to emitted clusters heavier than24Ne.

  8. Shell Model Description of the Odd-Odd Co and Cu Nuclei

    SciTech Connect

    Medina, N. H.; Allegro, P. R. P.; Oliveira, J. R. B. de; Ribas, R. V.; Seale, W. A.; Toufen, D. L.; Silveira, M. A. G.

    2007-10-26

    The known excited states of the odd-odd nuclei {sup 54,56,58,60}Co and 60,62,64,66Cu were interpreted in the framework of the large scale shell model (LSSM), using several effective interactions and configuration spaces. For the description of the negative parity states, we have allowed one particle excitation to the g{sub 9/2} orbital. The LSSM using the GXPF1 effective interaction reproduces well the first excited states in all of these nuclei.

  9. Proton emission from the deformed odd-odd nuclei near drip line

    NASA Astrophysics Data System (ADS)

    Patial, M.; Arumugam, P.; Jain, A. K.; Maglione, E.; Ferreira, L. S.

    2016-01-01

    Proton emission from odd-odd nuclei is studied within the two quasiparticle plus rotor model which includes the non-adiabatic effects and the residual interaction between valence proton and neutron. Justification of the formalism is discussed through corroboration of our results with the experimental spectrum of 180Ta. Exact calculations are performed to get the proton emission halflives. Our results for the proton emitter 130Eu leads to the assignment of spin and parity Jπ = 1+ for the ground state. The role of Coriolis and residual neutron-proton interactions on the proton emission halflives and their interplay are also discussed.

  10. Comparative study of Gamow-Teller strength distributions in the odd-odd nucleus V50 and its impact on electron capture rates in astrophysical environments

    NASA Astrophysics Data System (ADS)

    Nabi, Jameel-Un; Sajjad, Muhammad

    2007-11-01

    Gamow-Teller (GT) strength transitions are an ideal probe for testing nuclear structure models. In addition to nuclear structure, GT transitions in nuclei directly affect the early phases of Type Ia and Type-II supernovae core collapse since the electron capture rates are partly determined by these GT transitions. In astrophysics, GT transitions provide an important input for model calculations and element formation during the explosive phase of a massive star at the end of its life-time. Recent nucleosynthesis calculations show that odd-odd and odd-A nuclei cause the largest contribution in the rate of change of lepton-to-baryon ratio. In the present manuscript, we have calculated the GT strength distributions and electron capture rates for odd-odd nucleus V50 by using the pn-QRPA theory. At present V50 is the first experimentally available odd-odd nucleus in fp-shell nuclei. We also compare our GT strength distribution with the recently measured results of a V50(d, He2)Ti50 experiment, with the earlier work of Fuller, Fowler, and Newman (referred to as FFN) and subsequently with the large-scale shell model calculations. One curious finding of the paper is that the Brink's hypothesis, usually employed in large-scale shell model calculations, is not a good approximation to use at least in the case of V50. SNe Ia model calculations performed using FFN rates result in overproduction of Ti50, and were brought to a much acceptable value by employing shell model results. It might be interesting to study how the composition of the ejecta using presently reported QRPA rates compare with the observed abundances.

  11. Allele-specific MMP-3 transcription under in vivo conditions

    SciTech Connect

    Zhu Chaoyong; Odeberg, Jacob; Hamsten, Anders; Eriksson, Per . E-mail: Per.Eriksson@ki.se

    2006-09-29

    A common matrix metalloproteinases-3 (MMP-3) -1612 5A/6A promoter polymorphism is associated with risk for cardiovascular disease, rheumatoid arthritis, and other diseases. Here we used the haplotype chromatin immunoprecipitation method to study allele-specific MMP-3 expression under in vivo conditions in heterozygous THP-1 cells. Pyrosequencing was used to analyse the ratio of 5A-allele to 6A-allele after chromatin immunoprecipitation using an antibody against phosphorylated active RNA polymerase II. There was no allele-specific difference in transcriptional activity during basal conditions, i.e., in unstimulated monocytic THP-1 cells. However, after stimulation of MMP-3 expression by monocyte differentiation or incubation with IL-1{beta}, the haplotype containing the 5A-allele was associated with higher transcriptional activity compared with the 6A-containing haplotype. Electromobility shift assay demonstrated increased binding of nuclear proteins to the 5A-allele after monocyte differentiation. In conclusion, the common MMP-3 5A/6A promoter polymorphism appears to be functional only during specific environmental conditions involving inflammation.

  12. Combined effects of current-smoking and the aldehyde dehydrogenase 2*2 allele on the risk of myocardial infarction in Japanese patients.

    PubMed

    Morita, Kazunori; Miyazaki, Hiroko; Saruwatari, Junji; Oniki, Kentaro; Kumagae, Naoki; Tanaka, Takahiro; Kajiwara, Ayami; Otake, Koji; Ogata, Yasuhiro; Arima, Yuichiro; Hokimoto, Seiji; Ogawa, Hisao; Nakagawa, Kazuko

    2015-01-05

    Aldehyde dehydrogenase 2 (ALDH2) detoxifies toxic aldehydes, e.g. acetaldehyde in cigarette smoke; however, the interactive effects between smoking status and the ALDH2 genotype on coronary artery disease (CAD) have not been reported. We investigated the effects of smoking status and the ALDH2 genotype, and assessed their interactive and combined effects on the risk of myocardial infarction (MI) or stable angina (SA), including 221 MI and 175 SA subjects and 473 age- and sex-matched controls without CAD. Current-smoking and the ALDH2*2 allele additively increased the risk of MI (adjusted odds ratio 4.54, 95% confidence interval 2.25-9.15), although this combination was not associated with the risk of SA. This combination also increased the peak creatine kinase (CK) level synergistically in the acute MI (AMI) subjects. Moreover, current-smoking was found to be a significant risk factor for an increased peak CK level in the ALDH2*2 allele carriers (B 2220.2IU/L, p=0.008), but not the non-carriers. Additionally, a synergistic effect of this combination on the triglycerides levels was also found in the AMI subjects. These preliminary findings suggest that the combination of current-smoking and the inactive ALDH2*2 allele may increase the risk of MI additively and the infarct size synergistically.

  13. W${'}$ signatures with odd Higgs particles

    SciTech Connect

    Dobrescu, Bogdan A.; Peterson, Andrea D.

    2014-08-13

    We point out that W' bosons may decay predominantly into Higgs particles associated with their broken gauge symmetry. We demonstrate this in a renormalizable model where the W' and W couplings to fermions differ only by an overall normalization. This "meta-sequential" W' boson decays into a scalar pair, with the charged one subsequently decaying into a W boson and a neutral scalar. These scalars are odd under a parity of the Higgs sector, which consists of a complex bidoublet and a doublet. Finally, the W' and Z' bosons have the same mass and branching fractions into scalars, and may show up at the LHC in final states involving one or two electroweak bosons and missing transverse energy.

  14. W$${'}$$ signatures with odd Higgs particles

    DOE PAGES

    Dobrescu, Bogdan A.; Peterson, Andrea D.

    2014-08-13

    We point out that W' bosons may decay predominantly into Higgs particles associated with their broken gauge symmetry. We demonstrate this in a renormalizable model where the W' and W couplings to fermions differ only by an overall normalization. This "meta-sequential" W' boson decays into a scalar pair, with the charged one subsequently decaying into a W boson and a neutral scalar. These scalars are odd under a parity of the Higgs sector, which consists of a complex bidoublet and a doublet. Finally, the W' and Z' bosons have the same mass and branching fractions into scalars, and may showmore » up at the LHC in final states involving one or two electroweak bosons and missing transverse energy.« less

  15. A prevalent cancer susceptibility APOBEC3A hybrid allele bearing APOBEC3B 3'UTR enhances chromosomal DNA damage.

    PubMed

    Caval, Vincent; Suspène, Rodolphe; Shapira, Milana; Vartanian, Jean-Pierre; Wain-Hobson, Simon

    2014-10-09

    Human APOBEC3A (A3A) cytidine deaminase is a host enzyme that can introduce mutations into chromosomal DNA. As APOBEC3B (A3B) encodes a C-terminal catalytic domain ~91% identical to A3A, we examined its genotoxic potential as well as that of a highly prevalent chimaeric A3A-A3B deletion allele (ΔA3B), which is linked to a higher odds ratio of developing breast, ovarian and liver cancer. Interestingly, breast cancer genomes from ΔA3B(-/-) patients show a higher overall mutation burden. Here it is shown that germline A3B can hypermutate nuclear DNA, albeit less efficiently than A3A. Chimaeric A3A mRNA resulting from ΔA3B was more stable, resulting in higher intracellular A3A levels and greater DNA damage. The cancer burden implied by the higher A3A levels could be considerable given the high penetration of the ΔA3B allele in South East Asia.

  16. A recombined allele of the lipase gene CEL and its pseudogene CELP confers susceptibility to chronic pancreatitis.

    PubMed

    Fjeld, Karianne; Weiss, Frank Ulrich; Lasher, Denise; Rosendahl, Jonas; Chen, Jian-Min; Johansson, Bente B; Kirsten, Holger; Ruffert, Claudia; Masson, Emmanuelle; Steine, Solrun J; Bugert, Peter; Cnop, Miriam; Grützmann, Robert; Mayerle, Julia; Mössner, Joachim; Ringdal, Monika; Schulz, Hans-Ulrich; Sendler, Matthias; Simon, Peter; Sztromwasser, Paweł; Torsvik, Janniche; Scholz, Markus; Tjora, Erling; Férec, Claude; Witt, Heiko; Lerch, Markus M; Njølstad, Pål R; Johansson, Stefan; Molven, Anders

    2015-05-01

    Carboxyl ester lipase is a digestive pancreatic enzyme encoded by the CEL gene. Mutations in CEL cause maturity-onset diabetes of the young as well as pancreatic exocrine dysfunction. Here we describe a hybrid allele (CEL-HYB) originating from a crossover between CEL and its neighboring pseudogene, CELP. In a discovery series of familial chronic pancreatitis cases, we observed CEL-HYB in 14.1% (10/71) of cases compared to 1.0% (5/478) of controls (odds ratio (OR) = 15.5; 95% confidence interval (CI) = 5.1-46.9; P = 1.3 × 10(-6) by two-tailed Fisher's exact test). In three replication studies of nonalcoholic chronic pancreatitis, we identified CEL-HYB in a total of 3.7% (42/1,122) cases and 0.7% (30/4,152) controls (OR = 5.2; 95% CI = 3.2-8.5; P = 1.2 × 10(-11); formal meta-analysis). The allele was also enriched in alcoholic chronic pancreatitis. Expression of CEL-HYB in cellular models showed reduced lipolytic activity, impaired secretion, prominent intracellular accumulation and induced autophagy. These findings implicate a new pathway distinct from the protease-antiprotease system of pancreatic acinar cells in chronic pancreatitis.

  17. A recombined allele of the lipase gene CEL and its pseudogene CELP confers susceptibility to chronic pancreatitis

    PubMed Central

    Fjeld, Karianne; Johansson, Bente B.; Kirsten, Holger; Ruffert, Claudia; Masson, Emmanuelle; Steine, Solrun J.; Bugert, Peter; Cnop, Miriam; Grützmann, Robert; Mayerle, Julia; Mössner, Joachim; Ringdal, Monika; Schulz, Hans-Ulrich; Sendler, Matthias; Simon, Peter; Sztromwasser, Paweł; Torsvik, Janniche; Scholz, Markus; Tjora, Erling; Férec, Claude; Witt, Heiko; Lerch, Markus M.; Njølstad, Pål R.; Johansson, Stefan; Molven, Anders

    2015-01-01

    Carboxyl-ester lipase is a digestive pancreatic enzyme encoded by the highly polymorphic CEL gene1. Mutations in CEL cause maturity-onset diabetes of the young (MODY) with pancreatic exocrine dysfunction2. Here we identified a hybrid allele (CEL-HYB), originating from a crossover between CEL and its neighboring pseudogene CELP. In a discovery cohort of familial chronic pancreatitis cases, the carrier frequency of CEL-HYB was 14.1% (10/71) compared with 1.0% (5/478) in controls (odds ratio [OR] = 15.5, 95% confidence interval [CI] = 5.1-46.9, P = 1.3 × 10−6). Three replication studies in non-alcoholic chronic pancreatitis cohorts identified CEL-HYB in a total of 3.7% (42/1,122) cases and 0.7% (30/4,152) controls (OR = 5.2, 95% CI = 3.2-8.5, P = 1.2 × 10−11; formal meta-analysis). The allele was also enriched in alcoholic chronic pancreatitis. Expression of CEL-HYB in cellular models revealed reduced lipolytic activity, impaired secretion, prominent intracellular accumulation and induced autophagy. The hybrid variant of CEL is the first chronic pancreatitis gene identified outside the protease/antiprotease system of pancreatic acinar cells. PMID:25774637

  18. Health-protective and Adverse Effects of the Apolipoprotein E ε2 Allele in Older Males

    PubMed Central

    Kulminski, Alexander M.; Ukraintseva, Svetlana V.; Arbeev, Konstantin G.; Manton, Kenneth G.; Oshima, Junko; Martin, George M.; Il'yasova, Dora; Yashin, Anatoli I.

    2009-01-01

    OBJECTIVES: To re-examine a health-protective role of the common Apolipoprotein E (APOE) polymorphism focusing on connections between the APOE ε2-containing genotypes and impairments in instrumental activities of daily living [IADL] in older (65+) males and females. To examine how these connections may be mediated by diagnosed coronary heart disease (CHD), Alzheimer's disease, colorectal cancer, macular degeneration (MD), and atherosclerosis. DESIGN: Retrospective cross-sectional study. SETTING: The unique disability-focused data from a genetic sub-sample of the 1999 National Long Term Care Survey linked with Medicare service use files. PARTICIPANTS: 1733 genotyped individuals interviewed on IADL disabilities. MEASUREMENTS: Indicators of IADL impairments, five geriatric disorders, and ε2-containing genotypes. RESULTS: The ε2/3 genotype is a major contributor to adverse associations between the ε2 allele and IADL disability in males [Odds Ratio (OR)=3.09, Confidence Interval (CI)=1.53-6.26)]. It shows, however, significant protective effects for CHD (OR=0.55, CI=0.33-0.92), while CHD is adversely associated with IADL disability (OR=2.18, CI=1.28-3.72). The presence of five diseases does not significantly alter the adverse association between ε2-containing genotypes and disability. Protective effects of the ε2/3 genotype for CHD (OR=0.52, CI=0.27-0.99) and deleterious effects for IADL (OR=3.50, CI=1.71-7.14) for males hold in multivariate models with both these factors included. No significant associations between the ε2-containing genotypes and IADL are found in females. CONCLUSIONS: The ε2 allele can play a dual role in males, protecting them against some health disorders, while promoting others. Strong adverse relationships with disability suggest that ε2-containing genotypes can be unfavorable factors for the health/well-being of aging males. PMID:18179501

  19. Immune-mediated disorders among women carriers of fragile X premutation alleles.

    PubMed

    Winarni, Tri Indah; Chonchaiya, Weerasak; Sumekar, Tanjung Ayu; Ashwood, Paul; Morales, Guadalupe Mendoza; Tassone, Flora; Nguyen, Danh V; Faradz, Sultana M H; Van de Water, Judy; Cook, Kylee; Hamlin, Alyssa; Mu, Yi; Hagerman, Paul J; Hagerman, Randi J

    2012-10-01

    The relative risk of immune-mediated disorders (IMDs) among women carriers of premutation alleles is estimated by a survey for IMDs among 344 carrier women (age 19-81 years; mean 46.35 and SD 12.60) and 72 controls (age 18-87 years; mean 52.40 and SD 15.40). One hundred fifty four (44.77%) women carrier had at least one IMD, as did 20 controls (27.78%). Among women carriers, autoimmune thyroid disorder was the most common (24.4%), then fibromyalgia (10.2%), irritable bowel syndrome (IBS; 9.9%), Raynaud's phenomenon (7.6%), rheumatoid arthritis (RA; 3.8%), Sjögren syndrome (2.6%), systemic lupus erythematosus (SLE; 2.03%), multiple sclerosis (1.74%). Of 55 carriers age 40 or older with FXTAS, 72.73% had at least one IMD, compared to 46.54% of those without FXTAS (n = 159), and 31.58% of controls (n = 57). The estimated odds ratio (OR) for IMD is 2.6 (95% CI 1.2-5.6, P = 0.015) for women with FXTAS relative to those without FXTAS; the likelihood of IMD in carriers without or with FXTAS was also significantly higher than for controls (OR 2.1, 95% CI 1.1-4.2, P = 0.034; OR 5.5, 95% CI 2.4-12.5, P < 0.001, respectively). Similarly, the odds of having an IMD among carriers with FXPOI is about 2.4 times higher when compared to carriers without FXPOI (95% CI 1.1-5.0; P = 0.021). The likelihood of IMD in carriers with or without FXPOI is greater (OR 2.4, 95% CI 1.1-5.0; P = 0.021) compared to that of controls.

  20. Extensive allelic variation in gene expression in populus F1 hybrids.

    PubMed

    Zhuang, Yan; Adams, Keith L

    2007-12-01

    Hybridization between plant species can induce speciation as well as phenotypic novelty and heterosis. Hybrids also can show genome rearrangements and gene expression changes compared with their parents. Here we determined the allelic variation in gene expression in Populus trichocarpa x Populus deltoides F(1) hybrids. Among 30 genes analyzed in four independently formed hybrids, 17 showed >1.5-fold expression biases for one of the two alleles, and there was monoallelic expression of one gene. Expression ratios of the alleles differed between leaves and stems for 10 genes. The results suggest differential regulation of the two parental alleles in the hybrids. To determine if the allelic expression biases were caused by hybridization we compared the ratios of species-specific transcripts between an F(1) hybrid and its parents. Thirteen of 19 genes showed allelic expression ratios in the hybrid that were significantly different from the ratios of the parental species. The P. deltoides allele of one gene was silenced in the hybrid. Modes of gene regulation were inferred from the hybrid-parent comparisons. Cis-regulation was inferred for 6 genes, trans-regulation for 1 gene, and combined cis- and trans-regulation for 9 genes. The results from this study indicate that hybridization between plant species can have extensive effects on allelic expression patterns, some of which might lead to phenotypic changes.

  1. The bipolar disorder risk allele at CACNA1C also confers risk of recurrent major depression and of schizophrenia.

    PubMed

    Green, E K; Grozeva, D; Jones, I; Jones, L; Kirov, G; Caesar, S; Gordon-Smith, K; Fraser, C; Forty, L; Russell, E; Hamshere, M L; Moskvina, V; Nikolov, I; Farmer, A; McGuffin, P; Holmans, P A; Owen, M J; O'Donovan, M C; Craddock, N

    2010-10-01

    Molecular genetic analysis offers opportunities to advance our understanding of the nosological relationship between psychiatric diagnostic categories in general, and the mood and psychotic disorders in particular. Strong evidence (P=7.0 × 10(-7)) of association at the polymorphism rs1006737 (within CACNA1C, the gene encoding the α-1C subunit of the L-type voltage-gated calcium channel) with the risk of bipolar disorder (BD) has recently been reported in a meta-analysis of three genome-wide association studies of BD, including our BD sample (N=1868) studied within the Wellcome Trust Case Control Consortium. Here, we have used our UK case samples of recurrent major depression (N=1196) and schizophrenia (N=479) and UK non-psychiatric comparison groups (N=15316) to examine the spectrum of phenotypic effect of the bipolar risk allele at rs1006737. We found that the risk allele conferred increased risk for schizophrenia (P=0.034) and recurrent major depression (P=0.013) with similar effect sizes to those previously observed in BD (allelic odds ratio ∼1.15). Our findings are evidence of some degree of overlap in the biological underpinnings of susceptibility to mental illness across the clinical spectrum of mood and psychotic disorders, and show that at least some loci can have a relatively general effect on susceptibility to diagnostic categories, as currently defined. Our findings will contribute to a better understanding of the pathogenesis of major psychiatric illness, and such knowledge should be useful in providing an etiological rationale for shaping psychiatric nosology, which is currently reliant entirely on descriptive clinical data.

  2. How Salmonella survive against the odds.

    PubMed

    Foster, J W; Spector, M P

    1995-01-01

    The enteric pathogen Salmonella typhimurium faces daunting odds during its voyages in the natural environment and through an infected host. It must manage stresses ranging from feast to famine, acid to base, and high to low osmolarity, among others, as well as counter various types of oxidative stress and a variety of antimicrobial peptides. The defenses used to survive these encounters can be specific or can provide cross protection to a variety of hostile conditions. Once inside a host, Salmonella spp. escape the extracellular environment and thus humoral immunity by invading professional and nonprofessional phagocytes in which a new set of challenges await. Some of these stresses are similar to those encountered in the natural environment (e.g. acid, starvation) but the bacterial response is complicated by the simultaneous occurrence of multiple stresses. S. typhimurium appears to sense various in vivo cues and responds by seducing the host signal-transduction pathways that are required to phagocytize the bacterial cell. The pathogen then calls upon components of its stress-response arsenal to survive the intracellular environment. These survival strategies enable the organism to persist in nature, where conditions are usually suboptimal, and equip the bacterium with pathogenic properties that, if successful, will provide it with a very rich and stress-free growth environment, a dead host.

  3. Beating the odds--surviving extreme hyperkalemia.

    PubMed

    Muck, Philip M; Letterer, Sebastian; Lindner, Ulrich; Lehnert, Hendrik; Haas, Christian Stefan

    2012-01-01

    Severe hyperkalemia (>7 mmol/L) is a medical emergency because of possible fatal arrhythmias. We here report the case of a 58-year-old woman surviving extreme hyperkalemia (>10 mmol/L). The patient with a history of congestive heart failure, a DDD pacemaker and mild chronic renal insufficiency was admitted with progressive weakness and sudden onset of hypotension and bradycardia in the absence of any pacemaker action. Laboratory tests revealed an extreme serum potassium level of 10.1 mmol/L, with a slightly elevated serum creatinine of 149 μmol/L. Treatment with norepinephrine, sodium bicarbonate, and insulin improved both the hemodynamic situation and the serum potassium with subsequent regaining pacemaker actions even before additional hemodialysis normalized the potassium level. A thorough investigation demonstrated that several mechanisms contributed to the extreme potassium level: urinalysis and a low transtubular potassium gradient in the presence of metabolic acidosis with normal anion gap pointed to preexisting interstitial nephritis, with renal tubular acidosis type IV as the predisposing factor, whereas several drugs and acute impairment of renal function contributed to the dangerous situation. Despite the odds for fatal outcome, the patient recovered completely, and long-term management was initiated to prevent recurrent hyperkalemia.

  4. Hybrid configuration mixing model for odd nuclei

    NASA Astrophysics Data System (ADS)

    Colò, G.; Bortignon, P. F.; Bocchi, G.

    2017-03-01

    In this work, we introduce a new approach which is meant to be a first step towards complete self-consistent low-lying spectroscopy of odd nuclei. So far, we essentially limit ourselves to the description of a double-magic core plus an extra nucleon. The model does not contain any free adjustable parameter and is instead based on a Hartree-Fock (HF) description of the particle states in the core, together with self-consistent random-phase approximation (RPA) calculations for the core excitations. We include both collective and noncollective excitations, with proper care of the corrections due to the overlap between them (i.e., due to the nonorthonormality of the basis). As a consequence, with respect to traditional particle-vibration coupling calculations in which one can only address single-nucleon states and particle-vibration multiplets, we can also describe states of shell-model types like 2 particle-1 hole. We will report results for 49Ca and 133Sb and discuss future perspectives.

  5. Odd frequency pairing of interacting Majorana fermions

    NASA Astrophysics Data System (ADS)

    Huang, Zhoushen; Woelfle, Peter; Balatsky, Alexandar

    Majorana fermions are rising as a promising key component in quantum computation. While the prevalent approach is to use a quadratic (i.e. non-interacting) Majorana Hamiltonian, when expressed in terms of Dirac fermions, generically the Hamiltonian involves interaction terms. Here we focus on the possible pair correlations in a simple model system. We study a model of Majorana fermions coupled to a boson mode and show that the anomalous correlator between different Majorana fermions, located at opposite ends of a topological wire, exhibits odd frequency behavior. It is stabilized when the coupling strength g is above a critical value gc. We use both, conventional diagrammatic theory and a functional integral approach, to derive the gap equation, the critical temperature, the gap function, the critical coupling, and a Ginzburg-Landau theory allowing to discuss a possible subleading admixture of even-frequency pairing. Work supported by USDOE DE-AC52-06NA25396 E304, Knut and Alice Wallenberg Foundation, and ERC DM-321031.

  6. The ODD protocol: A review and first update

    USGS Publications Warehouse

    Grimm, Volker; Berger, Uta; DeAngelis, Donald L.; Polhill, J. Gary; Giske, Jarl; Railsback, Steve F.

    2010-01-01

    The 'ODD' (Overview, Design concepts, and Details) protocol was published in 2006 to standardize the published descriptions of individual-based and agent-based models (ABMs). The primary objectives of ODD are to make model descriptions more understandable and complete, thereby making ABMs less subject to criticism for being irreproducible. We have systematically evaluated existing uses of the ODD protocol and identified, as expected, parts of ODD needing improvement and clarification. Accordingly, we revise the definition of ODD to clarify aspects of the original version and thereby facilitate future standardization of ABM descriptions. We discuss frequently raised critiques in ODD but also two emerging, and unanticipated, benefits: ODD improves the rigorous formulation of models and helps make the theoretical foundations of large models more visible. Although the protocol was designed for ABMs, it can help with documenting any large, complex model, alleviating some general objections against such models.

  7. The distributions of odd nitrogen and odd hydrogen in the natural and perturbed stratosphere

    NASA Technical Reports Server (NTRS)

    Prinn, R. G.; Alyea, F. N.; Cunnold, D. M.; Katz, A.

    1974-01-01

    In order to quantitatively illustrate the effects of quasi-horizontal transport of certain gases and of the reactions influencing their concentrations, a vertical-meridional pole-to-pole stratospheric model is presented which explicitly predicts concentrations of odd nitrogen and odd hydrogen compounds in the natural stratosphere and also in a perturbed stratosphere incorporating artificial injection of nitrogen oxides by an SST fleet. The northern hemisphere SST operations clearly have a very large local effect on the nitrogen oxide distribution and also have a significant effect on the southern hemisphere. The largest changes are seen at the point of injection of the nitrogen oxides. Results are in agreement with previous one-dimensional models.

  8. Structure of the yrast band in the odd-odd deformed nucleus {sup 156}Pm

    SciTech Connect

    Sood, P. C.; Sai, K. Vijay; Gowrishankar, R.; Sainath, M.

    2011-05-15

    The six-level sequence deduced for the odd-odd nucleus {sup 156}Pm in the high-spin studies following spontaneous fission of {sup 252}Cf is shown to constitute the K{sup {pi}=}4{sup +} yrast band having the two-quasiparticle configuration {l_brace}p:5/2[532]+ n:3/2[521]{r_brace}. Spin parities I{sup {pi}=}4{sup +} through 9{sup +} are assigned to the earlier suggested six levels. The location and the decay {gamma}'s of the 10{sup +} level of this band are indicated. It is also pointed out that there are no {gamma} rays common to these postfission high-spin spectra and those seen in the {sup 156}Nd {beta}-decay studies.

  9. Human Leukocyte Antigens and Systemic Lupus Erythematosus: A Protective Role for the HLA-DR6 Alleles DRB1*13:02 and *14:03

    PubMed Central

    Furukawa, Hiroshi; Kawasaki, Aya; Oka, Shomi; Ito, Ikue; Shimada, Kota; Sugii, Shoji; Hashimoto, Atsushi; Komiya, Akiko; Fukui, Naoshi; Kondo, Yuya; Ito, Satoshi; Hayashi, Taichi; Matsumoto, Isao; Kusaoi, Makio; Amano, Hirofumi; Nagai, Tatsuo; Hirohata, Shunsei; Setoguchi, Keigo; Kono, Hajime; Okamoto, Akira; Chiba, Noriyuki; Suematsu, Eiichi; Katayama, Masao; Migita, Kiyoshi; Suda, Akiko; Ohno, Shigeru; Hashimoto, Hiroshi; Takasaki, Yoshinari; Sumida, Takayuki; Nagaoka, Shouhei

    2014-01-01

    Many studies on associations between human leukocyte antigen (HLA) allele frequencies and susceptibility to systemic lupus erythematosus (SLE) have been performed. However, few protective associations with HLA-DRB1 alleles have been reported. Here, we sought protective, as well as predispositional, alleles of HLA-DRB1 in Japanese SLE patients. An association study was conducted for HLA-DRB1 in Japanese SLE patients. Relative predispositional effects were analyzed by sequential elimination of carriers of each allele with the strongest association. We also explored the association of DRB1 alleles with SLE phenotypes including the presence of autoantibody and clinical manifestations. Significantly different carrier frequencies of certain DRB1 alleles were found to be associated with SLE as follows: increased DRB1*15:01 (P = 5.48×10−10, corrected P (Pc) = 1.59×10−8, odds ratio [OR] 2.17, 95% confidence interval [CI] 1.69–2.79), decreased DRB1*13:02 (P = 7.17×10−5, Pc = 0.0020, OR 0.46, 95% CI 0.34–0.63) and decreased DRB1*14:03 (P = 0.0010, Pc = 0.0272, OR 0.34, 95% CI 0.18–0.63). Additionally, the “*15:01/*13:02 or *14:03” genotype tended to be negatively associated with SLE (P = 0.4209, OR 0.66), despite there being significant positive associations with *15:01 when present together with alleles other than *13:02 or *14:03 (P = 1.79×10−11, OR 2.39, 95% CI 1.84–3.10). This protective effect of *13:02 and *14:03 was also confirmed in SLE patients with different clinical phenotypes. To the best of our knowledge, this is the first report of a protective association between the carrier frequencies of HLA-DRB1*13:02 and *14:03 and SLE in the Japanese population. PMID:24498373

  10. Type 2 Diabetes Risk Allele Loci in the Qatari Population

    PubMed Central

    Abi Khalil, Charbel; Fakhro, Khalid A.; Robay, Amal; Ramstetter, Monica D.; Al-Azwani, Iman K.; Malek, Joel A.; Zirie, Mahmoud; Jayyousi, Amin; Badii, Ramin; Al-Nabet Al-Marri, Ajayeb; Chiuchiolo, Maria J.; Al-Shakaki, Alya; Chidiac, Omar; Gharbiah, Maey; Bener, Abdulbari; Stadler, Dora; Hackett, Neil R.; Mezey, Jason G.; Crystal, Ronald G.

    2016-01-01

    Background The prevalence of type 2 diabetes (T2D) is increasing in the Middle East. However, the genetic risk factors for T2D in the Middle Eastern populations are not known, as the majority of studies of genetic risk for T2D are in Europeans and Asians. Methods All subjects were ≥3 generation Qataris. Cases with T2D (n = 1,124) and controls (n = 590) were randomly recruited and assigned to the 3 known Qatari genetic subpopulations [Bedouin (Q1), Persian/South Asian (Q2) and African (Q3)]. Subjects underwent genotyping for 37 single nucleotide polymorphisms (SNPs) in 29 genes known to be associated with T2D in Europeans and/or Asian populations, and an additional 27 tag SNPs related to these susceptibility loci. Pre-study power analysis suggested that with the known incidence of T2D in adult Qataris (22%), the study population size would be sufficient to detect significant differences if the SNPs were risk factors among Qataris, assuming that the odds ratio (OR) for T2D SNPs in Qatari’s is greater than or equal to the SNP with highest known OR in other populations. Results Haplotype analysis demonstrated that Qatari haplotypes in the region of known T2D risk alleles in Q1 and Q2 genetic subpopulations were similar to European haplotypes. After Benjamini-Hochberg adjustment for multiple testing, only two SNPs (rs7903146 and rs4506565), both associated with transcription factor 7-like 2 (TCF7L2), achieved statistical significance in the whole study population. When T2D subjects and control subjects were assigned to the known 3 Qatari subpopulations, and analyzed individually and with the Q1 and Q2 genetic subpopulations combined, one of these SNPs (rs4506565) was also significant in the admixed group. No other SNPs associated with T2D in all Qataris or individual genetic subpopulations. Conclusions With the caveats of the power analysis, the European/Asian T2D SNPs do not contribute significantly to the high prevalence of T2D in the Qatari population, suggesting

  11. Even-odd effects in Z and N distributions of fragments emitted at intermediate energies

    SciTech Connect

    Lombardo, I.; Lanzalone, G.; Agodi, C.; Amorini, F.; Anzalone, A.; Han, J.; Maiolino, C.; Auditore, L.; Loria, D.; Trifiro, A.; Trimarchi, M.; Berceanu, I.; Cardella, G.; De Filippo, E.; Pagano, A.; Papa, M.; Pirrone, S.; Cavallaro, S.; Porto, F.; Rizzo, F.

    2011-08-15

    Even-odd effects in Z and N distributions of light fragments emitted at forward angles in nuclear collisions {sup 40}Ca + {sup 40}Ca, {sup 40}Ca + {sup 48}Ca, and {sup 48}Ca + {sup 48}Ca at 25 MeV/nucleon and identified in charge and mass with the Chimera multidetector have been analyzed. The amplitude of even-odd staggering effects seems to be related to the neutron to proton ratio N/Z of the entrance channels. A qualitative explanation of this effect, taking into account the deexcitation phase of primary excited fragments, is discussed.

  12. GT Strength in Odd-A Nuclei^*

    NASA Astrophysics Data System (ADS)

    Watson, J. W.; Du, Q. Q.

    1998-04-01

    We measured the complete set of polarization-transfer observables (D_ij) for the ^13C(p,n)^13N and ^15N(p,n)^15O reactions at 135 MeV. From the D_ijs we constructed the spin-independent, spin-longitudinal, and spin-transverse responses [1] D_0, D_q, Dn and D_p. From these responses we extracted, in a model-independent way, the Δ J=0 and Δ J=1 (``F'' and ``GT'') fractions of the J^π=1/2^-arrow1/2^- g.s. to g.s. transitions for these reactions. The ``F'' fraction, f_F=D_0(0^circ); the ``GT'' fraction, f_GT=D_q(0^circ)+D_n(0^circ)+D_p(0^circ)= 1- D_0(0^circ). The extracted GT fractions, f_GT, are substantially larger than one would predict from β-decay matrix elements and the systematics of the (p,n) reaction on even-A nuclei. These results confirm earlier, model-dependent determinations of f_GT obtained from the (p,n) reaction on ^13C, ^15N and ^39K at other energies [2], [3], [4], indicating that considerable caution must be used when extracting B(GT) matrix elements from odd-A (p,n) data. * Research supported in part by the U.S. NSF. [1] M. Ichimura, K. Kawahigashi, Phys. Rev. C 45 1822 (1992). [2] T. N. Taddeucci, C. A. Goulding, T. A. Carey, R. C. Byrd, C. D. Goodman, C. Gaarde, J. Larsen, D. Horen, J. Rapaport, and E. Sugarbaker, Nucl. Phys. A469 125 (1987). [3] H. Sakai, H. Okamura, N. Matsuoka, A. Shimizu, T. Suda, M. Ieiri and H. M. Shimizu, Nuclear Physics A579 45-61 (1994). [4] W. Huang, Ph.D. dissertation, Indiana U., 1991, (unpublished).

  13. Allelic differences between Europeans and Chinese for CREB1 SNPs and their implications in gene expression regulation, hippocampal structure and function, and bipolar disorder susceptibility.

    PubMed

    Li, M; Luo, X-J; Rietschel, M; Lewis, C M; Mattheisen, M; Müller-Myhsok, B; Jamain, S; Leboyer, M; Landén, M; Thompson, P M; Cichon, S; Nöthen, M M; Schulze, T G; Sullivan, P F; Bergen, S E; Donohoe, G; Morris, D W; Hargreaves, A; Gill, M; Corvin, A; Hultman, C; Toga, A W; Shi, L; Lin, Q; Shi, H; Gan, L; Meyer-Lindenberg, A; Czamara, D; Henry, C; Etain, B; Bis, J C; Ikram, M A; Fornage, M; Debette, S; Launer, L J; Seshadri, S; Erk, S; Walter, H; Heinz, A; Bellivier, F; Stein, J L; Medland, S E; Arias Vasquez, A; Hibar, D P; Franke, B; Martin, N G; Wright, M J; Su, B

    2014-04-01

    Bipolar disorder (BD) is a polygenic disorder that shares substantial genetic risk factors with major depressive disorder (MDD). Genetic analyses have reported numerous BD susceptibility genes, while some variants, such as single-nucleotide polymorphisms (SNPs) in CACNA1C have been successfully replicated, many others have not and subsequently their effects on the intermediate phenotypes cannot be verified. Here, we studied the MDD-related gene CREB1 in a set of independent BD sample groups of European ancestry (a total of 64,888 subjects) and identified multiple SNPs significantly associated with BD (the most significant being SNP rs6785[A], P=6.32 × 10(-5), odds ratio (OR)=1.090). Risk SNPs were then subjected to further analyses in healthy Europeans for intermediate phenotypes of BD, including hippocampal volume, hippocampal function and cognitive performance. Our results showed that the risk SNPs were significantly associated with hippocampal volume and hippocampal function, with the risk alleles showing a decreased hippocampal volume and diminished activation of the left hippocampus, adding further evidence for their involvement in BD susceptibility. We also found the risk SNPs were strongly associated with CREB1 expression in lymphoblastoid cells (P<0.005) and the prefrontal cortex (P<1.0 × 10(-6)). Remarkably, population genetic analysis indicated that CREB1 displayed striking differences in allele frequencies between continental populations, and the risk alleles were completely absent in East Asian populations. We demonstrated that the regional prevalence of the CREB1 risk alleles in Europeans is likely caused by genetic hitchhiking due to natural selection acting on a nearby gene. Our results suggest that differential population histories due to natural selection on regional populations may lead to genetic heterogeneity of susceptibility to complex diseases, such as BD, and explain inconsistencies in detecting the genetic markers of these diseases among

  14. Cosmic impact: What are the odds?

    NASA Astrophysics Data System (ADS)

    Harris, A. W.

    2009-12-01

    Firestone et al. (PNAS 104, 16016-16021, 2007) propose that the impact of a ~4 km diameter comet (or multiple bodies making up a similar mass) led to the Younger Dryas cooling and extinction of megafauna in North America, 12,900 years ago. Even more provocatively, Firestone et al. (Cycle of Cosmic Catastrophes, Bear & Co. Books, 2006, 392pp), suggest that a nearby supernova may have produced a comet shower leading to the impact event, either by disturbing the Oort Cloud or by direct injection of 4-km comet-like bodies to the solar neighborhood. Here we show: (a) A supernova shockwave or mass ejection is not capable of triggering a shower of comets from the Oort Cloud. (b) An Oort Cloud shower from whatever cause would take 100,000 years or more for the perturbed comets to arrive in the inner solar system, and the peak flux would persist for some hundreds of thousands more years. (c) Even if all 20 solar masses or so of ejected matter from a SN were in the form of 4-km diameter balls, the probability of even one such ball hitting the Earth from an event 100 light years away would be about 3e-5. (d) A 4-km diameter ball traveling fast enough to get here from 100 LY away in some tens of thousands of years would deliver the energy of a 50 km diameter impactor traveling at typical Earth-impact velocity (~20 km/sec). We review the current impact flux on the Earth from asteroids and comets, and show that the probability of an impact of a 4-km diameter asteroid in an interval of 13,000 years is about one in a thousand, and the probability of a comet impact of that size is a few in a million. An "impact shower" caused by the injection or breakup of comets or asteroids in the inner solar system by whatever means would take tens to hundreds of thousands of years to clear out, thus the population of NEOs we see now with our telescopic surveys is what we’ve had for the last few tens of thousands of years, at least. Faced with such low odds, the evidence that such a large

  15. High-spin states and shell structure of the odd-odd nucleus {sup 90}Nb

    SciTech Connect

    Cui, X.Z.; Zhang, Z.L.; Meng, R.; Yang, C.X.; Zhu, L.H.; Wu, X.G.; Wang, Z.M.; He, C.Y.; Li, G.S.; Wen, S.X.; Ma, R.G.; Liu, Y.; Luo, P.; Zheng, Y.; Ndontchueng, M.M.; Huo, J.D.

    2005-10-01

    The high-spin states of the odd-odd nucleus {sup 90}Nb have been investigated with in-beam {gamma}-spectroscopic techniques via the {sup 76}Ge({sup 19}F,5n){sup 90}Nb reaction at a beam energy of 80 MeV. {gamma}-{gamma} coincidences were measured using a {gamma}-ray detector array. Twenty new {gamma} rays have been assigned to {sup 90}Nb and the level scheme has been extended up to an excitation energy of 8.095 MeV at spin 18({Dirac_h}/2{pi}). The level structure of {sup 90}Nb at high spin states has been well reproduced using semiempirical shell-model calculations in the model space {pi}(1p{sub 1/2},0f{sub 5/2},0g{sub 9/2}){nu}(0g{sub 9/2}). The results show that the excitation of protons plays an important role in generating the high-spin states of {sup 90}Nb.

  16. Diabatic crossing of chiral "twins" in the odd-odd 106Ag nucleus: A theoretical perspective

    NASA Astrophysics Data System (ADS)

    Malik, Sham S.

    2016-07-01

    A systematic study of both the observed positive-parity magnetic rotation band and the negative-parity Δ I =1 doublet bands in an odd-odd 106Ag nucleus is carried out. The negative-parity doublet bands depict some unusual features that have not been observed in any isotope in the mass A =100 region. For instance, (i) the moment of inertia of the partner band is quite different from that of the yrast band, and (ii) these bands cross each other at an angular momentum of I =14 ℏ . Also, the observed significantly large but constant B (M 1 ) transitions confirm that the strong M 1 transitions are being reinforced by the contributions from collective rotation. To explain these features, a collective model has been developed whose kinetic and potential energies are extracted from the tilted-axis cranking model. Instead of the triaxial parameter γ , a second-order phase transition is found to be responsible for the spontaneous breakdown of chiral symmetry. Analytical solution of the Schrödinger equation has generated a doublet nondegenerate eigenvalue spectrum. The ensuing model results based on the two-quasiparticle configuration π g9/2⊗ν h11/2 exhibit similarities with many observed features of the negative-parity doublet bands and hence confirm their chiral character. The cranking mass parameter in kinetic energy plays an important role in diabatic crossing between these emerged chiral twin bands.

  17. Neutron-proton multiplets in the odd-odd nucleus 53 37 90Rb

    NASA Astrophysics Data System (ADS)

    Czerwiński, M.; RzÄ ca-Urban, T.; Urban, W.; BÄ czyk, P.; Sieja, K.; Timár, J.; Nyakó, B. M.; Kuti, I.; Tornyi, T. G.; Atanasova, L.; Blanc, A.; Jentschel, M.; Mutti, P.; Köster, U.; Soldner, T.; de France, G.; Simpson, G. S.; Ur, C. A.

    2016-03-01

    Medium-spin excited levels in 90Rb, populated in the fission of 235U induced by neutrons, have been observed for the first time. γ radiation from fission has been measured by using the EXILL array of Ge detectors at the cold-neutron-beam facility PF1B of the Institut Laue-Langevin, Grenoble. Low-energy levels are interpreted as members of the π p3/2 -1ν (d5/2) 3 , π f5/2 -1ν (d5/2) 3 , and π g9 /2ν (d5/2) 3 multiplets with the 0- ground state due to the seniority-3 coupling in the ν d5 /2 shell. Analogous anomalous coupling within the π g9 /2ν (d5/2) 3 configuration explains the 5+, 6+, and 7+ triplet of states, observed at medium spins, similar to the triplet seen in the N =53 isotone, 88Br. Shell-model calculations reproduce well the proposed structures in Rb,9088 and support the seniority-3 coupling in N =53 isotones and its absence in N =51 isotones. The structure of the odd-odd 88Rb and 90Rb nuclei provides an argument in favor of the collectivity building up at the neutron number N =53 .

  18. Engineering Escherichia coli for odd straight medium chain free fatty acid production.

    PubMed

    Wu, Hui; San, Ka-Yiu

    2014-10-01

    Microbial biosynthesis of free fatty acids (FFAs) can be achieved by introducing an acyl-acyl carrier protein thioesterase gene into Escherichia coli. The engineered E. coli usually produced even chain FFAs. In this study, propionyl-CoA synthetase (prpE) from Salmonella enterica was overexpressed in two efficient even chain FFAs producers, ML103 (pXZM12) carrying the acyl-ACP thioesterase gene from Umbellularia californica and ML103 (pXZ18) carrying the acyl-ACP thioesterase gene from Ricinus communis combined with supplement of extracellular propionate. With these metabolically engineered E. coli, the odd straight chain FFAs, undecanoic acid (C11:0), tridecanoic acid (C13:0), and pentadecanoic acid (C15:0) were produced from glucose and propionate. The highest total odd straight chain FFAs produced by ML103 (pXZM12, pBAD-prpE) reached 276 mg/l with a ratio of 23.43 % of the total FFAs. In ML103 (pXZ18, pBAD-prpE), the highest total odd straight chain FFAs accumulated to 297 mg/l, and the ratio reached 17.68 % of the total FFAs. Due to the different substrate specificity of the acyl-ACP thioesterases, the major odd straight chain FFA components of ML103 (pXZM12, pBAD-prpE) were undecanoic acid and tridecanoic acid, while the ML103 (pXZ18, pBAD-prpE) preferred pentadecanoic acid.

  19. Allele-specific disparity in breast cancer

    PubMed Central

    2011-01-01

    Background In a cancer cell the number of copies of a locus may vary due to amplification and deletion and these variations are denoted as copy number alterations (CNAs). We focus on the disparity of CNAs in tumour samples, which were compared to those in blood in order to identify the directional loss of heterozygosity. Methods We propose a numerical algorithm and apply it to data from the Illumina 109K-SNP array on 112 samples from breast cancer patients. B-allele frequency (BAF) and log R ratio (LRR) of Illumina were used to estimate Euclidian distances. For each locus, we compared genotypes in blood and tumour for subset of samples being heterozygous in blood. We identified loci showing preferential disparity from heterozygous toward either the A/B-allele homozygous (allelic disparity). The chi-squared and Cochran-Armitage trend tests were used to examine whether there is an association between high levels of disparity in single nucleotide polymorphisms (SNPs) and molecular, clinical and tumour-related parameters. To identify pathways and network functions over-represented within the resulting gene sets, we used Ingenuity Pathway Analysis (IPA). Results To identify loci with a high level of disparity, we selected SNPs 1) with a substantial degree of disparity and 2) with substantial frequency (at least 50% of the samples heterozygous for the respective locus). We report the overall difference in disparity in high-grade tumours compared to low-grade tumours (p-value < 0.001) and significant associations between disparity in multiple single loci and clinical parameters. The most significantly associated network functions within the genes represented in the loci of disparity were identified, including lipid metabolism, small-molecule biochemistry, and nervous system development and function. No evidence for over-representation of directional disparity in a list of stem cell genes was obtained, however genes appeared to be more often altered by deletion than by

  20. Odds of Getting Adequate Physical Activity by Dog Walking

    PubMed Central

    Soares, Jesus; Epping, Jacqueline N.; Owens, Chantelle J.; Brown, David R.; Lankford, Tina J.; Simoes, Eduardo J.; Caspersen, Carl J.

    2015-01-01

    Background We aimed to determine the likelihood that adult dog owners who walk their dogs will achieve a healthy level of moderate-intensity (MI) physical activity (PA), defined as at least 150 mins/wk. Methods We conducted a systematic search of 6 databases with data from 1990–2012 on dog owners’ PA, to identify those who achieved MIPA. To compare dog-walkers’ performance with non–dog walkers, we used a random effects model to estimate the unadjusted odds ratio (OR) and corresponding 95% confidence interval (CI). Results We retrieved 9 studies that met our inclusion criterion and allowed OR calculations. These yielded data on 6980 dog owners aged 18 to 81 years (41% men). Among them, 4463 (63.9%) walked their dogs. Based on total weekly PA, 2710 (60.7%) dog walkers, and 950 (37.7%) non–dog walkers achieved at least MIPA. The estimated OR was 2.74 (95% CI 2.09–3.60). Conclusion Across 9 published studies, almost 2 in 3 dog owners reported walking their dogs, and the walkers are more than 2.5 times more likely to achieve at least MIPA. These findings suggest that dog walking may be a viable strategy for dog owners to help achieve levels of PA that may enhance their health. PMID:24733365

  1. The C allele of JAK2 rs4495487 is an additional candidate locus that contributes to myeloproliferative neoplasm predisposition in the Japanese population

    PubMed Central

    2012-01-01

    Background Polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF) are myeloproliferative neoplasms (MPNs) characterized in most cases by a unique somatic mutation, JAK2 V617F. Recent studies revealed that JAK2 V617F occurs more frequently in a specific JAK2 haplotype, named JAK2 46/1 or GGCC haplotype, which is tagged by rs10974944 (C/G) and/or rs12343867 (T/C). This study examined the impact of single nucleotide polymorphisms (SNPs) of the JAK2 locus on MPNs in a Japanese population. Methods We sequenced 24 JAK2 SNPs in Japanese patients with PV. We then genotyped 138 MPN patients (33 PV, 96 ET, and 9 PMF) with known JAK2 mutational status and 107 controls for a novel SNP, in addition to two SNPs known to be part of the 46/1 haplotype (rs10974944 and rs12343867). Associations with risk of MPN were estimated by odds ratios and their 95% confidence intervals using logistic regression. Results A novel locus, rs4495487 (T/C), with a mutated T allele was significantly associated with PV. Similar to rs10974944 and rs12343867, rs4495487 in the JAK2 locus is significantly associated with JAK2-positive MPN. Based on the results of SNP analysis of the three JAK2 locus, we defined the "GCC genotype" as having at least one minor allele in each SNP (G allele in rs10974944, C allele in rs4495487, and C allele in rs12343867). The GCC genotype was associated with increased risk of both JAK2 V617F-positive and JAK2 V617F-negative MPN. In ET patients, leukocyte count and hemoglobin were significantly associated with JAK2 V617F, rather than the GCC genotype. In contrast, none of the JAK2 V617F-negative ET patients without the GCC genotype had thrombosis, and splenomegaly was frequently seen in this subset of ET patients. PV patients without the GCC genotype were significantly associated with high platelet count. Conclusions Our results indicate that the C allele of JAK2 rs4495487, in addition to the 46/1 haplotype, contributes significantly to the

  2. Low-penetrance alleles predisposing to sporadic colorectal cancers: a French case-controlled genetic association study

    PubMed Central

    Küry, Sébastien; Buecher, Bruno; Robiou-du-Pont, Sébastien; Scoul, Catherine; Colman, Hélène; Le Neel, Tanguy; Le Houérou, Claire; Faroux, Roger; Ollivry, Jean; Lafraise, Bernard; Chupin, Louis-Dominique; Sébille, Véronique; Bézieau, Stéphane

    2008-01-01

    Background Sporadic colorectal cancers (CRC) are multifactorial diseases resulting from the combined effects of numerous genetic, environmental and behavioral risk factors. Genetic association studies have suggested low-penetrance alleles of extremely varied genes to be involved in susceptibility to CRC in Caucasian populations. Methods Through a large genetic association study based on 1023 patients with sporadic CRC and 1121 controls, we tested a panel of these low-penetrance alleles to find out whether they could determine "genotypic profiles" at risk for CRC among individuals of the French population. We examined 52 polymorphisms of 35 genes – drawn from inflammation, xenobiotic detoxification, one-carbon, insulin signaling, and DNA repair pathways – for their possible contribution to colorectal carcinogenesis. The risk of cancer associated with these polymorphisms was assessed by calculation of odds ratios (OR) using multivariate analyses and logistic regression. Results Whereas all these polymorphisms had previously been found to be associated with CRC risk, especially in Caucasian populations, we were able to replicate the association for only five of them. Three SNPs were shown to increase CRC risk: PTGS1 c.639C>A (p.Gly213Gly), IL8 c.-352T>A, and MTHFR c.1286A>C (p.Ala429Glu). On the contrary, two other SNPs, PLA2G2A c.435+230C>T and PPARG c.1431C>T (p.His477His), were associated with a decrease in CRC risk. Further analyses highlighted genotypic combinations having a greater predisposing effect on CRC (OR 1.97, 95%CI 1.31–2.97, p = 0.0009) than the allelic variants that were examined separately. Conclusion The identification of CRC-predisposing combinations, composed of alleles PTGS1 c.639A, PLA2G2A c.435+230C, PPARG c.1431C, IL8 c.-352A, and MTHFR c.1286C, highlights the importance of inflammatory processes in susceptibility to sporadic CRC, as well as a possible crosstalk between inflammation and one-carbon pathways. PMID:18992148

  3. Level Density In Interacting Boson-Fermion-Fermion Model (IBFFM) Of The Odd-Odd Nucleus 196Au

    SciTech Connect

    Kabashi, Skender; Bekteshi, Sadik

    2007-04-23

    The level density of the odd-odd nucleus 196Au is investigated in the interacting boson-fermion-fermion model (IBFFM) which accounts for collectivity and complex interaction between quasiparticle and collective modes.The IBFFM total level density is fitted by Gaussian and its tail is also fitted by Bethe formula and constant temperature Fermi gas model.

  4. A-1012G promoter polymorphism of vitamin D receptor gene is associated with psoriasis risk and lower allele-specific expression.

    PubMed

    Richetta, Antonio Giovanni; Silvestri, Valentina; Giancristoforo, Simona; Rizzolo, Piera; D'Epiro, Sara; Graziano, Veronica; Mattozzi, Carlo; Navazio, Anna Sara; Campoli, Marco; D'Amico, Cristina; Scarnò, Marco; Calvieri, Stefano; Ottini, Laura

    2014-02-01

    Psoriasis is caused by a combination of genetic, immunologic, and environmental factors. The vitamin D receptor (VDR) is involved in antiproliferative and prodifferentiation pathways in keratinocytes and exerts immunosuppressive effects. We aimed to investigate possible associations between VDR polymorphisms and psoriasis susceptibility and to evaluate functional effects of potential psoriasis-associated polymorphisms. We genotyped 108 patients with psoriasis and 268 healthy controls at 5 VDR polymorphisms (A-1012G, FokI, BsmI, ApaI, and TaqI) by TaqMan allelic-discrimination real-time polymerase chain reaction. We found a significant increased overall risk of psoriasis for the VDR A-1012G promoter polymorphism (odds ratio [OR]=2.43, 95% confidence interval [CI]: 1.15-5.13; p=0.05). A significant higher frequency (p=0.035) of the A allele was found in psoriatic cases compared with controls. In a case-case analysis, a statistically significant association between A-1012G and family history emerged (p=0.033). Furthermore, a significant association of A-1012G risk genotypes with a lower expression of VDR mRNA emerged (p=0.0028). Our data show that VDR promoter A-1012G polymorphism is associated with psoriasis risk and suggest that this polymorphism may modulate psoriasis risk by affecting VDR expression.

  5. The competition between alpha decay and spontaneous fission in odd-even and odd-odd nuclei in the range 99 ≤ Z ≤ 129

    NASA Astrophysics Data System (ADS)

    Santhosh, K. P.; Priyanka, B.

    2015-08-01

    The predictions on the mode of decay of the odd-even and odd-odd isotopes of heavy and superheavy nuclei with Z = 99- 129, in the range 228 ≤ A ≤ 336, have been done within the Coulomb and proximity potential model for deformed nuclei (CPPMDN). A comparison of our calculated alpha half lives with the values computed using other theoretical models shows good agreement with each other. An extensive study on the spontaneous fission half lives of all the isotopes under study has been performed to identify the long-lived isotopes in the mass region. The study reveals that the alpha decay half lives and the mode of decay of the isotopes with Z = 109, 111, 113, 115 and 117, evaluated using our formalisms, agree well with the experimental observations. As our study on the odd-even and odd-odd isotopes of Z = 99- 129 predicts that, the isotopes 238,240-25499, 244,246-258101, 248,250,252-260,262103, 254,256,258-262,264105, 258,260,262-264,266107, 262,264,266-274109, 266,268-279111, 270-284,286113, 272-289,291115, 274-299117, 276-307119, 281-314121, 287-320,322123, 295-325125, 302-327127 and 309-329129 survive fission and have alpha decay channel as the prominent mode of decay, these nuclei could possibly be synthesized in the laboratory and this could be of great interest to the experimentalists. The behavior of these nuclei against the proton decay has also been studied to identify the probable proton emitters in this region of nuclei.

  6. Colorings of odd or even chirality on hexagonal lattices

    NASA Astrophysics Data System (ADS)

    Cépas, O.

    2017-02-01

    We define two classes of colorings that have odd or even chirality on hexagonal lattices. This parity is an invariant in the dynamics of all loops, and explains why standard Monte Carlo algorithms are nonergodic. We argue that adding the motion of "stranded" loops allows for parity changes. By implementing this algorithm, we show that the even and odd classes have the same entropy. In general, they do not have the same number of states, except for the special geometry of long strips, where a Z2 symmetry between even and odd states occurs in the thermodynamic limit.

  7. Superdeformation studies in the odd-odd nucleus {sup 192}Tl

    SciTech Connect

    Fischer, S.; Carpenter, M.P.; Janssens, R.V.F.

    1995-08-01

    The study of yrast and near-yrast structures of odd-odd nuclei to high spins is somewhat limited due to the complexity of the spectra resulting from the many proton-neutron couplings near the Fermi surface. In superdeformed nuclei, the number of available protons and neutrons near the Fermi surface is somewhat limited due to the presence of large-shell gaps which stabilize the nuclear shape. A relatively small number of available neutron and proton configurations can lead to fragmentation of the SD intensity into a number of different bands. Two good examples of this phenomenon were found in {sup 192}Tl and {sup 194}Tl where the presence of six superdeformed bands were reported in both nuclei. We reexamined {sup 192}Tl at Gammasphere using the {sup 160}Gd({sup 37}Cl,5n) reaction at 178 MeV to populate states in the superdeformed well of this nucleus. While our previous study on {sup 192}Tl at ATLAS was very successful, a number of questions remained which formed the basis of our objectives in this experiment: obtain better {gamma}-ray energies for the known transitions and identify higher spin members in each band; determine how the bands feed the known yrast states in {sup 192}Tl as well as determine the complete spectrum in coincidence with the SD bands; look for M1 transitions connecting proposed signature partners; and attempt to identify other excitations in the superdeformed well. Analysis is underway and four of the six bands were confirmed. The reasons that two of the reported bands were not observed in this latest work is still under investigation. As of this time, no other superdeformed bands were identified in the data. Two of the confirmed SD bands have a constant moment of inertia and show indications of cross-talk between each other. This observation is not unexpected since the calculated M1 rates for the proposed configuration of the band, {pi}{sub 13/2} x {upsilon}j{sub 15/2}, indicate that M1 transitions linking the two SD bands should be observed.

  8. A novel measurement of allele discrimination for assessment of allele-specific silencing by RNA interference.

    PubMed

    Takahashi, Masaki; Hohjoh, Hirohiko

    2014-11-01

    Allele-specific silencing by RNA interference (ASP-RNAi) is an atypical RNAi that is capable of discriminating target alleles from non-target alleles, and may be therapeutically useful for specific inhibition of disease-causing alleles without affecting their corresponding normal alleles. However, it is difficult to design and select small interfering RNA (siRNAs) that confer ASP-RNAi. A major problem is that there are few appropriate measures in determining optimal allele-specific siRNAs. Here we show two novel formulas for calculating a new measure of allele-discrimination, named "ASP-score". The formulas and ASP-score allow for an unbiased determination of optimal siRNAs, and may contribute to characterizing such allele-specific siRNAs.

  9. Ovarian Cancer Susceptibility Alleles and Risk of Ovarian Cancer in BRCA1 and BRCA2 Mutation Carriers

    PubMed Central

    Ramus, Susan J.; Antoniou, Antonis C; Kuchenbaecker, Karoline B.; Soucy, Penny; Beesley, Jonathan; Chen, Xiaoqing; McGuffog, Lesley; Sinilnikova, Olga M.; Healey, Sue; Barrowdale, Daniel; Lee, Andrew; Thomassen, Mads; Gerdes, Anne-Marie; Kruse, Torben A.; Jensen, Uffe Birk; Skytte, Anne-Bine; Caligo, Maria A.; Liljegren, Annelie; Lindblom, Annika; Olsson, Håkan; Kristoffersson, Ulf; Stenmark-Askmalm, Marie; Melin, Beatrice; Domchek, Susan M.; Nathanson, Katherine L.; Rebbeck, Timothy R.; Jakubowska, Anna; Lubinski, Jan; Jaworska, Katarzyna; Durda, Katarzyna; Złowocka, Elżbieta; Gronwald, Jacek; Huzarski, Tomasz; Byrski, Tomasz; Cybulski, Cezary; Toloczko-Grabarek, Aleksandra; Osorio, Ana; Benitez, Javier; Duran, Mercedes; Tejada, Maria-Isabel; Hamann, Ute; Rookus, Matti; van Leeuwen, Flora E.; Aalfs, Cora M.; Meijers-Heijboer, Hanne E.J.; van Asperen, Christi J.; van Roozendaal, K.E.P.; Hoogerbrugge, Nicoline; Collée, J. Margriet; Kriege, Mieke; van der Luijt, Rob B.; Peock, Susan; Frost, Debra; Ellis, Steve D.; Platte, Radka; Fineberg, Elena; Evans, D. Gareth; Lalloo, Fiona; Jacobs, Chris; Eeles, Ros; Adlard, Julian; Davidson, Rosemarie; Eccles, Diana; Cole, Trevor; Cook, Jackie; Paterson, Joan; Douglas, Fiona; Brewer, Carole; Hodgson, Shirley; Morrison, Patrick J.; Walker, Lisa; Porteous, Mary E.; Kennedy, M. John; Pathak, Harsh; Godwin, Andrew K.; Stoppa-Lyonnet, Dominique; Caux-Moncoutier, Virginie; de Pauw, Antoine; Gauthier-Villars, Marion; Mazoyer, Sylvie; Léoné, Mélanie; Calender, Alain; Lasset, Christine; Bonadona, Valérie; Hardouin, Agnès; Berthet, Pascaline; Bignon, Yves-Jean; Uhrhammer, Nancy; Faivre, Laurence; Loustalot, Catherine; Buys, Saundra; Daly, Mary; Miron, Alex; Terry, Mary Beth; Chung, Wendy K.; John, Esther M; Southey, Melissa; Goldgar, David; Singer, Christian F; Tea, Muy-Kheng; Pfeiler, Georg; Fink-Retter, Anneliese; Hansen, Thomas v. O.; Ejlertsen, Bent; Johannsson, Oskar Th.; Offit, Kenneth; Kirchhoff, Tomas; Gaudet, Mia M.; Vijai, Joseph; Robson, Mark; Piedmonte, Marion; Phillips, Kelly-Anne; Van Le, Linda; Hoffman, James S; Toland, Amanda Ewart; Montagna, Marco; Tognazzo, Silvia; Imyanitov, Evgeny; Isaacs, Claudine; Janavicius, Ramunas; Lazaro, Conxi; Blanco, Ignacio; Tornero, Eva; Navarro, Matilde; Moysich, Kirsten B.; Karlan, Beth Y.; Gross, Jenny; Olah, Edith; Vaszko, Tibor; Teo, Soo-Hwang; Ganz, Patricia A.; Beattie, Mary S.; Dorfling, Cecelia M; van Rensburg, Elizabeth J; Diez, Orland; Kwong, Ava; Schmutzler, Rita K.; Wappenschmidt, Barbara; Engel, Christoph; Meindl, Alfons; Ditsch, Nina; Arnold, Norbert; Heidemann, Simone; Niederacher, Dieter; Preisler-Adams, Sabine; Gadzicki, Dorotehea; Varon-Mateeva, Raymonda; Deissler, Helmut; Gehrig, Andrea; Sutter, Christian; Kast, Karin; Fiebig, Britta; Schäfer, Dieter; Caldes, Trinidad; de la Hoya, Miguel; Nevanlinna, Heli; Aittomäki, Kristiina; Plante, Marie; Spurdle, Amanda B.; Neuhausen, Susan L.; Ding, Yuan Chun; Wang, Xianshu; Lindor, Noralane; Fredericksen, Zachary; Pankratz, V. Shane; Peterlongo, Paolo; Manoukian, Siranoush; Peissel, Bernard; Zaffaroni, Daniela; Bonanni, Bernardo; Bernard, Loris; Dolcetti, Riccardo; Papi, Laura; Ottini, Laura; Radice, Paolo; Greene, Mark H.; Mai, Phuong L.; Andrulis, Irene L.; Glendon, Gord; Ozcelik, Hilmi; Pharoah, Paul D.P.; Gayther, Simon A.; Simard, Jacques; Easton, Douglas F.; Couch, Fergus J.; Chenevix-Trench, Georgia

    2012-01-01

    Germline mutations in BRCA1 and BRCA2 are associated with increased risks of breast and ovarian cancer. A genome-wide association study (GWAS) identified six alleles associated with risk of ovarian cancer for women in the general population. We evaluated four of these loci as potential modifiers of ovarian cancer risk for BRCA1 and BRCA2 mutation carriers. Four single-nucleotide polymorphisms (SNPs), rs10088218 (at 8q24), rs2665390 (at 3q25), rs717852 (at 2q31), and rs9303542 (at 17q21), were genotyped in 12,599 BRCA1 and 7,132 BRCA2 carriers, including 2,678 ovarian cancer cases. Associations were evaluated within a retrospective cohort approach. All four loci were associated with ovarian cancer risk in BRCA2 carriers; rs10088218 per-allele hazard ratio (HR) = 0.81 (95% CI: 0.67–0.98) P-trend = 0.033, rs2665390 HR = 1.48 (95% CI: 1.21–1.83) P-trend = 1.8 × 10−4, rs717852 HR = 1.25 (95% CI: 1.10–1.42) P-trend = 6.6 × 10−4, rs9303542 HR = 1.16 (95% CI: 1.02–1.33) P-trend = 0.026. Two loci were associated with ovarian cancer risk in BRCA1 carriers; rs10088218 per-allele HR = 0.89 (95% CI: 0.81–0.99) P-trend = 0.029, rs2665390 HR = 1.25 (95% CI: 1.10–1.42) P-trend = 6.1 × 10−4. The HR estimates for the remaining loci were consistent with odds ratio estimates for the general population. The identification of multiple loci modifying ovarian cancer risk may be useful for counseling women with BRCA1 and BRCA2 mutations regarding their risk of ovarian cancer. PMID:22253144

  10. Characterization of isomers in the neutron-rich odd-odd nucleus {sup 156}Pm

    SciTech Connect

    Sood, P. C.; Gowrishankar, R; Sai, K. Vijay; Sainath, M.

    2011-02-15

    Critical examination of the experimental data from {sup 156}Nd and {sup 156}Pm {beta} decays and the observed location of relevant neutron and proton orbitals in the neighboring odd-A isotones and isotopes, taken together with the low-lying two-quasiparticle (2qp) structures expected in {sup 156}Pm from the rotor-particle model, lead to the conclusion that a consistent description of all the available data is achieved with the I{sup {pi}}=4{sup +} spin-parity assignment to the 26.7s {sup 156}Pm ground state (g.s.) and assignment of I{sup {pi}}=1{sup +} to its 150.3-keV isomer with the 2qp configuration 4{sub g.s.}{sup +}{l_brace}p{sub o}:5/2[532{up_arrow}]{+-}n{sub o}:3/2[521{up_arrow}]{r_brace}1{sub 150}{sup +}. In the process, a two-neutron configuration is also suggested for the 1509-keV 4{sup +} level in the daughter nucleus {sup 156}Sm. The present analysis reiterates the important question of whether the {beta}-decay log ft value, by itself, can be employed to deduce the relative parity of the {beta}-connected states.

  11. Genes Plus Erratic Sleep May Raise Odds for Obesity

    MedlinePlus

    ... Search Search MedlinePlus GO GO About MedlinePlus Site Map FAQs Customer ... of this page: https://medlineplus.gov/news/fullstory_164039.html Genes Plus Erratic Sleep May Raise Odds for Obesity ...

  12. Can Depression Up Odds for Arthritis Linked to Psoriasis?

    MedlinePlus

    ... https://medlineplus.gov/news/fullstory_163780.html Can Depression Up Odds for Arthritis Linked to Psoriasis? Mood ... 24, 2017 FRIDAY, Feb. 24, 2017 (HealthDay News) -- Depression in people with the chronic inflammatory skin disease ...

  13. Fixation probability and the crossing time in the Wright-Fisher multiple alleles model

    NASA Astrophysics Data System (ADS)

    Gill, Wonpyong

    2009-08-01

    The fixation probability and crossing time in the Wright-Fisher multiple alleles model, which describes a finite haploid population, were calculated by switching on an asymmetric sharply-peaked landscape with a positive asymmetric parameter, r, such that the reversal allele of the optimal allele has higher fitness than the optimal allele. The fixation probability, which was evaluated as the ratio of the first arrival time at the reversal allele to the origination time, was double the selective advantage of the reversal allele compared with the optimal allele in the strong selection region, where the fitness parameter, k, is much larger than the critical fitness parameter, kc. The crossing time in a finite population for r>0 and kallele in the first generation should be greater than one individual in an asymmetric sharply-peaked landscape. It was also found that the crossing time in a finite population for r>0 and k≫kc scaled as a power law in the fitness parameter with a similar scaling exponent as the crossing time in an infinite population for r=0, and that the critical fitness parameter decreased with increasing sequence length with a fixed population size.

  14. Selected class I and class II HLA alleles and haplotypes and risk of high-grade cervical intraepithelial neoplasia.

    PubMed

    Ades, Steven; Koushik, Anita; Duarte-Franco, Eliane; Mansour, Nabil; Arseneau, Jocelyne; Provencher, Diane; Gilbert, Lucy; Gotlieb, Walter; Ferenczy, Alex; Coutlée, François; Roger, Michel; Franco, Eduardo L

    2008-06-15

    Human leukocyte antigens (HLAs) present foreign antigens to the immune system and may be important determinants of cervical neoplasia. Previously published associations between HLA and cervical neoplasia exhibit considerable variation in findings. The biomarkers of cervical cancer risk (BCCR) case-control study addressed the role of specific HLA alleles as cofactors in the development of high-grade cervical intraepithelial neoplasia (HG-CIN) based on the most consistent evidence from published literature. Cases (N = 381) were women with histologically-confirmed HG-CIN attending colposcopy clinics and controls (N = 884) were women from outpatient clinics with normal cytological screening smears. Subjects were mainly of French-Canadian descent. Cervical specimens were tested for human papillomavirus (HPV) DNA and HLA genotypes by PGMY L1 consensus primer PCR and a PCR sequence-specific primer method, respectively. Unlike other studies, the DQB1*03 and DRB1*13 allele groups were not associated with risk of HG-CIN. The B7-DRB1*1501-DQB1*0602 haplotype was associated with a 41% overall reduction in HG-CIN risk (odds ratio [OR] = 0.59; 95% confidence interval [CI]: 0.36-0.96), and an 83% reduction in risk of HG-CIN among HPV 16 or HPV 18-positive subjects (OR = 0.17; 95%CI: 0.05-0.54). Paradoxically, however, the same haplotype was associated with HPV 16/18 infection risk among controls (OR = 8.44, 95%CI: 1.12-63.73). In conclusion, the B7-DRB1*1501-DQB1*0602 haplotype was protective against HG-CIN, especially in individuals infected with oncogenic HPV, but the mechanism of the association seems to involve multiple steps in the natural history of HPV and CIN.

  15. The Sp1-mediaded allelic regulation of MMP13 expression by an ESCC susceptibility SNP rs2252070

    PubMed Central

    Shi, Meng; Xia, Jianhong; Xing, Huaixin; Yang, Wenjun; Xiong, Xiangyu; Pan, Wenting; Han, Sichong; Shang, Jinhua; Zhou, Changchun; Zhou, Liqing; Yang, Ming

    2016-01-01

    Metallopeptidase 13 (MMP13), a well-known and highly regulated zinc-dependent MMP collagenase, plays a crucial part in development and progression of esophageal squamous cell carcinoma (ESCC). Therefore, we examined associations between ESCC susceptibility and four haplotype-tagging single nucleotide polymorphisms (htSNPs) using a two stage case-control strategy. Odds ratios (OR) and 95% confidence intervals (95% CI) were computed by logistic regression model. After analyzing 1588 ESCC patients and frequency-matched 1600 unaffected controls, we found that MMP13 rs2252070 G > A genetic polymorphism is significantly associated with ESCC risk in Chinese Han populations (GA: OR = 0.63, 95% CI = 0.54–0.74, P = 1.7 × 10−6, AA: OR = 0.73, 95% CI = 0.66–0.81, P = 1.8 × 10−6). Interestingly, the rs2252070 G-to-A change was shown to diminish a Sp1-binding site in ESCC cells. Reporter gene assays indicated that the rs2252070 A allele locating in a potential MMP13 promoter has low promoter activities. After measuring MMP13 gene expression in sixty-six pairs of esophageal cancer and normal tissues, we observed that the rs2252070 A protective allele carriers showed decreased oncogene MMP13 expression. Results of these analyses underline the support of the notion that MMP13 might function as a key oncogene in esophageal carcinogenesis. PMID:27245877

  16. The Sp1-mediaded allelic regulation of MMP13 expression by an ESCC susceptibility SNP rs2252070.

    PubMed

    Shi, Meng; Xia, Jianhong; Xing, Huaixin; Yang, Wenjun; Xiong, Xiangyu; Pan, Wenting; Han, Sichong; Shang, Jinhua; Zhou, Changchun; Zhou, Liqing; Yang, Ming

    2016-06-01

    Metallopeptidase 13 (MMP13), a well-known and highly regulated zinc-dependent MMP collagenase, plays a crucial part in development and progression of esophageal squamous cell carcinoma (ESCC). Therefore, we examined associations between ESCC susceptibility and four haplotype-tagging single nucleotide polymorphisms (htSNPs) using a two stage case-control strategy. Odds ratios (OR) and 95% confidence intervals (95% CI) were computed by logistic regression model. After analyzing 1588 ESCC patients and frequency-matched 1600 unaffected controls, we found that MMP13 rs2252070 G > A genetic polymorphism is significantly associated with ESCC risk in Chinese Han populations (GA: OR = 0.63, 95% CI = 0.54-0.74, P = 1.7 × 10(-6), AA: OR = 0.73, 95% CI = 0.66-0.81, P = 1.8 × 10(-6)). Interestingly, the rs2252070 G-to-A change was shown to diminish a Sp1-binding site in ESCC cells. Reporter gene assays indicated that the rs2252070 A allele locating in a potential MMP13 promoter has low promoter activities. After measuring MMP13 gene expression in sixty-six pairs of esophageal cancer and normal tissues, we observed that the rs2252070 A protective allele carriers showed decreased oncogene MMP13 expression. Results of these analyses underline the support of the notion that MMP13 might function as a key oncogene in esophageal carcinogenesis.

  17. HLA-DPB1*04:01 allele is associated with non-obstructive azoospermia in Japanese patients.

    PubMed

    Jinam, Timothy A; Nakaoka, Hirofumi; Hosomichi, Kazuyoshi; Mitsunaga, Shigeki; Okada, Hiroyuki; Tanaka, Atsushi; Tanaka, Kenichi; Inoue, Ituro

    2013-12-01

    Azoospermia is defined by absence of sperm in the semen and can either be caused by obstruction of the seminal tract (obstructive azoospermia) or by defects in spermatogenesis (non-obstructive azoospermia, NOA). Previous studies reported that specific alleles and single nucleotide polymorphisms (SNPs) in the human leukocyte antigen (HLA) region were associated with NOA in East Asians. We attempt to expand upon previous findings by genotyping more HLA genes and to replicate SNP associations by focusing on Japanese NOA patients. HLA typing of six genes (HLA-A, -B, -C, -DRB1, -DQB1, and -DPB1) was done on 355 NOA patients using SSO-Luminex assay while genotyping of two previously reported SNPs (rs498422 and rs3129878) was done on 443 patients and 544 fertile males using TaqMan assay. Association between the HLA alleles and SNP with NOA was assessed with Chi squared and logistic regression tests. We found that HLA-DPB1*04:01 [corrected p value, P(c) 7.13 × 10(-6); odds ratio (OR) 2.52], DRB1*13:02 (P(c) 4.93 × 10(-4), OR 1.97), DQB1*06:04 (P(c) 8.94 × 10(-4), OR 1.91) and rs3129878 (p value 3.98 × 10(-4); OR 1.32) showed significant association with NOA, however, these loci are in linkage disequilibrium with each other. The conditional logistic regression tests showed that DPB1*04:01 is independently associated with NOA, confirming the involvement of the HLA region in the etiology of NOA in Japanese patients.

  18. Cavity tests of parity-odd Lorentz violations in electrodynamics

    NASA Astrophysics Data System (ADS)

    Mewes, Matthew; Petroff, Alexander

    2007-03-01

    Electromagnetic resonant cavities form the basis for a number modern tests of Lorentz invariance. The geometry of most of these experiments implies unsuppressed sensitivities to parity-even Lorentz violations only. Parity-odd violations typically enter through suppressed boost effects, causing a reduction in sensitivity by roughly 4 orders of magnitude. Here we discuss possible techniques for achieving unsuppressed sensitivities to parity-odd violations using asymmetric resonators.

  19. The odd-number sequence: squares and sums

    NASA Astrophysics Data System (ADS)

    Leyendekkers, J. V.; Shannon, A. G.

    2015-11-01

    Direct study of various characteristics of integers and their interactions is readily accessible to undergraduate students. Integers obviously fall in different classes of modular rings and thus have features unique to that class which can result in a variety of formations, particularly with sums of squares. The sum of the first n odd numbers is itself the square of n within the odd number sequence, from which testing for primality within the Fibonacci sequence is investigated in this note.

  20. Allelic selection of human IL-2 gene.

    PubMed

    Matesanz, F; Delgado, C; Fresno, M; Alcina, A

    2000-12-01

    The allelic expression of mouse IL-2 cannot be definitely extrapolated to what might happen in humans. Therefore, we investigated the regulation of allelic expression of the IL-2 gene in non-genetically manipulated human T lymphocytes by following natural allelic polymorphisms. We found a phenotypically silent punctual change in the human IL-2 at position 114 after the first nucleotide of the initiation codon, which represents a dimorphic polymorphism at the first exon of the IL-2 gene. This allowed the study by single-cell PCR of the regulation of the human IL-2 allelic expression in heterozygous CD4(+) T cells, which was found to be tightly controlled monoallelically. These findings may be used as a suitable marker for monitoring the IL-2 allelic contribution to effector activities and in immune responses against different infections or in pathological situations.

  1. Reduced carriership of 4G allele of plasminogen activator inhibitor-1 4G/5G polymorphism in very young survivors of myocardial infarction.

    PubMed

    Rallidis, Loukianos S; Gialeraki, Argyri; Merkouri, Efrosyni; Liakos, George; Dagres, Nikolaos; Sionis, Dimitrios; Travlou, Anthi; Lekakis, John; Kremastinos, Dimitrios T

    2010-05-01

    There are limited and controversial data regarding the impact of 4G/5G polymorphism of the plasminogen activator inhibitor-1 (PAI-1) gene in the pathogenesis of premature myocardial infarction (MI). We explored whether 4G/5G polymorphism of the PAI-1 gene is associated with the development of MI allele carriers (4G/4G and 4G/5G genotypes) of PAI-1 were less frequent in patients than in controls (69.6 vs. 83.6%, P = 0.007). 4G carriership of the polymorphism of PAI-1 was associated with lower risk for acute MI (odds ratio 0.45, 95% confidence interval 0.23-0.88, P = 0.02) after adjusting for major cardiovascular risk factors. Patients possessing the 4G allele had higher PAI-1 plasma levels (32.2 +/- 25 vs. 22.2 +/- 11.3 ng/ml, P = 0.006) but lower lipoprotein(a) levels (10.1 [2.1-29.9] vs. 15.3 [8.2-57.1] mg/dl, P = 0.03) compared to 5G/5G homozygotes. Our data indicate that the 4G allele of the PAI-1 4G/5G polymorphism is less frequent among survivors of MI at very young age compared with matched controls.

  2. The ADA*2 allele of the adenosine deaminase gene (20q13.11) and recurrent spontaneous abortions: an age-dependent association

    PubMed Central

    Nunes, Daniela Prudente Teixeira; Spegiorin, Lígia Cosentino Junqueira Franco; de Mattos, Cinara Cássia Brandão; Oliani, Antonio Helio; Vaz-Oliani, Denise Cristina Mós; de Mattos, Luiz Carlos

    2011-01-01

    OBJECTIVE: Adenosine deaminase acts on adenosine and deoxyadenosine metabolism and modulates the immune response. The adenosine deaminase G22A polymorphism (20q.11.33) influences the level of adenosine deaminase enzyme expression, which seems to play a key role in maintaining pregnancy. The adenosine deaminase 2 phenotype has been associated with a protective effect against recurrent spontaneous abortions in European Caucasian women. The aim of this study was to investigate whether the G22A polymorphism of the adenosine deaminase gene is associated with recurrent spontaneous abortions in Brazilian women. METHODS: A total of 311 women were recruited to form two groups: G1, with a history of recurrent spontaneous abortions (N = 129), and G2, without a history of abortions (N = 182). Genomic DNA was extracted from peripheral blood with a commercial kit and PCR-RFLP analysis was used to identify the G22A genetic polymorphism. Fisher's exact test and odds ratio values were used to compare the proportions of adenosine deaminase genotypes and alleles between women with and without a history of recurrent spontaneous abortion (p<0.05). The differences between mean values for categorical data were calculated using unpaired t tests. The Hardy-Weinberg equilibrium was assessed with a chi-square test. RESULTS: Statistically significant differences were identified for the frequencies of adenosine deaminase genotypes and alleles between the G1 and G2 groups when adjusted for maternal age. CONCLUSIONS: The results suggest that the adenosine deaminase *2 allele is associated with a low risk for recurrent spontaneous abortions, but this association is dependent on older age. PMID:22086524

  3. Strong association of the HLA-DP6 supertype with childhood leukaemia is due to a single allele, DPB1*0601.

    PubMed

    Taylor, G M; Hussain, A; Verhage, V; Thompson, P D; Fergusson, W D; Watkins, G; Lightfoot, T; Harrison, C J; Birch, J M

    2009-05-01

    We previously reported that susceptibility to childhood B cell precursor ALL (BCP ALL) is associated with HLA-DPB1 alleles having glutamic acid (E) rather than lysine (K) in the P4 antigenic peptide-binding pocket. Clustering approximately 90% of DPB1 alleles into DPB69E (DP2, 6, 8) and DPB69K (DP1, 3, 4) supertypes revealed that DP2 and DP8 are associated with BCP ALL, but DP6 is also associated with non-BCP leukaemia. Here, we report that only one of seven alleles with the DP6 supertype (DPB1(*)0601) is associated with childhood leukaemia (leukaemia vs controls: odds ratio, 95% confidence interval [OR, CI]: 4.6, 2.0-10.4; corrected P=0.019), but not with childhood solid tumours or lymphomas. DPB1(*)0601 is also significantly associated with leukaemia subtypes, including BCP ALL, Pro-B ALL, T-ALL and AML. DPB1(*)0601 is significantly over-transmitted (76.9%) from parents to children with BCP ALL (OR; CI: 4.7; 1.01-22.2). Sequencing the coding region of DPB1(*)0601 revealed an exon 1-4 haplotype [T-DEAV-KIL-RVI] shared with DPB1(*)0301 and 0901, but no evidence of germline mutations in childhood leukaemia. These results suggest that the DPbeta0601 molecule may be functionally involved in childhood leukaemia. Analysis of peptide binding and T-cell activation by DPbeta0601-peptide complexes should help determine its role in childhood leukaemia causation.

  4. Projected shell model study of odd-odd f-p-g shell proton-rich nuclei

    NASA Astrophysics Data System (ADS)

    Palit, R.; Sheikh, J. A.; Sun, Y.; Jain, H. C.

    2003-01-01

    A systematic study of two-quasiparticle bands of the proton-rich odd-odd nuclei in the mass A˜70 80 region is performed using the projected shell model approach. The study includes Br, Rb, and Y isotopes with N=Z+2 and Z+4. We describe the energy spectra and electromagnetic transition strengths in terms of the configuration mixing of the angular-momentum projected multi-quasiparticle states. Signature splitting and signature inversion in the rotational bands are discussed and are shown to be well described. A preliminary study of the odd-odd N=Z nucleus 74Rb, using the concept of spontaneous symmetry breaking is also presented.

  5. Redundant prepuce increases the odds of chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS)

    PubMed Central

    Zhao, Yu-Yang; Xu, Dong-Liang; Zhao, Fu-Jun; Han, Bang-Min; Shao, Yi; Zhao, Wei; Xia, Shu-Jie

    2014-01-01

    Some published evidence has revealed that the dendritic cells can interact with pathogens that exist in the inner foreskin. This information provides a new vision that pathogens could play a role through the redundant prepuce; numerous studies have failed to find pathogens in prostates of patients who had chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS). However, no studies have reported an association between foreskin length and CP/CPPS. Hence, we conducted a retrospective case-control study of clinical data from 322 CP/CPPS patients (case group) and 341 nonCP/CPPS patients (control group). Demographic characteristics, lifestyle factors, and foreskin lengths were collected and analyzed. Multivariate logistic regression was adopted to calculate the odds of foreskin length for CP/CPPS. According to the multivariate logistic regression results, when the foreskin length covered up more than half of the glans penis, the odds for CP/CPPS were higher with an increased foreskin (odds ratio (OR): 1.66, 95% confidence interval (CI): 1.04–2.66). In comparison, when the glans penis was completely covered by the foreskin, the OR value increased to 1.86 (95% CI, 1.2–2.88). The study results showed an association between foreskin length and the odds of CP/CPPS. When the foreskin length covered up more than half of the glans penis, there were greater odds for CP/CPPS. This possible mechanism might result from interaction between pathogens and DCs in the inner foreskin, consequently activating T-cells to mediate allergic inflammation in the prostate and producing the autoimmunizations causing CP/CPPS. PMID:24875824

  6. Redundant prepuce increases the odds of chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS).

    PubMed

    Zhao, Yu-Yang; Xu, Dong-Liang; Zhao, Fu-Jun; Han, Bang-Min; Shao, Yi; Zhao, Wei; Xia, Shu-Jie

    2014-01-01

    Some published evidence has revealed that the dendritic cells can interact with pathogens that exist in the inner foreskin. This information provides a new vision that pathogens could play a role through the redundant prepuce; numerous studies have failed to find pathogens in prostates of patients who had chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS). However, no studies have reported an association between foreskin length and CP/CPPS. Hence, we conducted a retrospective case-control study of clinical data from 322 CP/CPPS patients (case group) and 341 nonCP/CPPS patients (control group). Demographic characteristics, lifestyle factors, and foreskin lengths were collected and analyzed. Multivariate logistic regression was adopted to calculate the odds of foreskin length for CP/CPPS. According to the multivariate logistic regression results, when the foreskin length covered up more than half of the glans penis, the odds for CP/CPPS were higher with an increased foreskin (odds ratio (OR): 1.66, 95% confidence interval (CI): 1.04-2.66). In comparison, when the glans penis was completely covered by the foreskin, the OR value increased to 1.86 (95% CI, 1.2-2.88). The study results showed an association between foreskin length and the odds of CP/CPPS. When the foreskin length covered up more than half of the glans penis, there were greater odds for CP/CPPS. This possible mechanism might result from interaction between pathogens and DCs in the inner foreskin, consequently activating T-cells to mediate allergic inflammation in the prostate and producing the autoimmunizations causing CP/CPPS.

  7. HLA-B alleles and complotypes in Mexican patients with seronegative spondyloarthropathies.

    PubMed Central

    Vargas-Alarcón, G; Garcia, A; Bahena, S; Melin-Aldana, H; Andrade, F; Ibañez-de-Kasep, G; Alcocer-Varela, J; Alarcón-Segovia, D; Granados, J

    1994-01-01

    OBJECTIVES--To analyse major histocompatibility complex (MHC) haplotypes in Mexican mestizo patients with seronegative spondyloarthropathies (SSpA) and normal controls, to discover if there are other antigens, besides B27, in the HLA region that might show association with the disease. METHODS--The study included 100 Mexican mestizo patients with SSpA and 200 of their first degree relatives. These groups were compared with 85 ethnically matched controls. The class I and class III MHC antigens were obtained by standard methods. The significance of differences between patients and controls was tested by chi 2 analysis; linkage disequilibrium among the different alleles in each haplotype was estimated by computing delta values. RESULTS--We found a significantly increased frequency of the HLA-B27 antigen (pcorr. = 1 x 10(-5), odds ratio (OR) = 33.4, 95% confidence interval (CI) = 9.3-142.0). In the group of 45 SSpA patients negative for the B27 antigen, independent increased frequencies of HLA-B49 antigen (pcorr. = 0.03, OR = 6.5, 95% CI = 1.5-32.8)) and the FC31 complotype (pcorr. = 0.04, OR = 3.7, 95% CI = 1.2-11.1) were found. Significant delta values were obtained for the [B27;SC30] haplotype (p = 0.0005) but not for haplotypes marked by the FC31 complotype. HLA-B antigens on the homologous chromosome in B27 positive patients were mainly HLA-B51 (18%) and HLA-B60 (16%); however, the observed genotypes B27/B51 and B27/B60 were not significantly different than expected from the allele frequencies alone. CONCLUSIONS--These data suggest that in Mexicans additional genes within the MHC region besides the HLA-B27 antigen, might be related to the genetic susceptibility for developing SSpA. Relevant antigens included the HLA-B49 and the FC31 complotype. PMID:7826137

  8. Executive functions in preschoolers with ADHD, ODD, and comorbid ADHD-ODD: Evidence from ecological and performance-based measures.

    PubMed

    Ezpeleta, Lourdes; Granero, Roser

    2015-09-01

    Executive functioning in 3-year-old preschoolers with attention-deficit hyperactivity disorder (ADHD), oppositional-defiant disorder (ODD), comorbid ADHD+ODD, and children without any of these conditions (control group) was examined. A community sample including 622 children was diagnosed using a diagnostic interview following DSM-IV criteria, and assessed using the Behavior Rating Inventory of Executive Function Preschool version (BRIEF-P) and the Kiddie-Conners' Continuous Performance Test. The children diagnosed with ADHD showed the poorest executive function (EF) profile in comparison with controls, and were closely followed up in this respect by the comorbid ADHD+ODD children. The ADHD and comorbid groups presented similar executive difficulties. The ODD group obtained mean scores statistically equal to those of controls in EF. These findings suggest that, in preschoolers, executive functioning deficits assessed with a performance-based measure or with behavioural descriptions are specific to children with ADHD, in comparison with those with ODD. This study contributes knowledge about EFs in two prevalent and comorbid disorders in preschool children, ADHD and ODD, knowledge that can help our understanding of specific deficits and the design of specific early intervention initiatives.

  9. Platelet serotonin uptake and paroxetine binding among allelic genotypes of the serotonin transporter in alcoholics.

    PubMed

    Javors, Martin A; Seneviratne, Chamindi; Roache, John D; Ait-Daoud, Nassima; Bergeson, Susan E; Walss-Bass, M Consuelo; Akhtar, Fatema Z; Johnson, Bankole A

    2005-01-01

    Expression rates of long (L) and short (S) alleles of the serotonin (5-HT) transporter (5-HTT) gene have been shown to differ under various circumstances. We compared 5-HTT uptake (function) level and paroxetine binding (density) in platelets of alcoholics as indices of 5-HTT expression rate among LL, LS, and SS genotypes. Concentration curves of [3H]5-HT and [3H]paroxetine were used to quantify the equilibrium constant (Km) and maximum 5-HT uptake rate (Vmax) for 5-HTT uptake into intact platelets and the dissociation constant (Kd) and maximum specific binding density (Bmax) for paroxetine binding to platelet membranes, respectively. Genotypes were determined using electrophoresis with fluorescent markers. Vmax for 5-HTT uptake did not correlate with Bmax for paroxetine binding (r=-0.095, P=0.415). Means of Vmax and Bmax did not differ in a statistically significant manner among LL, LS, and SS genotypes in these alcoholic subjects. However, Vmax for LL and SS appeared to have a bimodal distribution, so the percentage of subjects with Vmax <200 fmol/min-10(7) platelets was statistically significantly higher in LL than in SS (51.5% vs. 22.7%, respectively), with an odds ratio of 3.6 (P<0.05). The percentage of Vmax <200 fmol/min-10(7) platelets for LS was 39.3% (not significant vs. LL or SS). Previous studies of healthy human controls have shown that 5-HTT density in raphe nuclei and 5-HTT uptake in platelets are higher in the LL genotype than in S carriers. Our findings in currently drinking alcoholics support the hypothesis that those with the LL genotype of the 5'-HTTLPR region of the 5-HTT gene have reduced 5-HTT function.

  10. Variant alleles of the CYP1B1 gene are associated with colorectal cancer susceptibility

    PubMed Central

    2010-01-01

    Background CYP1B1 is a P450 enzyme which is involved in the activation of pro-carcinogens to carcinogens as well as sex hormone metabolism. Because differences in the activity of the enzyme have been correlated with variant alleles of single nucleotide polymorphisms (SNPs), it represents an attractive candidate gene for studies into colorectal cancer susceptibility. Methods We genotyped 597 cancer patients and 597controls for three CYP1B1 SNPs, which have previously been shown to be associated with altered enzymatic activity. Using the three SNPs, eight different haplotypes were constructed. The haplotype frequencies were estimated in cases and controls and then compared. The odds ratio for each tumour type, associated with each haplotype was estimated, with reference to the most common haplotype observed in the controls. Results The three SNPs rs10012, rs1056827 and rs1056836 alone did not provide any significant evidence of association with colorectal cancer risk. Haplotypes of rs1056827 and rs10012 or rs1056827 and rs1056836 revealed an association with colorectal cancer which was significantly stronger in the homozygous carriers. One haplotype was under represented in the colorectal cancer patient group compared to the control population suggesting a protective effect. Conclusion Genetic variants within the CYP1B1 that are associated with altered function appear to influence susceptibility to a colorectal cancer in Poland. Three haplotypes were associated with altered cancer risk; one conferred protection and two were associated with an increased risk of disease. These observations should be confirmed in other populations. PMID:20701755

  11. ABO Blood Group Alleles and Prostate Cancer Risk: Results from the Breast and Prostate Cancer Cohort Consortium (BPC3)

    PubMed Central

    Markt, Sarah C.; Shui, Irene M.; Unger, Robert H.; Urun, Yuksel; Berg, Christine D.; Black, Amanda; Brennan, Paul; Bueno-de-Mesquita, H. Bas; Gapstur, Susan M.; Giovannucci, Edward; Haiman, Christopher; Henderson, Brian; Hoover, Robert N.; Hunter, David J.; Key, Timothy J.; Khaw, Kay-Tee; Canzian, Federico; Larranga, Nerea; Le Marchand, Loic; Ma, Jing; Naccarati, Alessio; Siddiq, Afshan; Stampfer, Meir J.; Stattin, Par; Stevens, Victoria L.; Stram, Daniel O.; Tjønneland, Anne; Travis, Ruth C.; Trichopoulos, Dimitrios; Ziegler, Regina G.; Lindstrom, Sara; Kraft, Peter; Mucci, Lorelei A.; Choueiri, Toni K.; Wilson, Kathryn M.

    2015-01-01

    Background ABO blood group has been associated with risk of cancers of the pancreas, stomach, ovary, kidney and skin, but has not been evaluated in relation to risk of aggressive prostate cancer. Methods We used three single nucleotide polymorphisms (SNPs) (rs8176746, rs505922, and rs8176704) to determine ABO genotype in 2,774 aggressive prostate cancer cases and 4,443 controls from the Breast and Prostate Cancer Cohort Consortium (BPC3). Unconditional logistic regression was used to calculate age and study adjusted odds ratios and 95% confidence intervals for the association between blood type, genotype and risk of aggressive prostate cancer (Gleason score ≥8 or locally advanced/metastatic disease (stage T3/T4/N1/M1). Results We found no association between ABO blood type and risk of aggressive prostate cancer (Type A: OR=0.97, 95% CI=0.87-1.08; Type B: OR=0.92, 95% CI=0.77-1.09; Type AB: OR=1.25, 95% CI=0.98-1.59, compared to Type O, respectively). Similarly, there was no association between ‘dose’ of A or B alleles and aggressive prostate cancer risk. Conclusions ABO blood type was not associated with risk of aggressive prostate cancer. PMID:26268879

  12. Characterization of the treefrog null allele, 1991

    SciTech Connect

    Guttman, S.I.

    1992-04-01

    Spring peeper (Hyla crucifer) tadpoles collected from the waste storage area during the Biological and Ecological Site Characterization of the Feed Materials Production Center (FEMP) in 1986 and 1987 appeared to be unique. A null (inactive) allele was found at the glucose phosphate isomerase enzyme locus in significant frequencies (approximately 20%) each year; this allele did not appear to occur in the offsite sample collected approximately 15km from the FEMP. Null alleles at this locus have not been reported in other amphibian populations; when they have been found in other organisms they have invariably been lethal in the homozygous condition.

  13. Characterization of the treefrog null allele

    SciTech Connect

    Guttman, S.I. . Dept. of Zoology)

    1990-12-01

    As part of the authors intensive year-long baseline ecological study, they characterized the degree of genetic polymorphism and heterozygosity in selected Feed Materials Production Center (FMPC) populations using electrophoretic techniques. These data are being used as an indicator of stress by comparing populations on and off the FMPC site. The current study was initiated to determine whether this GPI null allele is lethal, when homozygous, in spring peepers. Also, a sampling protocol was implemented to determine whether a linear effect occurs relative to the frequency of the null allele offsite and to determine the origination site of the null allele. 18 refs., 2 figs., 4 tabs.

  14. Association of the HLA-B*52 allele with non-progression to AIDS in Brazilian HIV-1-infected individuals.

    PubMed

    Teixeira, S L M; de Sá, N B R; Campos, D P; Coelho, A B; Guimarães, M L; Leite, T C N F; Veloso, V G; Morgado, M G

    2014-04-01

    Several human leukocyte antigen (HLA) class I alleles are associated with the susceptibility to human immunodeficiency virus-1 (HIV-1) infection and/or AIDS progression. Of these, the HLA-B alleles are considered the strongest genetic determinant of disease outcome. We evaluated the influence of the HLA-B alleles on AIDS progression among HIV-1-positive individuals from Rio de Janeiro, Brazil, who were categorized as rapid progressors (RPs), typical progressors (TPs) or long-term non-progressors (LTNPs). In this study, significant differences in HLA-B allele frequencies were observed among the three progression groups for the B*48, B*49 and B*52 alleles. After controlling for other factors associated with AIDS progression, the presence of the B*52 allele was shown to be a significant protective factor (hazard ratio (HR) 0.49 (95% confidence interval (CI) 0.27-0.90) P<0.03). Although no direct association was observed between the presence of the B*27 or B*57 allele and the LTNP profile compared with the TP or RP groups, the adjusted model confirmed that these alleles are protective factors against AIDS progression (HR 0.62 (95% CI 0.38-0.99) P<0.05), as previously described. These data corroborate the existence of significant differences in HLA-B allele frequencies among the distinct AIDS progression profiles and further elucidate the role of HLA alleles in the outcome of HIV infections in diverse populations.

  15. Odds of fault and factors for out-of-state drivers in crashes in four states of the USA.

    PubMed

    Harootunian, Kristine; Lee, Brian H Y; Aultman-Hall, Lisa

    2014-11-01

    Drivers outside their country of residence are at a safety disadvantage when compared to native counterparts. This research aimed to (1) investigate if out-of-state drivers in the United States experienced the same vulnerabilities as foreign drivers, and (2) examine the relations of out-of-state crashes to various human and environmental factors. Crash data from Florida, Maine, Minnesota, and Nevada was analyzed to model fault using logistic regressions. Univariate regressions showed that out-of-state drivers had increased odds of fault, ranging from 17% to 92%, for a single-vehicle crash compared to in-state drivers in all states except Florida, where there was no difference between groups. Odds were elevated for out-of-state drivers in two-vehicle crashes by 3% to 19% in all states except Florida and Minnesota, where, again, there was no difference between groups. Human and environmental factors such as age, sex, driving conditions, and seasons were examined with multivariate regressions for in- and out-of-state groups separately, and their odds ratios were compared. For single-vehicle crashes age, sex, road grade, surface condition, light conditions, and day of week were factors that increased at least one of the two groups' odds of fault in all states. Sex, surface condition, and light conditions increased the odds of fault for at least one of the groups in two-vehicle crashes in all four states. Factors that consistently increased odds of fault for both single- and two-vehicle crashes were males, non-vehicle owners, curves, and inclement weather. Although there were several factors in each state that increased odds of fault for out-of-state drivers, no factors consistently increased odds of fault for out-of-state drivers across all four states.

  16. Nucleotide variation and identification of novel blast resistance alleles of Pib by allele mining strategy.

    PubMed

    Ramkumar, G; Madhav, M S; Devi, S J S Rama; Prasad, M S; Babu, V Ravindra

    2015-04-01

    Pib is one of significant rice blast resistant genes, which provides resistance to wide range of isolates of rice blast pathogen, Magnaporthe oryzae. Identification and isolation of novel and beneficial alleles help in crop enhancement. Allele mining is one of the best strategies for dissecting the allelic variations at candidate gene and identification of novel alleles. Hence, in the present study, Pib was analyzed by allele mining strategy, and coding and non-coding (upstream and intron) regions were examined to identify novel Pib alleles. Allelic sequences comparison revealed that nucleotide polymorphisms at coding regions affected the amino acid sequences, while the polymorphism at upstream (non-coding) region affected the motifs arrangements. Pib alleles from resistant landraces, Sercher and Krengosa showed better resistance than Pib donor variety, might be due to acquired mutations, especially at LRR region. The evolutionary distance, Ka/Ks and phylogenetic analyzes also supported these results. Transcription factor binding motif analysis revealed that Pib (Sr) had a unique motif (DPBFCOREDCDC3), while five different motifs differentiated the resistance and susceptible Pib alleles. As the Pib is an inducible gene, the identified differential motifs helps to understand the Pib expression mechanism. The identified novel Pib resistant alleles, which showed high resistance to the rice blast, can be used directly in blast resistance breeding program as alternative Pib resistant sources.

  17. Association of MMP7 -181A→G Promoter Polymorphism with Gastric Cancer Risk: INFLUENCE OF NICOTINE IN DIFFERENTIAL ALLELE-SPECIFIC TRANSCRIPTION VIA INCREASED PHOSPHORYLATION OF cAMP-RESPONSE ELEMENT-BINDING PROTEIN (CREB).

    PubMed

    Kesh, Kousik; Subramanian, Lakshmi; Ghosh, Nillu; Gupta, Vinayak; Gupta, Arnab; Bhattacharya, Samir; Mahapatra, Nitish R; Swarnakar, Snehasikta

    2015-06-05

    Elevated expression of matrix metalloproteinase7 (MMP7) has been demonstrated to play a pivotal role in cancer invasion. The -181A→G (rs11568818) polymorphism in the MMP7 promoter modulates gene expression and possibly affects cancer progression. Here, we evaluated the impact of -181A→G polymorphism on MMP7 promoter activity and its association with gastric cancer risk in eastern Indian case-control cohorts (n = 520). The GG genotype as compared with the AA genotype was predisposed (p = 0.02; odds ratio = 1.9, 95% confidence interval = 1.1-3.3) to gastric cancer risk. Stratification analysis showed that tobacco addiction enhanced gastric cancer risk in GG subjects when compared with AA subjects (p = 0.03, odds ratio = 2.46, and 95% confidence interval = 1.07-5.68). Meta-analysis revealed that tobacco enhanced the risk for cancer more markedly in AG and GG carriers. Activity and expression of MMP7 were significantly higher in GG than in AA carriers. In support, MMP7 promoter-reporter assays showed greater transcriptional activity toward A to G transition under basal/nicotine-induced/cAMP-response element-binding protein (CREB) overexpressed conditions in gastric adenocarcinoma cells. Moreover, nicotine (a major component of tobacco) treatment significantly up-regulated MMP7 expression due to enhanced CREB phosphorylation followed by its nuclear translocation in gastric adenocarcinoma cells. Furthermore, chromatin immunoprecipitation experiments revealed higher binding of phosphorylated CREB with the -181G than the -181A allele. Altogether, specific binding of phosphorylated CREB to the G allele-carrying promoter enhances MMP7 gene expression that is further augmented by nicotine due to increased CREB phosphorylation and thereby increases the risk for gastric cancer.

  18. Effects of Tooth Loss and the Apolipoprotein E ɛ4 Allele on Mild Memory Impairment in the Fujiwara-kyo Study of Japan: A Nested Case-Control Study

    PubMed Central

    Okamoto, Nozomi; Morikawa, Masayuki; Amano, Nobuko; Yanagi, Motokazu; Takasawa, Shin; Kurumatani, Norio

    2016-01-01

    Background: Several studies have suggested that periodontal disease can exacerbate the pro-inflammatory status of the brain. Tooth loss is one of the alternative evaluation indices of periodontal disease. There are few data on the relationship between tooth loss and memory impairment, depending on the apolipoprotein E (APOE) ɛ4 genotype. Objective: To determine if tooth loss is associated with mild memory impairment (MMI) and if this association is modified by the presence of the APOE ɛ4 allele. Methods: A nested case-control study was conducted from 2007 to 2012 in Japan. Five hundred and thirty-seven Japanese subjects aged 65 years and over who were cognitively intact at baseline were analyzed. MMI at follow-up was evaluated. Results: The median number of teeth at baseline was significantly lower in MMI participants (n = 179) than in controls (n = 358) (MMI: median 21.0, interquartile range 10.0–25.0 versus controls: 24.0, 14.0–27.0). After adjustment for demographics, vascular risk factors, and APOE ɛ4 allele, the multivariate adjusted odds ratio (OR) of ≤8 teeth was 1.97 (95% confidence interval [CI], 1.13–3.44) compared to 25–32 teeth. Participants with both the presence of at least 1 APOE ɛ4 allele and ≤8 teeth had a higher risk of MMI compared with those with neither (OR, 2.82; 95% CI, 1.15–6.91). Those with either risk factor alone did not have a higher risk of MMI. Conclusions: A lower number of teeth is related to risk of MMI. This may be primarily true for those individuals with an APOE ɛ4 allele. PMID:27716671

  19. Estimating Regression Parameters in an Extended Proportional Odds Model

    PubMed Central

    Chen, Ying Qing; Hu, Nan; Cheng, Su-Chun; Musoke, Philippa; Zhao, Lue Ping

    2012-01-01

    The proportional odds model may serve as a useful alternative to the Cox proportional hazards model to study association between covariates and their survival functions in medical studies. In this article, we study an extended proportional odds model that incorporates the so-called “external” time-varying covariates. In the extended model, regression parameters have a direct interpretation of comparing survival functions, without specifying the baseline survival odds function. Semiparametric and maximum likelihood estimation procedures are proposed to estimate the extended model. Our methods are demonstrated by Monte-Carlo simulations, and applied to a landmark randomized clinical trial of a short course Nevirapine (NVP) for mother-to-child transmission (MTCT) of human immunodeficiency virus type-1 (HIV-1). Additional application includes analysis of the well-known Veterans Administration (VA) Lung Cancer Trial. PMID:22904583

  20. Effective field theory for vibrations in odd-mass nuclei

    NASA Astrophysics Data System (ADS)

    Coello Pérez, E. A.; Papenbrock, T.

    2016-11-01

    Heavy even-even nuclei exhibit low-energy collective excitations that are separated in scale from the microscopic (fermion) degrees of freedom. This separation of scale allows us to approach nuclear vibrations within an effective field theory (EFT). In odd-mass nuclei collective and single-particle properties compete at low energies, and this makes their description more challenging. In this article we describe spherical odd-mass nuclei with ground-state spin I =1/2 by means of an EFT that couples a fermion to the collective degrees of freedom of an even-even core. The EFT relates observables such as energy levels, electric quadrupole transition strengths, and magnetic dipole moments of the odd-mass nucleus to those of its even-even neighbor and allows us to quantify theoretical uncertainties. For isotopes of rhodium and silver the theoretical description is consistent with data within experimental and theoretical uncertainties. Several testable predictions are made.

  1. Even and odd Wigner negative binomial states: Nonclassical properties

    NASA Astrophysics Data System (ADS)

    Mojaveri, B.; Dehghani, A.

    2015-10-01

    By using Wigner-Heisenberg algebra (WHA) and its Fock representation, even and odd Wigner negative binomial states (WNBSs) |M,ξ,ν>±W (ν = 0 corresponds to the ordinary even and odd negative binomial states (NBSs)) are introduced. These states can be reduced to the Wigner cat states in special limit. We establish the resolution of identity property for them through a positive definite measure on the unit disc. Some of their nonclassical properties, such as Mandel’s parameter and quadrature squeezing have been investigated numerically. We show that in contrast with the even NBSs, even WNBSs may exhibit sub-Poissonian statistics. Also squeezing in the field quadratures appears for both even and odd WNBSs. It is found that the deformation parameter ν plays an essential role in displaying highly nonclassical behaviors.

  2. Comparison of HLA allelic imputation programs.

    PubMed

    Karnes, Jason H; Shaffer, Christian M; Bastarache, Lisa; Gaudieri, Silvana; Glazer, Andrew M; Steiner, Heidi E; Mosley, Jonathan D; Mallal, Simon; Denny, Joshua C; Phillips, Elizabeth J; Roden, Dan M

    2017-01-01

    Imputation of human leukocyte antigen (HLA) alleles from SNP-level data is attractive due to importance of HLA alleles in human disease, widespread availability of genome-wide association study (GWAS) data, and expertise required for HLA sequencing. However, comprehensive evaluations of HLA imputations programs are limited. We compared HLA imputation results of HIBAG, SNP2HLA, and HLA*IMP:02 to sequenced HLA alleles in 3,265 samples from BioVU, a de-identified electronic health record database coupled to a DNA biorepository. We performed four-digit HLA sequencing for HLA-A, -B, -C, -DRB1, -DPB1, and -DQB1 using long-read 454 FLX sequencing. All samples were genotyped using both the Illumina HumanExome BeadChip platform and a GWAS platform. Call rates and concordance rates were compared by platform, frequency of allele, and race/ethnicity. Overall concordance rates were similar between programs in European Americans (EA) (0.975 [SNP2HLA]; 0.939 [HLA*IMP:02]; 0.976 [HIBAG]). SNP2HLA provided a significant advantage in terms of call rate and the number of alleles imputed. Concordance rates were lower overall for African Americans (AAs). These observations were consistent when accuracy was compared across HLA loci. All imputation programs performed similarly for low frequency HLA alleles. Higher concordance rates were observed when HLA alleles were imputed from GWAS platforms versus the HumanExome BeadChip, suggesting that high genomic coverage is preferred as input for HLA allelic imputation. These findings provide guidance on the best use of HLA imputation methods and elucidate their limitations.

  3. Comparison of HLA allelic imputation programs

    PubMed Central

    Shaffer, Christian M.; Bastarache, Lisa; Gaudieri, Silvana; Glazer, Andrew M.; Steiner, Heidi E.; Mosley, Jonathan D.; Mallal, Simon; Denny, Joshua C.; Phillips, Elizabeth J.; Roden, Dan M.

    2017-01-01

    Imputation of human leukocyte antigen (HLA) alleles from SNP-level data is attractive due to importance of HLA alleles in human disease, widespread availability of genome-wide association study (GWAS) data, and expertise required for HLA sequencing. However, comprehensive evaluations of HLA imputations programs are limited. We compared HLA imputation results of HIBAG, SNP2HLA, and HLA*IMP:02 to sequenced HLA alleles in 3,265 samples from BioVU, a de-identified electronic health record database coupled to a DNA biorepository. We performed four-digit HLA sequencing for HLA-A, -B, -C, -DRB1, -DPB1, and -DQB1 using long-read 454 FLX sequencing. All samples were genotyped using both the Illumina HumanExome BeadChip platform and a GWAS platform. Call rates and concordance rates were compared by platform, frequency of allele, and race/ethnicity. Overall concordance rates were similar between programs in European Americans (EA) (0.975 [SNP2HLA]; 0.939 [HLA*IMP:02]; 0.976 [HIBAG]). SNP2HLA provided a significant advantage in terms of call rate and the number of alleles imputed. Concordance rates were lower overall for African Americans (AAs). These observations were consistent when accuracy was compared across HLA loci. All imputation programs performed similarly for low frequency HLA alleles. Higher concordance rates were observed when HLA alleles were imputed from GWAS platforms versus the HumanExome BeadChip, suggesting that high genomic coverage is preferred as input for HLA allelic imputation. These findings provide guidance on the best use of HLA imputation methods and elucidate their limitations. PMID:28207879

  4. Rheumatoid Arthritis Risk Allele PTPRC Is Also Associated With Response to Anti–Tumor Necrosis Factor α Therapy

    PubMed Central

    Cui, Jing; Saevarsdottir, Saedis; Thomson, Brian; Padyukov, Leonid; van der Helm-van Mil, Annette H. M.; Nititham, Joanne; Hughes, Laura B.; de Vries, Niek; Raychaudhuri, Soumya; Alfredsson, Lars; Askling, Johan; Wedrén, Sara; Ding, Bo; Guiducci, Candace; Wolbink, Gert Jan; Crusius, J. Bart A.; van der Horst-Bruinsma, Irene E.; Herenius, Marieke; Weinblatt, Michael E.; Shadick, Nancy A.; Worthington, Jane; Batliwalla, Franak; Kern, Marlena; Morgan, Ann W.; Wilson, Anthony G.; Isaacs, John D.; Hyrich, Kimme; Seldin, Michael F.; Moreland, Larry W.; Behrens, Timothy W.; Allaart, Cornelia F.; Criswell, Lindsey A.; Huizinga, Tom W. J.; Tak, Paul P.; Bridges, S. Louis; Toes, Rene E. M.; Barton, Anne; Klareskog, Lars; Gregersen, Peter K.; Karlson, Elizabeth W.; Plenge, Robert M.

    2013-01-01

    Objective Anti–tumor necrosis factor α (anti-TNF) therapy is a mainstay of treatment in rheumatoid arthritis (RA). The aim of the present study was to test established RA genetic risk factors to determine whether the same alleles also influence the response to anti-TNF therapy. Methods A total of 1,283 RA patients receiving etanercept, infliximab, or adalimumab therapy were studied from among an international collaborative consortium of 9 different RA cohorts. The primary end point compared RA patients with a good treatment response according to the European League Against Rheumatism (EULAR) response criteria (n = 505) with RA patients considered to be nonresponders (n = 316). The secondary end point was the change from baseline in the level of disease activity according to the Disease Activity Score in 28 joints (ΔDAS28). Clinical factors such as age, sex, and concomitant medications were tested as possible correlates of treatment response. Thirty-one single-nucleotide polymorphisms (SNPs) associated with the risk of RA were genotyped and tested for any association with treatment response, using univariate and multivariate logistic regression models. Results Of the 31 RA-associated risk alleles, a SNP at the PTPRC (also known as CD45) gene locus (rs10919563) was associated with the primary end point, a EULAR good response versus no response (odds ratio [OR] 0.55, P = 0.0001 in the multivariate model). Similar results were obtained using the secondary end point, the ΔDAS28 (P = 0.0002). There was suggestive evidence of a stronger association in autoantibody-positive patients with RA (OR 0.55, 95% confidence interval [95% CI] 0.39–0.76) as compared with autoantibody-negative patients (OR 0.90, 95% CI 0.41–1.99). Conclusion Statistically significant associations were observed between the response to anti-TNF therapy and an RA risk allele at the PTPRC gene locus. Additional studies will be required to replicate this finding in additional patient collections

  5. Fine Mapping Seronegative and Seropositive Rheumatoid Arthritis to Shared and Distinct HLA Alleles by Adjusting for the Effects of Heterogeneity

    PubMed Central

    Han, Buhm; Diogo, Dorothée; Eyre, Steve; Kallberg, Henrik; Zhernakova, Alexandra; Bowes, John; Padyukov, Leonid; Okada, Yukinori; González-Gay, Miguel A.; Rantapää-Dahlqvist, Solbritt; Martin, Javier; Huizinga, Tom W.J.; Plenge, Robert M.; Worthington, Jane; Gregersen, Peter K.; Klareskog, Lars; de Bakker, Paul I.W.; Raychaudhuri, Soumya

    2014-01-01

    Despite progress in defining human leukocyte antigen (HLA) alleles for anti-citrullinated-protein-autoantibody-positive (ACPA+) rheumatoid arthritis (RA), identifying HLA alleles for ACPA-negative (ACPA−) RA has been challenging because of clinical heterogeneity within clinical cohorts. We imputed 8,961 classical HLA alleles, amino acids, and SNPs from Immunochip data in a discovery set of 2,406 ACPA− RA case and 13,930 control individuals. We developed a statistical approach to identify and adjust for clinical heterogeneity within ACPA− RA and observed independent associations for serine and leucine at position 11 in HLA-DRβ1 (p = 1.4 × 10−13, odds ratio [OR] = 1.30) and for aspartate at position 9 in HLA-B (p = 2.7 × 10−12, OR = 1.39) within the peptide binding grooves. These amino acid positions induced associations at HLA-DRB1∗03 (encoding serine at 11) and HLA-B∗08 (encoding aspartate at 9). We validated these findings in an independent set of 427 ACPA− case subjects, carefully phenotyped with a highly sensitive ACPA assay, and 1,691 control subjects (HLA-DRβ1 Ser11+Leu11: p = 5.8 × 10−4, OR = 1.28; HLA-B Asp9: p = 2.6 × 10−3, OR = 1.34). Although both amino acid sites drove risk of ACPA+ and ACPA− disease, the effects of individual residues at HLA-DRβ1 position 11 were distinct (p < 2.9 × 10−107). We also identified an association with ACPA+ RA at HLA-A position 77 (p = 2.7 × 10−8, OR = 0.85) in 7,279 ACPA+ RA case and 15,870 control subjects. These results contribute to mounting evidence that ACPA+ and ACPA− RA are genetically distinct and potentially have separate autoantigens contributing to pathogenesis. We expect that our approach might have broad applications in analyzing clinical conditions with heterogeneity at both major histocompatibility complex (MHC) and non-MHC regions. PMID:24656864

  6. Extremal charged rotating dilaton black holes in odd dimensions

    SciTech Connect

    Allahverdizadeh, Masoud; Kunz, Jutta; Navarro-Lerida, Francisco

    2010-09-15

    Employing higher-order perturbation theory, we find a new class of charged rotating black hole solutions of Einstein-Maxwell-dilaton theory with general dilaton coupling constant. Starting from the Myers-Perry solutions, we use the electric charge as the perturbative parameter, and focus on extremal black holes with equal-magnitude angular momenta in odd dimensions. We perform the perturbations up to 4th order for black holes in 5 dimensions and up to 3rd order in higher odd dimensions. We calculate the physical properties of these black holes and study their dependence on the charge and the dilaton coupling constant.

  7. Allele Workbench: transcriptome pipeline and interactive graphics for allele-specific expression.

    PubMed

    Soderlund, Carol A; Nelson, William M; Goff, Stephen A

    2014-01-01

    Sequencing the transcriptome can answer various questions such as determining the transcripts expressed in a given species for a specific tissue or condition, evaluating differential expression, discovering variants, and evaluating allele-specific expression. Differential expression evaluates the expression differences between different strains, tissues, and conditions. Allele-specific expression evaluates expression differences between parental alleles. Both differential expression and allele-specific expression have been studied for heterosis (hybrid vigor), where the hybrid has improved performance over the parents for one or more traits. The Allele Workbench software was developed for a heterosis study that evaluated allele-specific expression for a mouse F1 hybrid using libraries from multiple tissues with biological replicates. This software has been made into a distributable package, which includes a pipeline, a Java interface to build the database, and a Java interface for query and display of the results. The required input is a reference genome, annotation file, and one or more RNA-Seq libraries with optional replicates. It evaluates allelic imbalance at the SNP and transcript level and flags transcripts with significant opposite directional allele-specific expression. The Java interface allows the user to view data from libraries, replicates, genes, transcripts, exons, and variants, including queries on allele imbalance for selected libraries. To determine the impact of allele-specific SNPs on protein folding, variants are annotated with their effect (e.g., missense), and the parental protein sequences may be exported for protein folding analysis. The Allele Workbench processing results in transcript files and read counts that can be used as input to the previously published Transcriptome Computational Workbench, which has a new algorithm for determining a trimmed set of gene ontology terms. The software with demo files is available from https://code.google.com/p/allele

  8. Ten novel HLA-DRB1 alleles and one novel DRB3 allele.

    PubMed

    Lazaro, A M; Steiner, N K; Moraes, M E; Moraes, J R; Ng, J; Hartzman, R J; Hurley, C K

    2005-10-01

    Ten novel HLA-DRB1 and one DRB3 alleles are described. Eight of the variants are single-nucleotide substitutions, four resulting in an amino acid change (DRB1*1145, *1148, *0828 and *1514) and four with silent substitutions (DRB1*040504, *130103, *160502 and DRB3*020204). Two alleles differ by two nucleotide changes altering one (DRB1*1447 and *1361) amino acid and one allele alters three nucleotides and two amino acids.

  9. Abnormal segregation of alleles in CEPH pedigree DNAs arising from allele loss in lymphoblastoid DNA

    SciTech Connect

    Royle, N.J.; Armour, J.A.L.; Crosier, M.; Jeffreys, A.J. )

    1993-01-01

    Somatic events that result in the reduction to hemior homozygosity at all loci affected by the event have been identified in lymphoblastoid DNA from mothers of two CEPH families. Using suitably informative probes, the allele deficiencies were detected by the abnormal transmission of alleles from grandparents to grandchildren, with the apparent absence of the alleles from the parent. Undetected somatic deficiencies in family DNAs could result in misscoring of recombination events and consequently introduce errors into linkage analysis. 15 refs., 2 figs.

  10. Ten Novel HLA-DRB1 Alleles and One Novel DRB3 Allele

    DTIC Science & Technology

    2006-05-31

    BRIEF COMMUNICATION Ten novel HLA-DRB1 alleles and one novel DRB3 allele A. M. Lazaro1, N. K. Steiner1, M. E. Moraes2, J. R. Moraes2, J. Ng1, R. J...accepted for publication 31 May 2005 doi: 10.1111/j.1399-0039.2005.00459.x Abstract Ten novel HLA-DRB1 and one DRB3 alleles are described. Eight of the...substitutions (DRB1*040504, *130103, *160502 and DRB3 *020204). Two alleles differ by two nucleotide changes altering one (DRB1*1447 and *1361) amino acid and

  11. The Antarctic ozone minimum - Relationship to odd nitrogen, odd chlorine, the final warming, and the 11-year solar cycle

    NASA Technical Reports Server (NTRS)

    Callis, L. B.; Natarajan, M.

    1986-01-01

    Photochemical calculations along 'diabatic trajectories' in the meridional phase are used to search for the cause of the dramatic springtime minimum in Antarctic column ozone. The results indicate that the minimum is principally due to catalytic destruction of ozone by high levels of total odd nitrogen. Calculations suggest that these levels of odd nitrogen are transported within the polar vortex and during the polar night from the middle to upper stratosphere and lower mesosphere to the lower stratosphere. The possibility that these levels are related to the 11-year solar cycle and are increased by enhanced formation in the thermosphere and mesosphere during solar maximum conditions is discussed.

  12. High-spin level scheme of doubly odd 128I

    NASA Astrophysics Data System (ADS)

    Ding, B.; Wang, H. X.; Jiang, H.; Zhang, Y. H.; Zhou, X. H.; Zhao, Y. M.; Wang, S. T.; Liu, M. L.; Li, G. S.; Zheng, Y.; Zhang, N. T.; Zhou, H. B.; Ma, Y. J.; Sasakiz, Y.; Yamada, K.; Ohshima, H.; Yokose, S.; Ishizuka, M.; Komatsubara, T.; Furuno, K.

    2012-09-01

    High-spin states in the odd-odd 128I have been studied experimentally using the 124Sn(7Li, 3nγ)128I reaction at beam energies of 28 and 32 MeV. A level scheme built on the known T1/2=175 ns, (6-) isomer has been established. The low-lying states in the level scheme have been proposed to be associated with the πd5/2⊗νh11/2 and πg7/2⊗νh11/2 two-quasiparticle excitations. The strongly populated negative-parity states, forming a bandlike structure, have been assigned to be based on the πg7/2⊗νh11/2 configuration. The πh11/2⊗νh11/2 multiplet 9+, 10+, and 11+ members have been identified according to the systematics of the corresponding level structures observed in the lighter odd-odd iodine isotopes. The two-quasiparticle configuration assignments are supported by the nucleon pair approximation and empirical shell-model calculations.

  13. Band structure of doubly-odd nuclei around mass 130

    SciTech Connect

    Higashiyama, Koji; Yoshinaga, Naotaka

    2011-05-06

    Nuclear structure of the doublet bands in the doubly-odd nuclei with mass A{approx}130 is studied in terms of a pair-truncated shell model. The model reproduces quite well the energy levels of the doublet bands and the electromagnetic transitions. The analysis of the electromagnetic transitions reveals new band structure of the doublet bands.

  14. Are the Odds Against the Origin of Life Too Great?

    ERIC Educational Resources Information Center

    Carrier, Richard

    2000-01-01

    Statistics are offered to "prove" odds against the origin of life. Presents a summary analysis of all known examples to be used to check these claims whenever they are brought up in conversations, debates, books, or articles. Addresses scientific work misused by anti-evolutionists and the pseudoscientific assertions of the…

  15. Stacking the Odds: A National Directory of Exemplary Programs.

    ERIC Educational Resources Information Center

    Snyder, Jon D.; Spindel, Ann

    A recent study found that many students have dreams for the future, but many of them are on paths that do not lead to that future. Many institutions are already taking steps to close the gap between aspirations and reality, and some of the programs that are working to stack the odds in children's favor are profiled in this directory. Educational…

  16. Odd Laplacians: geometrical meaning of potential and modular class

    NASA Astrophysics Data System (ADS)

    Khudaverdian, Hovhannes M.; Peddie, Matthew T.

    2017-01-01

    A second-order self-adjoint operator Δ =Spartial ^2+U is uniquely defined by its principal symbol S and potential U if it acts on half-densities. We analyse the potential U as a compensating field (gauge field) in the sense that it compensates the action of coordinate transformations on the second derivatives in the same way as an affine connection compensates the action of coordinate transformations on first derivatives in the first-order operator, a covariant derivative, nabla =partial +Γ . Usually a potential U is derived from other geometrical constructions such as a volume form, an affine connection, or a Riemannian structure, etc. The story is different if Δ is an odd operator on a supermanifold. In this case, the second-order potential becomes a primary object. For example, in the case of an odd symplectic supermanifold, the compensating field of the canonical odd Laplacian depends only on this symplectic structure and can be expressed by the formula obtained by K. Bering. We also study modular classes of odd Poisson manifolds via Δ -operators, and consider an example of a non-trivial modular class which is related with the Nijenhuis bracket.

  17. A Study of Odd- and Even-Number Cultures

    ERIC Educational Resources Information Center

    Nishiyama, Yutaka

    2006-01-01

    Japanese prefer odd numbers, whereas Westerners emphasize even numbers, an observation that is clear from the distribution of number-related words in Japanese and English dictionaries. In this article, the author explains why these two cultures differ by surveying the history of numbers, including yin-yang thought from ancient China, ancient Greek…

  18. Search for very light CP-odd Higgs Boson in radiative decays of Upsilon(1S).

    PubMed

    Love, W; Savinov, V; Mendez, H; Ge, J Y; Miller, D H; Shipsey, I P J; Xin, B; Adams, G S; Anderson, M; Cummings, J P; Danko, I; Hu, D; Moziak, B; Napolitano, J; He, Q; Insler, J; Muramatsu, H; Park, C S; Thorndike, E H; Yang, F; Artuso, M; Blusk, S; Khalil, S; Li, J; Mountain, R; Nisar, S; Randrianarivony, K; Sultana, N; Skwarnicki, T; Stone, S; Wang, J C; Zhang, L M; Bonvicini, G; Cinabro, D; Dubrovin, M; Lincoln, A; Naik, P; Rademacker, J; Asner, D M; Edwards, K W; Reed, J; Briere, R A; Ferguson, T; Tatishvili, G; Vogel, H; Watkins, M E; Rosner, J L; Alexander, J P; Cassel, D G; Duboscq, J E; Ehrlich, R; Fields, L; Galik, R S; Gibbons, L; Gray, R; Gray, S W; Hartill, D L; Heltsley, B K; Hertz, D; Hunt, J M; Kandaswamy, J; Kreinick, D L; Kuznetsov, V E; Ledoux, J; Mahlke-Krüger, H; Mohapatra, D; Onyisi, P U E; Patterson, J R; Peterson, D; Riley, D; Ryd, A; Sadoff, A J; Shi, X; Stroiney, S; Sun, W M; Wilksen, T; Athar, S B; Patel, R; Yelton, J; Rubin, P; Eisenstein, B I; Karliner, I; Mehrabyan, S; Lowrey, N; Selen, M; White, E J; Wiss, J; Mitchell, R E; Shepherd, M R; Besson, D; Pedlar, T K; Cronin-Hennessy, D; Gao, K Y; Hietala, J; Kubota, Y; Klein, T; Lang, B W; Poling, R; Scott, A W; Zweber, P; Dobbs, S; Metreveli, Z; Seth, K K; Tomaradze, A; Libby, J; Martin, L; Powell, A; Wilkinson, G; Ecklund, K M

    2008-10-10

    We search for a non-SM-like CP-odd Higgs boson (a(1)(0)) decaying to tau(+)tau(-) or mu(+)mu(-) in radiative decays of the Upsilon(1S). No significant signal is found, and upper limits on the product branching ratios are set. Our tau(+)tau(-) results are almost 2 orders of magnitude more stringent than previous upper limits. Our data provide no evidence for a Higgs state with a mass of 214 MeV decaying to mu(+)mu(-), previously proposed as an explanation for 3 Sigma(+)-->pmu(+)mu(-) events observed by the HyperCP experiment. Our results constrain NMSSM models.

  19. High-Throughput SNP Allele-Frequency Determination in Pooled DNA Samples by Kinetic PCR

    PubMed Central

    Germer, Søren; Holland, Michael J.; Higuchi, Russell

    2000-01-01

    We have developed an accurate, yet inexpensive and high-throughput, method for determining the allele frequency of biallelic polymorphisms in pools of DNA samples. The assay combines kinetic (real-time quantitative) PCR with allele-specific amplification and requires no post-PCR processing. The relative amounts of each allele in a sample are quantified. This is performed by dividing equal aliquots of the pooled DNA between two separate PCR reactions, each of which contains a primer pair specific to one or the other allelic SNP variant. For pools with equal amounts of the two alleles, the two amplifications should reach a detectable level of fluorescence at the same cycle number. For pools that contain unequal ratios of the two alleles, the difference in cycle number between the two amplification reactions can be used to calculate the relative allele amounts. We demonstrate the accuracy and reliability of the assay on samples with known predetermined SNP allele frequencies from 5% to 95%, including pools of both human and mouse DNAs using eight different SNPs altogether. The accuracy of measuring known allele frequencies is very high, with the strength of correlation between measured and known frequencies having an r2 = 0.997. The loss of sensitivity as a result of measurement error is typically minimal, compared with that due to sampling error alone, for population samples up to 1000. We believe that by providing a means for SNP genotyping up to thousands of samples simultaneously, inexpensively, and reproducibly, this method is a powerful strategy for detecting meaningful polymorphic differences in candidate gene association studies and genome-wide linkage disequilibrium scans. PMID:10673283

  20. Biosynthesis of odd-chain fatty alcohols in Escherichia coli.

    PubMed

    Cao, Ying-Xiu; Xiao, Wen-Hai; Liu, Duo; Zhang, Jin-Lai; Ding, Ming-Zhu; Yuan, Ying-Jin

    2015-05-01

    Engineered microbes offer the opportunity to design and implement artificial molecular pathways for renewable production of tailored chemical commodities. Targeted biosynthesis of odd-chain fatty alcohols is very challenging in microbe, due to the specificity of fatty acids synthase for two-carbon unit elongation. Here, we developed a novel strategy to directly tailor carbon number in fatty aldehydes formation step by incorporating α-dioxygenase (αDOX) from Oryza sativa (rice) into Escherichia coli αDOX oxidizes Cn fatty acids (even-chain) to form Cn-1 fatty aldehydes (odd-chain). Through combining αDOX with fatty acyl-acyl carrier protein (-ACP) thioesterase (TE) and aldehyde reductase (AHR), the medium odd-chain fatty alcohols profile (C11, C13, C15) was firstly established in E. coli. Also, medium even-chain alkanes (C12, C14) were obtained by substitution of AHR to aldehyde decarbonylase (AD). The titer of odd-chain fatty alcohols was improved from 7.4mg/L to 101.5mg/L in tube cultivation by means of fine-tuning endogenous fatty acyl-ACP TE (TesA'), αDOX, AHRs and the genes involved in fatty acids metabolism pathway. Through high cell density fed-batch fermentation, a titer of 1.95g/L odd-chain fatty alcohols was achieved, which was the highest reported titer in E. coli. Our system has greatly expanded the current microbial fatty alcohols profile that provides a new brand solution for producing complex and desired molecules in microbes.

  1. Antiferromagnetic molecular nanomagnets with odd-numbered coupled spins

    NASA Astrophysics Data System (ADS)

    Owerre, S. A.; Nsofini, J.

    2015-05-01

    In recent years, studies on cyclic molecular nanomagnets have captivated the attention of researchers. These magnets are finite in size and contain very large spins. They are interesting because they possess macroscopic quantum tunneling of Néel vectors. For antiferromagnetic molecular nanomagnets with finite number of even-numbered coupled spins, tunneling involves two classical localized Néel ground states separated by a magnetic energy barrier. The question is: can such phenomena be observed in nanomagnets with odd number of magnetic ions? The answer is not directly obvious because cyclic chains with odd-numbered coupled spins are frustrated as one cannot obtain a perfect Néel order. These frustrated spins can indeed be observed experimentally, so they are of interest. In this letter, we theoretically investigate macroscopic quantum tunneling in this odd spin system with arbitrary spins s, in the presence of a magnetic field applied along the plane of the magnet. In contrast to systems with an even-numbered coupled spins, the ground state of the cyclic odd-spin system contains a topological soliton due to spin frustration. Thus, the classical ground state is 2N-fold degenerate as the soliton can be placed anywhere along the ring with total S_z=+/- s . Small quantum fluctuations delocalize the soliton with a formation of an energy band. We obtain this energy band using degenerate perturbation theory at order 2s. We show that the soliton ground state is chiral for half-odd integer spins and non-chiral for integer spins. From the structure of the energy band we infer that as the value of the spin increases the inelastic polarized neutron-scattering intensity may increase or decrease depending on the strengths of the parameters of the Hamiltonian.

  2. Entrance-channel effects in odd-Z tranactinide compound nucleus reactions

    SciTech Connect

    Nelson, S.L.; Gregorich, K.E.; Dragojevic, I.; Dullmann, Ch.E.; Eichler, R.; Folden III, C.M.; Garcia, M.A.; Gates, J.M.; Stavsetra, L.; Sudowe, R.; Nitsche, H.

    2007-09-01

    Swiatecki, Siwek-Wilczynska, and Wilczynski's 'Fusion By Diffusion' description [1] of transactinide (TAN) compound nucleus (CN) formation utilizes a three-step model. The first step is the 'sticking', or capture, which can be calculated relatively accurately. The second step is the probability for the formation of a CN by 'diffusion' analogous to that of Brownian motion. Lastly, there exists the probability of the CN 'surviving' deexcitation by neutron emission, which competes with fission and other de-excitation modes. This model predicts and reproduces cross sections typically within a factor of two. Producing the same CN with different projectile-target pairs is a very sensitive way to test entrance channel effects on heavy element production cross sections. If the same CN is produced at or near the same excitation energy the survival portion of the theory is nearly identical for the two reactions. This method can be used as a critical test of the novel 'diffusion' portion of the model. The reactions producing odd-Z TAN CN such as Db, Bh, Mt, and Rg (Z = 105, 107, 109, and 111, respectively) were first studied using even-Z projectiles on {sup 209}Bi targets (as opposed to odd-Z projectiles on {sup 208}Pb targets) because lower effective fissility [2] was expected to lead to larger cross sections. Many odd-Z projectile reactions producing odd-Z CN had not been studied in-depth until very recently. We have completed studies of these reaction pairs with the 88-Inch Cyclotron and the Berkeley Gas-Filled Separator (BGS) at the Lawrence Berkeley National Laboratory (LBNL), see Figure 1. Cross section ratios for several pairs of reactions will be presented and compared with theory.

  3. Odds, prevalence and predictors of sleep problems in school-age normal children.

    PubMed

    Spruyt, Karen; O'Brien, Louise M; Cluydts, Raymond; Verleye, Gino Benjamin; Ferri, Raffaele

    2005-06-01

    The objectives of the study were to describe the prevalence, odds, and predictors of 36 paediatric sleep behaviours and describe their coexistence in a school-age normal population. The design was community-based questionnaire survey of sleep-wake patterns, sleep environment, and 36 sleep behaviours indicative of six sleep disorder-subscales using the Health-Behaviour Questionnaire. A caregivers' report of 3045 children aged 6-13 years in Belgium constituted the participants. Prevalence of each sleep behaviour was calculated. Log-linear modelling within and between the sleep disorder-subscales was used to screen for coexistence. The effect size of selected night-time parameters to the likelihood of sleep behaviours and disorder-subscale was expressed as odds ratios via logit regression analysis. Significant differences in sleep-wake patterns were found between weekday and weekend. Ranking by odds showed that: (1) sleep problems such as 'tired when waking up', 'repetitive limb movements', 'going to bed reluctantly', and 'sleep paralysis' and; (2) the disorder-subscale 'excessive somnolence' are common in children. Coexistences within and between disorder-subscales of sleep problems are evident in a school-age, normal population. These results suggest that disorders of excessive somnolence (DES) are highly prevalent in a non-clinical sample of school-age children. Furthermore, sleep-onset latency and a noisy, not well-darkened room are predictive towards the odds for exhibiting sleep problems and disorders. It is advocated that more information on the importance of good sleep-wake hygiene should reach parents and children.

  4. Allele-specific DNA methylation: beyond imprinting.

    PubMed

    Tycko, Benjamin

    2010-10-15

    Allele-specific DNA methylation (ASM) and allele-specific gene expression (ASE) have long been studied in genomic imprinting and X chromosome inactivation. But these types of allelic asymmetries, along with allele-specific transcription factor binding (ASTF), have turned out to be far more pervasive-affecting many non-imprinted autosomal genes in normal human tissues. ASM, ASE and ASTF have now been mapped genome-wide by microarray-based methods and NextGen sequencing. Multiple studies agree that all three types of allelic asymmetries, as well as the related phenomena of expression and methylation quantitative trait loci, are mostly accounted for by cis-acting regulatory polymorphisms. The precise mechanisms by which this occurs are not yet understood, but there are some testable hypotheses and already a few direct clues. Future challenges include achieving higher resolution maps to locate the epicenters of cis-regulated ASM, using this information to test mechanistic models, and applying genome-wide maps of ASE/ASM/ASTF to pinpoint functional regulatory polymorphisms influencing disease susceptibility.

  5. AlleleSeq: analysis of allele-specific expression and binding in a network framework.

    PubMed

    Rozowsky, Joel; Abyzov, Alexej; Wang, Jing; Alves, Pedro; Raha, Debasish; Harmanci, Arif; Leng, Jing; Bjornson, Robert; Kong, Yong; Kitabayashi, Naoki; Bhardwaj, Nitin; Rubin, Mark; Snyder, Michael; Gerstein, Mark

    2011-08-02

    To study allele-specific expression (ASE) and binding (ASB), that is, differences between the maternally and paternally derived alleles, we have developed a computational pipeline (AlleleSeq). Our pipeline initially constructs a diploid personal genome sequence (and corresponding personalized gene annotation) using genomic sequence variants (SNPs, indels, and structural variants), and then identifies allele-specific events with significant differences in the number of mapped reads between maternal and paternal alleles. There are many technical challenges in the construction and alignment of reads to a personal diploid genome sequence that we address, for example, bias of reads mapping to the reference allele. We have applied AlleleSeq to variation data for NA12878 from the 1000 Genomes Project as well as matched, deeply sequenced RNA-Seq and ChIP-Seq data sets generated for this purpose. In addition to observing fairly widespread allele-specific behavior within individual functional genomic data sets (including results consistent with X-chromosome inactivation), we can study the interaction between ASE and ASB. Furthermore, we investigate the coordination between ASE and ASB from multiple transcription factors events using a regulatory network framework. Correlation analyses and network motifs show mostly coordinated ASB and ASE.

  6. Forensic Loci Allele Database (FLAD): Automatically generated, permanent identifiers for sequenced forensic alleles.

    PubMed

    Van Neste, Christophe; Van Criekinge, Wim; Deforce, Dieter; Van Nieuwerburgh, Filip

    2016-01-01

    It is difficult to predict if and when massively parallel sequencing of forensic STR loci will replace capillary electrophoresis as the new standard technology in forensic genetics. The main benefits of sequencing are increased multiplexing scales and SNP detection. There is not yet a consensus on how sequenced profiles should be reported. We present the Forensic Loci Allele Database (FLAD) service, made freely available on http://forensic.ugent.be/FLAD/. It offers permanent identifiers for sequenced forensic alleles (STR or SNP) and their microvariants for use in forensic allele nomenclature. Analogous to Genbank, its aim is to provide permanent identifiers for forensically relevant allele sequences. Researchers that are developing forensic sequencing kits or are performing population studies, can register on http://forensic.ugent.be/FLAD/ and add loci and allele sequences with a short and simple application interface (API).

  7. Transformation of QTL genotypic effects to allelic effects

    PubMed Central

    Nagamine, Yoshitaka

    2005-01-01

    The genotypic and allelic effect models are equivalent in terms of QTL detection in a simple additive model, but the QTL allelic model has the advantage of providing direct information for marker-assisted selection. However, the allelic matrix is four times as large as the genotypic IBD matrix, causing computational problems, especially in genome scans examining multiple positions. Transformation from genotypic to allelic effects, after estimating the genotypic effects with a smaller IBD matrix, can solve this problem. Although the validity of transformation from genotypic to allelic effects has been disputed, this work proves that transformation can successfully yield unique allelic effects when genotypic and allelic IBD matrixes exist. PMID:16093016

  8. Mesospheric Odd Nitrogen Enhancements During Relativistic Electron Precipitation Events

    NASA Technical Reports Server (NTRS)

    Aikin, A. C.; Smith, H. J. P.

    1999-01-01

    The behavior of mesospheric odd nitrogen species during and following relativistic and diffuse auroral precipitation events is simulated, Below 75 km nitric oxide is enhanced in proportion to the ion pair production function associated with the electron precipitation and the length of the event. Nitrogen dioxide and nitric acid are also enhanced. At 65 km the percentage of odd nitrogen for N is 0.1%, HNO3 is 1.6%, NO2 is 15%, and NO is 83.3%. Between 75 and 85 km NO is depleted during particle events due to the faster destruction of NO by N relative to the production of NO by N reacting with O2. Recovery of NO depends on transport from the lower thermosphere, where NO is produced in abundant amounts during particle events.

  9. Flexible Viologen Cyclophanes: Odd/Even Effects on Intramolecular Interactions.

    PubMed

    Berville, Mathilde; Choua, Sylvie; Gourlaouen, Christophe; Boudon, Corinne; Ruhlmann, Laurent; Bailly, Corinne; Cobo, Saioa; Saint-Aman, Eric; Wytko, Jennifer; Weiss, Jean

    2017-01-04

    The ability of three bis-viologen cyclophanes to act as redox-triggered contractile switches is investigated. Odd/even effects in the formation of cyclic bis-viologens are circumvented by the use of a Zincke salt intermediate and a tetrathiafulvalene template to prepare a flexible cyclophane with hexyl linkers. Comparative spectro-electrochemical studies of this macrocycle with two other pentyl- or heptyl-linked cyclic bis-viologens show that the development of intramolecular interactions in aqueous solution depends on the length of the bridges. This dependence is confirmed by EPR and DFT studies of the magnetic coupling in the diradical dication species. The anti-ferromagnetic or ferromagnetic nature of the coupling depend, respectively, on the odd or even number of methylene groups in the spacer.

  10. Investigation of odd-order nonlinear susceptibilities in atomic vapors

    SciTech Connect

    Yan, Yaqi; Wu, Zhenkun; Si, Jinhai; Yan, Lihe; Zhang, Yiqi; Yuan, Chenzhi; Sun, Jia; Zhang, Yanpeng

    2013-06-15

    We theoretically deduce the macroscopic symmetry constraints for arbitrary odd-order nonlinear susceptibilities in homogeneous media including atomic vapors for the first time. After theoretically calculating the expressions using a semiclassical method, we demonstrate that the expressions for third- and fifth-order nonlinear susceptibilities for undressed and dressed four- and six-wave mixing (FWM and SWM) in atomic vapors satisfy the macroscopic symmetry constraints. We experimentally demonstrate consistence between the macroscopic symmetry constraints and the semiclassical expressions for atomic vapors by observing polarization control of FWM and SWM processes. The experimental results are in reasonable agreement with our theoretical calculations. -- Highlights: •The macroscopic symmetry constraints are deduced for homogeneous media including atomic vapors. •We demonstrate that odd-order nonlinear susceptibilities satisfy the constraints. •We experimentally demonstrate the deduction in part.

  11. Odd-frequency triplet pairing in mixed-parity superconductors

    NASA Astrophysics Data System (ADS)

    Cuoco, Mario; Gentile, Paola; Noce, Canio; Romano, Alfonso; Annunziata, Gaetano; Linder, Jacob

    2012-02-01

    We show that mixed-parity superconductors may exhibit equal-spin pair correlations that are odd-in-time and can be tuned by means of an applied field. The direction and the amplitude of the pair correlator in the spin space turn out to be strongly dependent on the symmetry of the order parameter, and thus provide a tool to identify different types of singlet-triplet mixed configurations. We suggest that odd-in-time spin-polarized pair correlations can be generated without magnetic inhomogeneities in superconducting/ferromagnetic hybrids with non-centrosymmetric superconductor or when parity mixing is induced at the interface. Paola Gentile, Canio Noce, Alfonso Romano, Gaetano Annunziata, Jacob Linder, Mario Cuoco, arXiv:1109.4885

  12. Shape phase transitions in odd-A nuclei

    SciTech Connect

    Alonso, C. E.; Arias, J. M.; Fortunato, L.; Vitturi, A.

    2008-11-11

    We investigate shape phase transitions in odd nuclei within the Interacting Boson Fermion Model. Special attention is given to the case of the transition from the vibrational behaviour to the stable axial deformation. The odd particle is assumed to be moving in the three single particle orbitals j = 1/2,3/2,5/2 with a boson-fermion Hamiltonian that leads to the occurrence of the SU{sup BF}(3) boson-fermion symmetry when the boson part approaches the SU(3) condition. Both energy spectra and electromagnetic transitions show characteristic patterns similar to those displayed by the even nuclei at the corresponding critical point. The role of the additional particle in characterizing the properties of the critical points in finite quantal systems is investigated by resorting to the formalism based on the intrinsic frame.

  13. Odd Harmonics in Exoplanet Photometry: Weather or Artifact?

    NASA Astrophysics Data System (ADS)

    Cowan, Nicolas B.; Chayes, Victoria; Bouffard, Élie; Meynig, Max; Haggard, Hal M.

    2017-01-01

    In addition to the transits of a planet in front of its star and the eclipses of the planet by its star, researchers have reported flux variations at the orbital frequency and its harmonics: planetary reflection and/or emission and Doppler beaming of starlight produce one peak per orbit, while ellipsoidal variations of a tidally distorted star and/or planet produce two maxima per orbit. Researchers have also reported significant photometric variability at three times the orbital frequency, as yet unexplained. Reflected phase variations of homogeneous planets only contain power at the orbital frequency and its even harmonics. We show that odd harmonics can, however, be produced by an edge-on planet with a time-variable map, or an inclined planet with a North-South (N-S) asymmetric map. For tidally-locked planets with thick atmospheres, either of these scenarios entail weather: planets with zero obliquity experience N-S symmetric stellar forcing. North-South asymmetry would therefore suggest stochastic localized features, i.e., weather. However, we find that previous claims of large-amplitude odd modes in Kepler photometry are artifacts of removing planetary transits rather than modeling them. The only reliable claims of odd harmonics remain HAT-P-7b and Kepler-13Ab, for which the third mode amplitude is 6-8% of the planetary flux. Although time-variable albedo maps could in principle explain these odd harmonics, upper-limits on the infrared variability of other hot Jupiters make this scenario unlikely. We recommend further studying the tidal effects of close-in planets on their host stars, as this remains the only plausible hypothesis.

  14. OPE of Green functions in the odd sector of QCD

    NASA Astrophysics Data System (ADS)

    Kadavý, T.; Kampf, K.; Novotný, J.

    2017-03-01

    A review of familiar results of the three-point Green functions of currents in the odd-intrinsic parity sector of QCD is presented. Such Green functions include very well-known examples of VVP, VAS or AAP correlators. We also present new results for VVA and AAA Green functions that have not yet been studied extensively in the literature before, more importantly with a phenomenological study and a discussion of the highenergy behaviour and its relation to the QCD condensates.

  15. Decoupling and anomalous bandcrossings in odd-proton nuclei

    SciTech Connect

    Wu, C.S. , Center of Theoretical Physics, P.O. Box 8730, Beijing 100080 Department of Physics, Peking University, Beijing 100871 Institute of Theoretical Physics, Academia Sinica, Beijing 100080 )

    1995-04-01

    The anomalous bandcrossing observed in the [541] [down arrow] bands of odd-[ital Z] nuclei from the rare-earth region was investigated in the framework of the particle-rotor model. The participation of the decoupling term in the [ital K]=1/2 band will give rise to a significant shift of the bandcrossing frequency, with an amplitude comparable to the observed values.

  16. Alternating parity structure in doubly odd /sup 218/Ac

    SciTech Connect

    Debray, M.E.; Davidson, M.; Kreiner, A.J.; Davidson, J.; Falcone, G.; Hojman, D.; Santos, D.

    1989-03-01

    States in doubly odd /sup 218/Ac have been studied using in-beam ..cap alpha..-, ..gamma..-, and e/sup -/-spectroscopy techniques mainly through the /sup 209/Bi(/sup 12/C,3n)= fusion-evaporation reaction. /sup 218/Ac shows a band structure, with interleaved states of alternating parities connected by enhanced B(E1) transitions, which is strikingly similar to the one in its isotone /sup 217/Ra.

  17. Observations of Chiral Odd GPDs and Their Implications

    NASA Astrophysics Data System (ADS)

    Goldstein, Gary R.; Liuti, Simonetta; Gonzalez-Hernandez, J. Osvaldo

    2014-01-01

    Our original suggestion to investigate exclusive π0 electroproduction as a method for extracting the tensor charge, transversity, and other quantities related to chiral odd generalized parton distributions from cross section and asymmetry data is reviewed. We explain some of the details of the process: i) the connection between the helicity description and the cartesian basis; ii) the dependence on the momentum transfer squared, Q2, and iii) the angular momentum, parity, and charge conjugation constraints (JPC quantum numbers).

  18. Fluctuation theorems and entropy production with odd-parity variables

    NASA Astrophysics Data System (ADS)

    Park, Hyunggyu; Lee, Hyun Keun; Kwon, Chulan

    2013-03-01

    We show that the total entropy production in stochastic processes with odd-parity variables (under time reversal) is separated into three parts, only two of which satisfy the integral fluctuation theorems in general. One is the usual excess contribution, which can appear only transiently and is called non-adiabatic. Another one is attributed solely to the breakage of detailed balance. The last part not satisfying the fluctuation theorem comes from the steady-state distribution asymmetry for odd-parity variables, which is activated in a non-transient manner. The latter two parts combine together as the house-keeping (adiabatic) contribution, whose positivity is not guaranteed except when the excess contribution completely vanishes. Our finding reveals that the equilibrium requires the steady-state distribution symmetry for odd-parity variables independently, in addition to the usual detailed balance. This work was supported by Mid-career Researcher Program through NRF grant (No. 2010-0026627) funded by the MEST.

  19. Decline in Cardiorespiratory Fitness and Odds of Incident Sleep Complaints

    PubMed Central

    Dishman, Rodney K.; Sui, Xuemei; Church, Timothy S.; Kline, Christopher E.; Youngstedt, Shawn D.; Blair, Steven N.

    2014-01-01

    Purpose To examine longitudinal change in cardiorespiratory fitness and odds of incident sleep problems. Methods A cohort of 7368 men and 1155 women, aged 20–85 years, from the Aerobics Center Longitudinal Study. The cohort did not complain of sleep problems, depression, or anxiety at their first clinic visit. Cardiorespiratory fitness assessed at 4 clinic visits between 1971–2006, each separated by an average of 2–3 years, was used as a proxy measure of cumulative physical activity exposure. Sleep complaints were made to a physician during follow-up. Results Across visits, there were 784 incident cases of sleep complaints in men and 207 cases in women. After adjustment for age, time between visits, body mass index, smoking, alcohol use, chronic medical conditions, complaints of depression or anxiety at each visit, and fitness at Visit 1, each minute decline in treadmill endurance (i.e., a decline in cardiorespiratory fitness of approximately one-half MET) between ages 51 to 56 increased the odds of incident sleep complaints by 1.7% (1.0–2.4%) in men and 1.3% (0.0–2.8%) in women. Odds were ~8% higher per minute decline in people with sleep complaints at 2 or 3 visits. Conclusion The results indicate that maintenance of cardiorespiratory fitness during middle-age, when decline in fitness typically accelerates and risk of sleep problems is elevated, helps protect against the onset of sleep complaints made to a physician. PMID:25207930

  20. Signatures of shape phase transitions in odd-mass nuclei

    NASA Astrophysics Data System (ADS)

    Nomura, K.; Nikšić, T.; Vretenar, D.

    2016-12-01

    Quantum phase transitions between competing ground-state shapes of atomic nuclei with an odd number of protons or neutrons are investigated in a microscopic framework based on nuclear energy density functional theory and the particle-plus-boson-core coupling scheme. The boson-core Hamiltonian, as well as the single-particle energies and occupation probabilities of the unpaired nucleon, are completely determined by constrained self-consistent mean-field calculations for a specific choice of the energy density functional and paring interaction, and only the strength parameters of the particle-core coupling are adjusted to reproduce selected spectroscopic properties of the odd-mass system. We apply this method to odd-A Eu and Sm isotopes with neutron number N ≈90 , and explore the influence of the single unpaired fermion on the occurrence of a shape phase transition. Collective wave functions of low-energy states are used to compute quantities that can be related to quantum order parameters: deformations, excitation energies, E 2 transition rates, and separation energies, and their evolution with the control parameter (neutron number) is analyzed.

  1. Balancing Selection at a Frog Antimicrobial Peptide Locus: Fluctuating Immune Effector Alleles?

    PubMed Central

    Blouin, Michael S.

    2008-01-01

    Balancing selection is common on many defense genes, but it has rarely been reported for immune effector proteins such as antimicrobial peptides (AMPs). We describe genetic diversity at a brevinin-1 AMP locus in three species of leopard frogs (Rana pipiens, Rana blairi, and Rana palustris). Several highly divergent allelic lineages are segregating at this locus. That this unusual pattern results from balancing selection is demonstrated by multiple lines of evidence, including a ratio of nonsynonymous/synonymous polymorphism significantly higher than 1, the ZnS test, incongruence between the number of segregating sites and haplotype diversity, and significant Tajima's D values. Our data are more consistent with a model of fluctuating selection in which alleles change frequencies over time than with a model of stable balancing selection such as overdominance. Evidence for fluctuating selection includes skewed allele frequencies, low levels of synonymous variation, nonneutral values of Tajima's D within allelic lineages, an inverse relationship between the frequency of an allelic lineage and its degree of polymorphism, and divergent allele frequencies among populations. AMP loci could be important sites of adaptive genetic diversity, with consequences for host–pathogen coevolution and the ability of species to resist disease epidemics. PMID:18799711

  2. Effect of donor CTLA-4 alleles and haplotypes on graft-versus-host disease occurrence in Tunisian patients receiving a human leukocyte antigen-identical sibling hematopoietic stem cell transplant.

    PubMed

    Sellami, Mohamed Hichem; Bani, Meriem; Torjemane, Lamia; Kaabi, Houda; Ladeb, Saloua; Ben Othmane, Tarek; Hmida, Slama

    2011-02-01

    The CTLA-4 genetic variation, such as single nucleotide polymorphisms (SNPs) may be critical and can affect the functional activity of cells that initiate the graft-versus-host disease (GVHD) effects. The aim of this study is to examine the effect of donor CTLA-4 alleles and haplotypes for the -318C>T and the 49A>G polymorphisms on the occurrence of GVHD in Tunisians recipients of HSCs. A total of 112 patients and their 112 respective sibling donors of HSCs were enrolled in this study. All patients had either grades 0-I or grades II-IV acute GVHD, or chronic GVHD. The SNPs genotyping assay was performed using sets of sequence specific primers (SSP-PCR). The single marker association analysis showed that the 49G allele, in a genetic recessive model, may be a potential risk factor only for the chronic GVHD (p = 0.032, odds ratio [OR] = 2.58, 95% confidence interval = 1.05-6.32). The haplotypes analyses showed that the CTLA-4 -318C49G nucleotide combination is significantly associated with the incidence of chronic GVHD (p = 0.043, χ² = 3.27). Donor CTLA-4 -318C49G haplotype may be a significant risk factor for developing chronic GVHD after allo-stem cell transplantation. We suppose that donor T cells expressing this haplotype in a homozygous state have higher proliferation than those expressing other haplotypes, especially after recognition of the recipient's minor histocompatibility antigens.

  3. The CIITA genetic polymorphism rs4774*C in combination with the HLA-DRB1*15:01 allele as a putative susceptibility factor to multiple sclerosis in Brazilian females.

    PubMed

    Paradela, Eduardo R; Alves-Leon, Soniza V; Figueiredo, André L S; Pereira, Valéria C S R; Malfetano, Fabíola; Mansur, Letícia F; Scherpenhuijzen, Simone; Agostinho, Luciana A; Rocha, Catielly F; Rueda-Lopes, Fernanda; Gasparetto, Emerson; Paiva, Carmen L A

    2015-04-01

    The objective of this study was to investigate the association between the HLA alleles at the DQA1, DQB1 and DRB1 loci, the CIITA genetic polymorphisms -168A/G and +1614G/C, and susceptibility to multiple sclerosis (MS) in a sample from Rio de Janeiro State, Brazil. Furthermore, we wished to determine whether any of these associations might be more significant in women compared with men. DNA samples from 52 relapsing-remitting MS (RRMS) patients and 126 healthy controls matched for sex and age were analyzed. We identified a significant HLA-DRB1*15:01-MS association that was female-specific (Odds Ratio (OR) = 4.78; p = 0.001). Furthermore, we observed that the +1614G/C mutation in combination with the HLA-DRB1*15:01 allele increased susceptibility to MS in females (OR = 4.55; p = 0.01). Together, these findings highlight the polygenic nature of MS.

  4. Diversity Outbred Mice at 21: Maintaining Allelic Variation in the Face of Selection

    PubMed Central

    Chesler, Elissa J.; Gatti, Daniel M.; Morgan, Andrew P.; Strobel, Marge; Trepanier, Laura; Oberbeck, Denesa; McWeeney, Shannon; Hitzemann, Robert; Ferris, Martin; McMullan, Rachel; Clayshultle, Amelia; Bell, Timothy A.; Manuel de Villena, Fernando Pardo; Churchill, Gary A.

    2016-01-01

    Multi-parent populations (MPPs) capture and maintain the genetic diversity from multiple inbred founder strains to provide a resource for high-resolution genetic mapping through the accumulation of recombination events over many generations. Breeding designs that maintain a large effective population size with randomized assignment of breeders at each generation can minimize the impact of selection, inbreeding, and genetic drift on allele frequencies. Small deviations from expected allele frequencies will have little effect on the power and precision of genetic analysis, but a major distortion could result in reduced power and loss of important functional alleles. We detected strong transmission ratio distortion in the Diversity Outbred (DO) mouse population on chromosome 2, caused by meiotic drive favoring transmission of the WSB/EiJ allele at the R2d2 locus. The distorted region harbors thousands of polymorphisms derived from the seven non-WSB founder strains and many of these would be lost if the sweep was allowed to continue. To ensure the utility of the DO population to study genetic variation on chromosome 2, we performed an artificial selection against WSB/EiJ alleles at the R2d2 locus. Here, we report that we have purged the WSB/EiJ allele from the drive locus while preserving WSB/EiJ alleles in the flanking regions. We observed minimal disruption to allele frequencies across the rest of the autosomal genome. However, there was a shift in haplotype frequencies of the mitochondrial genome and an increase in the rate of an unusual sex chromosome aneuploidy. The DO population has been restored to genome-wide utility for genetic analysis, but our experience underscores that vigilant monitoring of similar genetic resource populations is needed to ensure their long-term utility. PMID:27694113

  5. Diversity Outbred Mice at 21: Maintaining Allelic Variation in the Face of Selection.

    PubMed

    Chesler, Elissa J; Gatti, Daniel M; Morgan, Andrew P; Strobel, Marge; Trepanier, Laura; Oberbeck, Denesa; McWeeney, Shannon; Hitzemann, Robert; Ferris, Martin; McMullan, Rachel; Clayshultle, Amelia; Bell, Timothy A; Manuel de Villena, Fernando Pardo; Churchill, Gary A

    2016-12-07

    Multi-parent populations (MPPs) capture and maintain the genetic diversity from multiple inbred founder strains to provide a resource for high-resolution genetic mapping through the accumulation of recombination events over many generations. Breeding designs that maintain a large effective population size with randomized assignment of breeders at each generation can minimize the impact of selection, inbreeding, and genetic drift on allele frequencies. Small deviations from expected allele frequencies will have little effect on the power and precision of genetic analysis, but a major distortion could result in reduced power and loss of important functional alleles. We detected strong transmission ratio distortion in the Diversity Outbred (DO) mouse population on chromosome 2, caused by meiotic drive favoring transmission of the WSB/EiJ allele at the R2d2 locus. The distorted region harbors thousands of polymorphisms derived from the seven non-WSB founder strains and many of these would be lost if the sweep was allowed to continue. To ensure the utility of the DO population to study genetic variation on chromosome 2, we performed an artificial selection against WSB/EiJ alleles at the R2d2 locus. Here, we report that we have purged the WSB/EiJ allele from the drive locus while preserving WSB/EiJ alleles in the flanking regions. We observed minimal disruption to allele frequencies across the rest of the autosomal genome. However, there was a shift in haplotype frequencies of the mitochondrial genome and an increase in the rate of an unusual sex chromosome aneuploidy. The DO population has been restored to genome-wide utility for genetic analysis, but our experience underscores that vigilant monitoring of similar genetic resource populations is needed to ensure their long-term utility.

  6. [Using log-binomial model for estimating the prevalence ratio].

    PubMed

    Ye, Rong; Gao, Yan-hui; Yang, Yi; Chen, Yue

    2010-05-01

    To estimate the prevalence ratios, using a log-binomial model with or without continuous covariates. Prevalence ratios for individuals' attitude towards smoking-ban legislation associated with smoking status, estimated by using a log-binomial model were compared with odds ratios estimated by logistic regression model. In the log-binomial modeling, maximum likelihood method was used when there were no continuous covariates and COPY approach was used if the model did not converge, for example due to the existence of continuous covariates. We examined the association between individuals' attitude towards smoking-ban legislation and smoking status in men and women. Prevalence ratio and odds ratio estimation provided similar results for the association in women since smoking was not common. In men however, the odds ratio estimates were markedly larger than the prevalence ratios due to a higher prevalence of outcome. The log-binomial model did not converge when age was included as a continuous covariate and COPY method was used to deal with the situation. All analysis was performed by SAS. Prevalence ratio seemed to better measure the association than odds ratio when prevalence is high. SAS programs were provided to calculate the prevalence ratios with or without continuous covariates in the log-binomial regression analysis.

  7. Intragenic allele pyramiding combines different specificities of wheat Pm3 resistance alleles.

    PubMed

    Brunner, Susanne; Hurni, Severine; Streckeisen, Philipp; Mayr, Gabriele; Albrecht, Mario; Yahiaoui, Nabila; Keller, Beat

    2010-11-01

    Some plant resistance genes occur as allelic series, with each member conferring specific resistance against a subset of pathogen races. In wheat, there are 17 alleles of the Pm3 gene. They encode nucleotide-binding (NB-ARC) and leucine-rich-repeat (LRR) domain proteins, which mediate resistance to distinct race spectra of powdery mildew. It is not known if specificities from different alleles can be combined to create resistance genes with broader specificity. Here, we used an approach based on avirulence analysis of pathogen populations to characterize the molecular basis of Pm3 recognition spectra. A large survey of mildew races for avirulence on the Pm3 alleles revealed that Pm3a has a resistance spectrum that completely contains that of Pm3f, but also extends towards additional races. The same is true for the Pm3b and Pm3c gene pair. The molecular analysis of these allelic pairs revealed a role of the NB-ARC protein domain in the efficiency of effector-dependent resistance. Analysis of the wild-type and chimeric Pm3 alleles identified single residues in the C-terminal LRR motifs as the main determinant of allele specificity. Variable residues of the N-terminal LRRs are necessary, but not sufficient, to confer resistance specificity. Based on these data, we constructed a chimeric Pm3 gene by intragenic allele pyramiding of Pm3d and Pm3e that showed the combined resistance specificity and, thus, a broader recognition spectrum compared with the parental alleles. Our findings support a model of stepwise evolution of Pm3 recognition specificities.

  8. Estimating the probability of allelic drop-out of STR alleles in forensic genetics.

    PubMed

    Tvedebrink, Torben; Eriksen, Poul Svante; Mogensen, Helle Smidt; Morling, Niels

    2009-09-01

    In crime cases with available DNA evidence, the amount of DNA is often sparse due to the setting of the crime. In such cases, allelic drop-out of one or more true alleles in STR typing is possible. We present a statistical model for estimating the per locus and overall probability of allelic drop-out using the results of all STR loci in the case sample as reference. The methodology of logistic regression is appropriate for this analysis, and we demonstrate how to incorporate this in a forensic genetic framework.

  9. The allele combinations of three loci based on, liver, stomach cancers, hematencephalon, COPD and normal population: A preliminary study.

    PubMed

    Gai, Liping; Liu, Hui; Cui, Jing-Hui; Yu, Weijian; Ding, Xiao-Dong

    2017-03-20

    The purpose of this study was to examine the specific allele combinations of three loci connected with the liver cancers, stomach cancers, hematencephalon and patients with chronic obstructive pulmonary disease (COPD) and to explore the feasibility of the research methods. We explored different mathematical methods for statistical analyses to assess the association between the genotype and phenotype. At the same time we still analyses the statistical results of allele combinations of three loci by difference value method and ratio method. All the DNA blood samples were collected from patients with 50 liver cancers, 75 stomach cancers, 50 hematencephalon, 72 COPD and 200 normal populations. All the samples were from Chinese. Alleles from short tandem repeat (STR) loci were determined using the STR Profiler plus PCR amplification kit (15 STR loci). Previous research was based on combinations of single-locus alleles, and combinations of cross-loci (two loci) alleles. Allele combinations of three loci were obtained by computer counting and stronger genetic signal was obtained. The methods of allele combinations of three loci can help to identify the statistically significant differences of allele combinations between liver cancers, stomach cancers, patients with hematencephalon, COPD and the normal population. The probability of illness followed different rules and had apparent specificity. This method can be extended to other diseases and provide reference for early clinical diagnosis.

  10. Meta-analysis of Methylenetetrahydrofolate reductase maternal gene in Down syndrome: increased susceptibility in women carriers of the MTHFR 677T allele.

    PubMed

    Victorino, D B; Godoy, M F; Goloni-Bertollo, E M; Pavarino, E C

    2014-08-01

    Because a number of data studies include some controversial results about Methylenetetrahydrofolate reductase (MTHFR) polymorphisms and Down syndrome (DS), we performed a meta-analysis to determine a more precise estimation of this association. Studies were searched on PubMed, EMBASE and Lilacs-Scielo, up to April 2013, and they were eligible if they included case mothers (DSM) that have gave birth to children with DS, and controls mothers (CM) that have gave birth to healthy children without chromosomal abnormality, syndrome or malformation. The combined odds ratio with 95% confidence intervals was calculated by fixed or random effects models to assess the strength of associations. Potential sources of heterogeneity between studies were evaluated using Q test and the I(2). Publication bias was estimated using Begg's test and Egger's linear regression test. Sensitivity analyses were performed by using allelic, dominant, recessive and codominant genetic models, Hardy-Weinberg equilibrium (HWE) and ethnicity. Twenty-two studies with 2,223 DSM and 2,807 CM were included for MTHFR C677T and 15 studies with 1,601 DSM and 1,849 CM were included for MTHFR A1298C. Overall analysis suggests an association of the MTHFR C677T polymorphism with maternal risk for DS. Moreover, no association between the MTHFR A1298C polymorphism and maternal risk for DS was found. There is also evidence of higher heterogeneity, with I(2) test values ranging from 8 to 89%. No evidence of publication bias was found. Taken together, our meta-analysis implied that the T allele carriers might carry an increased maternal risk for DS.

  11. Inheritance of 15 microsatellites in the Pacific oyster Crassostrea gigas: segregation and null allele identification for linkage analysis

    NASA Astrophysics Data System (ADS)

    Li, Li; Guo, Ximing; Zhang, Guofan

    2009-02-01

    Microsatellites were screened in a backcross family of the Pacific oyster, Crassostrea gigas. Fifteen microsatellite loci were distinguishable and polymorphic with 6 types of allele-combinations. Null alleles were detected in 46.7% of loci, accounting for 11.7% of the total alleles. Four loci did not segregate in Mendelian Ratios. Three linkage groups were identified among 7 of the 15 segregating loci. Fluorescence-based automated capillary electrophoresis (ABI 310 Genetic Analyzer) that used to detect the microsatellite loci, has been proved a fast, precise, and reliable method in microsatellite genotyping.

  12. High-Throughput Genotyping with TaqMan Allelic Discrimination and Allele-Specific Genotyping Assays.

    PubMed

    Heissl, Angelika; Arbeithuber, Barbara; Tiemann-Boege, Irene

    2017-01-01

    Real-time PCR-based genotyping methods, such as TaqMan allelic discrimination assays and allele-specific genotyping, are particularly useful when screening a handful of single nucleotide polymorphisms in hundreds of samples; either derived from different individuals, tissues, or pre-amplified DNA. Although real-time PCR-based methods such as TaqMan are well-established, alternative methods, like allele-specific genotyping, are powerful alternatives, especially for genotyping short tandem repeat (STR) length polymorphisms. Here, we describe all relevant aspects when developing an assay for a new SNP or STR using either TaqMan or allele-specific genotyping, respectively, such as primer and probe design, optimization of reaction conditions, the experimental procedure for typing hundreds of samples, and finally the data evaluation. Our goal is to provide a guideline for developing genotyping assays using these two approaches that render reliable and reproducible genotype calls involving minimal optimization.

  13. Isospin odd @pK scattering length [rapid communication

    NASA Astrophysics Data System (ADS)

    Schweizer, J.

    2005-10-01

    We make use of the chiral two-loop representation of the πK scattering amplitude [J. Bijnens, P. Dhonte, P. Talavera, JHEP 0405 (2004) 036] to investigate the isospin odd scattering length at next-to-next-to-leading order in the SU (3) expansion. This scattering length is protected against contributions of ms in the chiral expansion, in the sense that the corrections to the current algebra result are of order Mπ2. In view of the planned lifetime measurement on πK atoms at CERN it is important to understand the size of these corrections.

  14. Neutron-proton pairing correlations in odd mass systems

    SciTech Connect

    Fellah, M. Allal, N. H.; Oudih, M. R.

    2015-03-30

    An expression of the ground-state which describes odd mass systems within the BCS approach in the isovector neutron-proton pairing case is proposed using the blocked level technique. The gap equations as well as the energy expression are then derived. It is shown that they exactly generalize the expressions obtained in the pairing between like-particles case. The various gap parameters and the energy are then numerically studied as a function of the pairing-strength within the schematic one-level model.

  15. HLA-B alleles of the Cayapa of Ecuador: new B39 and B15 alleles.

    PubMed

    Garber, T L; Butler, L M; Trachtenberg, E A; Erlich, H A; Rickards, O; De Stefano, G; Watkins, D I

    1995-01-01

    Recent data suggest that HLA-B locus alleles can evolve quickly in native South American populations. To investigate further this phenomenon of new HLA-B variants among Amerindians, we studied samples from another South American tribe, the Cayapa from Ecuador. We selected individuals for HLA-B molecular typing based upon their HLA class II typing results. Three new variants of HLA-B39 and one new variant of HLA-B15 were found in the Cayapa: HLA-B*3905, HLA-B*3906, HLA-B*3907, and HLA-B*1522. A total of thirteen new HLA-B alleles have now been found in the four South American tribes studied. Each of these four tribes studied, including the Cayapa, had novel alleles that were not found in any of the other tribes, suggesting that many of these new HLA-B alleles may have evolved since the Paleo-Indians originally populated South America. Each of these 13 new alleles contained predicted amino acid replacements that were located in the peptide binding site. These amino acid replacements may affect the sequence motif of the bound peptides, suggesting that these new alleles have been maintained by selection. New allelic variants have been found for all common HLA-B locus antigenic groups present in South American tribes with the exception of B48. In spite of its high frequency in South American tribes, no evidence for variants of B48 has been found in all the Amerindians studied, suggesting that B48 may have unique characteristics among the B locus alleles.

  16. Closely Spaced Pregnancies Are Associated With Increased Odds of Autism in California Sibling Births

    PubMed Central

    Liu, Kayuet; Bearman, Peter S.

    2011-01-01

    OBJECTIVE: To determine whether the interpregnancy interval (IPI) is associated with the risk of autism in subsequent births. METHODS: Pairs of first- and second-born singleton full siblings were identified from all California births that occurred from 1992 to 2002 using birth records, and autism diagnoses were identified by using linked records of the California Department of Developmental Services. IPI was calculated as the time interval between birth dates minus the gestational age of the second sibling. In the primary analysis, logistic regression models were used to determine whether odds of autism in second-born children varied according to IPI. To address potential confounding by unmeasured family-level factors, a case-sibling control analysis determined whether affected sibling (first versus second) varied with IPI. RESULTS: An inverse association between IPI and odds of autism among 662 730 second-born children was observed. In particular, IPIs of <12, 12 to 23, and 24 to 35 months were associated with odds ratios (95% confidence intervals) for autism of 3.39 (3.00–3.82), 1.86 (1.65–2.10), and 1.26 (1.10–1.45) relative to IPIs of ≥36 months. The association was not mediated by preterm birth or low birth weight and persisted across categories of sociodemographic characteristics, with some attenuation in the oldest and youngest parents. Second-born children were at increased risk of autism relative to their firstborn siblings only in pairs with short IPIs. CONCLUSIONS: These results suggest that children born after shorter intervals between pregnancies are at increased risk of developing autism; the highest risk was associated with pregnancies spaced <1 year apart. PMID:21220394

  17. Type of Diabetes Mellitus and the Odds of Gleason Score 8 to 10 Prostate Cancer

    SciTech Connect

    Kang, Josephine; Chen Minghui; Zhang Yuanye; Moran, Brian J.; Dosoretz, Daniel E.; Katin, Michael J.; Braccioforte, Michelle H.; Salenius, Sharon A.; D'Amico, Anthony V.

    2012-03-01

    Purpose: It has been recently shown that diabetes mellitus (DM) is significantly associated with the likelihood of presenting with high-grade prostate cancer (PCa) or Gleason score (GS) 8 to 10; however, whether this association holds for both Type 1 and 2 DM is unknown. In this study we evaluated whether DM Type 1, 2, or both are associated with high-grade PCa after adjusting for known predictors of high-grade disease. Methods and Materials: Between 1991 and 2010, a total of 15,330 men diagnosed with PCa and treated with radiation therapy were analyzed. A polychotomous logistic regression analysis was performed to evaluate whether Type 1 or 2 DM was associated with odds of GS 7 or GS 8 to 10 compared with 6 or lower PCa, adjusting for African American race, age, prostate-specific antigen (PSA) level, and digital rectal examination findings. Results: Men with Type 1 DM (adjusted odds ratio [AOR], 2.05; 95% confidence interval [CI], 1.28-3.27; p = 0.003) or Type 2 DM (AOR, 1.58; 95% CI, 1.26-1.99; p < 0.001) were significantly more likely to be diagnosed with GS 8 to 10 PCa compared with nondiabetic men. However this was not true for GS 7, for which these respective results were AOR, 1.30; 95% CI, 0.93-1.82; p = 0.12 and AOR, 1.13; 95% CI, 0.98-1.32; p = 0.10. Conclusion: Type 1 and 2 DM were associated with a higher odds of being diagnosed with Gleason score 8 to 10 but not 7 PCa. Pending validation, men who are diagnosed with Type I DM with GS 7 or lower should be considered for additional workup to rule out occult high-grade disease.

  18. Initial invasion of gametophytic self-incompatibility alleles in the absence of tight linkage between pollen and pistil S alleles.

    PubMed

    Sakai, Satoki; Wakoh, Haluka

    2014-08-01

    In homomorphic self-incompatibility (SI) systems of plants, the loci controlling the pollen and pistil types are tightly linked, and this prevents the generation of compatible combinations of alleles expressing pollen and pistil types, which would result in self-fertilization. We modeled the initial invasion of the first pollen and pistil alleles in gametophytic SI to determine whether these alleles can stably coexist in a population without tight linkage. We assume pollen and pistil loci each carry an incompatibility allele S and an allele without an incompatibility function N. We assume that pollen with an S allele are incompatible with pistils carrying S alleles, whereas other crosses are compatible. Ovules in pistils carrying an S allele suffer viability costs because recognition consumes resources. We found that the cost of carrying a pistil S allele allows pollen and pistil S alleles to coexist in a stable equilibrium if linkage is partial. This occurs because parents that carry pistil S alleles but are homozygous for pollen N alleles cannot avoid self-fertilization; however, they suffer viability costs. Hence, pollen N alleles are selected again. When pollen and pistil S alleles can coexist in a polymorphic equilibrium, selection will favor tighter linkage.

  19. Do Heliconius butterfly species exchange mimicry alleles?

    PubMed Central

    Smith, Joel; Kronforst, Marcus R.

    2013-01-01

    Hybridization has the potential to transfer beneficial alleles across species boundaries, and there are a growing number of examples in which this has apparently occurred. Recent studies suggest that Heliconius butterflies have transferred wing pattern mimicry alleles between species via hybridization, but ancestral polymorphism could also produce a signature of shared ancestry around mimicry genes. To distinguish between these alternative hypotheses, we measured DNA sequence divergence around putatively introgressed mimicry loci and compared this with the rest of the genome. Our results reveal that putatively introgressed regions show strongly reduced sequence divergence between co-mimetic species, suggesting that their divergence times are younger than the rest of the genome. This is consistent with introgression and not ancestral variation. We further show that this signature of introgression occurs at sites throughout the genome, not just around mimicry genes. PMID:23864282

  20. Structure of dipole bands in doubly odd 102Ag

    NASA Astrophysics Data System (ADS)

    Singh, V.; Sihotra, S.; Malik, S. S.; Bhat, G. H.; Palit, R.; Sheikh, J. A.; Kumar, S.; Singh, N.; Singh, K.; Goswamy, J.; Sethi, J.; Saha, S.; Trivedi, T.; Mehta, D.

    2016-10-01

    Excited states in the transitional doubly odd 102Ag nucleus were populated in the 75As(31P,p 3 n ) fusion-evaporation reaction using the 125 MeV incident 31P beam. The subsequent deexcitations were investigated through in-beam γ -ray spectroscopic techniques using the Indian National Gamma Array spectrometer equipped with 21 clover Ge detectors. The level scheme in 102Ag has been established up to excitation energy ˜6.5 MeV and angular momentum 19 ℏ . The earlier reported level scheme is considerably extended and modified to result in a pair of nearly degenerate negative-parity dipole bands. Lifetime measurements for the states of these two dipole bands have been performed by using the Doppler-shift attenuation method. The two nearly degenerate bands exhibit different features with regard to kinetic moment of inertia, and the reduced transition probabilities B (M 1 ) and B (E 2 ) , which do not favor these to be chiral partners. These bands are discussed in the framework of the hybrid version of tilted-axis cranking (tac) model calculations and assigned the π g9 /2⊗ν h11 /2 and π g9 /2⊗ν h11 /2(d5/2/g7 /2) 2 configurations. The tac model calculations are extended to the nearly degenerate bands observed in the heavier doubly odd Ag-108104 isotopes.

  1. The distribution of odd nitrogen in the lower stratosphere and possible perturbations caused by stratospheric air transport

    NASA Technical Reports Server (NTRS)

    Isaksen, I. S. A.; Hesstvedt, E.

    1973-01-01

    In the lower stratosphere a significant production of odd nitrogen results from the reaction N2O + O(D-1) yields 2NO. Since the transport is relatively slow, odd nitrogen builds up with a maximum mixing ratio of 2 x 10 to the minus 8th power at 30 Km. Profiles of odd nitrogen, for different latitudes, winter and summer, are computed from one-dimensional transport models. Variations with latitude are small. Horizontal transport is therefore not believed to alter our results significantly. In order to evaluate the effect of odd nitrogen upon the ozone layer, NO(x) profiles are calculated. OH is here a key component, since it converts NO2 to HNO3. In the region where ozone is determined by chemistry rather than by transport (above 25 km), NO2 is found to be relatively abundant. The effect of stratospheric transport on the NO(x) distribution is shown to depend critically upon the height of emission. The effect increases by a factor of 5 or more for a change of flight level from 18 km to 23 km. This strong dependence should be duely considered when future stratospheric transport is discussed.

  2. Genome-wide Association Study of Subtype-Specific Epithelial Ovarian Cancer Risk Alleles Using Pooled DNA

    PubMed Central

    Earp, Madalene A.; Kelemen, Linda E.; Magliocco, Anthony M.; Swenerton, Kenneth D.; Chenevix–Trench, Georgia; Lu, Yi; Hein, Alexander; Ekici, Arif B.; Beckmann, Matthias W.; Fasching, Peter A.; Lambrechts, Diether; Despierre, Evelyn; Vergote, Ignace; Lambrechts, Sandrina; Doherty, Jennifer A.; Rossing, Mary Anne; Chang-Claude, Jenny; Rudolph, Anja; Friel, Grace; Moysich, Kirsten B.; Odunsi, Kunle; Sucheston-Campbell, Lara; Lurie, Galina; Goodman, Marc T.; Carney, Michael E.; Thompson, Pamela J.; Runnebaum, Ingo B.; Dürst, Matthias; Hillemanns, Peter; Dörk, Thilo; Antonenkova, Natalia; Bogdanova, Natalia; Leminen, Arto; Nevanlinna, Heli; Pelttari, Liisa M.; Butzow, Ralf; Bunker, Clareann H.; Modugno, Francesmary; Edwards, Robert P.; Ness, Roberta B.; du Bois, Andreas; Heitz, Florian; Schwaab, Ira; Harter, Philipp; Karlan, Beth Y.; Walsh, Christine; Lester, Jenny; Jensen, Allan; Kjær, Susanne K.; Høgdall, Claus K.; Høgdall, Estrid; Lundvall, Lene; Sellers, Thomas A.; Fridley, Brooke L.; Goode, Ellen L.; Cunningham, Julie M.; Vierkant, Robert A.; Giles, Graham G.; Baglietto, Laura; Severi, Gianluca; Southey, Melissa C.; Liang, Dong; Wu, Xifeng; Lu, Karen; Hildebrandt, Michelle A.T.; Levine, Douglas A.; Bisogna, Maria; Schildkraut, Joellen M.; Iversen, Edwin S.; Weber, Rachel Palmieri; Berchuck, Andrew; Cramer, Daniel W.; Terry, Kathryn L.; Poole, Elizabeth M.; Tworoger, Shelley S.; Bandera, Elisa V.; Chandran, Urmila; Orlow, Irene; Olson, Sara H.; Wik, Elisabeth; Salvesen, Helga B.; Bjorge, Line; Halle, Mari K.; van Altena, Anne M.; Aben, Katja K.H.; Kiemeney, Lambertus A.; Massuger, Leon F.A.G.; Pejovic, Tanja; Bean, Yukie T.; Cybulski, Cezary; Gronwald, Jacek; Lubinski, Jan; Wentzensen, Nicolas; Brinton, Louise A.; Lissowska, Jolanta; Garcia–Closas, Montserrat; Dicks, Ed; Dennis, Joe; Easton, Douglas F.; Song, Honglin; Tyrer, Jonathan P.; Pharoah, Paul D. P.; Eccles, Diana; Campbell, Ian G.; Whittemore, Alice S.; McGuire, Valerie; Sieh, Weiva; Rothstein, Joseph H.; Flanagan, James M.; Paul, James; Brown, Robert; Phelan, Catherine M.; Risch, Harvey A.; McLaughlin, John R.; Narod, Steven A.; Ziogas, Argyrios; Anton-Culver, Hoda; Gentry-Maharaj, Aleksandra; Menon, Usha; Gayther, Simon A.; Ramus, Susan J.; Wu, Anna H.; Pearce, Celeste L.; Pike, Malcolm C.; Dansonka-Mieszkowska, Agnieszka; Rzepecka, Iwona K; Szafron, Lukasz M; Kupryjanczyk, Jolanta; Cook, Linda S.; Le, Nhu D.; Brooks–Wilson, Angela

    2014-01-01

    Epithelial ovarian cancer (EOC) is a heterogeneous cancer with both genetic and environmental risk factors. Variants influencing the risk of developing the less-common EOC subtypes have not been fully investigated. We performed a genome-wide association study (GWAS) of EOC according to subtype by pooling genomic DNA from 545 cases and 398 controls of European descent, and testing for allelic associations. We evaluated for replication 188 variants from the GWAS (56 variants for mucinous, 55 for endometrioid and clear cell, 53 for low malignant potential (LMP) serous, and 24 for invasive serous EOC), selected using pre-defined criteria. Genotypes from 13,188 cases and 23,164 controls of European descent were used to perform unconditional logistic regression under the log-additive genetic model; odds ratios (OR) and 95% confidence intervals are reported. Nine variants tagging 6 loci were associated with subtype-specific EOC risk at P<0.05, and had an OR that agreed in direction of effect with the GWAS results. Several of these variants are in or near genes with a biological rationale for conferring EOC risk, including ZFP36L1 and RAD51B for mucinous EOC (rs17106154, OR=1.17, P=0.029, n=1,483 cases), GRB10 for endometrioid and clear cell EOC (rs2190503, P=0.014, n=2,903 cases), and C22orf26/BPIL2 for LMP serous EOC (rs9609538, OR=0.86, P=0.0043, n=892 cases). In analyses that included the 75 GWAS samples, the association between rs9609538 (OR=0.84, P=0.0007) and LMP serous EOC risk remained statistically significant at P<0.0012 adjusted for multiple testing. Replication in additional samples will be important to verify these results for the less-common EOC subtypes. PMID:24190013

  3. Correlations of Energy Ratios for Collective Nuclear Bands

    NASA Astrophysics Data System (ADS)

    Zamfir, N. V.; Bucurescu, D.; Căta-Danil, G.; Ivaşcu, M.; Mărginean, N.

    2009-01-01

    It is shown that the Mallmann's energy correlations, introduced a long time ago for the ground state bands of the even-even nuclei are, in fact, universal. Various bands in all collective nuclei (even-even, odd-even, and odd-odd) obey the same systematics. This unique, universal behaviour indicates the same spin dependence of the energy of the levels and, consequently, a common structure of all collective bands. Based on the second-order anharmonic vibrator description, parameter-free recurrence relations between energy ratios are deduced. These relations can be used to predict levels of higher spins in various bands.

  4. Correlations of Energy Ratios for Collective Nuclear Bands

    NASA Astrophysics Data System (ADS)

    Zamfir, N. V.; Bucurescu, D.; Căta-Danil, G.; Ivaşcu, M.; Mărginean, N.

    2009-03-01

    It is shown that the Mallmann's energy correlations, introduced a long time ago for the ground state bands of the even-even nuclei are, in fact, universal. Various bands in all collective nuclei (even-even, odd-even, and odd-odd) obey the same systematics. This unique, universal behaviour indicates the same spin dependence of the energy of the levels in all bands in all collective nuclei. Based on a second-order anharmonic vibrator description, parameter-free recurrence relations between energy ratios are deduced. These relations can be used to predict levels of higher spins in various bands.

  5. Allelic variation contributes to bacterial host specificity

    SciTech Connect

    Yue, Min; Han, Xiangan; Masi, Leon De; Zhu, Chunhong; Ma, Xun; Zhang, Junjie; Wu, Renwei; Schmieder, Robert; Kaushik, Radhey S.; Fraser, George P.; Zhao, Shaohua; McDermott, Patrick F.; Weill, François-Xavier; Mainil, Jacques G.; Arze, Cesar; Fricke, W. Florian; Edwards, Robert A.; Brisson, Dustin; Zhang, Nancy R.; Rankin, Shelley C.; Schifferli, Dieter M.

    2015-10-30

    Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. In conclusion, together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts.

  6. Allelic variation contributes to bacterial host specificity

    DOE PAGES

    Yue, Min; Han, Xiangan; Masi, Leon De; ...

    2015-10-30

    Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population andmore » functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. In conclusion, together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts.« less

  7. Additive composite ABCG2, SLC2A9 and SLC22A12 scores of high-risk alleles with alcohol use modulate gout risk.

    PubMed

    Tu, Hung-Pin; Chung, Chia-Min; Min-Shan Ko, Albert; Lee, Su-Shin; Lai, Han-Ming; Lee, Chien-Hung; Huang, Chung-Ming; Liu, Chiu-Shong; Ko, Ying-Chin

    2016-09-01

    The aim of the present study was to evaluate the contribution of urate transporter genes and alcohol use to the risk of gout/tophi. Eight variants of ABCG2, SLC2A9, SLC22A12, SLC22A11 and SLC17A3 were genotyped in male individuals in a case-control study with 157 gout (33% tophi), 106 asymptomatic hyperuricaemia and 295 control subjects from Taiwan. The multilocus profiles of the genetic risk scores for urate gene variants were used to evaluate the risk of asymptomatic hyperuricaemia, gout and tophi. ABCG2 Q141K (T), SLC2A9 rs1014290 (A) and SLC22A12 rs475688 (C) under an additive model and alcohol use independently predicted the risk of gout (respective odds ratio for each factor=2.48, 2.03, 1.95 and 2.48). The additive composite Q141K, rs1014290 and rs475688 scores of high-risk alleles were associated with gout risk (P<0.0001). We observed the supramultiplicative interaction effect of genetic urate scores and alcohol use on gout and tophi risk (P for interaction=0.0452, 0.0033). The synergistic effect of genetic urate score 5-6 and alcohol use indicates that these combined factors correlate with gout and tophi occurrence.

  8. Enhanced low-template DNA analysis conditions and investigation of allele dropout patterns.

    PubMed

    Hedell, Ronny; Dufva, Charlotte; Ansell, Ricky; Mostad, Petter; Hedman, Johannes

    2015-01-01

    Forensic DNA analysis applying PCR enables profiling of minute biological samples. Enhanced analysis conditions can be applied to further push the limit of detection, coming with the risk of visualising artefacts and allele imbalances. We have evaluated the consecutive increase of PCR cycles from 30 to 35 to investigate the limitations of low-template (LT) DNA analysis, applying the short tandem repeat (STR) analysis kit PowerPlex ESX 16. Mock crime scene DNA extracts of four different quantities (from around 8-84 pg) were tested. All PCR products were analysed using 5, 10 and 20 capillary electrophoresis (CE) injection seconds. Bayesian models describing allele dropout patterns, allele peak heights and heterozygote balance were developed to assess the overall improvements in EPG quality with altered PCR/CE settings. The models were also used to evaluate the impact of amplicon length, STR marker and fluorescent label on the risk for allele dropout. The allele dropout probability decreased for each PCR cycle increment from 30 to 33 PCR cycles. Irrespective of DNA amount, the dropout probability was not affected by further increasing the number of PCR cycles. For the 42 and 84 pg samples, mainly complete DNA profiles were generated applying 32 PCR cycles. For the 8 and 17 pg samples, the allele dropouts decreased from 100% using 30 cycles to about 75% and 20%, respectively. The results for 33, 34 and 35 PCR cycles indicated that heterozygote balance and stutter ratio were mainly affected by DNA amount, and not directly by PCR cycle number and CE injection settings. We found 32 and 33 PCR cycles with 10 CE injection seconds to be optimal, as 34 and 35 PCR cycles did not improve allele detection and also included CE saturation problems. We find allele dropout probability differences between several STR markers. Markers labelled with the fluorescent dyes CXR-ET (red in electropherogram) and TMR-ET (shown as black) generally have higher dropout risks compared with those

  9. The Relative Odds of Progressing by Structural and Functional Tests in Glaucoma

    PubMed Central

    Abe, Ricardo Y.; Diniz-Filho, Alberto; Zangwill, Linda M.; Gracitelli, Carolina P. B.; Marvasti, Amir H.; Weinreb, Robert N.; Baig, Saif; Medeiros, Felipe A.

    2016-01-01

    Purpose The purpose of this study was to evaluate the effect of disease severity and number of tests acquired during follow-up on the relative odds of identifying progression by structural or functional tests in glaucoma. Methods This was an observational cohort study involving 462 eyes of 305 patients with glaucoma and 62 eyes of 49 healthy subjects. Glaucoma patients and healthy subjects were followed for an average of 3.6 ± 0.9 and 3.8 ± 0.9 years, with a median (interquantile range) of 8 (6–9) and 7 (6–8) visits, respectively. At each visit, subjects underwent visual field assessment with standard automated perimetry (SAP) and retinal nerve fiber layer (RNFL) evaluation by spectral-domain optical coherence tomography (SD-OCT). Slopes of change in SAP mean sensitivity and OCT RNFL thickness over time were estimated by linear regression using progressively cumulative visits over time. Cutoff values for age-related expected rates of change for each test were obtained from the healthy group. Progression by SD-OCT and/or SAP was determined if the slope of change was statistically significant and also lower (faster) than the fifth percentile cutoff calculated from the healthy group. A generalized estimating equation logistic regression model was used to evaluate the relative odds of progressing by OCT versus SAP in glaucoma eyes. Results Eyes with less severe disease at baseline had a higher chance of being detected as progressing by SD-OCT but not by SAP, whereas an increase in disease severity at baseline increased the chance that the eye would be detected as progressing by SAP but not SD-OCT. Each 1 dB higher MD was associated with a 5% increase in the odds of detecting progression by SD-OCT versus SAP (odds ratio = 1.05 per 1 dB; 95% confidence interval: 1.01–1.09; P = 0.005). Conclusions The ability to detect glaucoma progression by SAP versus SD-OCT is significantly influenced by the stage of disease. Our results may provide useful information for

  10. A fast degrading odd-odd aliphatic polyester-5,7 made by condensation polymerization for biomedical applications.

    PubMed

    Chen, Fei; Nölle, Jan Martin; Wietzke, Steffen; Reuter, Marco; Chatterjee, Sangam; Koch, Martin; Agarwal, Seema

    2012-01-01

    A fast enzymatic degradable aliphatic all-odd-polyester-5,7, based on 1,7-heptanedioic acid (pimelic acid) and 1,5-pentanediol, was synthesized by polycondensation. The structural characterization of the polyester was done using 1D- and 2D-NMR spectroscopic techniques. The properties of the resulting polyester-like crystallization behavior, enzymatic degradation, thermal stability, etc., were investigated using differential scanning calorimetry, wide-angle X-ray diffraction, scanning electron microscopy and gel-permeation chromatography. Terahertz time-domain spectroscopy was employed to determine the glass transition temperature, which could not be revealed reliably by conventional thermal analysis. The properties of all-odd-polyester-5,7 were compared with a well-known enzymatic degradable polyester (polycaprolactone). The results indicated that polyester-5,7 has a crystal structure similar to PCL, but a much faster degradation rate. The morphology of polyester-5,7 film during enzymatic degradation showed a fibrillar structure and degradation began by surface erosion.

  11. Evidence of antimagnetic rotation in odd-A {sup 105}Cd

    SciTech Connect

    Choudhury, Deepika; Jain, A. K.; Patial, M.; Gupta, N.; Arumugam, P.; Dhal, A.; Sinha, R. K.; Chaturvedi, L.; Joshi, P. K.; Trivedi, T.; Palit, R.; Kumar, S.; Garg, R.; Mandal, S.; Negi, D.; Mohanto, G.; Muralithar, S.; Singh, R. P.; Madhavan, N.; Bhowmik, R. K.

    2010-12-15

    The lifetimes of the levels above spin 23/2{sup -} in the negative-parity yrast band of {sup 105}Cd have been measured using the Doppler shift attenuation method. The obtained B(E2) values are small and show a decrease with an increase in spin. This establishes, for the first time, antimagnetic rotation (AMR) in an odd-A nucleus. An excellent agreement between the theoretical (semiclassical model) and experimental results along with a large I{sup (2)}/B(E2) ratio for the states strongly suggests that the structure of the levels beyond spin 23/2{sup -} has the character of a twin-shears type AMR band resulting from the coupling of a pair of g{sub 9/2} proton holes with aligned h{sub 11/2} and (g{sub 7/2}){sup 2} neutron particles, along with a small contribution from the core rotation.

  12. Optimal odd-periodic complementary sequences for diffuse wireless optical communications

    NASA Astrophysics Data System (ADS)

    Wang, Jun-Bo; Xie, Xiu-Xiu; Jiao, Yuan; Song, Xiaoyu; Zhao, Xibin; Gu, Ming; Sheng, Ming

    2012-09-01

    Indoor wireless optical communication (WOC) systems become promising because of their distinct advantages over their radio frequency counterparts. We address the optimal odd-periodic complementary sequences (OPCSs) for estimating a channel impulse response in WOC systems. Based on the Cramer-Rao bound, a criterion for design the optimal OPCSs is introduced. Optimum OPCSs are obtained and tabulated by computer search for different channel responses and OPCS length. Moreover, the sequence detection performance measured by bit error ratio (BER) for OPCSs-based channel estimation is also investigated. Simulation results show that the sequence detection performance can be significantly improved by using the optimal OPCS pairs. Moreover, the longer OPCS is, the better a BER performance can be obtained when the channel order is held fixed.

  13. On strontium isotopic anomalies and odd-A p-process abundances. [in solar system

    NASA Technical Reports Server (NTRS)

    Clayton, D. D.

    1978-01-01

    Several aspects of the nucleosynthesis of Sr isotopes are considered in an attempt to shed light on the problem of the Sr isotopic anomalies discovered in an inclusion of the Allende meteorite. Decomposition of the Sr isotopes into average r-, s-, and p-process nucleosynthetic classes is performed. It is suggested that the Allende inclusion most likely has an excess of s-process Sr and that the initial Sr-87/Sr-86 isotopic ratio is probably slightly more primitive than basaltic achondrites. The results also show that Sn-115 is mostly due to the r-process and that odd-A yields are very small. It is concluded that if the Sr anomaly in the inclusion is an average s enhancement, it argues somewhat in favor of a model of gas/dust fractionation of s and r isotopes during accumulation of the inclusion parent in the protosolar cloud.

  14. Systematics of fine structure in the α decay of deformed odd-mass nuclei

    NASA Astrophysics Data System (ADS)

    Ren, Zhongzhou; Ni, Dongdong

    2014-12-01

    We present a detailed analysis of the a-decay fine structure in 32 deformed odd-mass nuclei from Z = 93 to Z = 102. The α-decay half-lives are systematically calculated within the multichannel cluster model (MCCM), which turns out to well reproduce the experimental data and show the neutron deformed shell structure. The branching ratios for various daughter states are investigated in the MCCM and in the WKB barrier penetration approach, respectively. It is found that the MCCM results agree well with the experimental data, while the WKB results have relatively large deviations from the experimental data for the α transitions to the high-lying members of the rotational band.

  15. Self-incompatibility of Prunus tenella and evidence that reproductively isolated species of Prunus have different SFB alleles coupled with an identical S-RNase allele.

    PubMed

    Surbanovski, Nada; Tobutt, Kenneth R; Konstantinović, Miroslav; Maksimović, Vesna; Sargent, Daniel J; Stevanović, Vladimir; Bosković, Radovan I

    2007-05-01

    Many species of Prunus display an S-RNase-based gametophytic self-incompatibility (SI), controlled by a single highly polymorphic multigene complex termed the S-locus. This comprises tightly linked stylar- and pollen-expressed genes that determine the specificity of the SI response. We investigated SI of Prunus tenella, a wild species found in small, isolated populations on the Balkan peninsula, initially by pollination experiments and identifying stylar-expressed RNase alleles. Nine P. tenella S-RNase alleles (S(1)-S(9)) were cloned; their sequence analysis showed a very high ratio of non-synonymous to synonymous nucleotide substitutions (K(a)/K(s)) and revealed that S-RNase alleles of P. tenella, unlike those of Prunus dulcis, show positive selection in all regions except the conserved regions and that between C2 and RHV. Remarkably, S(8)-RNase, was found to be identical to S(1)-RNase from Prunus avium, a species that does not interbreed with P. tenella and, except for just one amino acid, to S(11) of P. dulcis. However, the corresponding introns and S-RNase-SFB intergenic regions showed considerable differences. Moreover, protein sequences of the pollen-expressed SFB alleles were not identical, harbouring 12 amino-acid replacements between those of P. tenella SFB(8) and P. avium SFB(1). Implications of this finding for hypotheses about the evolution of new S-specificities are discussed.

  16. Increasing long term response by selecting for favorable minor alleles

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Long-term response of genomic selection can be improved by considering allele frequencies of selected markers or quantitative trait loci (QTLs). A previous formula to weight allele frequency of favorable minor alleles was tested, and 2 new formulas were developed. The previous formula used nonlinear...

  17. Mutant maize variety containing the glt1-1 allele

    DOEpatents

    Nelson, O.E.; Pan, D.

    1994-07-19

    A maize plant has in its genome a non-mutable form of a mutant allele designated vitX-8132. The allele is located at a locus designated as glt which conditions kernels having an altered starch characteristic. Maize plants including such a mutant allele produce a starch that does not increase in viscosity on cooling, after heating. 2 figs.

  18. Mutant maize variety containing the glt1-1 allele

    DOEpatents

    Nelson, Oliver E.; Pan, David

    1994-01-01

    A maize plant has in its genome a non-mutable form of a mutant allele designated vitX-8132. The allele is located at a locus designated as glt which conditions kernels having an altered starch characteristic. Maize plants including such a mutant allele produce a starch that does not increase in viscosity on cooling, after heating.

  19. Phase transition in odd-N Pd-isotopes

    NASA Astrophysics Data System (ADS)

    Zhou, Hou-Bing; Dong, Guo-Xiang; Sun, Xiao-Jun; Xu, Fu-Rong

    2015-11-01

    Phase transition in odd-N isotopes 99,101,103Pd are investigated via the E-GOS (E-Gamma Over Spin) curves, which strongly suggest a structure evolution from vibration to rotation along the yrast lines with increasing spin. Theoretical calculations have been performed for the ground state bands of 99,101,103Pd in the framework of the cranked shell model (CSM) and the alignment properties observed experimentally are analyzed employing this model. The results show that the phase transition in the ground state bands of 99,101,103Pd can be interpreted as the valence nucleons start to occupy the g9/2 proton orbitals with increasing spin which would polarize the core to a small, but rigid quadrupole deformation. Supported by Natural Science Foundation of Guangxi (2014jjBA10016, 2014jjDA10012) and National Natural Science Foundation of China (11465005)

  20. Near yrast states in doubly odd [sup 214]Fr

    SciTech Connect

    Debray, M.E.; Kreiner, A.J.; Kesque, J.M.; Ozafran, M.; Romo, A.; Somacal, H.; Vazquez, M.E. ); Davidson, J.; Davidson, M. ); Ahn, K.; Fossan, D.B.; Liang, Y.; Ma, R.; Paul, E.S.; Piel, W.F. Jr.; Xu, N. )

    1993-11-01

    High spin states of doubly odd [sup 214]Fr[sub 127] have been investigated using in-beam [gamma]-ray and conversion electron spectroscopy techniques through the [sup 206]Pb([sup 11]B, 3[ital n]) and [sup 208]Pb([sup 11]B, 5[ital n]) fusion-evaporation reactions. Completely new spectrocopic information has been obtained. The yrast level structure is established up to spin (19[sup +]) and some information on [gamma] transitions from higher-lying levels is also obtained. Two new isomers [ital T][sub 1/2]=174(20) ns and [ital T][sub 1/2]=11(2) ns were found. Configuration assignments for the low-lying levels are discussed. Information on residual proton-neutron interactions is extracted.

  1. Odd-frequency pairing of interacting Majorana fermions

    DOE PAGES

    Huang, Zhoushen; Wolfle, P.; Balatsky, Alexander V.

    2015-09-14

    In this study, Majorana fermions are rising as a promising key component in quantum computation. Although the prevalent approach is to use a quadratic (i.e., noninteracting) Majorana Hamiltonian, when expressed in terms of Dirac fermions, generically the Hamiltonian involves interaction terms. Here we focus on the possible pair correlations in a simple model system. We study a model of Majorana fermions coupled to a boson mode and show that the anomalous correlator between different Majorana fermions, located at opposite ends of a topological wire, exhibits odd-frequency behavior. It is stabilized when the coupling strength g is above a critical valuemore » gc. We use both, conventional diagrammatic theory and a functional integral approach, to derive the gap equation, the critical temperature, the gap function, the critical coupling, and a Ginzburg-Landau theory that allows discussing a possible subleading admixture of even-frequency pairing.« less

  2. Odd-frequency pairing of interacting Majorana fermions

    NASA Astrophysics Data System (ADS)

    Huang, Zhoushen; Wölfle, P.; Balatsky, A. V.

    2015-09-01

    Majorana fermions are rising as a promising key component in quantum computation. Although the prevalent approach is to use a quadratic (i.e., noninteracting) Majorana Hamiltonian, when expressed in terms of Dirac fermions, generically the Hamiltonian involves interaction terms. Here we focus on the possible pair correlations in a simple model system. We study a model of Majorana fermions coupled to a boson mode and show that the anomalous correlator between different Majorana fermions, located at opposite ends of a topological wire, exhibits odd-frequency behavior. It is stabilized when the coupling strength g is above a critical value gc. We use both, conventional diagrammatic theory and a functional integral approach, to derive the gap equation, the critical temperature, the gap function, the critical coupling, and a Ginzburg-Landau theory that allows discussing a possible subleading admixture of even-frequency pairing.

  3. Odd-frequency pairing of interacting Majorana fermions

    SciTech Connect

    Huang, Zhoushen; Wolfle, P.; Balatsky, Alexander V.

    2015-09-14

    In this study, Majorana fermions are rising as a promising key component in quantum computation. Although the prevalent approach is to use a quadratic (i.e., noninteracting) Majorana Hamiltonian, when expressed in terms of Dirac fermions, generically the Hamiltonian involves interaction terms. Here we focus on the possible pair correlations in a simple model system. We study a model of Majorana fermions coupled to a boson mode and show that the anomalous correlator between different Majorana fermions, located at opposite ends of a topological wire, exhibits odd-frequency behavior. It is stabilized when the coupling strength g is above a critical value gc. We use both, conventional diagrammatic theory and a functional integral approach, to derive the gap equation, the critical temperature, the gap function, the critical coupling, and a Ginzburg-Landau theory that allows discussing a possible subleading admixture of even-frequency pairing.

  4. Torsion, parity-odd response, and anomalies in topological states

    NASA Astrophysics Data System (ADS)

    Parrikar, Onkar; Hughes, Taylor L.; Leigh, Robert G.

    2014-11-01

    We study the response of a class of topological systems to electromagnetic and gravitational sources, including torsion and curvature. By using the technology of anomaly polynomials, we derive the parity-odd response of a massive Dirac fermion in d =2 +1 and d =4 +1 , which provides a simple model for a topological insulator. We discuss the covariant anomalies of the corresponding edge states, from a Callan-Harvey anomaly inflow, as well as a Hamiltonian spectral flow point of view. We also discuss the applicability of our results to other systems such as Weyl semimetals. Finally, using dimensional reduction from d =4 +1 , we derive the effective action for a d =3 +1 time-reversal invariant topological insulator in the presence of torsion and curvature, and discuss its various physical consequences.

  5. Dimension-5 CP -odd operators: QCD mixing and renormalization

    DOE PAGES

    Bhattacharya, Tanmoy; Cirigliano, Vincenzo; Gupta, Rajan; ...

    2015-12-23

    Here, we study the off-shell mixing and renormalization of flavor-diagonal dimension-five T- and P-odd operators involving quarks, gluons, and photons, including quark electric dipole and chromoelectric dipole operators. Furthermore, we present the renormalization matrix to one loop in themore » $$\\bar{MS}$$ scheme. We also provide a definition of the quark chromoelectric dipole operator in a regularization-independent momentum-subtraction scheme suitable for nonperturbative lattice calculations and present the matching coefficients with the $$\\bar{MS}$$ scheme to one loop in perturbation theory, using both the naïve dimensional regularization and ’t Hooft–Veltman prescriptions for γ5.« less

  6. Alleles versus mutations: Understanding the evolution of genetic architecture requires a molecular perspective on allelic origins.

    PubMed

    Remington, David L

    2015-12-01

    Perspectives on the role of large-effect quantitative trait loci (QTL) in the evolution of complex traits have shifted back and forth over the past few decades. Different sets of studies have produced contradictory insights on the evolution of genetic architecture. I argue that much of the confusion results from a failure to distinguish mutational and allelic effects, a limitation of using the Fisherian model of adaptive evolution as the lens through which the evolution of adaptive variation is examined. A molecular-based perspective reveals that allelic differences can involve the cumulative effects of many mutations plus intragenic recombination, a model that is supported by extensive empirical evidence. I discuss how different selection regimes could produce very different architectures of allelic effects under a molecular-based model, which may explain conflicting insights on genetic architecture from studies of variation within populations versus between divergently selected populations. I address shortcomings of genome-wide association study (GWAS) practices in light of more suitable models of allelic evolution, and suggest alternate GWAS strategies to generate more valid inferences about genetic architecture. Finally, I discuss how adopting more suitable models of allelic evolution could help redirect research on complex trait evolution toward addressing more meaningful questions in evolutionary biology.

  7. Exposure to Childhood Traumas Ups the Odds of Giving Birth to Daughters

    PubMed Central

    Kaitz, Marsha; Rokem, Ann Marie; Mankuta, David; Davidov, Maayan; Faraone, Stephen V.

    2014-01-01

    Purpose This study examined the likelihood of giving birth to a daughter as a function of women’s exposure to four categories of stressors: Childhood Trauma, Adult Trauma, Chronic Stressors, and Recent (adverse) Life Events. Hypothesis 1 stated that that exposure to Recent Life Events (near conception) and to childhood traumas would increase women’s chances of having a girl baby. Hypothesis 2 stated that the relation between stress and gender outcome is mediated by persistent PTSD symptoms. Method The final sample was comprised of 225 women. The design was Prospective Observational. At first contact, women were retained if they were < 27 weeks pregnant and met initial inclusion criteria. In interview 2, at 27–30 weeks, women were excluded for positive diagnoses of anxiety disorders besides PTSD with or without depression (Structured Clinical Interview for DSM disorders). In interview 3 (30–34 weeks), reports on stress categories (Social Stress Indicator Questionnaire, SSI) and PTSD symptoms (Post Traumatic Checklist) were obtained. Infant Gender was obtained from medical records. The relation between stress categories and the distribution of girl/boy infants was examined with Chi Squares and Logistic Regression analyses. Mediation was tested with the macro PROCESS (Hayes 2012). Results Childhood Trauma was the only stress category that increased the odds of having a girl; with an odds ratio of > 3.0 for women who had been exposed to more than two such events. PTSD symptoms (partially) mediated the relation between Childhood Trauma and infant gender. Conclusions Findings suggest that women’s exposure to childhood trauma contributes to the determination of the sex ratio at birth and that PTSD symptoms are part of the cause. PMID:24221408

  8. Exposure to childhood traumas ups the odds of giving birth to daughters.

    PubMed

    Kaitz, Marsha; Rokem, Ann Marie; Mankuta, David; Davidov, Maayan; Faraone, Stephen V

    2014-04-01

    This study examined the likelihood of giving birth to a daughter as a function of women's exposure to four categories of stressors: childhood trauma, adult trauma, chronic stressors, and recent (adverse) life events. Hypothesis 1 stated that exposure to recent life events (near conception) and to childhood traumas would increase women's chances of having a girl baby. Hypothesis 2 stated that the relationship between stress and gender outcome is mediated by persistent posttraumatic stress disorder (PTSD) symptoms. The final sample was comprised of 225 women. The design was prospective observational. At first contact, women were retained if they were <27 weeks pregnant and met initial inclusion criteria. In interview 2, at 27-30 weeks, women were excluded for positive diagnoses of anxiety disorders besides PTSD with or without depression (Structured Clinical Interview for DSM-IV Disorders). In interview 3 (30-34 weeks), reports on stress categories (Social Stress Indicator Questionnaire) and PTSD symptoms (Post-Traumatic Checklist) were obtained. Infant gender was obtained from medical records. The relationship between stress categories and the distribution of girl/boy infants was examined with Chi Squares and logistic regression analyses. Mediation was tested with the macro PROCESS (Hayes 2012). Childhood trauma was the only stress category that increased the odds of having a girl, with an odds ratio of >3.0 for women who had been exposed to more than two such events. PTSD symptoms (partially) mediated the relationship between childhood trauma and infant gender. Findings suggest that women's exposure to childhood trauma contributes to the determination of the sex ratio at birth and that PTSD symptoms are part of the cause.

  9. Decline in Cardiorespiratory Fitness and Odds of Incident Depression

    PubMed Central

    Dishman, Rodney K.; Sui, Xuemei; Church, Timothy S.; Hand, Gregory A.; Trivedi, Madhukar H.; Blair, Steven N.

    2012-01-01

    Background Studies of physical activity and incidence of physician-diagnosed depression have been limited to a single estimate of self-reported physical activity exposure, despite follow-up periods lasting many years. Purpose To examine longitudinal change in cardiorespiratory fitness, an objective marker of habitual physical activity, and incident depression complaints made to a physician. Methods Cardiorespiratory fitness assessed at four clinic visits between 1971 and 2006, each separated by an average of 2–3 years, was used to objectively measure cumulative physical activity exposure in cohorts of 7936 men and 1261 women, aged 20–85 years, from the Aerobics Center Longitudinal Study who did not complain of depression at their first clinic visit in 1971–2003. Data were analyzed in August 2010. Results Across subsequent visits, there were 446 incident cases in men and 153 cases in women. After adjustment for age, time between visits, BMI at each visit, and fitness at Visit 1, each 1-minute decline in treadmill endurance (i.e., a decline in cardiorespiratory fitness of approximately 1 half-MET) between ages 51 and 55 years in men and ages 53 and 56 years in women, increased the odds of incident depression complaints by approximately 2% and 9.5%, respectively. The increased odds remained significant but were attenuated to 1.3% and 5.4% after further adjustment at each visit for smoking, alcohol use, chronic medical conditions, anxiety, and sleep problems. Conclusions Maintenance of cardiorespiratory fitness during late middle-age, when decline in fitness typically accelerates, helps protect against the onset of depression complaints made to a physician. PMID:22992353

  10. An Overview of Modeling Middle Atmospheric Odd Nitrogen

    NASA Technical Reports Server (NTRS)

    Jackman, Charles H.; Kawa, S. Randolph; Einaudi, Franco (Technical Monitor)

    2001-01-01

    Odd nitrogen (N, NO, NO2, NO3, N2O5, HNO3, HO2NO2, ClONO2, and BrONO2) constituents are important components in the control of middle atmospheric ozone. Several processes lead to the production of odd nitrogen (NO(sub y)) in the middle atmosphere (stratosphere and mesosphere) including the oxidation of nitrous oxide (N2O), lightning, downflux from the thermosphere, and energetic charged particles (e.g., galactic cosmic rays, solar proton events, and energetic electron precipitation). The dominant production mechanism of NO(sub y) in the stratosphere is N2O oxidation, although other processes contribute. Mesospheric NO(sub y) is influenced by N2O oxidation, downflux from the thermosphere, and energetic charged particles. NO(sub y) is destroyed in the middle atmosphere primarily via two processes: 1) dissociation of NO to form N and O followed by N + NO yielding N2 + O to reform even nitrogen; and 2) transport to the troposphere where HNO3 can be rapidly scavenged in water droplets and rained out of the atmosphere. There are fairly significant differences among global models that predict NO(sub y). NO(sub y) has a fairly long lifetime in the stratosphere (months to years), thus disparate transport in the models probably contributes to many of these differences. Satellite and aircraft measurement provide modeling tests of the various components of NO(sub y). Although some recent reaction rate measurements have led to improvements in model/measurement agreement, significant differences do remain. This presentation will provide an overview of several proposed sources and sinks of NO(sub y) and their regions of importance. Multi-dimensional modeling results for NO(sub y) and its components with comparisons to observations will also be presented.

  11. Identification of the third/extra allele for forensic application in cases with TPOX tri-allelic pattern.

    PubMed

    Picanço, Juliane Bentes; Raimann, Paulo Eduardo; da Motta, Carlos Henrique Ares Silveira; Rodenbusch, Rodrigo; Gusmão, Leonor; Alho, Clarice Sampaio

    2015-05-01

    Genotyping of polymorphic short tandem repeats (STRs) loci is widely used in forensic DNA analysis. STR loci eventually present tri-allelic pattern as a genotyping irregularity and, in that situation, the doubt about the tri-allele locus frequency calculation can reduce the analysis strength. In the TPOX human STR locus, tri-allelic genotypes have been reported with a widely varied frequency among human populations. We investigate whether there is a single extra allele (the third allele) in the TPOX tri-allelic pattern, what it is, and where it is, aiming to understand its genomic anatomy and to propose the knowledge of this TPOX extra allele from genetic profile, thus preserving the two standard TPOX alleles in forensic analyses. We looked for TPOX tri-allelic subjects in 75,113 Brazilian families. Considering only the parental generation (mother+father) we had 150,226 unrelated subjects evaluated. From this total, we found 88 unrelated subjects with tri-allelic pattern in the TPOX locus (0.06%; 88/150,226). Seventy three of these 88 subjects (73/88; 83%) had the Clayton's original Type 2 tri-allelic pattern (three peaks of even intensity). The remaining 17% (15/88) show a new Type 2 derived category with heterozygote peak imbalance (one double dose peak plus one regular sized peak). In this paper we present detailed data from 66 trios (mother+father+child) with true biological relationships. In 39 of these families (39/66; 59%) the extra TPOX allele was transmitted either from the mother or from the father to the child. Evidences indicated the allele 10 as the extra TPOX allele, and it is on the X chromosome. The present data, which support the previous Lane hypothesis, improve the knowledge about tri-allelic pattern of TPOX CODIS' locus allowing the use of TPOX profile in forensic analyses even when with tri-allelic pattern. This evaluation is now available for different forensic applications.

  12. CFH haplotypes and ARMS2, C2, C3, and CFB alleles show association with susceptibility to age-related macular degeneration in Mexicans

    PubMed Central

    Zenteno, Juan Carlos; Fernández-López, Juan Carlos; Rodríguez-Corona, Ulises; Falfán-Valencia, Ramcés; Sebastian, Leticia; Morales, Fabiola; Ochoa-Contreras, Daniel; Carnevale, Alessandra; Silva-Zolezzi, Irma

    2014-01-01

    Purpose To evaluate the contribution of genetic variants of complement factor H (CFH), complement component 2 and 3 (C2 and C3), complement factor B (CFB), and age-related maculopathy susceptibility 2 (ARMS2) to age-related macular degeneration (AMD) risk in the Mexican Mestizo population. Methods Analysis included 282 unrelated Mexican patients with advanced AMD, 205 healthy controls, and 280 population controls. Stereoscopic fundus images were graded on the Clinical Age-Related Maculopathy System (CARMS). We designed a resequencing strategy using primers with M13 adaptor for the 23 exons of the CFH gene in a subgroup of 96 individuals clinically evaluated: 48 AMD cases and 48 age- and sex-matched healthy controls. Single nucleotide polymorphisms (SNPs) in C3 (Arg80Gly and Pro292Leu), C2 (rs547154), CFB (Leu9His), and ARMS2 (Ala69Ser) were genotyped in all patients, healthy and population controls using TaqMan assay. Results All evaluated individuals were Mexican Mestizos, and their genetic ancestry was validated using 224 ancestry informative markers and calculating Fst values. The CFH resequencing revealed 19 SNPs and a common variant in the intron 2 splice acceptor site; three CFH haplotypes inferred from individual genotypes, showed significant differences between cases and controls. The risk alleles in C3 (rs1047286, odds ratio [OR]=2.48, 95% confidence interval [CI]=1.64–3.75, p=1.59E-05; rs2230199, OR=2.15, 95% CI=1.48–3.13, p=6.28E-05) and in ARMS2 (rs10490924, OR=3.09, 95% CI=2.48–3.86, p=5.42E-23) were strongly associated with risk of AMD. The protective effect of alleles in C2 (rs547154) and CFB (rs4151667) showed a trend but was not significantly associated after correction for multiple testing. Conclusions Our results show that ARMS2 and C3 are major contributors to advanced AMD in Mexican patients, while the contributions of CFH, C2, and CFB are minor to those of other populations, reveling significant ethnic differences in minor allele

  13. Update on allele nomenclature for human cytochromes P450 and the Human Cytochrome P450 Allele (CYP-allele) Nomenclature Database.

    PubMed

    Sim, Sarah C; Ingelman-Sundberg, Magnus

    2013-01-01

    Interindividual variability in xenobiotic metabolism and drug response is extensive and genetic factors play an important role in this variation. A majority of clinically used drugs are substrates for the cytochrome P450 (CYP) enzyme system and interindividual variability in expression and function of these enzymes is a major factor for explaining individual susceptibility for adverse drug reactions and drug response. Because of the existence of many polymorphic CYP genes, for many of which the number of allelic variants is continually increasing, a universal and official nomenclature system is important. Since 1999, all functionally relevant polymorphic CYP alleles are named and published on the Human Cytochrome P450 Allele (CYP-allele) Nomenclature Web site (http://www.cypalleles.ki.se). Currently, the database covers nomenclature of more than 660 alleles in a total of 30 genes that includes 29 CYPs as well as the cytochrome P450 oxidoreductase (POR) gene. On the CYP-allele Web site, each gene has its own Webpage, which lists the alleles with their nucleotide changes, their functional consequences, and links to publications identifying or characterizing the alleles. CYP2D6, CYP2C9, CYP2C19, and CYP3A4 are the most important CYPs in terms of drug metabolism, which is also reflected in their corresponding highest number of Webpage hits at the CYP-allele Web site.The main advantage of the CYP-allele database is that it offers a rapid online publication of CYP-alleles and their effects and provides an overview of peer-reviewed data to the scientific community. Here, we provide an update of the CYP-allele database and the associated nomenclature.

  14. Borrowed alleles and convergence in serpentine adaptation

    PubMed Central

    Arnold, Brian J.; Lahner, Brett; DaCosta, Jeffrey M.; Weisman, Caroline M.; Hollister, Jesse D.; Salt, David E.; Bomblies, Kirsten; Yant, Levi

    2016-01-01

    Serpentine barrens represent extreme hazards for plant colonists. These sites are characterized by high porosity leading to drought, lack of essential mineral nutrients, and phytotoxic levels of metals. Nevertheless, nature forged populations adapted to these challenges. Here, we use a population-based evolutionary genomic approach coupled with elemental profiling to assess how autotetraploid Arabidopsis arenosa adapted to a multichallenge serpentine habitat in the Austrian Alps. We first demonstrate that serpentine-adapted plants exhibit dramatically altered elemental accumulation levels in common conditions, and then resequence 24 autotetraploid individuals from three populations to perform a genome scan. We find evidence for highly localized selective sweeps that point to a polygenic, multitrait basis for serpentine adaptation. Comparing our results to a previous study of independent serpentine colonizations in the closely related diploid Arabidopsis lyrata in the United Kingdom and United States, we find the highest levels of differentiation in 11 of the same loci, providing candidate alleles for mediating convergent evolution. This overlap between independent colonizations in different species suggests that a limited number of evolutionary strategies are suited to overcome the multiple challenges of serpentine adaptation. Interestingly, we detect footprints of selection in A. arenosa in the context of substantial gene flow from nearby off-serpentine populations of A. arenosa, as well as from A. lyrata. In several cases, quantitative tests of introgression indicate that some alleles exhibiting strong selective sweep signatures appear to have been introgressed from A. lyrata. This finding suggests that migrant alleles may have facilitated adaptation of A. arenosa to this multihazard environment. PMID:27357660

  15. Biased gene conversion skews allele frequencies in human populations, increasing the disease burden of recessive alleles.

    PubMed

    Lachance, Joseph; Tishkoff, Sarah A

    2014-10-02

    Gene conversion results in the nonreciprocal transfer of genetic information between two recombining sequences, and there is evidence that this process is biased toward G and C alleles. However, the strength of GC-biased gene conversion (gBGC) in human populations and its effects on hereditary disease have yet to be assessed on a genomic scale. Using high-coverage whole-genome sequences of African hunter-gatherers, agricultural populations, and primate outgroups, we quantified the effects of GC-biased gene conversion on population genomic data sets. We find that genetic distances (FST and population branch statistics) are modified by gBGC. In addition, the site frequency spectrum is left-shifted when ancestral alleles are favored by gBGC and right-shifted when derived alleles are favored by gBGC. Allele frequency shifts due to gBGC mimic the effects of natural selection. As expected, these effects are strongest in high-recombination regions of the human genome. By comparing the relative rates of fixation of unbiased and biased sites, the strength of gene conversion was estimated to be on the order of Nb ≈ 0.05 to 0.09. We also find that derived alleles favored by gBGC are much more likely to be homozygous than derived alleles at unbiased SNPs (+42.2% to 62.8%). This results in a curse of the converted, whereby gBGC causes substantial increases in hereditary disease risks. Taken together, our findings reveal that GC-biased gene conversion has important population genetic and public health implications.

  16. Unique first-forbidden β-decay transitions in odd-odd and even-even heavy nuclei

    NASA Astrophysics Data System (ADS)

    Nabi, Jameel-Un; Çakmak, Necla; Majid, Muhammad; Selam, Cevad

    2017-01-01

    The allowed Gamow-Teller (GT) transitions are the most common weak nuclear processes of spin-isospin (στ) type. These transitions play a key role in numerous processes in the domain of nuclear physics. Equally important is their contribution in astrophysics, particularly in nuclear synthesis and supernova-explosions. In situations where allowed GT transitions are not favored, first-forbidden transitions become significant, specifically in medium heavy and heavy nuclei. For neutron-rich nuclei, first-forbidden transitions are favored mainly due to the phase-space amplification for these transitions. In this work we calculate the allowed GT as well as unique first-forbidden (U1F) | ΔJ | = 2 transitions strength in odd-odd and even-even nuclei in mass range 70 ≤ A ≤ 214. Two different pn-QRPA models were used with a schematic separable interaction to calculate GT and U1F transitions. The inclusion of U1F strength improved the overall comparison of calculated terrestrial β-decay half-lives in both models. The ft values and reduced transition probabilities for the 2- ⟷0+ transitions were also calculated. We compared our calculations with the previously reported correlated RPA calculation and experimental results. Our calculations are in better agreement with measured data. For stellar applications we further calculated the allowed GT and U1F weak rates. These include β±-decay rates and electron/positron capture rates of heavy nuclei in stellar matter. Our study shows that positron and electron capture rates command the total weak rates of these heavy nuclei at high stellar temperatures.

  17. Allelic genealogies in sporophytic self-incompatibility systems in plants.

    PubMed Central

    Schierup, M H; Vekemans, X; Christiansen, F B

    1998-01-01

    Expectations for the time scale and structure of allelic genealogies in finite populations are formed under three models of sporophytic self-incompatibility. The models differ in the dominance interactions among the alleles that determine the self-incompatibility phenotype: In the SSIcod model, alleles act codominantly in both pollen and style, in the SSIdom model, alleles form a dominance hierarchy, and in SSIdomcod, alleles are codominant in the style and show a dominance hierarchy in the pollen. Coalescence times of alleles rarely differ more than threefold from those under gametophytic self-incompatibility, and transspecific polymorphism is therefore expected to be equally common. The previously reported directional turnover process of alleles in the SSIdomcod model results in coalescence times lower and substitution rates higher than those in the other models. The SSIdom model assumes strong asymmetries in allelic action, and the most recessive extant allele is likely to be the most recent common ancestor. Despite these asymmetries, the expected shape of the allele genealogies does not deviate markedly from the shape of a neutral gene genealogy. The application of the results to sequence surveys of alleles, including interspecific comparisons, is discussed. PMID:9799270

  18. Cytochrome P450 2D6 variants in a Caucasian population: Allele frequencies and phenotypic consequences

    SciTech Connect

    Sachse, C.; Brockmoeller, J.; Bauer, S.; Roots, I.

    1997-02-01

    Cytochrome P450 2D6 (CYP2D6) metabolizes many important drugs. CYP2D6 activity ranges from complete deficiency to ultrafast metabolism, depending on at least 16 different known alleles. Their frequencies were determined in 589 unrelated German volunteers and correlated with enzyme activity measured by phenotyping with dextromethorphan or debrisoquine. For genotyping, nested PCR-RFLP tests from a PCR amplificate of the entire CYP2D6 gene were developed. The frequency of the CYP2D6*1 allele coding for extensive metabolizer (EM) phenotype was .364. The alleles coding for slightly (CYP2D6*2) or moderately (*9 and *10) reduced activity (intermediate metabolizer phenotype [IM]) showed frequencies of .324, .018, and .015, respectively. By use of novel PCR tests for discrimination, CYP2D6 gene duplication alleles were found with frequencies of.005 (*1 x 2), .013 (* 2 x 2), and .001 (*4 x 2). Frequencies of alleles with complete deficiency (poor metabolizer phenotype [PM]) were .207 (*4), .020 (*3 and *5), .009 (*6), and .001 (*7, *15, and *16). The defective CYP2D6 alleles *8, *11, *12, *13, and *14 were not found. All 41 PMs (7.0%) in this sample were explained by five mutations detected by four PCR-RFLP tests, which may suffice, together with the gene duplication test, for clinical prediction of CYP2D6 capacity. Three novel variants of known CYP2D6 alleles were discovered: *1C (T{sub 1957}C), *2B (additional C{sub 2558}T), and *4E (additional C{sub 2938}T). Analysis of variance showed significant differences in enzymatic activity measured by the dextromethorphan metabolic ratio (MR) between carriers of EN/PM (mean MR = .006) and IM/PM (mean MR = .014) alleles and between carriers of one (mean MR = .009) and two (mean MR = .003) functional alleles. The results of this study provide a solid basis for prediction of CYP2D6 capacity, as required in drug research and routine drug treatment. 35 refs., 4 figs., 5 tabs.

  19. Exquisite allele discrimination by toehold hairpin primers

    PubMed Central

    Byrom, Michelle; Bhadra, Sanchita; Jiang, Yu Sherry; Ellington, Andrew D.

    2014-01-01

    The ability to detect and monitor single nucleotide polymorphisms (SNPs) in biological samples is an enabling research and clinical tool. We have developed a surprising, inexpensive primer design method that provides exquisite discrimination between SNPs. The field of DNA computation is largely reliant on using so-called toeholds to initiate strand displacement reactions, leading to the execution of kinetically trapped circuits. We have now similarly found that the short toehold sequence to a target of interest can initiate both strand displacement within the hairpin and extension of the primer by a polymerase, both of which will further stabilize the primer:template complex. However, if the short toehold does not bind, neither of these events can readily occur and thus amplification should not occur. Toehold hairpin primers were used to detect drug resistance alleles in two genes, rpoB and katG, in the Mycobacterium tuberculosis genome, and ten alleles in the Escherichia coli genome. During real-time PCR, the primers discriminate between mismatched templates with Cq delays that are frequently so large that the presence or absence of mismatches is essentially a ‘yes/no’ answer. PMID:24990378

  20. Odds ratio for 2 × 2 tables: Mantel-Haenszel estimator, profile likelihood, and presence of surrogate responses.

    PubMed

    Banerjee, Buddhananda; Biswas, Atanu

    2014-01-01

    Use of surrogate outcome to improve the inference in biomedical problems is an area of growing interest. Here, we consider a setup where both the true and surrogate endpoints are binary and we observe all the surrogate endpoints along with a few true endpoints. In a two-treatment setup we study the surrogate-augmented Mantel-Haenszel estimator based on observations from different groups when the group effect is present. We compare the Mantel-Haenszel estimator with the one obtained by maximizing profile likelihood in a surrogate augmented setup. We observe that the performances of these estimators are very close.

  1. Microarrays for high-throughput genotyping of MICA alleles using allele-specific primer extension.

    PubMed

    Baek, I C; Jang, J-P; Choi, H-B; Choi, E-J; Ko, W-Y; Kim, T-G

    2013-10-01

    The role of major histocompatibility complex (MHC) class I chain-related gene A (MICA), a ligand of NKG2D, has been defined in human diseases by its allele associations with various autoimmune diseases, hematopoietic stem cell transplantation (HSCT) and cancer. This study describes a practical system to develop MICA genotyping by allele-specific primer extension (ASPE) on microarrays. From the results of 20 control primers, strict and reliable cut-off values of more than 30,000 mean fluorescence intensity (MFI) as positive and less than 3000 MFI as negative, were applied to select high-quality specific extension primers. Among 55 allele-specific primers, 44 primers could be initially selected as optimal primer. Through adjusting the length, six primers were improved. The other failed five primers were corrected by refractory modification. MICA genotypes by ASPE on microarrays showed the same results as those by nucleotide sequencing. On the basis of these results, ASPE on microarrays may provide high-throughput genotyping for MICA alleles for population studies, disease-gene associations and HSCT.

  2. Massive and massless higher spinning particles in odd dimensions

    NASA Astrophysics Data System (ADS)

    Bastianelli, Fiorenzo; Bonezzi, Roberto; Corradini, Olindo; Latini, Emanuele

    2014-09-01

    We study actions for massive bosonic particles of higher spins by dimensionally reducing an action for massless particles. For the latter we take a model with a SO( N) extended local supersymmetry on the worldline, that is known to describe massless (conformal) particles of higher spins in flat spacetimes of even dimensions. Dimensional reduction produces an action for massive spinning particles in odd dimensions. The field equations that emerge in a quantization à la Dirac are shown to be equivalent to the Fierz-Pauli ones. The massless limit generates a multiplet of massless states with higher spins, whose first quantized field equations have a geometric form with fields belonging to various types of Young tableaux. These geometric equations can be partially integrated to show their equivalence with the standard Fronsdal-Labastida equations. We covariantize our model to check whether an extension to curved spacetimes can be achieved. Restricting to (A)dS spaces, we find that the worldline gauge algebra becomes nonlinear, but remains first class. This guarantees consistency on such backgrounds. A light cone analysis confirms the presence of the expected propagating degrees of freedom. A covariant analysis is worked out explicitly for the massive case, which is seen to give rise to the Fierz-Pauli equations extended to (A)dS spaces. It is worth noting that in D = 3 the massless limit of our model with N → ∞ has the same field content of the Vasiliev's theory that accommodates each spin exactly once.

  3. Ferroelectric behavior of the odd-numbered nylons

    SciTech Connect

    Scheinbeim, J.I.; Newman, B.A.

    1993-12-31

    Recent work in the Polymer Electroprocessing Laboratory. Rutgers University, has shown that the odd-numbered nylons (11, 9, 7, 5) constitute the second known family of ferroelectric polymers: poly(vinylidene fluoride) and its co-polymers are the only other known family of ferroelectric polymers. Using mel-quenched and cold-drawn samples of nylon 11 which exhibit double orientation (chain axes in the draw direction and hydrogen bonds in the plane of the films) the authors examined changes in orientation of the polar (hydrogen bonds) and non-polar (hydrocarbon) sections as a function of annealing temperature and applied electric field. Using FTIR and WAXD studies, the authors have found that the samples polarized by application of electric fields before high temperature annealing exhibit diffraction patterns rotated by 90{degrees} from those of samples exposed to only high temperature annealing. These studies also show that the polarized, annealed samples are triply oriented and that they hydrocarbon sections exhibit little crystal order unless samples are annealed at high temperature.

  4. Increasing the Odds: Applying Emergentist Theory in Language Intervention

    PubMed Central

    Poll, Gerard H.

    2011-01-01

    Purpose This review introduces a leading theory of language development, emergentism, the view that language ability is the product of interactions between the language environment and the learning capabilities of the child. It suggests ways in which emergentism provides a theoretical rationale for interventions designed to address developmental language delays in young children. Method A review of selected literature on emergentist theory and research is presented, with a focus on the acquisition of early morphology and syntax. A significant method for developing and testing emergentist theory, connectionist modeling, is described. Key themes from both connectionist and behavioral studies are summarized and applied with specific examples to language intervention techniques. A case study is presented to integrate elements of emergentism with language intervention. Conclusions Evaluating the theoretical foundation for language interventions is an important step in evidence-based practice. This article introduces three themes in the emergentist literature that have implications for language intervention: sufficiency of language input, active engagement of the child with the input, and the introduction of factors that increase the odds for correctly mapping language form to meaning. Evidence supporting the importance of these factors in effective language intervention is presented, along with limitations in that evidence. PMID:21616988

  5. Even-odd entanglement in boson and spin systems

    NASA Astrophysics Data System (ADS)

    Rossignoli, R.; Canosa, N.; Matera, J. M.

    2011-04-01

    We examine the entanglement entropy of the even half of a translationally invariant finite chain or lattice in its ground state. This entropy measures the entanglement between the even and odd halves (each forming a “comb” of n/2 sites) and can be expected to be extensive for short-range couplings away from criticality. We first consider bosonic systems with quadratic couplings, where analytic expressions for arbitrary dimensions can be provided. The bosonic treatment is then applied to finite spin chains and arrays by means of the random-phase approximation. Results for first-neighbor anisotropic XY couplings indicate that, while at strong magnetic fields this entropy is strictly extensive, at weak fields important deviations arise, stemming from parity-breaking effects and the presence of a factorizing field (in the vicinity of which it becomes size-independent and identical to the entropy of a contiguous half). Exact numerical results for small spin s chains are shown to be in agreement with the bosonic random-phase approximation prediction.

  6. Sex-specific allelic transmission bias suggests sexual conflict at MC1R.

    PubMed

    Ducret, Valérie; Gaigher, Arnaud; Simon, Céline; Goudet, Jérôme; Roulin, Alexandre

    2016-09-01

    Sexual conflict arises when selection in one sex causes the displacement of the other sex from its phenotypic optimum, leading to an inevitable tension within the genome - called intralocus sexual conflict. Although the autosomal melanocortin-1-receptor gene (MC1R) can generate colour variation in sexually dichromatic species, most previous studies have not considered the possibility that MC1R may be subject to sexual conflict. In the barn owl (Tyto alba), the allele MC1RWHITE is associated with whitish plumage coloration, typical of males, and the allele MC1RRUFOUS is associated with dark rufous coloration, typical of females, although each sex can express any phenotype. Because each colour variant is adapted to specific environmental conditions, the allele MC1RWHITE may be more strongly selected in males and the allele MC1RRUFOUS in females. We therefore investigated whether MC1R genotypes are in excess or deficit in male and female fledglings compared with the expected Hardy-Weinberg proportions. Our results show an overall deficit of 7.5% in the proportion of heterozygotes in males and of 12.9% in females. In males, interannual variation in assortative pairing with respect to MC1R explained the year-specific deviations from Hardy-Weinberg proportions, whereas in females, the deficit was better explained by the interannual variation in the probability of inheriting the MC1RWHITE or MC1RRUFOUS allele. Additionally, we observed that sons inherit the MC1RRUFOUS allele from their fathers on average slightly less often than expected under the first Mendelian law. Transmission ratio distortion may be adaptive in this sexually dichromatic species if males and females are, respectively, selected to display white and rufous plumages.

  7. Odd-even staggering in the neutron-proton interaction and nuclear mass models

    NASA Astrophysics Data System (ADS)

    Cheng, Y. Y.; Zhao, Y. M.; Arima, A.

    2015-02-01

    In this paper we study odd-even staggering of the empirical neutron-proton interaction between the last neutron and the last proton, denoted as δ V1 n -1 p , and its consequence in the Garvey-Kelson mass relations (GKs) and nuclear mass models. The root-mean-squared deviations of predicted masses respectively for even-A and odd-A nuclei by using two combinatorial GKs suggest a large odd-even staggering of δ V1 n -1 p between even-odd and odd-even nuclei, while the odd-even difference of δ V1 n -1 p between even-even and odd-odd nuclei is much smaller. The contribution of the odd-even staggering of δ V1 n -1 p between even-A and odd-A nuclei in deviations of theoretical δ V1 n -1 p values of the Duflo-Zuker model and the improved Weizs a ̈cker -Skyrme model are well represented by an isospin-dependent term. The consideration of this odd-even staggering improves our description of binding energies and one-neutron separation energies in both the Duflo-Zuker model and the improved Weizs a ̈cker -Skyrme model.

  8. Use of allele scores as instrumental variables for Mendelian randomization

    PubMed Central

    Burgess, Stephen; Thompson, Simon G

    2013-01-01

    Background An allele score is a single variable summarizing multiple genetic variants associated with a risk factor. It is calculated as the total number of risk factor-increasing alleles for an individual (unweighted score), or the sum of weights for each allele corresponding to estimated genetic effect sizes (weighted score). An allele score can be used in a Mendelian randomization analysis to estimate the causal effect of the risk factor on an outcome. Methods Data were simulated to investigate the use of allele scores in Mendelian randomization where conventional instrumental variable techniques using multiple genetic variants demonstrate ‘weak instrument’ bias. The robustness of estimates using the allele score to misspecification (for example non-linearity, effect modification) and to violations of the instrumental variable assumptions was assessed. Results Causal estimates using a correctly specified allele score were unbiased with appropriate coverage levels. The estimates were generally robust to misspecification of the allele score, but not to instrumental variable violations, even if the majority of variants in the allele score were valid instruments. Using a weighted rather than an unweighted allele score increased power, but the increase was small when genetic variants had similar effect sizes. Naive use of the data under analysis to choose which variants to include in an allele score, or for deriving weights, resulted in substantial biases. Conclusions Allele scores enable valid causal estimates with large numbers of genetic variants. The stringency of criteria for genetic variants in Mendelian randomization should be maintained for all variants in an allele score. PMID:24062299

  9. Characterization of long-lived isomers in the odd-odd heavy actinide 254Md

    NASA Astrophysics Data System (ADS)

    Sood, P. C.; Gowrishankar, R.

    2017-02-01

    Bandhead energies of all the physically admissible low-lying two-quasiparticle configuration states in the doubly-odd heavy actinide Md 153 101 254 are evaluated using the well-tested two-quasiparticle rotor model with explicit inclusion of the residual proton-neutron interaction. A critical examination of these results, aimed at characterization of the long-lived (t1 /2=10 min and 28 min; %ɛ ≤100 ) isomer pair, conclusively rules out a high-spin (J ≥5 ) assignment for either of the isomers. Our analysis leads to JπK =1-0 {p :1 /2-[521 ] ⊗n :1 /2+) [620 ] } and 3-3 {p :7 /2-[514 ] ⊗n :1 /2+[620 ] } assignments, respectively, to these isomers and designates the 10-min isomer as its ground state. Our study reveals a "landmark" position for 254Md in the decay path of super heavy elements. The as-yet unobserved electron capture decay branches from each of the two 254Md isomers to 254Fm levels are specified.

  10. Preconception maternal polychlorinated biphenyl concentrations and the secondary sex ratio

    SciTech Connect

    Taylor, Kira C.; Jackson, Leila W.; Lynch, Courtney D.; Kostyniak, Paul J.; Buck Louis, Germaine M. . E-mail: louisg@mail.nih.gov

    2007-01-15

    The secondary sex ratio is the ratio of male to female live births and historically has ranged from 102 to 106 males to 100 females. Temporal declines have been reported in many countries prompting authors to hypothesize an environmental etiology. Blood specimens were obtained from 99 women aged 24-34 prior to attempting pregnancy and quantified for 76 polychlorinated biphenyl (PCB) congeners using dual column gas chromatography with electron capture detection. Women were prospectively followed until pregnancy or 12 cycles of trying. The odds of a male birth for three PCB groupings (total, estrogenic, anti-estrogenic) controlling for maternal characteristics were estimated using logistic regression. Among the 50 women with live births and PCB data, 26 female and 24 male infants were born (ratio 0.92). After adjusting for age and body mass index, odds of a male birth were elevated among women in the second (OR=1.29) and third (OR=1.48) tertiles of estrogenic PCBs; odds (OR=0.70) were reduced among women in the highest tertile of anti-estrogenic PCBs. All confidence intervals included one. The direction of the odds ratios in this preliminary study varied by PCB groupings, supporting the need to study specific PCB patterns when assessing environmental influences on the secondary sex ratio.

  11. Identification of a novel HLA-A allele, A*3120.

    PubMed

    Chang, Y; Pascual, C J; Alonzo, P; Chamizo, A

    2009-03-01

    A novel human leukocyte antigen (HLA)-A allele, HLA-A*3120, was first identified in a National Marrow Donor Program (NMDP) donor. The A*3120 allele resulted from a single nucleotide substitution (T to G) at codon 92 of exon 3 of A*310102. The substitution caused an amino acid change (serine to alanine). This novel allele was also seen in two other unrelated NMDP donors.

  12. Investigation of the correlation between odd oxygen and secondary organic aerosol in Mexico City and Houston

    NASA Astrophysics Data System (ADS)

    Wood, E. C.; Canagaratna, M. R.; Herndon, S. C.; Kroll, J. H.; Onasch, T. B.; Kolb, C. E.; Worsnop, D. R.; Knighton, W. B.; Seila, R.; Zavala, M.; Molina, L. T.; Decarlo, P. F.; Jimenez, J. L.; Weinheimer, A. J.; Knapp, D. J.; Jobson, B. T.; Stutz, J.; Kuster, W. C.; Williams, E. J.

    2010-02-01

    Many recent models underpredict secondary organic aerosol (SOA) particulate matter (PM) concentrations in polluted regions, indicating serious deficiencies in the models' chemical mechanisms and/or missing SOA precursors. Since tropospheric photochemical ozone production is much better understood, we investigate the correlation of odd-oxygen ([Ox]≡[O3]+[NO2]) and the oxygenated component of organic aerosol (OOA), which is interpreted as a surrogate for SOA. OOA and Ox measured in Mexico City in 2006 and Houston in 2000 were well correlated in air masses where both species were formed on similar timescales (less than 8 h) and not well correlated when their formation timescales or location differed greatly. When correlated, the ratio of these two species ranged from 30 μg m-3 ppm-1 (STP) in Houston during time periods affected by large petrochemical plant emissions to as high as 160 μg m-3 ppm-1 in Mexico City, where typical values were near 120 μg m-3 ppm-1. On several days in Mexico City, the [OOA]/[Ox] ratio decreased by a factor of ~2 between 08:00 and 13:00 LT. This decrease is only partially attributable to evaporation of the least oxidized and most volatile components of OOA; differences in the diurnal emission trends and timescales for photochemical processing of SOA precursors compared to ozone precursors also likely contribute to the observed decrease. The extent of OOA oxidation increased with photochemical aging. Calculations of the ratio of the SOA formation rate to the Ox production rate using ambient VOC measurements and traditional laboratory SOA yields are lower than the observed [OOA]/[Ox] ratios by factors of 5 to 15, consistent with several other models' underestimates of SOA. Calculations of this ratio using emission factors for organic compounds from gasoline and diesel exhaust do not reproduce the observed ratio. Although not succesful in reproducing the atmospheric observations presented, modeling P(SOA)/P(Ox) can serve as a useful test

  13. Investigation of the correlation between odd oxygen and secondary organic aerosol in Mexico City and Houston

    NASA Astrophysics Data System (ADS)

    Wood, E. C.; Canagaratna, M. R.; Herndon, S. C.; Onasch, T. B.; Kolb, C. E.; Worsnop, D. R.; Kroll, J. H.; Knighton, W. B.; Seila, R.; Zavala, M.; Molina, L. T.; Decarlo, P. F.; Jimenez, J. L.; Weinheimer, A. J.; Knapp, D. J.; Jobson, B. T.; Stutz, J.; Kuster, W. C.; Williams, E. J.

    2010-09-01

    Many recent models underpredict secondary organic aerosol (SOA) particulate matter (PM) concentrations in polluted regions, indicating serious deficiencies in the models' chemical mechanisms and/or missing SOA precursors. Since tropospheric photochemical ozone production is much better understood, we investigate the correlation of odd-oxygen ([Ox]≡[O3]+[NO2]) and the oxygenated component of organic aerosol (OOA), which is interpreted as a surrogate for SOA. OOA and Ox measured in Mexico City in 2006 and Houston in 2000 were well correlated in air masses where both species were formed on similar timescales (less than 8 h) and not well correlated when their formation timescales or location differed greatly. When correlated, the ratio of these two species ranged from 30 μg m-3/ppm (STP) in Houston during time periods affected by large petrochemical plant emissions to as high as 160 μg m-3/ppm in Mexico City, where typical values were near 120 μg m-3/ppm. On several days in Mexico City, the [OOA]/[Ox] ratio decreased by a factor of ~2 between 08:00 and 13:00 local time. This decrease is only partially attributable to evaporation of the least oxidized and most volatile components of OOA; differences in the diurnal emission trends and timescales for photochemical processing of SOA precursors compared to ozone precursors also likely contribute to the observed decrease. The extent of OOA oxidation increased with photochemical aging. Calculations of the ratio of the SOA formation rate to the Ox production rate using ambient VOC measurements and traditional laboratory SOA yields are lower than the observed [OOA]/[Ox] ratios by factors of 5 to 15, consistent with several other models' underestimates of SOA. Calculations of this ratio using emission factors for organic compounds from gasoline and diesel exhaust do not reproduce the observed ratio. Although not succesful in reproducing the atmospheric observations presented, modeling P(SOA)/P(Ox) can serve as a useful test

  14. Novel HLA-A and HLA-B alleles.

    PubMed

    Hurley, C K; Steiner, N; Kosman, C; Mitton, W; Koester, R; Bei, M; Bush, J; McCormack, J; Hahn, A; Henson, V; Hoyer, R; Wade, J A; Hartzman, R J; Ng, J

    1998-07-01

    Nine novel HLA-A and HLA-B alleles are described: A*2609, A*6803, A*6806, B*1539, B*1540, B*2712, B*4103, B*5109, and B*5603. Most appear to have arisen by gene conversion events. B*5603 appears to have arisen by a reciprocal recombination event joining exon 2 of a B*55/ *56 allele with exon 3 of a B*15 allele. Serologically, the antigen encoded by this allele types with broad B22- and Bw6-specific alloantisera. Also unique, the antigen encoded by B*2712 does not react with B27-specific alloantisera but does react with Bw6-specific alloantisera.

  15. Mutated tumor alleles are expressed according to their DNA frequency.

    PubMed

    Castle, John C; Loewer, Martin; Boegel, Sebastian; Tadmor, Arbel D; Boisguerin, Valesca; de Graaf, Jos; Paret, Claudia; Diken, Mustafa; Kreiter, Sebastian; Türeci, Özlem; Sahin, Ugur

    2014-04-22

    The transcription of tumor mutations from DNA into RNA has implications for biology, epigenetics and clinical practice. It is not clear if mutations are in general transcribed and, if so, at what proportion to the wild-type allele. Here, we examined the correlation between DNA mutation allele frequency and RNA mutation allele frequency. We sequenced the exome and transcriptome of tumor cell lines with large copy number variations, identified heterozygous single nucleotide mutations and absolute DNA copy number, and determined the corresponding DNA and RNA mutation allele fraction. We found that 99% of the DNA mutations in expressed genes are expressed as RNA. Moreover, we found a high correlation between the DNA and RNA mutation allele frequency. Exceptions are mutations that cause premature termination codons and therefore activate nonsense-mediated decay. Beyond this, we did not find evidence of any wide-scale mechanism, such as allele-specific epigenetic silencing, preferentially promoting mutated or wild-type alleles. In conclusion, our data strongly suggest that genes are equally transcribed from all alleles, mutated and wild-type, and thus transcribed in proportion to their DNA allele frequency.

  16. Comparison between subjects with long- and short-allele carriers in the BOLD signal within amygdala during emotional tasks

    NASA Astrophysics Data System (ADS)

    Hadi, Shamil; Siadat, Mohamad R.; Babajani-Feremi, Abbas

    2012-03-01

    Emotional tasks may result in a strong blood oxygen level-dependent (BOLD) signal in the amygdala in 5- HTTLRP short-allele. Reduced anterior cingulate cortex (ACC)-amygdala connectivity in short-allele provides a potential mechanistic account for the observed increase in amygdala activity. In our study, fearful and threatening facial expressions were presented to two groups of 12 subjects with long- and short-allele carriers. The BOLD signals of the left amygdala of each group were averaged to increase the signal-to-noise ratio. A Bayesian approach was used to estimate the model parameters to elucidate the underlying hemodynamic mechanism. Our results showed a positive BOLD signal in the left amygdala for short-allele individuals, and a negative BOLD signal in the same region for long-allele individuals. This is due to the fact that short-allele is associated with lower availability of serotonin transporter (5-HTT) and this leads to an increase of serotonin (5-HT) concentration in the cACC-amygdala synapse.

  17. Analyses of Allele-Specific Gene Expression in Highly Divergent Mouse Crosses Identifies Pervasive Allelic Imbalance

    PubMed Central

    Crowley, James J; Zhabotynsky, Vasyl; Sun, Wei; Huang, Shunping; Pakatci, Isa Kemal; Kim, Yunjung; Wang, Jeremy R; Morgan, Andrew P; Calaway, John D; Aylor, David L; Yun, Zaining; Bell, Timothy A; Buus, Ryan J; Calaway, Mark E; Didion, John P; Gooch, Terry J; Hansen, Stephanie D; Robinson, Nashiya N; Shaw, Ginger D; Spence, Jason S; Quackenbush, Corey R; Barrick, Cordelia J; Nonneman, Randal J.; Kim, Kyungsu; Xenakis, James; Xie, Yuying; Valdar, William; Lenarcic, Alan B; Wang, Wei; Welsh, Catherine E; Fu, Chen-Ping; Zhang, Zhaojun; Holt, James; Guo, Zhishan; Threadgill, David W; Tarantino, Lisa M; Miller, Darla R; Zou, Fei; McMillan, Leonard; Sullivan, Patrick F; de Villena, Fernando Pardo-Manuel

    2015-01-01

    Complex human traits are influenced by variation in regulatory DNA through mechanisms that are not fully understood. Since regulatory elements are conserved between humans and mice, a thorough annotation of cis regulatory variants in mice could aid in this process. Here we provide a detailed portrait of mouse gene expression across multiple tissues in a three-way diallel. Greater than 80% of mouse genes have cis regulatory variation. These effects influence complex traits and usually extend to the human ortholog. Further, we estimate that at least one in every thousand SNPs creates a cis regulatory effect. We also observe two types of parent-of-origin effects, including classical imprinting and a novel, global allelic imbalance in favor of the paternal allele. We conclude that, as with humans, pervasive regulatory variation influences complex genetic traits in mice and provide a new resource toward understanding the genetic control of transcription in mammals. PMID:25730764

  18. Pure odd-order oscillators with constant excitation

    NASA Astrophysics Data System (ADS)

    Cveticanin, L.

    2011-02-01

    In this paper the excited vibrations of a truly nonlinear oscillator are analyzed. The excitation is assumed to be constant and the nonlinearity is pure (without a linear term). The mathematical model is a second-order nonhomogeneous differential equation with strong nonlinear term. Using the first integral, the exact value of period of vibration i.e., angular frequency of oscillator described with a pure nonlinear differential equation with constant excitation is analytically obtained. The closed form solution has the form of gamma function. The period of vibration depends on the value of excitation and of the order and coefficient of the nonlinear term. For the case of pure odd-order-oscillators the approximate solution of differential equation is obtained in the form of trigonometric function. The solution is based on the exact value of period of vibration. For the case when additional small perturbation of the pure oscillator acts, the so called 'Cveticanin's averaging method' for a truly nonlinear oscillator is applied. Two special cases are considered: one, when the additional term is a function of distance, and the second, when damping acts. To prove the correctness of the method the obtained results are compared with those for the linear oscillator. Example of pure cubic oscillator with constant excitation and linear damping is widely discussed. Comparing the analytically obtained results with exact numerical ones it is concluded that they are in a good agreement. The investigations reported in the paper are of special interest for those who are dealing with the problem of vibration reduction in the oscillator with constant excitation and pure nonlinear restoring force the examples of which can be found in various scientific and engineering systems. For example, such mechanical systems are seats in vehicles, supports for machines, cutting machines with periodical motion of the cutting tools, presses, etc. The examples can be find in electronics

  19. Nuclear Shell Structure and Beta Decay I. Odd A Nuclei II. Even A Nuclei

    DOE R&D Accomplishments Database

    Mayer, M.G.; Moszkowski, S.A.; Nordheim, L.W.

    1951-05-01

    In Part I a systematics is given of all transitions for odd A nuclei for which sufficiently reliable data are available. The allowed or forbidden characters of the transitions are correlated with the positions of the initial and final odd nucleon groups in the nuclear shell scheme. The nuclear shells show definite characteristics with respect to parity of the ground states. The latter is the same as the one obtained from known spins and magnetic moments in a one-particle interpretation. In Part II a systematics of the beta transitions of even-A nuclei is given. An interpretation of the character of the transitions in terms of nuclear shell structure is achieved on the hypothesis that the odd nucleon groups have the same structure as in odd-A nuclei, together with a simple coupling rule between the neutron and proton groups in odd-odd nuclei.

  20. Experimental identification of intruder bandheads in odd-mass {sup 187-193}Pb

    SciTech Connect

    Andreyev, A. N.; Huyse, M.; Van de Vel, K.; Van Duppen, P.; Cocks, J. F. C.; Dorvaux, O.; Greenlees, P.; Jones, P.; Julin, R.; Juutinen, S.; Helariutta, K.; Kettunen, H.; Kuusiniemi, P.; Leino, M.; Muikku, M.; Trzaska, W. H.; Eskola, K.; Wyss, R.

    1999-11-16

    Fine-structure {alpha}-decays of the odd mass {sup 191-197}Po identifying proton based intruder states in the daughter lead nuclei have been observed, leading to a systematics of intruder states in odd mass lead isotopes from {sup 197}Pb down to {sup 187}Pb. The interpretation of these states involves the coupling of the i{sub 13/2} or p{sub 3/2} odd neutron to the oblate deformed even lead core.

  1. Experimental Identification of Intruder Bandheads in Odd-Mass {sup 187-193}Pb

    SciTech Connect

    A.N. Andreyev; J.F.C. Cocks; O. Dorvaux; K. Eskola; P. Greenlees; P. Jones; R. Julin; S. Juutinen; K. Helariutta; M. Huyse; H. Kettunen; P. Kuusiniemi; M. Leino; M. Muikku; W.H. Trzaska; K. Van de Vel; P. Van Duppen; R. Wyss

    1999-12-31

    Fine-structure {alpha}-decays of the odd mass {sup 191-197}Po identifying proton based intruder states in the daughter lead nuclei have been observed, leading to a systematics of intruder states in odd mass lead isotopes from {sup 197}Pb down to {sup 187}Pb. The interpretation of these states involves the coupling of the i{sub 13/2} or p{sub 3/2} odd neutron to the oblate deformed even lead core.

  2. The odds of delivering one, two or three extremely low birth weight (< 1000 g) triplet infants: a study of 3288 sets.

    PubMed

    Blickstein, Isaac; Jacques, Debbie L; Keith, Louis G

    2002-01-01

    The odds of an individual triplet pregnancy to end with neonates weighing < 1000 g (extremely low birth weight [ELBW]) are unknown. We analyzed a nationwide perinatal database collected by Matria Healthcare, Inc. (Marietta, GA) to select from 3288 triplets those weighing 500-1000 g, delivered during the period 1988-2000 in the United States. We counted the number of sets with one, two, and three ELBW neonates and compared the incidence of ELBW infants between the subsets of nulliparas and multiparas. The odds of delivering at least one ELBW infant was significantly higher among nulliparas (1:8) than among multiparas (1:14), Odds Ratio (OR) 1.9, 95% Confidence Interval (CI) 1.9, 2.5. The odds of having at least two ELBW sibs in nulliparas (1:16) is twice higher than in multiparas (1:31), OR 2.0, 95% CI 1.3, 2.9. Nulliparas and multiparas had similar odds of delivering three ELBW infants (1:29 versus 1:40, OR 1.3, 95% CI 0.9, 2.1). Nulliparas are at significantly increased risk of delivering one or two ELBW triplets. This observation is no less than alarming and highlighted by the exceptionally high risk of major neurological deficits reported among ELBW infants.

  3. Combined Effects of GSTM1 Null Allele and APOL1 Renal Risk Alleles in CKD Progression in the African American Study of Kidney Disease and Hypertension Trial.

    PubMed

    Bodonyi-Kovacs, Gabor; Ma, Jennie Z; Chang, Jamison; Lipkowitz, Michael S; Kopp, Jeffrey B; Winkler, Cheryl Ann; Le, Thu H

    2016-10-01

    Apolipoprotein L-1 (APOL1) high-risk alleles and the glutathione-S-transferase-μ1 (GSTM1) null allele have been shown separately to associate with CKD progression in the African American Study of Kidney Disease and Hypertension (AASK) trial participants. Here, we determined combined effects of GSTM1 null and APOL1 high-risk alleles on clinical outcomes in 682 AASK participants who were classified into four groups by GSTM1 null or active genotype and APOL1 high- or low-risk genotype. We assessed survival differences among these groups by log-rank test and Cox regression adjusted for important clinical variables for time to GFR event (change in GFR of 50% or 25-ml/min per 1.73 m(2) decline), incident ESRD, death, or composite outcomes. The groups differed significantly in event-free survival for incident ESRD and composite outcomes (P≤0.001 by log-rank test). Compared with the reference GSTM1 active/APOL1 low-risk group, other groups had these hazard ratios for the composite outcome of incident ESRD and change in GFR: GSTM1 active/APOL1 high-risk hazard ratio, 2.13; 95% confidence interval, 0.76 to 5.90 (P=0.15); GSTM1 null/APOL1 low-risk hazard ratio, 2.05; 95% confidence interval, 1.08 to 3.88 (P=0.03); and GSTM1 null/APOL1 high-risk hazard ratio, 3.0; 95% confidence interval, 1.51 to 5.96 (P=0.002). In conclusion, GSTM1 null and APOL1 high-risk alleles deleteriously affect CKD progression among blacks with hypertension, and subjects with both GSTM1 null and APOL1 high-risk genotypes had highest risk of adverse renal outcomes. Larger cohorts are needed to fully explore interactions of GSTM1 and APOL1 genotypes in other subgroups.

  4. Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots

    PubMed Central

    Baker, Christopher L.; Petkova, Pavlina; Walker, Michael; Flachs, Petr; Mihola, Ondrej; Trachtulec, Zdenek; Petkov, Petko M.; Paigen, Kenneth

    2015-01-01

    Genetic recombination during meiosis functions to increase genetic diversity, promotes elimination of deleterious alleles, and helps assure proper segregation of chromatids. Mammalian recombination events are concentrated at specialized sites, termed hotspots, whose locations are determined by PRDM9, a zinc finger DNA-binding histone methyltransferase. Prdm9 is highly polymorphic with most alleles activating their own set of hotspots. In populations exhibiting high frequencies of heterozygosity, questions remain about the influences different alleles have in heterozygous individuals where the two variant forms of PRDM9 typically do not activate equivalent populations of hotspots. We now find that, in addition to activating its own hotspots, the presence of one Prdm9 allele can modify the activity of hotspots activated by the other allele. PRDM9 function is also dosage sensitive; Prdm9 +/- heterozygous null mice have reduced numbers and less active hotspots and increased numbers of aberrant germ cells. In mice carrying two Prdm9 alleles, there is allelic competition; the stronger Prdm9 allele can partially or entirely suppress chromatin modification and recombination at hotspots of the weaker allele. In cell cultures, PRDM9 protein variants form functional heteromeric complexes which can bind hotspots sequences. When a heteromeric complex binds at a hotspot of one PRDM9 variant, the other PRDM9 variant, which would otherwise not bind, can still methylate hotspot nucleosomes. We propose that in heterozygous individuals the underlying molecular mechanism of allelic suppression results from formation of PRDM9 heteromers, where the DNA binding activity of one protein variant dominantly directs recombination initiation towards its own hotspots, effectively titrating down recombination by the other protein variant. In natural populations with many heterozygous individuals, allelic competition will influence the recombination landscape. PMID:26368021

  5. Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots.

    PubMed

    Baker, Christopher L; Petkova, Pavlina; Walker, Michael; Flachs, Petr; Mihola, Ondrej; Trachtulec, Zdenek; Petkov, Petko M; Paigen, Kenneth

    2015-09-01

    Genetic recombination during meiosis functions to increase genetic diversity, promotes elimination of deleterious alleles, and helps assure proper segregation of chromatids. Mammalian recombination events are concentrated at specialized sites, termed hotspots, whose locations are determined by PRDM9, a zinc finger DNA-binding histone methyltransferase. Prdm9 is highly polymorphic with most alleles activating their own set of hotspots. In populations exhibiting high frequencies of heterozygosity, questions remain about the influences different alleles have in heterozygous individuals where the two variant forms of PRDM9 typically do not activate equivalent populations of hotspots. We now find that, in addition to activating its own hotspots, the presence of one Prdm9 allele can modify the activity of hotspots activated by the other allele. PRDM9 function is also dosage sensitive; Prdm9+/- heterozygous null mice have reduced numbers and less active hotspots and increased numbers of aberrant germ cells. In mice carrying two Prdm9 alleles, there is allelic competition; the stronger Prdm9 allele can partially or entirely suppress chromatin modification and recombination at hotspots of the weaker allele. In cell cultures, PRDM9 protein variants form functional heteromeric complexes which can bind hotspots sequences. When a heteromeric complex binds at a hotspot of one PRDM9 variant, the other PRDM9 variant, which would otherwise not bind, can still methylate hotspot nucleosomes. We propose that in heterozygous individuals the underlying molecular mechanism of allelic suppression results from formation of PRDM9 heteromers, where the DNA binding activity of one protein variant dominantly directs recombination initiation towards its own hotspots, effectively titrating down recombination by the other protein variant. In natural populations with many heterozygous individuals, allelic competition will influence the recombination landscape.

  6. Even the Odd Numbers Help: Failure Modes of SAM-Based Tunnel Junctions Probed via Odd-Even Effects Revealed in Synchrotrons and Supercomputers.

    PubMed

    Thompson, Damien; Nijhuis, Christian A

    2016-10-18

    This Account describes a body of research in atomic level design, synthesis, physicochemical characterization, and macroscopic electrical testing of molecular devices made from ferrocene-functionalized alkanethiol molecules, which are molecular diodes, with the aim to identify, and resolve, the failure modes that cause leakage currents. The mismatch in size between the ferrocene headgroup and alkane rod makes waxlike highly dynamic self-assembled monolayers (SAMs) on coinage metals that show remarkable atomic-scale sensitivity in their electrical properties. Our results make clear that molecular tunnel junction devices provide an excellent testbed to probe the electronic and supramolecular structures of SAMs on inorganic substrates. Contacting these SAMs to a eutectic "EGaIn" alloy top-electrode, we designed highly stable long-lived molecular switches of the form electrode-SAM-electrode with robust rectification ratios of up to 3 orders of magnitude. The graphic that accompanies this conspectus displays a computed SAM packing structure, illustrating the lollipop shape of the molecules that gives dynamic SAM supramolecular structures and also the molecule-electrode van der Waals (vdW) contacts that must be controlled to form good SAM-based devices. In this Account, we first trace the evolution of SAM-based electronic devices and rationalize their operation using energy level diagrams. We describe the measurement of device properties using near edge X-ray absorption fine structure spectroscopy, cyclic voltammetry, and X-ray photoelectron spectroscopy complemented by molecular dynamics and electronic structure calculations together with large numbers of electrical measurements. We discuss how data obtained from these combined experimental/simulation codesign studies demonstrate control over the supramolecular and electronic structure of the devices, tuning odd-even effects to optimize inherent packing tendencies of the molecules in order to minimize leakage currents

  7. Universal one-dimensional atomic gases near odd-wave resonance

    NASA Astrophysics Data System (ADS)

    Cui, Xiaoling

    2016-10-01

    We show the renormalization of the contact interaction for odd-wave scattering in one-dimension (1D). Based on the renormalized interaction, we exactly solve the two-body problem in a harmonic trap and further explore the universal properties of spin-polarized fermions near odd-wave resonance by using the operator-product-expansion method. It is found that the high-momentum distribution behaves as C /k2 , with C being the odd-wave contact. Various universal relations are derived. Our work suggests a universal system emergent in 1D with large odd-wave scattering length.

  8. Invasion, Coexistence, and Extinction Driven by Preemptive Competition and Sex Ratio

    NASA Astrophysics Data System (ADS)

    Molnar, Ferenc; Caraco, Thomas; Korniss, Gyorgy

    2012-02-01

    We investigate competitive invasion in a simple population dynamics model, where females can differ genetically in the sex ratio of their offspring, and males can differ in mortality. Analyzing of the mean-field dynamics, we obtain conditions for ecological stability of a given sex-ratio allele for any mortality rate parameters. We also found that stable coexistence of the two alleles is possible, but only males can differ; one female phenotype is present. Our results show that the success of invasion is determined by the female birth sex ratio. A lower female ratio never excludes a larger female sex ratio; in case of coexistence, the surviving female phenotype always has the greater female sex ratio. Finally, we identified an interesting invasion-to-extinction scenario: successful invasion followed by extinction occurs when the invader initially propagates with the resident allele, but after excluding the resident, cannot survive on its own.

  9. Allele-Selective Transcriptome Recruitment to Polysomes Primed for Translation: Protein-Coding and Noncoding RNAs, and RNA Isoforms.

    PubMed

    Mascarenhas, Roshan; Pietrzak, Maciej; Smith, Ryan M; Webb, Amy; Wang, Danxin; Papp, Audrey C; Pinsonneault, Julia K; Seweryn, Michal; Rempala, Grzegorz; Sadee, Wolfgang

    2015-01-01

    mRNA translation into proteins is highly regulated, but the role of mRNA isoforms, noncoding RNAs (ncRNAs), and genetic variants remains poorly understood. mRNA levels on polysomes have been shown to correlate well with expressed protein levels, pointing to polysomal loading as a critical factor. To study regulation and genetic factors of protein translation we measured levels and allelic ratios of mRNAs and ncRNAs (including microRNAs) in lymphoblast cell lines (LCL) and in polysomal fractions. We first used targeted assays to measure polysomal loading of mRNA alleles, confirming reported genetic effects on translation of OPRM1 and NAT1, and detecting no effect of rs1045642 (3435C>T) in ABCB1 (MDR1) on polysomal loading while supporting previous results showing increased mRNA turnover of the 3435T allele. Use of high-throughput sequencing of complete transcript profiles (RNA-Seq) in three LCLs revealed significant differences in polysomal loading of individual RNA classes and isoforms. Correlated polysomal distribution between protein-coding and non-coding RNAs suggests interactions between them. Allele-selective polysome recruitment revealed strong genetic influence for multiple RNAs, attributable either to differential expression of RNA isoforms or to differential loading onto polysomes, the latter defining a direct genetic effect on translation. Genes identified by different allelic RNA ratios between cytosol and polysomes were enriched with published expression quantitative trait loci (eQTLs) affecting RNA functions, and associations with clinical phenotypes. Polysomal RNA-Seq combined with allelic ratio analysis provides a powerful approach to study polysomal RNA recruitment and regulatory variants affecting protein translation.

  10. Allele-Selective Transcriptome Recruitment to Polysomes Primed for Translation: Protein-Coding and Noncoding RNAs, and RNA Isoforms

    PubMed Central

    Smith, Ryan M.; Webb, Amy; Wang, Danxin; Papp, Audrey C.; Pinsonneault, Julia K.; Seweryn, Michal; Rempala, Grzegorz; Sadee, Wolfgang

    2015-01-01

    mRNA translation into proteins is highly regulated, but the role of mRNA isoforms, noncoding RNAs (ncRNAs), and genetic variants remains poorly understood. mRNA levels on polysomes have been shown to correlate well with expressed protein levels, pointing to polysomal loading as a critical factor. To study regulation and genetic factors of protein translation we measured levels and allelic ratios of mRNAs and ncRNAs (including microRNAs) in lymphoblast cell lines (LCL) and in polysomal fractions. We first used targeted assays to measure polysomal loading of mRNA alleles, confirming reported genetic effects on translation of OPRM1 and NAT1, and detecting no effect of rs1045642 (3435C>T) in ABCB1 (MDR1) on polysomal loading while supporting previous results showing increased mRNA turnover of the 3435T allele. Use of high-throughput sequencing of complete transcript profiles (RNA-Seq) in three LCLs revealed significant differences in polysomal loading of individual RNA classes and isoforms. Correlated polysomal distribution between protein-coding and non-coding RNAs suggests interactions between them. Allele-selective polysome recruitment revealed strong genetic influence for multiple RNAs, attributable either to differential expression of RNA isoforms or to differential loading onto polysomes, the latter defining a direct genetic effect on translation. Genes identified by different allelic RNA ratios between cytosol and polysomes were enriched with published expression quantitative trait loci (eQTLs) affecting RNA functions, and associations with clinical phenotypes. Polysomal RNA-Seq combined with allelic ratio analysis provides a powerful approach to study polysomal RNA recruitment and regulatory variants affecting protein translation. PMID:26331722

  11. Observations Suggesting Allelism of the Achondroplasia and Hypochondroplasia Genes

    PubMed Central

    McKusick, Victor A.; Kelly, Thaddeus E.; Dorst, John P.

    1973-01-01

    It is argued that there are at least two alleles at the achondroplasia locus: one responsible for classic achondroplasia and one responsible for hypochondroplasia. Homozygosity for the achondroplasia gene produces a lethal skeletal dysplasia; homozygosity for hypochondroplasia has not been described. We report here a child considered to be a genetic compound for the achondroplasia and hypochondroplasia alleles. Images PMID:4697848

  12. Selection of Heterodera glycines chorismate mutase-1 alleles on nematode-resistant soybean.

    PubMed

    Lambert, Kris N; Bekal, Sadia; Domier, Leslie L; Niblack, Terry L; Noel, Gregory R; Smyth, Charles A

    2005-06-01

    The soybean cyst nematode Heterodera glycines is the most destructive pathogen of soybean in the Unites States. Diversity in the parasitic ability of the nematode allows it to reproduce on nematode-resistant soybean. H. glycines chorismate mutase-1 (Hg-CM-1) is a nematode enzyme with the potential to suppress host plant defense compounds; therefore, it has the potential to enhance the parasitic ability of nematodes expressing the gene. Hg-cm-1 is a member of a gene family where two alleles, Hg-cm-1A and Hg-cm-1B, have been identified. Analysis of the Hg-cm-1 gene copy number revealed that there are multiple copies of Hg-cm-1 alleles in the H. glycines genome. H. glycines inbred lines were crossed to ultimately generate three F2 populations of second-stage juveniles (J2s) segregating for Hg-cm-1A and Hg-cm-1B. Segregation of Hg-cm-1A and 1B approximated a 1:2:1 ratio, which suggested that Hg-cm-1 is organized in a cluster of genes that segregate roughly as a single locus. The F2 H. glycines J2 populations were used to infect nematode-resistant (Hartwig, PI88788, and PI90763) and susceptible (Lee 74) soybean plants. H. glycines grown on Hartwig, Lee 74, and PI90763 showed allelic frequencies similar to Hg-cm-1A/B, but nematodes grown on PI88788 contained predominately Hg-cm-1A allele as a result of a statistically significant drop of Hg-cm-1B in the population. This result suggests that specific Hg-cm-1 alleles, or a closely linked gene, may aid H. glycines in adapting to particular soybean hosts.

  13. Assortative mating can impede or facilitate fixation of underdominant alleles.

    PubMed

    Newberry, Mitchell G; McCandlish, David M; Plotkin, Joshua B

    2016-12-01

    Underdominant mutations have fixed between divergent species, yet classical models suggest that rare underdominant alleles are purged quickly except in small or subdivided populations. We predict that underdominant alleles that also influence mate choice, such as those affecting coloration patterns visible to mates and predators alike, can fix more readily. We analyze a mechanistic model of positive assortative mating in which individuals have n chances to sample compatible mates. This one-parameter model naturally spans random mating (n=1) and complete assortment (n→∞), yet it produces sexual selection whose strength depends non-monotonically on n. This sexual selection interacts with viability selection to either inhibit or facilitate fixation. As mating opportunities increase, underdominant alleles fix as frequently as neutral mutations, even though sexual selection and underdominance independently each suppress rare alleles. This mechanism allows underdominant alleles to fix in large populations and illustrates how life history can affect evolutionary change.

  14. Estimating Relatedness in the Presence of Null Alleles.

    PubMed

    Huang, Kang; Ritland, Kermit; Dunn, Derek W; Qi, Xiaoguang; Guo, Songtao; Li, Baoguo

    2016-01-01

    Studies of genetics and ecology often require estimates of relatedness coefficients based on genetic marker data. However, with the presence of null alleles, an observed genotype can represent one of several possible true genotypes. This results in biased estimates of relatedness. As the numbers of marker loci are often limited, loci with null alleles cannot be abandoned without substantial loss of statistical power. Here, we show how loci with null alleles can be incorporated into six estimators of relatedness (two novel). We evaluate the performance of various estimators before and after correction for null alleles. If the frequency of a null allele is <0.1, some estimators can be used directly without adjustment; if it is >0.5, the potency of estimation is too low and such a locus should be excluded. We make available a software package entitled PolyRelatedness v1.6, which enables researchers to optimize these estimators to best fit a particular data set.

  15. A gene feature enumeration approach for describing HLA allele polymorphism.

    PubMed

    Mack, Steven J

    2015-12-01

    HLA genotyping via next generation sequencing (NGS) poses challenges for the use of HLA allele names to analyze and discuss sequence polymorphism. NGS will identify many new synonymous and non-coding HLA sequence variants. Allele names identify the types of nucleotide polymorphism that define an allele (non-synonymous, synonymous and non-coding changes), but do not describe how polymorphism is distributed among the individual features (the flanking untranslated regions, exons and introns) of a gene. Further, HLA alleles cannot be named in the absence of antigen-recognition domain (ARD) encoding exons. Here, a system for describing HLA polymorphism in terms of HLA gene features (GFs) is proposed. This system enumerates the unique nucleotide sequences for each GF in an HLA gene, and records these in a GF enumeration notation that allows both more granular dissection of allele-level HLA polymorphism and the discussion and analysis of GFs in the absence of ARD-encoding exon sequences.

  16. Assignment of single particle configurations in odd-A nuclei near A~100 with angular correlation measurements

    NASA Astrophysics Data System (ADS)

    Ramayya, A. V.; Hamilton, J. H.; Hwang, J. K.; Liu, S. H.; Daniel, A. V.; Goodin, C.; Luo, Y. X.; Rasmussen, J. O.; Stone, N. J.; Zhu, S. J.; Li, K.

    2011-01-01

    The multipole mixing ratios of ΔI = 1 transitions between levels in rotational bands built on single-particle states in odd neutron nuclei are dependent on the configurations of the states. In particular, the mixing ratio can be used to distinguish between several possible single-particle configurations if interpreted with the particle plus axial-rotor model (PRM). This work features the first determination of the ground-state configurations of 109,111Ru. The single-particle structures of the ground states of 101Zr and 103,105,107Mo as well as excited states in 103,107Mo are also investigated, with a new result found in 107Mo.

  17. Nuclear Data Evaluation for Mass Chain A=217:Odd-Proton Nuclei.

    PubMed

    Nafee, Sherif S; Shaheen, Salem A; Al-Ramady, Amir M

    2016-01-01

    Thallium (81(217)Tl, Bismuth (83(217)Bi), Astatine (85(217)At), Francium (87(217)Fr), Actinium (89(217)Ac) and Protactinium (91(217)Pa) are of odd-proton numbers among the mass chain A = 217. In the present work, the half-lives and gamma transitions for the six nuclei have been studied and adopted based on the recently published interactions or unevaluated nuclear data sets XUNDL. The Q (α) has been updated based on the recent published work of the Atomic Mass Evaluation AME2012 as well. Moreover, the total conversion electrons as well as the K-Shell to L-Shell, L-Shell to M-Shell and L-Shell to N-Shell Conversion Electron Ratios have been calculated using BrIcc code v2.3. An updated skeleton decay scheme for each of the above nuclei has been presented here. The decay hindrance factors (HF) calculated using the ALPHAD program, which is available from Brookhaven National Laboratory's website, have been calculated for the α- decay data sets for (221)Fr-, (221)Ac- and (221)Pa-α-decays.

  18. Nuclear Data Evaluation for Mass Chain A=217:Odd-Proton Nuclei

    PubMed Central

    Nafee, Sherif S.; Shaheen, Salem A.; Al-Ramady, Amir M.

    2016-01-01

    Thallium (Tl81217), Bismuth (Bi83217), Astatine (At85217), Francium (Fr87217), Actinium (Ac89217) and Protactinium (Pa91217) are of odd-proton numbers among the mass chain A = 217. In the present work, the half-lives and gamma transitions for the six nuclei have been studied and adopted based on the recently published interactions or unevaluated nuclear data sets XUNDL. The Q (α) has been updated based on the recent published work of the Atomic Mass Evaluation AME2012 as well. Moreover, the total conversion electrons as well as the K-Shell to L-Shell, L-Shell to M-Shell and L-Shell to N-Shell Conversion Electron Ratios have been calculated using BrIcc code v2.3. An updated skeleton decay scheme for each of the above nuclei has been presented here. The decay hindrance factors (HF) calculated using the ALPHAD program, which is available from Brookhaven National Laboratory’s website, have been calculated for the α- decay data sets for 221Fr-, 221Ac- and 221Pa- α-decays. PMID:26761207

  19. Frequency of FCGR3B Alleles in Thai Blood Donors

    PubMed Central

    Kaset, Chollanot; Leetrakool, Nipapan; Intharanut, Kamphon

    2013-01-01

    Background Human neutrophil antigens (HNAs) are involved in autoimmune and alloimmune neutropenia and transfusion-related acute lung injury. The HNA-1 system is important in immunogenetics, and allele frequencies have been described in different populations. This study investigated the frequency of FCGR3B alleles encoding HNA-1a, HNA-1b, and HNA-1c among Thai blood donors and compared these frequencies with those previously reported for other populations. Methods Eight hundred DNA samples obtained from unrelated healthy blood donors at the National Blood Centre, Thai Red Cross Society, Bangkok, and the Blood Bank, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand, were included. Samples were simultaneously typed for each FCGR3B allele using an in-house polymerase chain reaction with sequence-specific primer (PCR-SSP) technique. Results The frequencies of FCGR3B*1, FCGR3B*2, and FCGR3B*3 alleles in central Thai blood donors were 0.548, 0.452, and 0.004, respectively; only FCGR3B*1 and FCGR3B*2 alleles were found in northern Thai blood donors (0.68 and 0.32, respectively). Compared with other Asian populations, central Thais had higher frequencies of the FCGR3B*2 allele (P<0.001), while the frequencies of the FCGR3B*1 and FCGR3B*2 alleles in northern Thais were similar to those previously reported in Taiwanese and Japanese populations. In contrast, the frequencies of the FCGR3B*1 and FCGR3B*2 alleles in the northern Thai population were statistically different from those observed in central Thai, Korean, German, and Turkish populations. Conclusions FCGR3B allele frequencies were significantly different between central and northern Thai blood donors. Our in-house PCR-SSP method is a simple, cost-effective, and convenient method for FCGR3B allele detection. PMID:24205492

  20. Microsatellite null alleles and estimation of population differentiation.

    PubMed

    Chapuis, Marie-Pierre; Estoup, Arnaud

    2007-03-01

    Microsatellite null alleles are commonly encountered in population genetics studies, yet little is known about their impact on the estimation of population differentiation. Computer simulations based on the coalescent were used to investigate the evolutionary dynamics of null alleles, their impact on F(ST) and genetic distances, and the efficiency of estimators of null allele frequency. Further, we explored how the existing method for correcting genotype data for null alleles performed in estimating F(ST) and genetic distances, and we compared this method with a new method proposed here (for F(ST) only). Null alleles were likely to be encountered in populations with a large effective size, with an unusually high mutation rate in the flanking regions, and that have diverged from the population from which the cloned allele state was drawn and the primers designed. When populations were significantly differentiated, F(ST) and genetic distances were overestimated in the presence of null alleles. Frequency of null alleles was estimated precisely with the algorithm presented in Dempster et al. (1977). The conventional method for correcting genotype data for null alleles did not provide an accurate estimate of F(ST) and genetic distances. However, the use of the genetic distance of Cavalli-Sforza and Edwards (1967) corrected by the conventional method gave better estimates than those obtained without correction. F(ST) estimation from corrected genotype frequencies performed well when restricted to visible allele sizes. Both the proposed method and the traditional correction method have been implemented in a program that is available free of charge at http://www.montpellier.inra.fr/URLB/. We used 2 published microsatellite data sets based on original and redesigned pairs of primers to empirically confirm our simulation results.

  1. Allele-Specific Reduction of the Mutant Huntingtin Allele Using Transcription Activator-Like Effectors in Human Huntington's Disease Fibroblasts.

    PubMed

    Fink, Kyle D; Deng, Peter; Gutierrez, Josh; Anderson, Joseph S; Torrest, Audrey; Komarla, Anvita; Kalomoiris, Stefanos; Cary, Whitney; Anderson, Johnathon D; Gruenloh, William; Duffy, Alexandra; Tempkin, Teresa; Annett, Geralyn; Wheelock, Vicki; Segal, David J; Nolta, Jan A

    2016-01-01

    Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder caused by an abnormal expansion of CAG repeats. Although pathogenesis has been attributed to this polyglutamine expansion, the underlying mechanisms through which the huntingtin protein functions have yet to be elucidated. It has been suggested that postnatal reduction of mutant huntingtin through protein interference or conditional gene knockout could prove to be an effective therapy for patients suffering from HD. For allele-specific targeting, transcription activator-like effectors (TALE) were designed to target single-nucleotide polymorphisms (SNP) in the mutant allele and packaged into a vector backbone containing KRAB to promote transcriptional repression of the disease-associated allele. Additional TALEs were packaged into a vector backbone containing heterodimeric FokI and were designed to be used as nucleases (TALEN) to cause a CAG-collapse in the mutant allele. Human HD fibroblasts were treated with each TALE-SNP or TALEN. Allele-expression was measured using a SNP-genotyping assay and mutant protein aggregation was quantified with Western blots for anti-ubiquitin. The TALE-SNP and TALEN significantly reduced mutant allele expression (p < 0.05) when compared to control transfections while not affecting expression of the nondisease allele. This study demonstrates the potential of allele-specific gene modification using TALE proteins, and provides a foundation for targeted treatment for individuals suffering from Huntington's or other genetically linked diseases.

  2. Allele-specific H3K79 Di- versus trimethylation distinguishes opposite parental alleles at imprinted regions.

    PubMed

    Singh, Purnima; Han, Li; Rivas, Guillermo E; Lee, Dong-Hoon; Nicholson, Thomas B; Larson, Garrett P; Chen, Taiping; Szabó, Piroska E

    2010-06-01

    Imprinted gene expression corresponds to parental allele-specific DNA CpG methylation and chromatin composition. Histone tail covalent modifications have been extensively studied, but it is not known whether modifications in the histone globular domains can also discriminate between the parental alleles. Using multiplex chromatin immunoprecipitation-single nucleotide primer extension (ChIP-SNuPE) assays, we measured the allele-specific enrichment of H3K79 methylation and H4K91 acetylation along the H19/Igf2 imprinted domain. Whereas H3K79me1, H3K79me2, and H4K91ac displayed a paternal-specific enrichment at the paternally expressed Igf2 locus, H3K79me3 was paternally biased at the maternally expressed H19 locus, including the paternally methylated imprinting control region (ICR). We found that these allele-specific differences depended on CTCF binding in the maternal ICR allele. We analyzed an additional 11 differentially methylated regions (DMRs) and found that, in general, H3K79me3 was associated with the CpG-methylated alleles, whereas H3K79me1, H3K79me2, and H4K91ac enrichment was specific to the unmethylated alleles. Our data suggest that allele-specific differences in the globular histone domains may constitute a layer of the "histone code" at imprinted genes.

  3. Into the Cuckoo's Nest: "Silver Linings Playbook" and Movies about Odd People

    ERIC Educational Resources Information Center

    Beck, Bernard

    2013-01-01

    Odd people have always been identified and often treated differently in human societies. In modern times, they have been described as being afflicted with a psychological condition to be treated by specialists and assigned to a "crazy" category by general society. Movies about such odd people have a long history. A recent movie,…

  4. Investigation of Cool and Hot Executive Function in ODD/CD Independently of ADHD

    ERIC Educational Resources Information Center

    Hobson, Christopher W.; Scott, Stephen; Rubia, Katya

    2011-01-01

    Background: Children with oppositional defiant disorder/conduct disorder (ODD/CD) have shown deficits in "cool" abstract-cognitive, and "hot" reward-related executive function (EF) tasks. However, it is currently unclear to what extent ODD/CD is associated with neuropsychological deficits, independently of attention deficit hyperactivity disorder…

  5. ODD and ADHD Symptoms in Ukrainian Children: External Validators and Comorbidity

    ERIC Educational Resources Information Center

    Drabick, Deborah A. G.; Gadow, Kenneth D.; Carlson, Gabrielle A.; Bromet, Evelyn J.

    2004-01-01

    Objective: To examine potential external validators for oppositional defiant disorder (ODD) and attention-deficient/hyperactive disorder (ADHD) symptoms in a Ukrainian community-based sample of 600 children age 10 to 12 years old and evaluate the nature of co-occurring ODD and ADHD symptoms using mother- and teacher-defined groups. Method: In…

  6. Fitting Proportional Odds Models to Educational Data in Ordinal Logistic Regression Using Stata, SAS and SPSS

    ERIC Educational Resources Information Center

    Liu, Xing

    2008-01-01

    The proportional odds (PO) model, which is also called cumulative odds model (Agresti, 1996, 2002 ; Armstrong & Sloan, 1989; Long, 1997, Long & Freese, 2006; McCullagh, 1980; McCullagh & Nelder, 1989; Powers & Xie, 2000; O'Connell, 2006), is one of the most commonly used models for the analysis of ordinal categorical data and comes from the class…

  7. The Correlation of Secondary Organic Aerosol with Odd Oxygen in Mexico City

    EPA Science Inventory

    Data from a mountain location intercepting the Mexico City emission plume demonstrate a strong correlation between secondary organic aerosol and odd-oxygen (O3 + NO2). The measured oxygenated-organic aerosol correlates with odd-oxygen measurements with an a...

  8. Association of Anxiety and ODD/CD in Children with and without ADHD

    ERIC Educational Resources Information Center

    Humphreys, Kathryn L.; Aguirre, Vincent P.; Lee, Steve S.

    2012-01-01

    The goal of this study is to examine levels of oppositional defiant disorder (ODD) and conduct disorder (CD) in four groups of children: attention-deficit/hyperactivity disorder (ADHD) only, anxiety only, ADHD and anxiety, and controls (i.e., non-ADHD youth). Although children with ADHD exhibit more ODD and CD than non-ADHD youth, it is unknown if…

  9. Why Some Schools with Latino Children Beat the Odds...and Others Don't

    ERIC Educational Resources Information Center

    Waits, Mary Jo; Campbell, Heather E.; Gau, Rebecca; Jacobs, Ellen; Rex, Tom; Hess, Robert K.

    2006-01-01

    Throughout Arizona and the Southwest, the odds are against high achievement in schools with a mostly Latino, mostly poor student enrollment. Some schools, however, "beat the odds" and achieve consistently high results or show steady gains. Why do these schools succeed where others fail? Using the methodology of business guru Jim Collins…

  10. The Interplay among Preschool Child and Family Factors and the Development of ODD Symptoms

    ERIC Educational Resources Information Center

    Harvey, Elizabeth A.; Metcalfe, Lindsay A.

    2012-01-01

    The present study examined (a) the interactions between early behavior, early parenting, and early family adversity in predicting later oppositional defiant disorder (ODD) symptoms, and (b) the reciprocal relations between parent functioning and ODD symptoms across the preschool years. Participants were 258 three-year-old children (138 boys, 120…

  11. Clinically Referred ODD Children with or without CD and Healthy Controls: Comparisons across Contextual Domains

    ERIC Educational Resources Information Center

    Kolko, David J.; Dorn, Lorah D.; Bukstein, Oscar; Burke, Jeffrey D.

    2008-01-01

    This study compares 6-11-year-old, clinically referred boys and girls diagnosed with Oppositional Defiant Disorder, either with (ODD + CD, n = 40) or without Conduct Disorder (ODD only; n = 136), to a matched sample of healthy control children (HC; n = 69). Multiple informants completed intake diagnostic interviews and self-reports to evaluate…

  12. Cooperation of Adhesin Alleles in Salmonella-Host Tropism

    PubMed Central

    De Masi, Leon; Yue, Min; Hu, Changmin; Rakov, Alexey V.; Rankin, Shelley C.

    2017-01-01

    ABSTRACT Allelic combinations and host specificities for three fimbrial adhesins, FimH, BcfD, and StfH, were compared for 262 strains of Salmonella enterica serovar Newport, a frequent human and livestock pathogen. Like FimH, BcfD had two major alleles (designated A and B), whereas StfH had two allelic groups, each with two alleles (subgroup A1 and A2 and subgroup B1 and B2). The most prevalent combinations of FimH/BcfD/StfH alleles in S. Newport were A/A/A1 and B/B/B1. The former set was most frequently found in bovine and porcine strains, whereas the latter combination was most frequently found in environmental and human isolates. Bacteria genetically engineered to express Fim, Bcf, or Stf fimbriae on their surface were tested with the different alleles for binding to human, porcine, and bovine intestinal epithelial cells. The major allelic combinations with bovine and porcine strains (A/A/A1) or with human isolates (B/B/B1) provided at least two alleles capable of binding significantly better than the other alleles to an intestinal epithelial cell line from the respective host(s). However, each combination of alleles kept at least one allele mediating binding to an intestinal epithelial cell from another host. These findings indicated that allelic variation in multiple adhesins of S. Newport contributes to bacterial adaptation to certain preferential hosts without losing the capacity to maintain a broad host range. IMPORTANCE Salmonella enterica remains a leading foodborne bacterial pathogen in the United States; infected livestock serve often as the source of contaminated food products. A study estimated that over a billion Salmonella gastroenteritis cases and up to 33 million typhoid cases occur annually worldwide, with 3.5 million deaths. Although many Salmonella strains with a broad host range present preferential associations with certain host species, it is not clear what determines the various levels of host adaptation. Here, causal properties of host

  13. Human Leukocyte Antigen-E Alleles are Associated with Hepatitis C Virus, Torque Teno Virus, and Toxoplasma Co-infections but are not Associated with Hepatitis B Virus, Hepatitis D Virus, and GB Virus C Co-infections in Human Immunodeficiency Virus Patients

    PubMed Central

    Prasetyo, Afiono Agung; Dharmawan, Ruben; Raharjo, Irvan; Hudiyono

    2016-01-01

    Context: Data regarding the distribution of Human Leukocyte Antigen (HLA)-E alleles and their association with blood-borne pathogen infections/co-infections are limited for many populations, including Indonesia. Aims: The aim of this study was to analyze the association between HLA-E allelic variants and infection with blood-borne pathogens such as hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis D virus (HDV), torque teno virus (TTV), GB virus C (GBV-C), and Toxoplasma gondii (T. gondii) in Indonesian Javanese human immunodeficiency virus (HIV) patients. Settings and Design: A total of 320 anti-HIV-positive blood samples were analyzed for HBV, HCV, HDV, TTV, GBV-C, and T. gondii infection status and its association with HLA-E allelic variants. Materials and Methods: Nucleic acid was extracted from plasma samples and used for the molecular detection of HBV DNA, HCV RNA, HDV RNA, TTV DNA, and GBV-C RNA, whereas hepatitis B surface antigen, anti-HCV, immunoglobulin M and G (IgM and IgG) anti-T. gondii were detected through serological testing. The blood samples were genotyped for HLA-E loci using a sequence-specific primer-polymerase chain reaction. Statistical Analysis Used: Either the Chi-square or Fisher's exact test was performed to analyze the frequency of HLA-E alleles and blood-borne pathogen infections in the population. Odds ratios (ORs) were calculated to measure the association between the antibodies found and the participants’ possible risk behaviors. A logistic regression analysis was used to assess the associations. Results: HLA-E*101/0101 was associated with HCV/TTV co-infection (adjusted OR [aOR]: 3.5; 95% confidence interval [CI]: 1.156-10.734; P = 0.027) and IgM/IgG anti-Toxo positivity (aOR: 27.0; 95% CI: 3.626-200.472; P = 0.001). HLA-E*103/0103 was associated with TTV co-infection (aOR: 2.7; 95% CI: 1.509-4.796; P = 0.001). Conclusions: HLA-E alleles in Indonesian Javanese HIV patients were found to be associated with HCV, TTV, and

  14. Odd-even effect in heavy-ion collisions at intermediate energies

    SciTech Connect

    Su Jun; Zhang Fengshou; Bian Baoan

    2011-01-15

    Heavy-ion collisions at intermediate energies are studied by the isospin-dependent quantum molecular dynamics model in the company of the GEMINI model. The isospin-dependent quantum molecular dynamics model is applied to describe the violent stage of the collisions, while the GEMINI model is applied to simulate the decays of the prefragments. The present study mainly focuses on the odd-even effect in the yields of the final fragments. We find that the odd-even effect appears in the deexcitation process of the excited prefragments, and is affected by the excitation energies and the isotope distributions of the prefragments. Both the projectile-isospin-dependent odd-even effect in the region of -4{<=}T{sub Z}{<=}1 and the role of the symmetry energy on the odd-even effect are studied. We find that the odd-even effect depends sensitively on the symmetry energy.

  15. Odd-skipped maintains prohemocyte potency and blocks blood cell development in Drosophila.

    PubMed

    Gao, Hongjuan; Wu, Xiaorong; Fossett, Nancy

    2011-03-01

    Studies using Drosophila have contributed significantly to our understanding of regulatory mechanisms that control stem cell fate choice. The Drosophila blood cell progenitor or prohemocyte shares important characteristics with mammalian hematopoietic stem cells, including quiescence, niche dependence, and the capacity to form all three fly blood cell types. This report extends our understanding of prohemocyte fate choice by showing that the zinc-finger protein Odd-skipped promotes multipotency and blocks differentiation. Odd-skipped was expressed in prohemocytes and downregulated in terminally differentiated plasmatocytes. Furthermore, Odd-skipped maintained the prohemocyte population and blocked differentiation of plasmatocytes and lamellocytes but not crystal cells. A previous study showed that Odd-skipped expression is downregulated by Decapentaplegic signaling. This report provides a functional basis for this regulator/target pair by suggesting that Decapentaplegic signaling limits Odd-skipped expression to promote prohemocyte differentiation. Overall, these studies are the basis for a gene regulatory model of prohemocyte cell fate choice.

  16. Odd-Mode Surface Plasmon Polaritons Supported by Complementary Plasmonic Metamaterial

    PubMed Central

    Gao, Xi; Zhou, Liang; Cui, Tie Jun

    2015-01-01

    Surface plasmon polaritons (SPPs), either on metal-dielectric interfaces in optical frequencies or on structured metal surfaces in the lower frequencies, are dominantly even modes. Here we discover dominant odd-mode SPPs on a complementary plasmonic metamaterial, which is constructed by complementary symmetric grooves. We show that the fundamental SPP mode on such a plasmonic metamaterial is a tightly confined odd mode, whose dispersion curve can be tuned by the shape of groove. According to the electric field distributions of odd-mode SPPs, we propose a high-efficiency transducer using asymmetric coplanar waveguide and slot line to excite the odd-mode SPPs. Numerical simulations and experimental results validate the high-efficiency excitation and excellent propagation performance of odd-mode SPPs on the complementary plasmonic waveguides in the microwave frequencies. PMID:25783166

  17. Genome-wide association study of subtype-specific epithelial ovarian cancer risk alleles using pooled DNA.

    PubMed

    Earp, Madalene A; Kelemen, Linda E; Magliocco, Anthony M; Swenerton, Kenneth D; Chenevix-Trench, Georgia; Lu, Yi; Hein, Alexander; Ekici, Arif B; Beckmann, Matthias W; Fasching, Peter A; Lambrechts, Diether; Despierre, Evelyn; Vergote, Ignace; Lambrechts, Sandrina; Doherty, Jennifer A; Rossing, Mary Anne; Chang-Claude, Jenny; Rudolph, Anja; Friel, Grace; Moysich, Kirsten B; Odunsi, Kunle; Sucheston-Campbell, Lara; Lurie, Galina; Goodman, Marc T; Carney, Michael E; Thompson, Pamela J; Runnebaum, Ingo B; Dürst, Matthias; Hillemanns, Peter; Dörk, Thilo; Antonenkova, Natalia; Bogdanova, Natalia; Leminen, Arto; Nevanlinna, Heli; Pelttari, Liisa M; Butzow, Ralf; Bunker, Clareann H; Modugno, Francesmary; Edwards, Robert P; Ness, Roberta B; du Bois, Andreas; Heitz, Florian; Schwaab, Ira; Harter, Philipp; Karlan, Beth Y; Walsh, Christine; Lester, Jenny; Jensen, Allan; Kjær, Susanne K; Høgdall, Claus K; Høgdall, Estrid; Lundvall, Lene; Sellers, Thomas A; Fridley, Brooke L; Goode, Ellen L; Cunningham, Julie M; Vierkant, Robert A; Giles, Graham G; Baglietto, Laura; Severi, Gianluca; Southey, Melissa C; Liang, Dong; Wu, Xifeng; Lu, Karen; Hildebrandt, Michelle A T; Levine, Douglas A; Bisogna, Maria; Schildkraut, Joellen M; Iversen, Edwin S; Weber, Rachel Palmieri; Berchuck, Andrew; Cramer, Daniel W; Terry, Kathryn L; Poole, Elizabeth M; Tworoger, Shelley S; Bandera, Elisa V; Chandran, Urmila; Orlow, Irene; Olson, Sara H; Wik, Elisabeth; Salvesen, Helga B; Bjorge, Line; Halle, Mari K; van Altena, Anne M; Aben, Katja K H; Kiemeney, Lambertus A; Massuger, Leon F A G; Pejovic, Tanja; Bean, Yukie T; Cybulski, Cezary; Gronwald, Jacek; Lubinski, Jan; Wentzensen, Nicolas; Brinton, Louise A; Lissowska, Jolanta; Garcia-Closas, Montserrat; Dicks, Ed; Dennis, Joe; Easton, Douglas F; Song, Honglin; Tyrer, Jonathan P; Pharoah, Paul D P; Eccles, Diana; Campbell, Ian G; Whittemore, Alice S; McGuire, Valerie; Sieh, Weiva; Rothstein, Joseph H; Flanagan, James M; Paul, James; Brown, Robert; Phelan, Catherine M; Risch, Harvey A; McLaughlin, John R; Narod, Steven A; Ziogas, Argyrios; Anton-Culver, Hoda; Gentry-Maharaj, Aleksandra; Menon, Usha; Gayther, Simon A; Ramus, Susan J; Wu, Anna H; Pearce, Celeste L; Pike, Malcolm C; Dansonka-Mieszkowska, Agnieszka; Rzepecka, Iwona K; Szafron, Lukasz M; Kupryjanczyk, Jolanta; Cook, Linda S; Le, Nhu D; Brooks-Wilson, Angela

    2014-05-01

    Epithelial ovarian cancer (EOC) is a heterogeneous cancer with both genetic and environmental risk factors. Variants influencing the risk of developing the less-common EOC subtypes have not been fully investigated. We performed a genome-wide association study (GWAS) of EOC according to subtype by pooling genomic DNA from 545 cases and 398 controls of European descent, and testing for allelic associations. We evaluated for replication 188 variants from the GWAS [56 variants for mucinous, 55 for endometrioid and clear cell, 53 for low-malignant potential (LMP) serous, and 24 for invasive serous EOC], selected using pre-defined criteria. Genotypes from 13,188 cases and 23,164 controls of European descent were used to perform unconditional logistic regression under the log-additive genetic model; odds ratios (OR) and 95 % confidence intervals are reported. Nine variants tagging six loci were associated with subtype-specific EOC risk at P < 0.05, and had an OR that agreed in direction of effect with the GWAS results. Several of these variants are in or near genes with a biological rationale for conferring EOC risk, including ZFP36L1 and RAD51B for mucinous EOC (rs17106154, OR = 1.17, P = 0.029, n = 1,483 cases), GRB10 for endometrioid and clear cell EOC (rs2190503, P = 0.014, n = 2,903 cases), and C22orf26/BPIL2 for LMP serous EOC (rs9609538, OR = 0.86, P = 0.0043, n = 892 cases). In analyses that included the 75 GWAS samples, the association between rs9609538 (OR = 0.84, P = 0.0007) and LMP serous EOC risk remained statistically significant at P < 0.0012 adjusted for multiple testing. Replication in additional samples will be important to verify these results for the less-common EOC subtypes.

  18. Obesity increases the odds of acquiring and incarcerating noninguinal abdominal wall hernias.

    PubMed

    Lau, Briana; Kim, Hanjoo; Haigh, Philip I; Tejirian, Talar

    2012-10-01

    The current data available describing the relationship of obesity and abdominal wall hernias is sparse. The objective of this study was to investigate the current prevalence of noninguinal abdominal wall hernias and their correlation with body mass index (BMI) and other demographic risk factors. Patients with umbilical, incisional, ventral, epigastric, or Spigelian hernias with or without incarceration were identified using the regional database for 14 hospitals over a 3-year period. Patients were stratified based on their BMI. Univariate and multivariate analyses were performed to distinguish other significant risk factors associated with the hernias. Of 2,807,414 patients, 26,268 (0.9%) had one of the specified diagnoses. Average age of the patients was 52 years and 61 per cent were male. The majority of patients had nonincarcerated umbilical hernias (74%). Average BMI was 32 kg/m2. Compared with patients with a normal BMI, the odds of having a hernia increased with BMI: BMI of 25 to 29.9 kg/m2 odds ratio (OR) 1.63, BMI of 30 to 39.9 kg/m2 OR 2.62, BMI 40 to 49.9 kg/m2 OR 3.91, BMI 50 to 59.9 kg/m2 OR 4.85, and BMI greater than 60 kg/m2 OR 5.17 (P<0.0001). Age older than 50 years was associated with a higher risk for having a hernia (OR, 2.12; 95% [CI], 2.07 to 2.17), whereas female gender was associated with a lower risk (OR, 0.53; 95% CI, 0.52 to 0.55). Those with incarcerated hernias had a higher average BMI (32 kg/m2 vs 35 kg/m2; P<0.0001). Overall, BMI greater than 40 kg/m2 showed an increased chance of incarceration, and a BMI greater than 60 kg/m2 had the highest chance of incarceration, OR 12.7 (P<0.0001). Age older than 50 years and female gender were also associated with a higher risk of incarceration (OR, 1.28; 95% CI, 1.02 to 1.59 and OR, 1.80; CI, 1.45 to 2.24). Increasing BMI and increasing age are associated with a higher prevalence and an increased risk of incarceration of noninguinal abdominal wall hernias.

  19. Generation of a Conditional Null Allele of Jumonji

    PubMed Central

    Mysliwiec, Matthew R.; Chen, Junqin; Powers, Patricia A.; Bartley, Christopher R.; Schneider, Michael D.; Lee, Youngsook

    2007-01-01

    Summary: The jumonji (jmj) gene plays important roles in multiple organ development in mouse, including cardiovascular development. Since JMJ is expressed widely during mouse development, it is essential that conditional knockout approaches be employed to ablate JMJ in a tissue-specific manner to identify the cell lineage specific roles of JMJ. In this report, we describe the establishment of a jmj conditional null allele in mice by generating a loxP-flanked (floxed) jmj allele, which allows the in vivo ablation of jmj via Cre recombinase-mediated deletion. Gene targeting was used to introduce loxP sites flanking exon 3 of the jmj allele to mouse embryonic stem cells. Our results indicate that the jmj floxed allele converts to a null allele in a heart-specific manner when embryos homozygous for the floxed jmj allele and carrying the α-myosin heavy chain promoter-Cre transgene were analyzed by Southern and Northern blot analyses. Therefore, this mouse line harboring the conditional jmj null allele will provide a valuable tool for deciphering the tissue and cell lineage specific roles of JMJ. PMID:16900512

  20. Allele Frequencies at Microsatellite Loci: The Stepwise Mutation Model Revisited

    PubMed Central

    Valdes, A. M.; Slatkin, M.; Freimer, N. B.

    1993-01-01

    We summarize available data on the frequencies of alleles at microsatellite loci in human populations and compare observed distributions of allele frequencies to those generated by a simulation of the stepwise mutation model. We show that observed frequency distributions at 108 loci are consistent with the results of the model under the assumption that mutations cause an increase or decrease in repeat number by one and under the condition that the product Nu, where N is the effective population size and u is the mutation rate, is larger than one. We show that the variance of the distribution of allele sizes is a useful estimator of Nu and performs much better than previously suggested estimators for the stepwise mutation model. In the data, there is no correlation between the mean and variance in allele size at a locus or between the number of alleles and mean allele size, which suggests that the mutation rate at these loci is independent of allele size. PMID:8454213

  1. Estimating relatedness and relationships using microsatellite loci with null alleles.

    PubMed

    Wagner, A P; Creel, S; Kalinowski, S T

    2006-11-01

    Relatedness is often estimated from microsatellite genotypes that include null alleles. When null alleles are present, observed genotypes represent one of several possible true genotypes. If null alleles are detected, but analyses do not adjust for their presence (ie, observed genotypes are treated as true genotypes), then estimates of relatedness and relationship can be incorrect. The number of loci available in many wildlife studies is limited, and loci with null alleles are commonly a large proportion of data that cannot be discarded without substantial loss of power. To resolve this problem, we present a new approach for estimating relatedness and relationships from data sets that include null alleles. Once it is recognized that the probability of the observed genotypes is dependent on the probabilities of a limited number of possible true genotypes, the required adjustments are straightforward. The concept can be applied to any existing estimators of relatedness and relationships. We review established maximum likelihood estimators and apply the correction in that setting. In an application of the corrected method to data from striped hyenas, we demonstrate that correcting for the presence of null alleles affect results substantially. Finally, we use simulated data to confirm that this method works better than two common approaches, namely ignoring the presence of null alleles or discarding affected loci.

  2. Arylamine N-acetyltransferase (NAT2) mutations and their allelic linkage in unrelated caucasian individuals: Correlation with phenotypic activity

    SciTech Connect

    Cascorbi, I.; Drakoulis, N.; Brockmoeller, J.

    1995-09-01

    The polymorphic arylamine N-acetyltransferase (NAT2; EC2.3.1.5) is supposed to be a susceptibility factor for several drug side effects and certain malignancies. A group of 844 unrelated German subjects was genotyped for their acetylation type, and 563 of them were also phenotyped. Seven mutations of the NAT2 gene were evaluated by allele-specific PCR (mutation 341C to T) and PCR-RFLP for mutations at nt positions 191, 282, 481, 590, 803, and 857. From the mutation pattern eight different alleles, including the wild type coding for rapid acetylation and seven alleles coding for slow phenotype, were determined. Four hundred ninety-seven subjects had a genotype of slow acetylation (58.9%; 95% confidence limits 55.5%-62.2%). Phenotypic acetylation capacity was expressed as the ratio of 5-acetylamino-6-formylamino-3-methyluracil and 1-methylxanthine in urine after caffeine intake. Some 6.7% of the cases deviated in genotype and phenotype, but sequencing DNA of these probands revealed no new mutations. Furthermore, linkage pattern of the mutations was always confirmed, as tested in 533 subjects. In vivo acetylation capacity of homozygous wild-type subjects (NAT2{sup *}4/{sup *}4) was significantly higher than in heterozygous genotypes (P = .001). All mutant alleles showed low in vivo acetylation capacities, including the previously not-yet-defined alleles {sup *}5A, {sup *}5C, and {sup *}13. Moreover, distinct slow genotypes differed significantly among each other, as reflected in lower acetylation capacity of {sup *}6A, {sup *}7B, and {sup *}13 alleles than the group of {sup *}5 alleles. The study demonstrated differential phenotypic activity of various NAT2 genes and gives a solid basis for clinical and molecular-epidemiological investigations. 34 refs., 4 figs., 7 tabs.

  3. Analysis of the triaxial, strongly deformed bands in odd-odd nucleus 164Lu with the tops-on-top model

    NASA Astrophysics Data System (ADS)

    Sugawara-Tanabe, Kazuko; Tanabe, Kosai; Yoshinaga, Naotaka

    2014-06-01

    The top-on-top model with angular-momentum-dependent moments of inertia is extended to the tops-on-top model for an odd-odd nucleus, where one proton and one neutron in each single-j orbital are coupled to the triaxial rotor. For a pure rotor case, an explicit algebraic formula for the triaxial, strongly deformed (TSD) band levels is given, and its stability problem is discussed. Both positive and negative parity TSD bands are well reproduced by taking account of attenuation factors in the Coriolis interaction and the proton-neutron interaction in the recoil term. Difference in quantum numbers between the yrast and yrare TSD bands is confirmed by direct estimation of spin alignments. The electromagnetic transition rates of B(M1) are much reduced because of the different sign of g-factors in comparison with the odd-A case, while B(E2) are in the same order.

  4. Genetic Diversity and Elite Allele Mining for Grain Traits in Rice (Oryza sativa L.) by Association Mapping.

    PubMed

    Edzesi, Wisdom M; Dang, Xiaojing; Liang, Lijun; Liu, Erbao; Zaid, Imdad U; Hong, Delin

    2016-01-01

    Mining elite alleles for grain size and weight is of importance for the improvement of cultivated rice and selection for market demand. In this study, association mapping for grain traits was performed on a selected sample of 628 rice cultivars using 262 SSRs. Grain traits were evaluated by grain length (GL), grain width (GW), grain thickness (GT), grain length to width ratio (GL/GW), and 1000-grain weight (TGW) in 2013 and 2014. Our result showed abundant phenotypic and genetic diversities found in the studied population. In total, 2953 alleles were detected with an average of 11.3 alleles per locus. The population was divided into seven subpopulations and the levels of linkage disequilibrium (LD) ranged from 34 to 84 cM. Genome-wide association mapping detected 10 marker trait association (MTAs) loci for GL, 1MTAs locus for GW, 7 MTAs loci for GT, 3 MTAs loci for GL/GW, and 1 MTAs locus for TGW. Twenty-nine, 2, 10, 5, and 3 elite alleles were found for the GL, GW, GT, GL/GW, and TGW, respectively. Optimal cross designs were predicted for improving the target traits. The accessions containing elite alleles for grain traits mined in this study could be used for breeding rice cultivars and cloning the candidate genes.

  5. Genetic Diversity and Elite Allele Mining for Grain Traits in Rice (Oryza sativa L.) by Association Mapping

    PubMed Central

    Edzesi, Wisdom M.; Dang, Xiaojing; Liang, Lijun; Liu, Erbao; Zaid, Imdad U.; Hong, Delin

    2016-01-01

    Mining elite alleles for grain size and weight is of importance for the improvement of cultivated rice and selection for market demand. In this study, association mapping for grain traits was performed on a selected sample of 628 rice cultivars using 262 SSRs. Grain traits were evaluated by grain length (GL), grain width (GW), grain thickness (GT), grain length to width ratio (GL/GW), and 1000-grain weight (TGW) in 2013 and 2014. Our result showed abundant phenotypic and genetic diversities found in the studied population. In total, 2953 alleles were detected with an average of 11.3 alleles per locus. The population was divided into seven subpopulations and the levels of linkage disequilibrium (LD) ranged from 34 to 84 cM. Genome-wide association mapping detected 10 marker trait association (MTAs) loci for GL, 1MTAs locus for GW, 7 MTAs loci for GT, 3 MTAs loci for GL/GW, and 1 MTAs locus for TGW. Twenty-nine, 2, 10, 5, and 3 elite alleles were found for the GL, GW, GT, GL/GW, and TGW, respectively. Optimal cross designs were predicted for improving the target traits. The accessions containing elite alleles for grain traits mined in this study could be used for breeding rice cultivars and cloning the candidate genes. PMID:27375646

  6. Transmission ratio distortion in the human body louse, Pediculus humanus (Insecta: Phthiraptera).

    PubMed

    McMeniman, C J; Barker, S C

    2006-01-01

    We studied inheritance at three microsatellite loci in eight F, and two F2 families of the body (clothes) louse of humans, Pediculus humanus. The alleles of heterozygous female-parents were always inherited in a Mendelian fashion in these families. Alleles from heterozygous male-parents, however, were inherited in two different ways: (i) in a Mendelian fashion and (ii) in a non-Mendelian fashion, where males passed to their offspring only one of their two alleles, that is, 100% nonrandom transmission. In male body lice, where there was non-Mendelian inheritance, the paternally inherited set of alleles was eliminated. We interpret this pattern of inheritance as evidence for extreme transmission ratio distortion of paternal alleles in this species.

  7. Analysis and interpretation of short tandem repeat microvariants and three-banded allele patterns using multiple allele detection systems.

    PubMed

    Crouse, C A; Rogers, S; Amiott, E; Gibson, S; Masibay, A

    1999-01-01

    The Palm Beach County Sheriffs Office (PBSO) Crime Laboratory and the Alabama Department of Forensic Sciences (ADFS) have validated and implemented analysis of short tandem repeat (STR) sequences on casework using silver staining kit and SYBR Green I detection systems and are presently validating fluorescently tagged STR alleles using the Hitachi FMBIO 100 instrument. Concurrently, the Broward County Sheriff's Office (BSO) Crime Laboratory is validating the ABI Prism310 Genetic Analyzer capillary electrophoresis STR detection system (ABI CE310) from Perkin Elmer Applied BioSystems. During the course of analyzing over 10,000 individuals for the STR loci CSF1PO, TPOX and THO1 (CTT) using silver staining for allele detection, 42 samples demonstrated alleles that were "off ladder," contained three-banded patterns at a single locus, or exhibited an apparent THO1 "9.3,10" allele pattern. PBSO, ADFS and BSO Crime Laboratories have collaborated on the verification of the allele patterns observed in these 42 samples using the following allele detection systems: (1) manual silver staining, (2) SYBR Green I staining, and/or (3) fluorescently tagged amplified products separated by polyacrylamide gel electrophoresis or capillary electrophoresis followed by laser detection. Regardless of the CTT allele detection system utilized, concordant results were obtained for 41 of the 42 samples. The only exception was a sample in which a wide band within the THO1 locus was identified as a THO1 "9.3, 10" genotype by silver staining kit and SYBR Green I staining but was verified to be a THO1 "9.3" homozygote by all other allele detection systems. Manual allele detection could readily identify microvariants, as a visual assessment of stained gels clearly shows that alleles do not migrate coincident with well-characterized allele size standards. As would be predicted, however, the manual detection systems did not provide adequate resolution to approximate the basepair size for off

  8. A New Electrophoresis Technique to Seperate Microsatellite Alleles

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Traditional agarose and polyacrylamide gel electrophoresis have been used commonly for microsatellite (simple sequence repeats, SSRs) analysis, but they are labor- intensive and not always able to provide accurate sizes for different alleles. Capillary sequencers provide automated analysis and accur...

  9. The Golden Ratio

    ERIC Educational Resources Information Center

    Hyde, Hartley

    2004-01-01

    The Golden Ratio is sometimes called the "Golden Section" or the "Divine Proportion", in which three points: A, B, and C, divide a line in this proportion if AC/AB = AB/BC. "Donald in Mathmagicland" includes a section about the Golden Ratio and the ratios within a five-pointed star or pentagram. This article presents two computing exercises that…

  10. Nonexistence of small, odd breathers for a class of nonlinear wave equations

    NASA Astrophysics Data System (ADS)

    Kowalczyk, Michał; Martel, Yvan; Muñoz, Claudio

    2016-11-01

    In this note, we show that for a large class of nonlinear wave equations with odd nonlinearities, any globally defined odd solution which is small in the energy space decays to 0 in the local energy norm. In particular, this result shows nonexistence of small, odd breathers for some classical nonlinear Klein Gordon equations, such as the sine-Gordon equation and φ ^4 and φ ^6 models. It also partially answers a question of Soffer and Weinstein (Invent Math 136(1): 9-74, p 19 1999) about nonexistence of breathers for the cubic NLKG in dimension one.

  11. Even and odd coherent states of supersymmetric harmonic oscillators and their nonclassical properties

    NASA Astrophysics Data System (ADS)

    Afshar, Davood; Motamedinasab, Amin; Anbaraki, Azam; Jafarpour, Mojtaba

    2016-02-01

    In this paper, we have constructed even and odd superpositions of supercoherent states, similar to the standard even and odd coherent states of the harmonic oscillator. Then, their nonclassical properties, that is, squeezing and entanglement have been studied. We have observed that even supercoherent states show squeezing behavior for some values of parameters involved, while odd supercoherent states do not show squeezing at all. Also sub-Poissonian statistics have been observed for some ranges of the parameters in both states. We have also shown that these states may be considered as logical qubits which reduce to the Bell states at a limit, with concurrence equal to 1.

  12. Positive parity states and some electromagnetic transition properties of even-odd europium isotopes

    SciTech Connect

    Yazar, Harun Resit

    2013-06-15

    The positive-parity low-spin states of even-odd Europium isotopes ({sup 151-155}Eu) were studied within the framework of the interacting boson-fermion model. The calculated positive low-spin state energy spectra of the odd Eu isotope were found to agree quite well with the experimental data. The B(E2) values were also calculated and it was found that the calculated positive-parity low-spin state energy spectra of the odd-A Eu isotopes agree quite well with the experimental data.

  13. General Conditions for Proximity-Induced Odd-Frequency Superconductivity in Two-Dimensional Electronic Systems.

    PubMed

    Triola, Christopher; Badiane, Driss M; Balatsky, Alexander V; Rossi, E

    2016-06-24

    We obtain the general conditions for the emergence of odd-frequency superconducting pairing in a two-dimensional (2D) electronic system proximity coupled to a superconductor, making minimal assumptions about both the 2D system and the superconductor. Using our general results we show that a simple heterostructure formed by a monolayer of a group VI transition metal dichalcogenide, such as molybdenum disulfide, and an s-wave superconductor with Rashba spin-orbit coupling exhibits odd-frequency superconducting pairing. Our results allow the identification of a new class of systems among van der Waals heterostructures in which odd-frequency superconductivity should be present.

  14. Robust identification of local adaptation from allele frequencies.

    PubMed

    Günther, Torsten; Coop, Graham

    2013-09-01

    Comparing allele frequencies among populations that differ in environment has long been a tool for detecting loci involved in local adaptation. However, such analyses are complicated by an imperfect knowledge of population allele frequencies and neutral correlations of allele frequencies among populations due to shared population history and gene flow. Here we develop a set of methods to robustly test for unusual allele frequency patterns and correlations between environmental variables and allele frequencies while accounting for these complications based on a Bayesian model previously implemented in the software Bayenv. Using this model, we calculate a set of "standardized allele frequencies" that allows investigators to apply tests of their choice to multiple populations while accounting for sampling and covariance due to population history. We illustrate this first by showing that these standardized frequencies can be used to detect nonparametric correlations with environmental variables; these correlations are also less prone to spurious results due to outlier populations. We then demonstrate how these standardized allele frequencies can be used to construct a test to detect SNPs that deviate strongly from neutral population structure. This test is conceptually related to FST and is shown to be more powerful, as we account for population history. We also extend the model to next-generation sequencing of population pools-a cost-efficient way to estimate population allele frequencies, but one that introduces an additional level of sampling noise. The utility of these methods is demonstrated in simulations and by reanalyzing human SNP data from the Human Genome Diversity Panel populations and pooled next-generation sequencing data from Atlantic herring. An implementation of our method is available from http://gcbias.org.

  15. Sequencing of 15 new BoLA-DRB3 alleles.

    PubMed

    Wang, K; Sun, D; Zhang, Y

    2008-08-01

    The class II DR of bovine major histocompatibility complex of cattle (BoLA) plays a central role in the regulation of the immune response through their ability to present those peptides to T-cell receptors. In this work, we sequenced the exon2 of DRB3 to identify new alleles in Chinese yellow cattle, a total of 15 new BoLA-DRB3 alleles were found.

  16. DRD4 dopamine receptor allelic diversity in various primate species

    SciTech Connect

    Adamson, M.; Higley, D.; O`Brien, S.

    1994-09-01

    The DRD4 dopamine receptor is uniquely characterized by a 48 bp repeating segment within the coding region, located in exon III. Different DRD4 alleles are produced by the presence of additional 48 bp repeats, each of which adds 16 amino acids to the length of the 3rd intracytoplasmic loop of the receptor. The DRD4 receptor is therefore an intriguing candidate gene for behaviors which are influenced by dopamine function. In several human populations, DRD4 alleles with 2-8 and 10 repeats have previously been identified, and the 4 and 7 repeat alleles are the most abundant. We have determined DRD4 genotypes in the following nonhuman primate species: chimpanzee N=2, pygmy chimpanzee N=2, gorilla N=4, siamang N=2, Gelada baboon N=1, gibbon N=1, orangutan (Bornean and Sumatran) N=62, spider monkey N=4, owl monkey N=1, Colobus monkey N=1, Patas monkey N=1, ruffed lemur N=1, rhesus macaque N=8, and vervet monkey N=28. The degree of DRD4 polymorphism and which DRD4 alleles were present both showed considerable variation across primate species. In contrast to the human, rhesus macaque monkeys were monomorphic. The 4 and 7 repeat allels, highly abundant in the human, may not be present in certain other primates. For example, the four spider monkeys we studied showed the 7, 8 and 9 repeat length alleles and the only gibbon we analyzed was homozygous for the 9 repeat allele (thus far not observed in the human). Genotyping of other primate species and sequencing of the individual DRD4 repeat alleles in different species may help us determine the ancestral DRD4 repeat length and identify connections between DRD4 genotype and phenotype.

  17. Sustainable Odds: Towards Quantitative Decision Support when Relevant Probabilities are not Available

    NASA Astrophysics Data System (ADS)

    Smith, L. A.

    2012-04-01

    There is, at present, no attractive foundation for quantitative probabilistic decision support in the face of model inadequacy, or given ambiguity (deep uncertainty) regarding the relative likelihood of various outcomes, known or unknown. True model error arguably precludes the extraction of objective probabilities from an ensemble of model runs drawn from an available (inadequate) model class, while the acknowledgement of incomplete understanding precludes the justified use of (if not the very formation of) an individual's subjective probabilities. An alternative approach based on Sustainable Odds is proposed and investigated. Sustainable Odds differ from "fair odds" (and are easily distinguished any claim which implying well defined probabilities) as the probabilities implied by sustainable odds summed over all outcomes is expected to exceed one. Traditionally, a person's fair odds are found by identifying the probability level at which one would happily accept either side of a bet, thus the probabilities implied by fair odds always sum to one. Knowing that one has incomplete information and perhaps even erroneous beliefs, there is no compelling reason a rational agent should accept the constraint implied by "fair odds" in any bet. Rather, a rational agent might insist on longer odds both on the event and against the event in order to account for acknowledged ignorance. Let probabilistic odds imply any set of odds for which the implied probabilities sum to one; once model error is acknowledged can one rationally demand non-probabilistic odds? The danger of using fair odds (or probabilities) in decision making is illustrated by considering the risk of ruin a cooperative insurance scheme using probabilistic odds is exposed to. Cases where knowing merely that the insurer's model is imperfect, and nothing else, is sufficient to place bets which drive the insurer to an unexpectedly early ruin are presented. Methodologies which allow the insurer to avoid this early

  18. Nonrandom duplication of the chromosome bearing a mutated Ha-ras-1 allele in mouse skin tumors.

    PubMed Central

    Bianchi, A B; Aldaz, C M; Conti, C J

    1990-01-01

    We analyzed the normal/mutated allelic ratio of the Ha-ras-1 gene in mouse skin squamous cell carcinomas induced by initiation with dimethylbenz[a]anthracene and promotion with phorbol 12-myristate 13-acetate. DNA for these studies was obtained from short-term tumor cultures (24-72 hr) to eliminate the contribution of stromal and inflammatory cells to the sample. The allelotypic analysis was performed in 25 squamous cell carcinomas by quantitative radio-analysis of the Xba I restriction fragment length polymorphism as detected by BS9, a v-Ha-ras probe, and rehybridization of the Southern blots with probes for chromosomes 7 and 8. Approximately 85% of the tumors presented overrepresentation of the mutated allele in the form of 1 normal/2 mutated (12 tumors), 0 normal/3 mutated (4 tumors), 0 normal/2 mutated (3 tumors), and gene amplification (3 tumors). No tumor was found with a 2 normal/1 mutated allelic ratio. These results support our previous cytogenetic studies, indicating that trisomy of chromosome 7 is present in the majority of these tumors and show that nonrandom duplication of the chromosome carrying the mutated Ha-ras-1 allele appears to be a major mechanism by which the mutated gene is overrepresented. Images PMID:1697691

  19. Construct Validity of ADHD/ODD Rating Scales: Recommendations for the Evaluation of Forthcoming DSM-V ADHD/ODD Scales

    ERIC Educational Resources Information Center

    Burns, G. Leonard; Walsh, James A.; Servera, Mateu; Lorenzo-Seva, Urbano; Cardo, Esther; Rodriguez-Fornells, Antoni

    2013-01-01

    Exploratory structural equation modeling (SEM) was applied to a multiple indicator (26 individual symptom ratings) by multitrait (ADHD-IN, ADHD-HI and ODD factors) by multiple source (mothers, fathers and teachers) model to test the invariance, convergent and discriminant validity of the Child and Adolescent Disruptive Behavior Inventory with 872…

  20. SSR allelic variation in almond (Prunus dulcis Mill.).

    PubMed

    Xie, Hua; Sui, Yi; Chang, Feng-Qi; Xu, Yong; Ma, Rong-Cai

    2006-01-01

    Sixteen SSR markers including eight EST-SSR and eight genomic SSRs were used for genetic diversity analysis of 23 Chinese and 15 international almond cultivars. EST- and genomic SSR markers previously reported in species of Prunus, mainly peach, proved to be useful for almond genetic analysis. DNA sequences of 117 alleles of six of the 16 SSR loci were analysed to reveal sequence variation among the 38 almond accessions. For the four SSR loci with AG/CT repeats, no insertions or deletions were observed in the flanking regions of the 98 alleles sequenced. Allelic size variation of these loci resulted exclusively from differences in the structures of repeat motifs, which involved interruptions or occurrences of new motif repeats in addition to varying number of AG/CT repeats. Some alleles had a high number of uninterrupted repeat motifs, indicating that SSR mutational patterns differ among alleles at a given SSR locus within the almond species. Allelic homoplasy was observed in the SSR loci because of base substitutions, interruptions or compound repeat motifs. Substitutions in the repeat regions were found at two SSR loci, suggesting that point mutations operate on SSRs and hinder the further SSR expansion by introducing repeat interruptions to stabilize SSR loci. Furthermore, it was shown that some potential point mutations in the flanking regions are linked with new SSR repeat motif variation in almond and peach.

  1. Mutable R-Navajo Alleles of Cyclic Origin in Maize

    PubMed Central

    Brink, R. Alexander; Williams, Elizabeth

    1973-01-01

    The generation in cyclic fashion of 26 mutable R-Navajo (mRnj) alleles in maize involved transposition of a non-specific repressor of gene action, Modulator (Mp), first away from, and then back to, the R locus represented by the R-Navajo (Rnj) allele on chromosome 10. The mRnj alleles reconstituted in this way varied widely, and continuously, in mutability to Rnj—that is, in transposition of Mp away from the R locus, thus derepressing the Rnj gene. They were alike, or nearly so, however, in activating Ds chromosome breakage and in increasing the stability of variegated pericarp, another unstable compound allele comprising Mp conjoined with Prr on chromosomal 1. These latter two phenomena are based primarily on loci elsewhere in the genome. It is postulated that the 26 reconstituted mRnj alleles carry a common Mp which, however, is intercalated at a different site within each allele. Nucleotide sequence in the regions adjacent to Mp is assumed to determine the frequency with which a form of micro-nondisjunction occurs whereby Mp is released from a donor site. Transposition to a new site is interpreted in terms of a chromosome model that gives effect to nicking, or single strand breaks, occurring throughout the genome as a prerequisite to unwinding, strand separation, and replication, of the DNA double helix. PMID:17248592

  2. Overdominant alleles in a population of variable size.

    PubMed Central

    Slatkin, M; Muirhead, C A

    1999-01-01

    An approximate method is developed to predict the number of strongly overdominant alleles in a population of which the size varies with time. The approximation relies on the strong-selection weak-mutation (SSWM) method introduced by J. H. Gillespie and leads to a Markov chain model that describes the number of common alleles in the population. The parameters of the transition matrix of the Markov chain depend in a simple way on the population size. For a population of constant size, the Markov chain leads to results that are nearly the same as those of N. Takahata. The Markov chain allows the prediction of the numbers of common alleles during and after a population bottleneck and the numbers of alleles surviving from before a bottleneck. This method is also adapted to modeling the case in which there are two classes of alleles, with one class causing a reduction in fitness relative to the other class. Very slight selection against one class can strongly affect the relative frequencies of the two classes and the relative ages of alleles in each class. PMID:10353917

  3. A model study of the effects of intermittent loss on odd nitrogen concentrations in the lower troposphere

    NASA Technical Reports Server (NTRS)

    Stewart, R. W.; Hameed, S.; Matloff, G.

    1983-01-01

    A time-dependent box model of the lower troposphere which includes a description of photochemical and physical processes has been developed. This model has been applied to the calculation of nitric acid and NO(x)(NO + NO2) concentrations over a diurnal cycle which includes precipitation. Nitric acid concentrations and the HNO3/NO(x) ratio are found to be highly variable under the assumptions regarding the frequency, duration, and intensity of precipitation employed in this model. The chemistry of odd nitrogen compounds during the night is potentially important in establishing the level of nitric acid in the lower troposphere. These calculations also indicate that relatively large errors may occur when the continuity equation describing nitric acid variations is averaged over a diurnal cycle which includes precipitation. Interpretation of simultaneous measurements of HNO3 and NO(x) will require some knowledge of the history of the observed air mass and may require an improved understanding of nighttime odd nitrogen chemistry.

  4. Effect of lipid supplementation on milk odd- and branched-chain fatty acids in dairy cows.

    PubMed

    Baumann, E; Chouinard, P Y; Lebeuf, Y; Rico, D E; Gervais, R

    2016-08-01

    Eight ruminally fistulated, multiparous Holstein cows were arranged in a double 4×4 Latin square with 14-d periods to investigate the effects of lipid supplementation on performance, rumen parameters, the milk odd- and branched-chain fatty acid (OBCFA) profile, and the relationships between milk OBCFA and rumen parameters. Lipid supplementation is known to inhibit microbial growth in the rumen, decrease de novo microbial fatty acid synthesis, and increase the uptake of circulating fatty acids by the mammary gland; treatments were selected to isolate these effects on the milk OBCFA profile. The 4 treatments were (1) a lipid-free emulsion medium infused in the rumen (CTL), (2) soybean oil as a source of polyunsaturated fatty acids infused in the rumen (RSO), (3) saturated fatty acids (38% 16:0, 40% 18:0) infused in the rumen (RSF), and (4) saturated fatty acids infused in the abomasum (ASF). Fat supplements were provided continuously as emulsions at a rate of 450g/d. Preplanned contrasts compared CTL to RSO, RSO to RSF, and RSF to ASF. Infusing RSO slightly decreased ruminal pH, but did not affect volatile fatty acids profile and milk fat concentration as compared with CTL. The yields of energy-corrected milk, fat, and protein were greater with RSF compared with RSO. The concentration of odd-chain fatty acids was decreased by RSO, whereas even-chain iso fatty acids were not affected. Milk fat concentration of 17:0 + cis-9 17:1 was higher for RSF than for RSO, due to the saturated fatty acids supplement containing 2% 17:0 + cis-9 17:1. Limited differences were observed in the milk OBCFA profile between RSF and ASF. A multiple regression analysis yielded the following equation for predicting rumen pH based on milk fatty acids: pH=6.24 - (0.56×4:0) + (1.67 × iso 14:0) + (4.22 × iso 15:0) + (9.41×22:0). Rumen propionate concentration was negatively correlated with milk fat concentration of iso 14:0 and positively correlated with milk 15:0, whereas the acetate

  5. High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus

    SciTech Connect

    Muchero, Wellington; Guo, Jianjun; Difazio, Stephen P.; Chen, Jay; Ranjan, Priya; Slavov, Gancho; Gunter, Lee E.; Jawdy, Sara; Bryan, Anthony C.; Sykes, Robert; Ziebell, Angela L.; Klapste, Jaroslav; Porth, Ilga; Skyba, Oleksandr; Unda, Faride; El-Kassaby, Yousry; Douglas, Carl; Mansfield, Shawn; Martin, Joel; Schackwitz, Wendy; Evans, Luke M.; Czarnecki, Olaf; Tuskan, Gerald A.

    2015-01-23

    We report the identification of six genetic loci and the allelic-variants associated with Populus cell wall phenotypes determined independently using pyrolysis Molecular Beam Mass Spectrometry (pyMBMS), saccharification assay and wet chemistry in two partially overlapping populations of P. trichocarpa genotypes sampled from multiple environments in the Pacific Northwest of North America. All 6 variants co-located with a quantitative trait locus (QTL) hotspot on chromosome XIV for lignin content, syringyl to guaiacyl (S/G) ratio, 5- and 6- carbon sugars identified in an interspecific P. trichocarpa x P. deltoides pseudo-backcross mapping pedigree. Genomic intervals containing an amino acid transporter, a MYB transcription factor, an angustifolia CtBP transcription factor, a copper transport protein ATOX1-related, a Ca2+ transporting ATPase and a protein kinase were identified within 5 QTL regions. Each interval contained single nucleotide polymorphisms (SNPs) that were significantly associated to cell-wall phenotypes, with associations exceeding the chromosome-wise Bonferroni-adjusted p-values in at least one environment. cDNA sequencing for allelic variants of 3 of the 6 genes identified polymorphisms leading to premature stop codons in the MYB transcription factor and protein kinase. On the other hand, variants of the Angustifolia CtBP transcription factor exhibited a polyglutamine (PolyQ) length polymorphism. Results from transient protoplast assays suggested that each of the polymorphisms conferred allelic differences in activation of cellulose, hemicelluloses and lignin pathway marker genes, with truncated and short PolyQ alleles exhibiting significantly reduced marker gene activation. Genes identified in this study represent novel targets for reducing cell wall recalcitrance for lignocellulosic biofuels production using plant biomass.

  6. High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus

    DOE PAGES

    Muchero, Wellington; Guo, Jianjun; Difazio, Stephen P.; ...

    2015-01-23

    We report the identification of six genetic loci and the allelic-variants associated with Populus cell wall phenotypes determined independently using pyrolysis Molecular Beam Mass Spectrometry (pyMBMS), saccharification assay and wet chemistry in two partially overlapping populations of P. trichocarpa genotypes sampled from multiple environments in the Pacific Northwest of North America. All 6 variants co-located with a quantitative trait locus (QTL) hotspot on chromosome XIV for lignin content, syringyl to guaiacyl (S/G) ratio, 5- and 6- carbon sugars identified in an interspecific P. trichocarpa x P. deltoides pseudo-backcross mapping pedigree. Genomic intervals containing an amino acid transporter, a MYB transcriptionmore » factor, an angustifolia CtBP transcription factor, a copper transport protein ATOX1-related, a Ca2+ transporting ATPase and a protein kinase were identified within 5 QTL regions. Each interval contained single nucleotide polymorphisms (SNPs) that were significantly associated to cell-wall phenotypes, with associations exceeding the chromosome-wise Bonferroni-adjusted p-values in at least one environment. cDNA sequencing for allelic variants of 3 of the 6 genes identified polymorphisms leading to premature stop codons in the MYB transcription factor and protein kinase. On the other hand, variants of the Angustifolia CtBP transcription factor exhibited a polyglutamine (PolyQ) length polymorphism. Results from transient protoplast assays suggested that each of the polymorphisms conferred allelic differences in activation of cellulose, hemicelluloses and lignin pathway marker genes, with truncated and short PolyQ alleles exhibiting significantly reduced marker gene activation. Genes identified in this study represent novel targets for reducing cell wall recalcitrance for lignocellulosic biofuels production using plant biomass.« less

  7. Against All Odds: Genocidal Trauma Is Associated with Longer Life-Expectancy of the Survivors

    PubMed Central

    Sagi-Schwartz, Abraham; Bakermans-Kranenburg, Marian J.; Linn, Shai; van IJzendoorn, Marinus H.

    2013-01-01

    Does surviving genocidal experiences, like the Holocaust, lead to shorter life-expectancy? Such an effect is conceivable given that most survivors not only suffered psychosocial trauma but also malnutrition, restriction in hygienic and sanitary facilities, and lack of preventive medical and health services, with potentially damaging effects for later health and life-expectancy. We explored whether genocidal survivors have a higher risk to die younger than comparisons without such background. This is the first population-based retrospective cohort study of the Holocaust, based on the entire population of immigrants from Poland to Israel (N = 55,220), 4–20 years old when the World War II started (1939), immigrating to Israel either between 1945 and 1950 (Holocaust group) or before 1939 (comparison group; not exposed to the Holocaust). Hazard of death – a long-term outcome of surviving genocidal trauma – was derived from the population-wide official data base of the National Insurance Institute of Israel. Cox regression yielded a significant hazard ratio (HR = 0.935, CI (95%) = 0.910–0.960), suggesting that the risk of death was reduced by 6.5 months for Holocaust survivors compared to non-Holocaust comparisons. The lower hazard was most substantial in males who were aged 10–15 (HR = 0.900, CI (95%) = 0.842–0.962, i.e., reduced by 10 months) or 16–20 years at the onset of the Holocaust (HR = 0.820, CI (95%) = 0.782–0.859, i.e., reduced by18 months). We found that against all odds genocidal survivors were likely to live longer. We suggest two explanations: Differential mortality during the Holocaust and “Posttraumatic Growth” associated with protective factors in Holocaust survivors or in their environment after World War II. PMID:23894427

  8. Strong odd-frequency correlations in fully gapped Zeeman-split superconductors

    PubMed Central

    Linder, Jacob; Robinson, Jason W. A.

    2015-01-01

    It is now well established that at a superconductor/ferromagnet (S/F) interface an unconventional superconducting state arises in which the pairing is odd-frequency. The hallmark signature of this superconducting state is generally understood to be an enhancement of the electronic density of states (DoS) at subgap energies close to the S/F interface. However, here we show that an odd frequency state can be present even if the DoS is fully gapped. As an example, we show that this is the case in the pioneering S/FI (where FI is a insulating ferromagnet) tunneling experiments of Meservey and Tedrow, and we derive a generalized analytical criterium to describe the effect of odd-frequency pairing on the DoS. Finally, we propose a simple experiment in which odd-frequency pairing in a Zeeman-split superconductor can be unambiguously detected via the application of an external magnetic field. PMID:26503380

  9. Odd versus even: a scientific study of the ‘rules’ of plating

    PubMed Central

    Michel, Charles; Spence, Charles

    2016-01-01

    We report on the results of a series of large-scale computer-based preference tests (conducted at The Science Museum in London and online) that evaluated the widely-held belief that food should be plated in odd rather than even numbers of elements in order to maximize the visual appeal of a dish. Participants were presented with pairs of plates of food showing odd versus even number of seared scallops (3 vs. 4; 1–6 in Experiment 7), arranged in a line, as a polygon or randomly, on either a round or square white plate. No consistent evidence for a preference for odd or even numbers of food items was found, thus questioning the oft-made assertion that odd number of items on a plate looks better than an even number. The implications of these results are discussed. PMID:26839741

  10. Testing Lorentz invariance using an odd-parity asymmetric optical resonator

    SciTech Connect

    Baynes, Fred N.; Luiten, Andre N.; Tobar, Michael E.

    2011-10-15

    We present the first experimental test of Lorentz invariance using the frequency difference between counter-propagating modes in an asymmetric odd-parity optical resonator. This type of test is {approx}10{sup 4} more sensitive to odd-parity and isotropic (scalar) violations of Lorentz invariance than equivalent conventional even-parity experiments due to the asymmetry of the optical resonator. The disadvantages of odd-parity resonators have been negated by the use of counter-propagating modes, delivering a high level of immunity to environmental fluctuations. With a nonrotating experiment our result limits the isotropic Lorentz violating parameter {kappa}-tilde{sub tr} to 3.4{+-}6.2x10{sup -9}, the best reported constraint from direct measurements. Using this technique the bounds on odd-parity and scalar violations of Lorentz invariance can be improved by many orders of magnitude.

  11. Odd-even dependence of rectifying behavior in carbon chains modified diphenyl-dimethyl molecule

    NASA Astrophysics Data System (ADS)

    Wu, Qiu-Hua; Zhao, Peng; Liu, Hai-Ying; Liu, De-Sheng; Chen, Gang

    2014-06-01

    Using density functional theory and non-equilibrium Green's function formalism, we investigate the effects of asymmetric nonequi-length carbon chains on the electron transport properties of diphenyl-dimethyl molecule. The results show significant odd-even dependence: the rectification appears only in the hybrid nanostructure with odd carbon chain on one side and even carbon chain on the other side, while it is negligible in those with odd/even carbon chain on both sides. The mechanism for the odd-even dependence of rectification is analyzed by the bias-dependent transmission spectra, evolution of molecular orbital levels, their spatial distributions, and projected density of states with the applied bias.

  12. Strong odd-frequency correlations in fully gapped Zeeman-split superconductors.

    PubMed

    Linder, Jacob; Robinson, Jason W A

    2015-10-27

    It is now well established that at a superconductor/ferromagnet (S/F) interface an unconventional superconducting state arises in which the pairing is odd-frequency. The hallmark signature of this superconducting state is generally understood to be an enhancement of the electronic density of states (DoS) at subgap energies close to the S/F interface. However, here we show that an odd frequency state can be present even if the DoS is fully gapped. As an example, we show that this is the case in the pioneering S/FI (where FI is a insulating ferromagnet) tunneling experiments of Meservey and Tedrow, and we derive a generalized analytical criterium to describe the effect of odd-frequency pairing on the DoS. Finally, we propose a simple experiment in which odd-frequency pairing in a Zeeman-split superconductor can be unambiguously detected via the application of an external magnetic field.

  13. Obesity in Youth Tied to Higher Odds for Liver Cancer in Men

    MedlinePlus

    ... page: https://medlineplus.gov/news/fullstory_164210.html Obesity in Youth Tied to Higher Odds for Liver ... risk, a new study warns. Efforts to reduce obesity, "should be implemented from an early age to ...

  14. Changing the Odds A North Carolina family's search to help those with TBI

    MedlinePlus

    ... Brain Injury Changing the Odds A North Carolina family's search to help those with TBI Past Issues / ... with traumatic brain injury (TBI)—and changed his family's life forever. "Back then there were no roadmaps ...

  15. Comparing T-odd and T-even spin sum rules

    SciTech Connect

    Teryaev, O.V.

    2015-04-10

    Sum rules for T-even and T-odd structure functions and parton distributions are considered. The case of spin-dependent distributions related to energy-momentum tensor (EMT) is specifically addressed. The Burkardt sum rule for T-odd Sivers functions may be related to EMT provided the imaginary prescription for gluonic pole correlator is incorporated. The momentum sum rule for deuteron tensor spin structure function allows one to probe indirectly the gravity couplings to quarks and gluons.

  16. Impriniting of human H19: Allele-specific CpG methylation, loss of the active allele in Wilms tumor, and potential for somatic allele switching

    SciTech Connect

    Zhang, Y.; Shields, T.; Crenshaw, T.; Hao, Y.; Moulton, T.; Tycko, B. )

    1993-07-01

    Genomic imprinting and monoallelic gene expression appear to play a role in human genetic disease and tumorigenesis. The human H19 gene, at chromosome 11p15, has previously been shown to be monoallelically expressed. Since CpG methylation has been implicated in imprinting, the authors analyzed methylation of H19 DNA. In fetal and adult organs the transcriptionally silent H19 allele was extensively hypermethylated through the entire gene and its promoter, and, consistent with a functional role for DNA methylation, expression of an H19 promoter-reporter construct was inhibited by in vitro methylation. Gynogenetic ovarian teratomas were found to contain only hypomethylated H19 DNA, suggesting that the expressed H19 allele might be maternal. This was confirmed by analysis of 11p15 polymorphisms in a patient with Wilms tumor. The tumor had lost the maternal 11p15, and H19 expression in the normal kidney was exclusively from this allele. Imprinting of human H19 appears to be susceptible to tissue-specific modulation in somatic development; in one individual, cerebellar cells were found to express only the otherwise silent allele. Implications of these findings for the role of DNA methylation in imprinting and for H19 as a candidate imprinted tumor-suppressor gene are discussed. 57 refs., 7 figs.

  17. Distribution of BoLA-DRB3 allelic frequencies and identification of two new alleles in Iranian buffalo breed.

    PubMed

    Mosafer, J; Heydarpour, M; Manshad, E; Russell, G; Sulimova, G E

    2012-01-01

    The role of the major histocompatibility complex (MHC) in the immune response makes it an attractive candidate gene for associations with disease resistance and susceptibility. This study describes genetic variability in the BoLA-DRB3 in Iranian buffaloes. Heminested PCR-RFLP method was used to identify the frequency of BoLA-DRB3 alleles. The BoLA-DRB3 locus is highly polymorphic in the study herd (12 alleles). Almost 63.50% of the alleles were accounted for by four alleles (BoLA-DRB3.2 ∗48, ∗20, ∗21, and obe) in Iranian buffalo. The DRB3.2 ∗48 allele frequency (24.20%) was higher than the others. The frequencies of the DRB3.2 ∗20 and DRB3.2 ∗21 are 14.52 and 14.00, respectively, and obe and gbb have a new pattern. Significant distinctions have been found between Iranian buffalo and other cattle breed studied. In the Iranian buffaloes studied alleles associated with resistance to various diseases are found.

  18. Distribution of BoLA-DRB3 Allelic Frequencies and Identification of Two New Alleles in Iranian Buffalo Breed

    PubMed Central

    Mosafer, J.; Heydarpour, M.; Manshad, E.; Russell, G.; Sulimova, G. E.

    2012-01-01

    The role of the major histocompatibility complex (MHC) in the immune response makes it an attractive candidate gene for associations with disease resistance and susceptibility. This study describes genetic variability in the BoLA-DRB3 in Iranian buffaloes. Heminested PCR-RFLP method was used to identify the frequency of BoLA-DRB3 alleles. The BoLA-DRB3 locus is highly polymorphic in the study herd (12 alleles). Almost 63.50% of the alleles were accounted for by four alleles (BoLA-DRB3.2 ∗48, ∗20, ∗21, and obe) in Iranian buffalo. The DRB3.2 ∗48 allele frequency (24.20%) was higher than the others. The frequencies of the DRB3.2 ∗20 and DRB3.2 ∗21 are 14.52 and 14.00, respectively, and obe and gbb have a new pattern. Significant distinctions have been found between Iranian buffalo and other cattle breed studied. In the Iranian buffaloes studied alleles associated with resistance to various diseases are found. PMID:22454612

  19. A limit to the divergent allele advantage model supported by variable pathogen recognition across HLA-DRB1 allele lineages.

    PubMed

    Lau, Q; Yasukochi, Y; Satta, Y

    2015-11-01

    Genetic diversity in human leukocyte antigen (HLA) molecules is thought to have arisen from the co-evolution between host and pathogen and maintained by balancing selection. Heterozygote advantage is a common proposed scenario for maintaining high levels of diversity in HLA genes, and extending from this, the divergent allele advantage (DAA) model suggests that individuals with more divergent HLA alleles bind and recognize a wider array of antigens. While the DAA model seems biologically suitable for driving HLA diversity, there is likely an upper threshold to the amount of sequence divergence. We used peptide-binding and pathogen-recognition capacity of DRB1 alleles as a model to further explore the DAA model; within the DRB1 locus, we examined binding predictions based on two distinct phylogenetic groups (denoted group A and B) previously identified based on non-peptide-binding region (PBR) nucleotide sequences. Predictions in this study support that group A allele and group B allele lineages have contrasting binding/recognition capacity, with only the latter supporting the DAA model. Furthermore, computer simulations revealed an inconsistency in the DAA model alone with observed extent of polymorphisms, supporting that the DAA model could only work effectively in combination with other mechanisms. Overall, we support that the mechanisms driving HLA diversity are non-exclusive. By investigating the relationships among HLA alleles, and pathogens recognized, we can provide further insights into the mechanisms on how humans have adapted to infectious diseases over time.

  20. Efficient odd straight medium chain free fatty acid production by metabolically engineered Escherichia coli.

    PubMed

    Wu, Hui; San, Ka-Yiu

    2014-11-01

    Free fatty acids (FFAs) can be used as precursors for the production of biofuels or chemicals. Different composition of FFAs will be useful for further modification of the biofuel/biochemical quality. Microbial biosynthesis of even chain FFAs can be achieved by introducing an acyl-acyl carrier protein thioesterase gene into E. coli. In this study, odd straight medium chain FFAs production was investigated by using metabolic engineered E. coli carrying acyl-ACP thioesterase (TE, Ricinus communis), propionyl-CoA synthase (Salmonella enterica), and β-ketoacyl-acyl carrier protein synthase III (four different sources) with supplement of extracellular propionate. By using these metabolically engineered E. coli, significant quantity of C13 and C15 odd straight-chain FFAs could be produced from glucose and propionate. The highest concentration of total odd straight chain FFAs attained was 1205 mg/L by the strain HWK201 (pXZ18, pBHE2), and 85% of the odd straight chain FFAs was C15. However, the highest percentage of odd straight chain FFAs was achieved by the strain HWK201 (pXZ18, pBHE3) of 83.2% at 48 h. This strategy was also applied successfully in strains carrying different TE, such as the medium length acyl-ACP thioesterase gene from Umbellularia californica. C11 and C13 became the major odd straight-chain FFAs.

  1. Swimming at low Reynolds number in fluids with odd, or Hall, viscosity.

    PubMed

    Lapa, Matthew F; Hughes, Taylor L

    2014-04-01

    We apply the geometric theory of swimming at low Reynolds number to the study of nearly circular swimmers in two-dimensional fluids with nonvanishing "odd," or Hall, viscosity. The odd viscosity gives an off-diagonal contribution to the fluid stress tensor, which results in a number of striking effects. In particular, we find that a swimmer whose area is changing will experience a torque proportional to the rate of change of the area, with the constant of proportionality given by the coefficient ηo of odd viscosity. After working out the general theory of swimming in fluids with odd viscosity for a class of simple swimmers, we give a number of example swimming strokes which clearly demonstrate the differences between swimming in a fluid with conventional viscosity and a fluid which also has an odd viscosity. We also include a discussion of the extension of the famous Scallop theorem of low Reynolds number swimming to the case where the fluid has a nonzero odd viscosity. A number of more technical results, including a proof of the torque-area relation for swimmers of more general shape, are explained in a set of Appendixes.

  2. Mother-teacher agreement on preschoolers' symptoms of ODD and CD: does context matter?

    PubMed

    Strickland, Jennifer; Hopkins, Joyce; Keenan, Kate

    2012-08-01

    The aims of this study were to examine mother-teacher agreement on oppositional defiant disorder (ODD) and conduct disorder (CD) symptoms and diagnoses in preschool children; to determine if context is a source of disagreement; and to explore if sex, referral status, and age moderated agreement rates. Participants included 158 male and 139 female 3- to 5-year old preschool children, their mothers, and teachers. A structured interview, the Kiddie-Disruptive Behavior Disorder Schedule was used for maternal report and teachers completed the Early Childhood Inventory. Results indicated that mothers reported more symptoms and diagnoses of ODD and CD than teachers, and mother-teacher agreement on both ODD and CD symptoms and diagnoses was low. Level of mother-teacher agreement increased when reporting on behavior in the same context; however, the rates remain modest. Referral status increased the likelihood of mother and teacher agreement on several ODD and CD symptoms, as well as ODD and CD diagnosis. These data suggest that context plays a role in mother-teacher agreement in the assessment of young children's ODD and CD symptoms.

  3. How the Number of Alleles Influences Gene Expression

    NASA Astrophysics Data System (ADS)

    Hat, Beata; Paszek, Pawel; Kimmel, Marek; Piechor, Kazimierz; Lipniacki, Tomasz

    2007-07-01

    The higher organisms, eukaryotes, are diploid and most of their genes have two homological copies (alleles). However, the number of alleles in a cell is not constant. In the S phase of the cell cycle all the genome is duplicated and then in the G2 phase and mitosis, which together last for several hours, most of the genes have four copies instead of two. Cancer development is, in many cases, associated with a change in allele number. Several genetic diseases are caused by haploinsufficiency: Lack of one of the alleles or its improper functioning. In the paper we consider the stochastic expression of a gene having a variable number of copies. We applied our previously developed method in which the reaction channels are split into slow (connected with change of gene state) and fast (connected with mRNA/protein synthesis/decay), the later being approximated by deterministic reaction rate equations. As a result we represent gene expression as a piecewise deterministic time-continuous Markov process, which is further related with a system of partial differential hyperbolic equations for probability density functions (pdfs) of protein distribution. The stationary pdfs are calculated analytically for haploidal gene or numerically for diploidal and tetraploidal ones. We distinguished nine classes of simultaneous activation of haploid, diploid and tetraploid genes. This allows for analysis of potential consequences of gene duplication or allele loss. We show that when gene activity is autoregulated by a positive feedback, the change in number of gene alleles may have dramatic consequences for its regulation and may not be compensated by the change of efficiency of mRNA synthesis per allele.

  4. Association between ACE D allele and elite short distance swimming.

    PubMed

    Costa, Aldo Matos; Silva, António José; Garrido, Nuno Domingos; Louro, Hugo; de Oliveira, Ricardo Jacó; Breitenfeld, Luiza

    2009-08-01

    The influence of ACE gene on athletic performance has been widely explored, and most of the published data refers to an I/D polymorphism leading to the presence (I allele) or absence (D allele) of a 287-bp sequence in intron 16, determining ACE activity in serum and tissues. A higher I allele frequency has been reported among elite endurance athletes, while the D allele was more frequent among those engaged in more power-orientated sports. However, on competitive swimming, the reproducibility of such associations is controversial. We thus compared the ACE genotype of elite swimmers with that of non-elite swimming cohort and of healthy control subjects. We thus sought an association of the ACE genotype of elite swimmers with their competitive distance. 39 Portuguese Olympic swimming candidates were classified as: short (<200 m) and middle (400-1,500 m) distance swimmers, respectively. A group of 32 non-elite swimmers were studied and classified as well, and a control group (n = 100) was selected from the Portuguese population. Chelex 100 was used for DNA extraction and genotype was determined by PCR-RFLP methods. We found that ACE genotype distribution and allelic frequency differs significantly by event distance only among elite swimmers (P < or = 0.05). Moreover, the allelic frequency of the elite short distance swimmers differed significantly from that of the controls (P = 0.021). No associations were found between middle distance swimmers and controls. Our results seem to support an association between the D allele and elite short distance swimming.

  5. Construction of a library of cloned short tandem repeat (STR) alleles as universal templates for allelic ladder preparation.

    PubMed

    Wang, Le; Zhao, Xing-Chun; Ye, Jian; Liu, Jin-Jie; Chen, Ting; Bai, Xue; Zhang, Jian; Ou, Yuan; Hu, Lan; Jiang, Bo-Wei; Wang, Feng

    2014-09-01

    Short tandem repeat (STR) genotyping methods are widely used for human identity testing applications, including forensic DNA analysis. Samples of DNA containing the length-variant STR alleles are typically separated and genotyped by comparison to an allelic ladder. Here, we describe a newly devised library of cloned STR alleles. The library covers alleles X and Y for the sex-determining locus Amelogenin and 259 other alleles for 22 autosomal STR loci (TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, vWA, D13S317, D16S539, D18S51, D21S11, D2S1338, D6S1043, D12S391, Penta E, D19S433, D11S4463, D17S974, D3S4529 and D12ATA63). New primers were designed for all these loci to construct recombinant plasmids so that the library retains core repeat elements of STR as well as 5'- and 3'-flanking sequences of ∼500 base pairs. Since amplicons of commercial STR genotyping kits and systems developed in laboratories are usually distributed from 50 to <500 base pairs, this library could provide universal templates for allelic ladder preparation. We prepared three different sets of allelic ladders for this locus TH01 and an updated version of an allelic ladder for the DNATyper(®)19 multiplex system using these plasmids to confirm the suitability of the library as a good source for allelic ladder preparation. Importantly, the authenticity of each construct was confirmed by bidirectional nucleotide sequencing and we report the repeat structures of the 259 STR alleles. The sequencing results showed all repeat structures we obtained for TPOX, CSF1PO, D7S820, TH01, D16S539, D18S51 and Penta E were the same as reported. However, we identified 102 unreported repeat structures from the other 15 STR loci, supplementing our current knowledge of repeat structures and leading to further understanding of these widely used loci.

  6. Which Executive Functioning Deficits Are Associated with AD/HD, ODD/CD and Comorbid AD/HD+ODD/CD? (Attention Deficit/hyperactivity Disorder)(Oppositional Defiant Disorder)

    ERIC Educational Resources Information Center

    Oosterlaan, Jaap; Scheres, Anouk; Sergeant, Joseph A.

    2005-01-01

    This study investigated (1) whether attention deficit/hyperactivity disorder (AD/HD) is associated with executive functioning (EF) deficits while controlling for oppositional defiant disorder/conduct disorder (ODD/CD), (2) whether ODD/CD is associated with EF deficits while controlling for AD/HD, and (3) whether a combination of AD/HD and ODD/CD…

  7. Characterization of a New Pm2 Allele Conferring Powdery Mildew Resistance in the Wheat Germplasm Line FG-1

    PubMed Central

    Ma, Pengtao; Xu, Hongxng; Li, Lihui; Zhang, Hongxia; Han, Guohao; Xu, Yunfeng; Fu, Xiaoyi; Zhang, Xiaotian; An, Diaoguo

    2016-01-01

    Powdery mildew has a negative impact on wheat production. Novel host resistance increases the diversity of resistance genes and helps to control the disease. In this study, wheat line FG-1 imported from France showed a high level of powdery mildew resistance at both the seedling and adult stages. An F2 population and F2:3 families from the cross FG-1 × Mingxian 169 both fit Mendelian ratios for a single dominant resistance gene when tested against multiple avirulent Blumeria tritici f. sp. tritici (Bgt) races. This gene was temporarily designated PmFG. PmFG was mapped on the multi-allelic Pm2 locus of chromosome 5DS using seven SSR, 10 single nucleotide polymorphism (SNP)-derived and two SCAR markers with the flanking markers Xbwm21/Xcfd81/Xscar112 (distal) and Xbwm25 (proximal) at 0.3 and 0.5 cM being the closest. Marker SCAR203 co-segregated with PmFG. Allelism tests between PmFG and documented Pm2 alleles confirmed that PmFG was allelic with Pm2. Line FG-1 produced a significantly different reaction pattern compared to other lines with genes at or near Pm2 when tested against 49 Bgt isolates. The PmFG-linked marker alleles detected by the SNP-derived markers revealed significant variation between FG-1 and other lines with genes at or near Pm2. It was concluded that PmFG is a new allele at the Pm2 locus. Data from seven closely linked markers tested on 31 wheat cultivars indicated opportunities for marker-assisted pyramiding of this gene with other genes for powdery mildew resistance and additional traits. PMID:27200022

  8. Characterization of a New Pm2 Allele Conferring Powdery Mildew Resistance in the Wheat Germplasm Line FG-1.

    PubMed

    Ma, Pengtao; Xu, Hongxng; Li, Lihui; Zhang, Hongxia; Han, Guohao; Xu, Yunfeng; Fu, Xiaoyi; Zhang, Xiaotian; An, Diaoguo

    2016-01-01

    Powdery mildew has a negative impact on wheat production. Novel host resistance increases the diversity of resistance genes and helps to control the disease. In this study, wheat line FG-1 imported from France showed a high level of powdery mildew resistance at both the seedling and adult stages. An F2 population and F2:3 families from the cross FG-1 × Mingxian 169 both fit Mendelian ratios for a single dominant resistance gene when tested against multiple avirulent Blumeria tritici f. sp. tritici (Bgt) races. This gene was temporarily designated PmFG. PmFG was mapped on the multi-allelic Pm2 locus of chromosome 5DS using seven SSR, 10 single nucleotide polymorphism (SNP)-derived and two SCAR markers with the flanking markers Xbwm21/Xcfd81/Xscar112 (distal) and Xbwm25 (proximal) at 0.3 and 0.5 cM being the closest. Marker SCAR203 co-segregated with PmFG. Allelism tests between PmFG and documented Pm2 alleles confirmed that PmFG was allelic with Pm2. Line FG-1 produced a significantly different reaction pattern compared to other lines with genes at or near Pm2 when tested against 49 Bgt isolates. The PmFG-linked marker alleles detected by the SNP-derived markers revealed significant variation between FG-1 and other lines with genes at or near Pm2. It was concluded that PmFG is a new allele at the Pm2 locus. Data from seven closely linked markers tested on 31 wheat cultivars indicated opportunities for marker-assisted pyramiding of this gene with other genes for powdery mildew resistance and additional traits.

  9. Testing for Ancient Selection Using Cross-population Allele Frequency Differentiation.

    PubMed

    Racimo, Fernando

    2016-02-01

    A powerful way to detect selection in a population is by modeling local allele frequency changes in a particular region of the genome under scenarios of selection and neutrality and finding which model is most compatible with the data. A previous method based on a cross-population composite likelihood ratio (XP-CLR) uses an outgroup population to detect departures from neutrality that could be compatible with hard or soft sweeps, at linked sites near a beneficial allele. However, this method is most sensitive to recent selection and may miss selective events that happened a long time ago. To overcome this, we developed an extension of XP-CLR that jointly models the behavior of a selected allele in a three-population tree. Our method - called "3-population composite likelihood ratio" (3P-CLR) - outperforms XP-CLR when testing for selection that occurred before two populations split from each other and can distinguish between those events and events that occurred specifically in each of the populations after the split. We applied our new test to population genomic data from the 1000 Genomes Project, to search for selective sweeps that occurred before the split of Yoruba and Eurasians, but after their split from Neanderthals, and that could have led to the spread of modern-human-specific phenotypes. We also searched for sweep events that occurred in East Asians, Europeans, and the ancestors of both populations, after their split from Yoruba. In both cases, we are able to confirm a number of regions identified by previous methods and find several new candidates for selection in recent and ancient times. For some of these, we also find suggestive functional mutations that may have driven the selective events.

  10. STR allele sequence variation: Current knowledge and future issues.

    PubMed

    Gettings, Katherine Butler; Aponte, Rachel A; Vallone, Peter M; Butler, John M

    2015-09-01

    This article reviews what is currently known about short tandem repeat (STR) allelic sequence variation in and around the twenty-four loci most commonly used throughout the world to perform forensic DNA investigations. These STR loci include D1S1656, TPOX, D2S441, D2S1338, D3S1358, FGA, CSF1PO, D5S818, SE33, D6S1043, D7S820, D8S1179, D10S1248, TH01, vWA, D12S391, D13S317, Penta E, D16S539, D18S51, D19S433, D21S11, Penta D, and D22S1045. All known reported variant alleles are compiled along with genomic information available from GenBank, dbSNP, and the 1000 Genomes Project. Supplementary files are included which provide annotated reference sequences for each STR locus, characterize genomic variation around the STR repeat region, and compare alleles present in currently available STR kit allelic ladders. Looking to the future, STR allele nomenclature options are discussed as they relate to next generation sequencing efforts underway.

  11. Estimating Relatedness in the Presence of Null Alleles

    PubMed Central

    Huang, Kang; Ritland, Kermit; Dunn, Derek W.; Qi, Xiaoguang; Guo, Songtao; Li, Baoguo

    2016-01-01

    Studies of genetics and ecology often require estimates of relatedness coefficients based on genetic marker data. However, with the presence of null alleles, an observed genotype can represent one of several possible true genotypes. This results in biased estimates of relatedness. As the numbers of marker loci are often limited, loci with null alleles cannot be abandoned without substantial loss of statistical power. Here, we show how loci with null alleles can be incorporated into six estimators of relatedness (two novel). We evaluate the performance of various estimators before and after correction for null alleles. If the frequency of a null allele is <0.1, some estimators can be used directly without adjustment; if it is >0.5, the potency of estimation is too low and such a locus should be excluded. We make available a software package entitled PolyRelatedness v1.6, which enables researchers to optimize these estimators to best fit a particular data set. PMID:26500259

  12. Assessing allelic dropout and genotype reliability using maximum likelihood.

    PubMed Central

    Miller, Craig R; Joyce, Paul; Waits, Lisette P

    2002-01-01

    A growing number of population genetic studies utilize nuclear DNA microsatellite data from museum specimens and noninvasive sources. Genotyping errors are elevated in these low quantity DNA sources, potentially compromising the power and accuracy of the data. The most conservative method for addressing this problem is effective, but requires extensive replication of individual genotypes. In search of a more efficient method, we developed a maximum-likelihood approach that minimizes errors by estimating genotype reliability and strategically directing replication at loci most likely to harbor errors. The model assumes that false and contaminant alleles can be removed from the dataset and that the allelic dropout rate is even across loci. Simulations demonstrate that the proposed method marks a vast improvement in efficiency while maintaining accuracy. When allelic dropout rates are low (0-30%), the reduction in the number of PCR replicates is typically 40-50%. The model is robust to moderate violations of the even dropout rate assumption. For datasets that contain false and contaminant alleles, a replication strategy is proposed. Our current model addresses only allelic dropout, the most prevalent source of genotyping error. However, the developed likelihood framework can incorporate additional error-generating processes as they become more clearly understood. PMID:11805071

  13. Rare allelic forms of PRDM9 associated with childhood leukemogenesis

    PubMed Central

    Hussin, Julie; Sinnett, Daniel; Casals, Ferran; Idaghdour, Youssef; Bruat, Vanessa; Saillour, Virginie; Healy, Jasmine; Grenier, Jean-Christophe; de Malliard, Thibault; Busche, Stephan; Spinella, Jean-François; Larivière, Mathieu; Gibson, Greg; Andersson, Anna; Holmfeldt, Linda; Ma, Jing; Wei, Lei; Zhang, Jinghui; Andelfinger, Gregor; Downing, James R.; Mullighan, Charles G.; Awadalla, Philip

    2013-01-01

    One of the most rapidly evolving genes in humans, PRDM9, is a key determinant of the distribution of meiotic recombination events. Mutations in this meiotic-specific gene have previously been associated with male infertility in humans and recent studies suggest that PRDM9 may be involved in pathological genomic rearrangements. In studying genomes from families with children affected by B-cell precursor acute lymphoblastic leukemia (B-ALL), we characterized meiotic recombination patterns within a family with two siblings having hyperdiploid childhood B-ALL and observed unusual localization of maternal recombination events. The mother of the family carries a rare PRDM9 allele, potentially explaining the unusual patterns found. From exomes sequenced in 44 additional parents of children affected with B-ALL, we discovered a substantial and significant excess of rare allelic forms of PRDM9. The rare PRDM9 alleles are transmitted to the affected children in half the cases; nonetheless there remains a significant excess of rare alleles among patients relative to controls. We successfully replicated this latter observation in an independent cohort of 50 children with B-ALL, where we found an excess of rare PRDM9 alleles in aneuploid and infant B-ALL patients. PRDM9 variability in humans is thought to influence genomic instability, and these data support a potential role for PRDM9 variation in risk of acquiring aneuploidies or genomic rearrangements associated with childhood leukemogenesis. PMID:23222848

  14. Rare allelic forms of PRDM9 associated with childhood leukemogenesis.

    PubMed

    Hussin, Julie; Sinnett, Daniel; Casals, Ferran; Idaghdour, Youssef; Bruat, Vanessa; Saillour, Virginie; Healy, Jasmine; Grenier, Jean-Christophe; de Malliard, Thibault; Busche, Stephan; Spinella, Jean-François; Larivière, Mathieu; Gibson, Greg; Andersson, Anna; Holmfeldt, Linda; Ma, Jing; Wei, Lei; Zhang, Jinghui; Andelfinger, Gregor; Downing, James R; Mullighan, Charles G; Awadalla, Philip

    2013-03-01

    One of the most rapidly evolving genes in humans, PRDM9, is a key determinant of the distribution of meiotic recombination events. Mutations in this meiotic-specific gene have previously been associated with male infertility in humans and recent studies suggest that PRDM9 may be involved in pathological genomic rearrangements. In studying genomes from families with children affected by B-cell precursor acute lymphoblastic leukemia (B-ALL), we characterized meiotic recombination patterns within a family with two siblings having hyperdiploid childhood B-ALL and observed unusual localization of maternal recombination events. The mother of the family carries a rare PRDM9 allele, potentially explaining the unusual patterns found. From exomes sequenced in 44 additional parents of children affected with B-ALL, we discovered a substantial and significant excess of rare allelic forms of PRDM9. The rare PRDM9 alleles are transmitted to the affected children in half the cases; nonetheless there remains a significant excess of rare alleles among patients relative to controls. We successfully replicated this latter observation in an independent cohort of 50 children with B-ALL, where we found an excess of rare PRDM9 alleles in aneuploid and infant B-ALL patients. PRDM9 variability in humans is thought to influence genomic instability, and these data support a potential role for PRDM9 variation in risk of acquiring aneuploidies or genomic rearrangements associated with childhood leukemogenesis.

  15. A Platform for Interrogating Cancer-Associated p53 Alleles

    PubMed Central

    D’Brot, Alejandro; Kurtz, Paula; Regan, Erin; Jakubowski, Brandon; Abrams, John M

    2016-01-01

    p53 is the most frequently mutated gene in human cancer. Compelling evidence argues that full transformation involves loss of growth suppression encoded by wild-type p53 together with poorly understood oncogenic activity encoded by missense mutations. Furthermore, distinguishing disease alleles from natural polymorphisms is an important clinical challenge. To interrogate the genetic activity of human p53 variants, we leveraged the Drosophila model as an in vivo platform. We engineered strains that replace the fly p53 gene with human alleles, producing a collection of stocks that are, in effect, ‘humanized’ for p53 variants. Like the fly counterpart, human p53 transcriptionally activated a biosensor and induced apoptosis after DNA damage. However, all humanized strains representing common alleles found in cancer patients failed to complement in these assays. Surprisingly, stimulus-dependent activation of hp53 occurred without stabilization, demonstrating that these two processes can be uncoupled. Like its fly counterpart, hp53 formed prominent nuclear foci in germline cells but cancer-associated p53 variants did not. Moreover, these same mutant alleles disrupted hp53 foci and inhibited biosensor activity, suggesting that these properties are functionally linked. Together these findings establish a functional platform for interrogating human p53 alleles and suggest that simple phenotypes could be used to stratify disease variants. PMID:26996664

  16. Identification and characterization of variant alleles at CODIS STR loci.

    PubMed

    Allor, Catherine; Einum, David D; Scarpetta, Marco

    2005-09-01

    Short tandem repeat (STR) profiles from 32,671 individuals generated by the ABI Profiler Plus and Cofiler systems were screened for variant alleles not represented within manufacturer-provided allelic ladders. A total of 85 distinct variants were identified at 12 of the 13 CODIS loci, most of which involve a truncated tetranucleotide repeat unit. Twelve novel alleles, identified at D3S1358, FGA, D18S51, D5S818, D7S820 and TPOX, were confirmed by nucleotide sequence analysis and include both insertions and deletions involving the repeat units themselves as well as DNA flanking the repeat regions. Population genetic data were collected for all variants and frequencies range from 0.0003 (many single observations) to 0.0042 (D7S820 '10.3' in North American Hispanics). In total, the variant alleles identified in this study are carried by 1.6% of the estimated 1 million individuals tested annually in the U.S. for the purposes of parentage resolution. A paternity case involving a recombination event of paternal origin is presented and demonstrates how variant alleles can significantly strengthen the genetic evidence in troublesome cases. In such instances, increased costs and turnaround time associated with additional testing may be eliminated.

  17. Offer/Acceptance Ratio.

    ERIC Educational Resources Information Center

    Collins, Mimi

    1997-01-01

    Explores how human resource professionals, with above average offer/acceptance ratios, streamline their recruitment efforts. Profiles company strategies with internships, internal promotion, cooperative education programs, and how to get candidates to accept offers. Also discusses how to use the offer/acceptance ratio as a measure of program…

  18. ADHD and Depression Symptoms in Parent Couples Predict Response to Child ADHD and ODD Behavior.

    PubMed

    Wymbs, Brian T; Dawson, Anne E; Egan, Theresa E; Sacchetti, Gina M; Tams, Sean T; Wymbs, Frances A

    2017-04-01

    Parents of children with attention-deficit hyperactivity disorder (ADHD) and oppositional defiant disorder (ODD) often have elevated ADHD and depressive symptoms, both of which increase the risk of ineffective parenting and interparental discord. However, little is known about whether child ADHD/ODD behavior and parent ADHD or depressive symptoms uniquely or synergistically predict the quality of parenting and interparental communication during triadic (mother-father-child) interactions. Ninety parent couples, including 51 who have children diagnosed with ADHD, were randomly assigned to interact with a 9-12 year-old confederate child (84 % male) exhibiting either ADHD/ODD-like behavior or typical behavior. Parents reported their own ADHD and depressive symptoms, and parents and observers rated the quality of parenting and interparental communication during the interaction. Actor-partner interdependence modeling indicated that child ADHD/ODD behavior predicted less positive and more negative parenting and communication, independent of adult ADHD and depressive symptoms. Parent couples including two parents with elevated ADHD communicated more positively while managing children exhibiting ADHD/ODD behavior than couples managing children behaving typically or couples with only one parent with elevated ADHD symptoms. Couples including one parent with, and one parent without, elevated ADHD or depressive symptoms parented less positively and more negatively, and communicated more negatively, when managing children exhibiting ADHD/ODD behavior than when managing children behaving typically. Taken together, depending on the similarity of ADHD and depressive symptom levels in parent couples, adults managing children exhibiting ADHD/ODD behavior may parent or communicate positively or negatively. Findings highlight the need to consider the psychopathology of both parents when treating children with ADHD in two-parent homes.

  19. Studies of a Large Odd-Numbered Odd-Electron Metal Ring: Inelastic Neutron Scattering and Muon Spin Relaxation Spectroscopy of Cr8 Mn.

    PubMed

    Baker, Michael L; Lancaster, Tom; Chiesa, Alessandro; Amoretti, Giuseppe; Baker, Peter J; Barker, Claire; Blundell, Stephen J; Carretta, Stefano; Collison, David; Güdel, Hans U; Guidi, Tatiana; McInnes, Eric J L; Möller, Johannes S; Mutka, Hannu; Ollivier, Jacques; Pratt, Francis L; Santini, Paolo; Tuna, Floriana; Tregenna-Piggott, Philip L W; Vitorica-Yrezabal, Iñigo J; Timco, Grigore A; Winpenny, Richard E P

    2016-01-26

    The spin dynamics of Cr8 Mn, a nine-membered antiferromagnetic (AF) molecular nanomagnet, are investigated. Cr8 Mn is a rare example of a large odd-membered AF ring, and has an odd-number of 3d-electrons present. Odd-membered AF rings are unusual and of interest due to the presence of competing exchange interactions that result in frustrated-spin ground states. The chemical synthesis and structures of two Cr8 Mn variants that differ only in their crystal packing are reported. Evidence of spin frustration is investigated by inelastic neutron scattering (INS) and muon spin relaxation spectroscopy (μSR). From INS studies we accurately determine an appropriate microscopic spin Hamiltonian and we show that μSR is sensitive to the ground-spin-state crossing from S=1/2 to S=3/2 in Cr8 Mn. The estimated width of the muon asymmetry resonance is consistent with the presence of an avoided crossing. The investigation of the internal spin structure of the ground state, through the analysis of spin-pair correlations and scalar-spin chirality, shows a non-collinear spin structure that fluctuates between non-planar states of opposite chiralities.

  20. Identification of two novel human CD1E alleles.

    PubMed

    Mirones, I; Oteo, M; Parra-Cuadrado, J F; Martínez-Naves, E

    2000-08-01

    CD1 is a family of proteins structurally related to major histocompatibility complex (MHC) molecules and specialized in presenting lipids or glycolipids to T cells. In humans, there are five CD1 genes (CD1A to CD1E). It has been shown that, in contrast with classical MHC genes, CD1 loci display a very limited polymorphism. In the present work we describe two novel CD1E alleles found in two healthy Caucasian individuals. One allele differs from the wild-type by a point mutation resulting in a replacement of arginine at position 154 by a tryptophan. In the second allele we found a substitution of the leucine 184 by a proline.

  1. Allele surfing promotes microbial adaptation from standing variation.

    PubMed

    Gralka, Matti; Stiewe, Fabian; Farrell, Fred; Möbius, Wolfram; Waclaw, Bartlomiej; Hallatschek, Oskar

    2016-08-01

    The coupling of ecology and evolution during range expansions enables mutations to establish at expanding range margins and reach high frequencies. This phenomenon, called allele surfing, is thought to have caused revolutions in the gene pool of many species, most evidently in microbial communities. It has remained unclear, however, under which conditions allele surfing promotes or hinders adaptation. Here, using microbial experiments and simulations, we show that, starting with standing adaptive variation, range expansions generate a larger increase in mean fitness than spatially uniform population expansions. The adaptation gain results from 'soft' selective sweeps emerging from surfing beneficial mutations. The rate of these surfing events is shown to sensitively depend on the strength of genetic drift, which varies among strains and environmental conditions. More generally, allele surfing promotes the rate of adaptation per biomass produced, which could help developing biofilms and other resource-limited populations to cope with environmental challenges.

  2. Generation and characterization of an analog-sensitive PERK allele.

    PubMed

    Maas, Nancy L; Singh, Nickpreet; Diehl, J Alan

    2014-08-01

    Restriction of nutrients and oxygen in the tumor microenvironment disrupts ER homeostasis and adaptation to such stress is mediated by the key UPR effector PERK. Given its pro-tumorigenic activity, significant efforts have been made to elucidate the molecular mechanisms that underlie PERK function. Chemical-genetic approaches have recently proven instrumental in pathway mapping and interrogating kinase function. To enable a detailed study of PERK signaling we have generated an analog-sensitive PERK allele that accepts N(6)-alkylated ATP analogs. We find that this allele can be regulated by bulky ATP-competitive inhibitors, confirming the identity of the PERK gatekeeper residue as methionine 886. Furthermore, this analog-sensitive allele can be used to specifically label substrates with thiophosphate both in vitro and in cells. These data highlight the potential for using chemical-genetic techniques to identify novel PERK substrates, thereby providing an expanded view of PERK function and further definition of its signaling networks.

  3. Extensive HLA class I allele promiscuity among viral CTL epitopes

    PubMed Central

    Frahm, Nicole; Yusim, Karina; Suscovich, Todd J.; Adams, Sharon; Sidney, John; Hraber, Peter; Hewitt, Hannah S.; Linde, Caitlyn H.; Kavanagh, Daniel G.; Woodberry, Tonia; Henry, Leah M.; Faircloth, Kellie; Listgarten, Jennifer; Kadie, Carl; Jojic, Nebojsa; Sango, Kaori; Brown, Nancy V.; Pae, Eunice; Zaman, M. Tauheed; Bihl, Florian; Khatri, Ashok; John, Mina; Mallal, Simon; Marincola, Francesco M.; Walker, Bruce D.; Sette, Alessandro; Heckerman, David; Korber, Bette T.; Brander, Christian

    2008-01-01

    Summary Promiscuous binding of T helper epitopes to MHC class II molecules has been well established, but few examples of promiscuous class I restricted epitopes exist. To address the extent of promiscuity of HLA class I peptides, responses to 242 well-defined viral epitopes were tested in 100 subjects regardless of the individuals’ HLA type. Surprisingly, half of all detected responses were seen in the absence of the originally reported restricting HLA class I allele, and only 3% of epitopes were recognized exclusively in the presence of their original allele. Functional assays confirmed the frequent recognition of HLA class I-restricted T cell epitopes on several alternative alleles across HLA class I supertypes and encoded on different class I loci. These data have significant implications for the understanding of MHC class I restricted antigen presentation and vaccine development. PMID:17705138

  4. Transmission ratio distortion results in asymmetric introgression in Louisiana Iris

    PubMed Central

    2010-01-01

    Background Linkage maps are useful tools for examining both the genetic architecture of quantitative traits and the evolution of reproductive incompatibilities. We describe the generation of two genetic maps using reciprocal interspecific backcross 1 (BC1) mapping populations from crosses between Iris brevicaulis and Iris fulva. These maps were constructed using expressed sequence tag (EST)- derived codominant microsatellite markers. Such a codominant marker system allowed for the ability to link the two reciprocal maps, and compare patterns of transmission ratio distortion observed between the two. Results Linkage mapping resulted in markers that coalesced into 21 linkage groups for each of the reciprocal backcross maps, presumably corresponding to the 21 haploid chromosomes of I. brevicaulis and I. fulva. The composite map was 1190.0-cM long, spanned 81% of the I. brevicaulis and I. fulva genomes, and had a mean density of 4.5 cM per locus. Transmission ratio distortion (TRD) was observed in 138 (48.5%) loci distributed in 19 of the 21 LGs in BCIB, BCIF, or both BC1 mapping populations. Of the distorted markers identified, I. fulva alleles were detected at consistently higher-than-expected frequencies in both mapping populations. Conclusions The observation that I. fulva alleles are overrepresented in both mapping populations suggests that I. fulva alleles are favored to introgress into I. brevicaulis genetic backgrounds, while I. brevicaulis alleles would tend to be prevented from introgressing into I. fulva. These data are consistent with the previously observed patterns of introgression in natural hybrid zones, where I. fulva alleles have been consistently shown to introgress across species boundaries. PMID:20298609

  5. Distribution of a pseudodeficiency allele among Tay-Sachs carriers

    SciTech Connect

    Tomczak, J.; Grebner, E.E. ); Boogen, C. )

    1993-08-01

    Recently Triggs-Raine et al. (1992) identified a new mutation in the gene coding for the [alpha]-subunit of [beta]-hexosaminidase A (hex A), the enzyme whose deficiency causes Tay-Sachs disease. This mutation, a C[sub 739]-to-T transition in exon 7, results in an altered enzyme that is active (albeit at reduced levels) in cells but that has essentially no activity in serum. This so-called pseudodeficient allele was first detected in compound heterozygotes who also carried a Tay-Sachs disease allele and therefore had no detectable hex A in their serum but who were in good health. Carriers of this apparently benign mutation are generally indistinguishable from carriers of a lethal mutation by means of routine enzyme-based screening tests, because the product of the pseudodeficient allele is not detectable in serum and has decreased activity in cells. This suggests that some individuals who have been classified as Tay-Sachs carriers are actually carriers of the pseudodeficient allele and are not at risk to have a child affected with Tay-Sachs disease. The pseudodeficient allele may also be responsible for some inconclusive diagnoses, where leukocyte values fall below the normal range but are still above the carrier range. The fact that there are now two mutant alleles (the psuedodeficient and the adult) that are indistinguishable from the lethal infantile mutations by means of enzyme assay yet that are phenotypically very different and that together may account for as much as 12% of enzyme-defined carriers on the basis of the data here suggests that DNA analysis should be part of a comprehensive screening program. It will be particularly useful to identify the mutations in couples at risk, before they undergo prenatal diagnosis. DNA analysis will also resolve some inconclusive diagnoses.

  6. α -decay spectra of odd nuclei using the effective Skyrme interaction

    NASA Astrophysics Data System (ADS)

    Ward, D. E.; Carlsson, B. G.; Åberg, S.

    2015-07-01

    Background: For nuclei heavier than 208Pb α decay is a dominating decay mode. α decay of odd nuclei can give spectroscopic information because different states in the daughter nucleus can be populated in the decay. Purpose: To explore and test microscopic descriptions of α decay of odd nuclei based on self-consistent models with effective nuclear interactions. To predict the hindrance of α decay of odd-A superheavy nuclei. Methods: We apply the method of our previous work [15e D. E. Ward, B. G. Carlsson, and S. Åberg, Phys. Rev. C 88, 064316 (2013), 10.1103/PhysRevC.88.064316] to the case of odd-A near-spherical nuclei. The Skyrme effective interaction SLy4 is used. Starting from the obtained Hartree-Fock-Bogoliubov vacuum and quasiparticle excitations, the α -particle formation amplitude is calculated giving the decay rates and hindrance of different α -decay channels. Result: The calculated relative decay rates show good agreement with available data. The hindrance of decay channels where the odd nucleon changes orbital is reasonably described by the microscopic calculation. Several hindered ground-state decays of superheavy nuclei are predicted, implying possible α -γ coincidences. Conclusions: The approach offers a practical method of making quantitative predictions for the relative hindrance of different α -decay channels.

  7. A common allele on chromosome 9 associated with coronary heartdisease

    SciTech Connect

    McPherson, Ruth; Pertsemlidis, Alexander; Kavaslar, Nihan; Stewart, Alexandre; Roberts, Robert; Cox, David R.; Hinds, David; Pennachio, Len; Tybjaerg-Hansen, Anne; Folsom, Aaron R.; Boerwinkle,Eric; Hobbs, Helen H.; Cohen, Jonathan C.

    2007-03-01

    Coronary heart disease (CHD) is a major cause of death in Western countries. Here we used genome-wide association scanning to identify a 58 kb interval on chromosome 9 that was consistently associated with CHD in six independent samples. The interval contains no annotated genes and is not associated with established CHD risk factors such as plasma lipoproteins, hypertension or diabetes. Homozygotes for the risk allele comprise 20-25% of Caucasians and have a {approx}30-40% increased risk of CHD. These data indicate that the susceptibility allele acts through a novel mechanism to increase CHD risk in a large fraction of the population.

  8. Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species.

    PubMed

    Waters, Amanda J; Bilinski, Paul; Eichten, Steven R; Vaughn, Matthew W; Ross-Ibarra, Jeffrey; Gehring, Mary; Springer, Nathan M

    2013-11-26

    In plants, a subset of genes exhibit imprinting in endosperm tissue such that expression is primarily from the maternal or paternal allele. Imprinting may arise as a consequence of mechanisms for silencing of transposons during reproduction, and in some cases imprinted expression of particular genes may provide a selective advantage such that it is conserved across species. Separate mechanisms for the origin of imprinted expression patterns and maintenance of these patterns may result in substantial variation in the targets of imprinting in different species. Here we present deep sequencing of RNAs isolated from reciprocal crosses of four diverse maize genotypes, providing a comprehensive analysis that allows evaluation of imprinting at more than 95% of endosperm-expressed genes. We find that over 500 genes exhibit statistically significant parent-of-origin effects in maize endosperm tissue, but focused our analyses on a subset of these genes that had >90% expression from the maternal allele (69 genes) or from the paternal allele (108 genes) in at least one reciprocal cross. Over 10% of imprinted genes show evidence of allelic variation for imprinting. A comparison of imprinting in maize and rice reveals that 13% of genes with syntenic orthologs in both species exhibit conserved imprinting. Genes that exhibit conserved imprinting between maize and rice have elevated nonsynonymous to synonymous substitution ratios compared with other imprinted genes, suggesting a history of more rapid evolution. Together, these data suggest that imprinting only has functional relevance at a subset of loci that currently exhibit imprinting in maize.

  9. Ground-state properties of even and odd Magnesium isotopes in a symmetry-conserving approach

    NASA Astrophysics Data System (ADS)

    Borrajo, Marta; Egido, J. Luis

    2017-01-01

    We present a self-consistent theory for odd nuclei with exact blocking and particle number and angular momentum projection. The demanding treatment of the pairing correlations in a variation-after-projection approach as well as the explicit consideration of the triaxial deformation parameters in a projection after variation method, together with the use of the finite-range density-dependent Gogny force, provides an excellent tool for the description of odd-even and even-even nuclei. We apply the theory to the Magnesium isotopic chain and obtain an outstanding description of the ground-state properties, in particular binding energies, odd-even mass differences, mass radii and electromagnetic moments among others.

  10. Global systematics of unique parity quasibands in odd-A collective nuclei

    NASA Astrophysics Data System (ADS)

    Bucurescu, D.; Cǎta-Danil, G.; Ivaşcu, M.; Stroe, L.; Ur, C. A.

    1994-04-01

    All known structures in the collective medium and heavy odd-A nuclei, based on the unique parity orbitals g9/2, h11/2, and i13/2, are collected and correlations between the energies within both the favored and unfavored quasibands are analyzed. A first startling result is that irrespective of the nature of the odd particle and the shell model orbital, for most of the nondeformed nuclei the energies within these quasibands, show a universal behavior of an anharmonic vibrator with a constant anharmonicity, identical with that found for the even-even nuclei. Second, the rapid transition between the anharmonic vibrator and the rotor regimes, which takes place in the even-even nuclei, is accompanied, in the adjacent odd-A nuclei, by an equally rapid transition from the anharmonic vibrator to the strong coupling regime.

  11. Positive parity low spin states of odd-mass tellurium isotopes

    NASA Astrophysics Data System (ADS)

    Yazar, Harun Reşit

    2006-11-01

    In this work, we analyse the positive parity of states of odd-mass nucleus within the framework of interacting boson fermion model. The result of an IBFM-1 multilevel calculation with the lg 9/2, 2d 5/2, 2d 3/2, 3s 1/2 and one level, 1h 11/2 with negative parity, single particle orbits is reported for the positive parity states of the odd mass nucleus 123-125Te. Also, an IBM-1 calculation is presented for the low-lying states in the even-even 124-126Te core nucleus. The energy levels and B (E2) transition probabilities were calculated and compared with the experimental data. It was found that the calculated positive parity low spin state energy spectra of the odd-mass 123-125Te isotopes agree quite well with the experimental data.

  12. Odd-parity superconductivity by competing spin-orbit coupling and orbital effect in artificial heterostructures

    NASA Astrophysics Data System (ADS)

    Watanabe, Tatsuya; Yoshida, Tomohiro; Yanase, Youichi

    2015-11-01

    We show that odd-parity superconductivity occurs in multilayer Rashba systems without requiring spin-triplet Cooper pairs. A pairing interaction in the spin-singlet channel stabilizes the odd-parity pair-density-wave (PDW) state in the magnetic field parallel to the two-dimensional conducting plane. It is shown that the layer-dependent Rashba spin-orbit coupling and the orbital effect play essential roles for the PDW state in binary and tricolor heterostructures. We demonstrate that the odd-parity PDW state is a symmetry-protected topological superconducting state characterized by the one-dimensional winding number in the symmetry class BDI. The superconductivity in the artificial heavy-fermion superlattice CeCoIn5/YbCoIn5 and bilayer interface SrTiO3/LaAlO3 is discussed.

  13. Influences of Vehicle Size and Mass and Selected Driver Factors on Odds of Driver Fatality

    PubMed Central

    Padmanaban, Jeya

    2003-01-01

    Research was undertaken to determine vehicle size parameters influencing driver fatality odds, independent of mass, in two-vehicle collisions. Forty vehicle parameters were evaluated for 1,500 vehicle groupings. Logistic regression analyses show driver factors (belt use, age, drinking) collectively contribute more to fatality odds than vehicle factors, and that mass is the most important vehicular parameter influencing fatality odds for all crash configurations. In car crashes, other vehicle parameters with statistical significance had a second order effect compared to mass. In light truck-to-car crashes, “vehicle type-striking vehicle is light truck” was the most important parameter after mass, followed by vehicle height and bumper height, with second order effect. To understand the importance of “vehicle type” variable, further investigation of vehicle “stiffness” and other passenger car/light truck differentiating parameters is warranted. PMID:12941244

  14. Even- and odd-parity finite-element transport solutions in the thick diffusion limit

    SciTech Connect

    Adams, M.L.

    1991-01-07

    We analyze the behavior of odd-parity continuous finite-element methods (CFEMs) for problems that contain diffusive regions. We find that each of these method produces a solution that, to leading order inside diffusive regions, satisfies a discretization of the diffusion equation. We find further that these leading-order solutions satisfy boundary conditions that can lead to large errors in the interior solution. We recognize, however, that we can combine an odd-purity CFEM solution and an even-parity CFEM solution and obtain a solution that satisfies very accurate boundary conditions. Our analysis holds in three-dimensional Cartesian geometry, with an arbitrary spatial grid. We give numerical results from slab-geometry; these invariably agree with the predictions of the analysis. Finally, we introduce a rapidly-convergent diffusion-synthetic acceleration scheme for the odd-parity CFEMs, which we believe is new. 18 refs., 3 figs.

  15. Atmospheric odd oxygen production due to the photodissociation of ordinary and isotopic molecular oxygen

    NASA Technical Reports Server (NTRS)

    Omidvar, K.; Frederick, J. E.

    1987-01-01

    Line-by-line calculations are performed to determine the contributions of the Schumann-Runge bands of ordinary and isotopic oxygen to the photodissociation of these molecules at different altitudes. The contributions to the dissociation rates of the satellite lines and of the first and higher vibrational states of the initial molecular states are found to be insignificant. At 70 km, (O-16)(O-18) is found to produce 10 times as much odd oxygen as would be produced if the isotope did not have selective absorption, and 6 percent of the odd oxygen produced is due to this isotope. It is noted that the excess odd oxygen produced is not enough to explain the excess quantity of ozone observed in the atmosphere, which cannot be accounted for in photochemical models. Comparison with previous results is made.

  16. High Aspect Ratio Wrinkles

    NASA Astrophysics Data System (ADS)

    Chen, Yu-Cheng; Crosby, Alfred

    2015-03-01

    Buckling-induced surface undulations are widely found in living creatures, for instance, gut villi and the surface of flower petal cells. These undulations provide unique functionalities with their extremely high aspect ratios. For the synthetic systems, sinusoidal wrinkles that are induced by buckling a thin film attached on a soft substrate have been proposed to many applications. However, the impact of the synthetic wrinkles have been restricted by limited aspect ratios, ranging from 0 to 0.35. Within this range, wrinkle aspect ratio is known to increase with increasing compressive strain until a critical strain is reached, at which point wrinkles transition to localizations, such as folds or period doublings. Inspired by the living creatures, we propose that wrinkles can be stabilized in high aspect ratio by manipulating the strain energy in the substrate. We experimentally demonstrate this idea by forming a secondary crosslinking network in the wrinkled surface and successfully achieve aspect ratio as large as 0.8. This work not only provides insights for the mechanism of high aspect ratio structures seen in living creatures, but also demonstrates significant promise for future wrinkle-based applications.

  17. Odd sensation induced by moving-phantom which triggers subconscious motor program.

    PubMed

    Fukui, Takao; Kimura, Toshitaka; Kadota, Koji; Shimojo, Shinsuke; Gomi, Hiroaki

    2009-06-03

    Our motor actions are sometimes not properly performed despite our having complete understanding of the environmental situation with a suitable action intention. In most cases, insufficient skill for motor control can explain the improper performance. A notable exception is the action of stepping onto a stopped escalator, which causes clumsy movements accompanied by an odd sensation. Previous studies have examined short-term sensorimotor adaptations to treadmills and moving sleds, but the relationship between the odd sensation and behavioral properties in a real stopped-escalator situation has never been examined. Understanding this unique action-perception linkage would help us to assess the brain function connecting automatic motor controls and the conscious awareness of action. Here we directly pose a question: Does the odd sensation emerge because of the unfamiliar motor behavior itself toward the irregular step-height of a stopped escalator or as a consequence of an automatic habitual motor program cued by the escalator itself. We compared the properties of motor behavior toward a stopped escalator (SE) with those toward moving escalator and toward a wooden stairs (WS) that mimicked the stopped escalator, and analyzed the subjective feeling of the odd sensation in the SE and WS conditions. The results show that moving escalator-specific motor actions emerged after participants had stepped onto the stopped escalator despite their full awareness that it was stopped, as if the motor behavior was guided by a "phantom" of a moving escalator. Additionally, statistical analysis reveals that postural forward sway that occurred after the stepping action is directly linked with the odd sensation. The results suggest a dissociation between conscious awareness and subconscious motor control: the former makes us perfectly aware of the current environmental situation, but the latter automatically emerges as a result of highly habituated visual input no matter how unsuitable

  18. Clonal Ordering of 17p and 5q Allelic Losses in Barrett Dysplasia and Adenocarcinoma

    NASA Astrophysics Data System (ADS)

    Blount, Patricia L.; Meltzer, Stephen J.; Yin, Jing; Huang, Ying; Krasna, Mark J.; Reid, Brian J.

    1993-04-01

    Both 17p and 5q allelic losses appear to be involved in the pathogenesis or progression of many human solid tumors. In colon carcinogenesis, there is strong evidence that the targets of the 17p and 5q allelic losses are TP53, the gene encoding p53, and APC, respectively. It is widely accepted that 5q allelic losses precede 17p allelic losses in the progression to colonic carcinoma. The data, however, supporting this proposed order are largely based on the prevalence of 17p and 5q allelic losses in adenomas and unrelated adenocarcinomas from different patients. We investigated the order in which 17p and 5q allelic losses developed during neoplastic progression in Barrett esophagus by evaluating multiple aneuploid cell populations from the same patient. Using DNA content flow cytometric cell sorting and polymerase chain reaction, 38 aneuploid cell populations from 14 patients with Barrett esophagus who had high grade dysplasia, cancer or both were evaluated for 17p and 5q allelic losses. 17p allelic losses preceded 5q allelic losses in 7 patients, both 17p and 5q allelic losses were present in all aneuploid populations of 4 patients, and only 17p (without 5q) allelic losses were present in the aneuploid populations of 3 patients. In no patient did we find that a 5q allelic loss preceded a 17p allelic loss. Our data suggest that 17p allelic losses typically occur before 5q allelic losses during neoplastic progression in Barrett esophagus.

  19. Association of BoLA DRB3 alleles with variability in immune response among the crossbred cattle vaccinated for foot-and-mouth disease (FMD).

    PubMed

    Gowane, G R; Sharma, A K; Sankar, M; Narayanan, K; Das, Biswajit; Subramaniam, S; Pattnaik, B

    2013-08-01

    Polymorphism of bovine leukocyte antigen (BoLA) DRB3 gene is being intensively investigated for potential association with economically important diseases of cattle. Accordingly, we investigated the association of DRB3 Exon 2 polymorphism as evidenced by the variation in the binding pockets with variability in immune response to inactivated trivalent (O, A and Asia1) foot and mouth disease virus (FMDV) vaccine in a closed population of crossbred cattle. Antibody titer of ≥ 1.8 was set as the cut off value to distinguish the protected (≥ 1.8) and unprotected (<1.8) animals. Eleven different alleles of over 3% frequency were detected in the population. We found that DRB3 alleles 0201, 0801 and 1501 always ranked high for protective immune response whereas alleles 0701, 1103 and 1101 consistently ranked low for unprotected immune response for all the three serotypes. Rank correlation of DRB3 alleles among the three serotypes was positive, high in magnitude and statistically significant (P<0.05). Logistic regression analysis revealed that odds of protection from the vaccine were highest for all the three serotypes if allele (∗)1501 was present and strengthened the results of allele ranking. Predicted amino acid substitution in the peptide binding pockets revealed that all the important sites had high Wu-Kabat index. Similarly, specific residues in pockets were crucial for immune response to FMD vaccine. There were specific substitutions in un-protected alleles such as absence of acidic amino acids substituted by basic amino acid at β71, presence of non-polar cysteine or basic histidine at β30 and presence of polar tyrosine at β37. From the observations, we hypothesize that the substitutions lead to unique conformational changes in the protein products of the studied alleles that would associate with the protective or unprotective antibody response to FMDV vaccine. The knowledge has potential implications in future selection programs if integrated with the

  20. Global correlations of unique parity structures in odd-A nuclei

    NASA Astrophysics Data System (ADS)

    Bucurescu, D.; Zamfir, N. V.; Cǎta-Danil, G.; Ivaşcu, M.; Stroe, L.; Ur, C. A.; Casten, R. F.

    1996-02-01

    All known unique parity structures in precollective odd-A nuclei (having cores with {E(4 1+) }/{E(2 1+) } < 2.0 ) are shown to behave similarly to the yrast quasibands in the neighboring even-even nuclei. This is interpreted in terms of a pair addition mode. With previous results on collective nuclei, this gives a tripartite classification of the evolution of the unique parity quasibands in odd-A nuclei. A simple index for signature splitting is also developed which avoids the need for complex analysis of Routhian structures.

  1. Sensitivity of odd-harmonic amplitudes to open quotient and skewing quotient in glottal airflow.

    PubMed

    Titze, Ingo R

    2015-01-01

    It is well known that a half-sinusoid has no odd harmonics other than the fundamental. If glottal flow in phonation were to approximate this exact waveshape, which is generally unlikely, some misperception of pitch and loss of vowel intelligibility would occur. The sensitivity of the glottal waveshape to this special shape is explored by systematically varying two parameters, open quotient and skewing quotient. Mild asymmetry (open quotient below 0.45 or above 0.55 and/or skewing quotient greater than 2.0) equalizes the odd-even harmonic series. Singers and speakers avoid the exact symmetry by skewing the flow pulse with source-filter interaction.

  2. High-purity Transmission of a Slow Light Odd Mode in a Photonic Crystal Waveguide

    DTIC Science & Technology

    2012-08-01

    Report (SAR) 18. NUMBER OF PAGES 3 19a. NAME OF RESPONSIBLE PERSON a. REPORT unclassified b. ABSTRACT unclassified c . THIS PAGE unclassified...the disper- sion of ng;odd. We have calculated Δng ng;odd − ng;even from the mixed-mode spectrum and plotted it in Fig. 4( c ). The peak spacing and...mode MZCs; (b) direct transmission with- out MZC and transmission with mixed-mode MZCs; ( c )Δng ob- tained from the mixed-mode spectrum; the solid

  3. An odd-number limitation of extended time-delayed feedback control in autonomous systems.

    PubMed

    Amann, Andreas; Hooton, Edward W

    2013-09-28

    We propose a necessary condition for the successful stabilization of a periodic orbit, using the extended version of time-delayed feedback control. This condition depends on the number of real Floquet multipliers larger than unity and is therefore related to the well-known odd-number limitation in non-autonomous systems. We show that the period of the orbit that is induced by mismatching the delay time of the control scheme and the period of the uncontrolled orbit plays an important role in the formulation of the odd-number limitation in the autonomous case.

  4. Nonminimal derivative coupling scalar-tensor theories: Odd-parity perturbations and black hole stability

    NASA Astrophysics Data System (ADS)

    Cisterna, Adolfo; Cruz, Miguel; Delsate, Térence; Saavedra, Joel

    2015-11-01

    We derive the odd-parity perturbation equation for the nonminimal kinetic coupling sector of the general Horndeski theory, where the kinetic term is coupled to the metric and the Einstein tensor. We derive the potential of the perturbation, by identifying a master function and switching to tortoise coordinates. We then prove the mode stability under linear odd-parity perturbations of hairy black holes in this sector of Horndeski theory, when a cosmological constant term in the action is included. Finally, we comment on the existence of slowly rotating black hole solutions in this setup and discuss their implications on the physics of compact object configurations, such as neutron stars.

  5. Collective states of odd nuclei in a model with quadrupole-octupole degrees of freedom

    SciTech Connect

    Minkov, N. Drenska, S. B.; Yotov, P.; Bonatsos, D. Scheid, W.

    2007-08-15

    We apply the collective axial quadrupole-octupole Hamiltonian to describe the rotation-vibration motion of odd nuclei with Coriolis coupling between the even-even core and the unpaired nucleon.We consider that the core oscillates coherently with respect to the quadrupole and octupole axialdeformation variables. The coupling between the core and the unpaired nucleon provides a split paritydoublet structure of the spectrum. The formalism successfully reproduces the parity-doublet splitting in a wide range of odd-A nuclei. It provides model estimations for the third angular-momentum projection K on the intrinsic symmetry axis and the related intrinsic nuclear structure.

  6. Microscopic multiphonon method for odd nuclei and its application to 17O

    NASA Astrophysics Data System (ADS)

    De Gregorio, G.; Knapp, F.; Lo Iudice, N.; Vesely, P.

    2016-12-01

    An equations of motion phonon method is extended to odd nuclei. It generates an orthonormal basis out of an odd particle coupled to n -phonon core states (n =0 ,1 ,2 ,⋯ ), built of Tamm-Dancoff phonons, and formulates the eigenvalue problem in such a multiphonon particle-core space. 17O is chosen as testing ground. An intrinsic chiral Hamiltonian is adopted in a large configuration space to perform a calculation using a Hartree-Fock (HF) basis in a space encompassing up to two and, under simplifying assumptions, three phonons. The impact of the different phonon components on spectrum, moments, transitions, and dipole cross section is discussed.

  7. General conditions for proximity induced odd-frequency superconductivity in two-dimensional electronic systems

    NASA Astrophysics Data System (ADS)

    Rossi, Enrico; Triola, Christopher; Badiane, Driss; Balatsky, Alexander V.

    We obtain the general conditions for the emergence of odd-frequency superconducting pairing in a two-dimensional (2D) electronic system proximity-coupled to a superconductor, making minimal assumptions about both the 2D system and the superconductor. Using our general results we show that a simple heterostructure formed by a monolayer of a group VI transition metal dichalcogenide, such as molybdenum disulfide, and an s-wave superconductor with Rashba spin-orbit coupling will exhibit odd-frequency superconducting pairing. Work supported by US DOE BES E304, KAW, ACS-PRF-53581-DNI5, and NSF-DMR-1455233.

  8. Stimulus-parity synaesthesia versus stimulus-dichotomy synaesthesia: Odd, even or something else?

    PubMed

    White, Rebekah C; Plassart, Anna

    2015-01-01

    In stimulus-parity synaesthesia, a range of stimuli-for example, letters, numbers, weekdays, months, and colours (the inducers)-elicit an automatic feeling of oddness or evenness (the concurrent). This phenomenon was first described by Théodore Flournoy in 1893, and has only recently been "rediscovered." Here, we describe an individual who experiences a comparable phenomenon, but uses the labels negative and positive rather than odd and even. Stimulus-parity synaesthesia may be broader than first supposed, and it is important that assessments are sensitive to this breadth.

  9. Tissue-specific patterns of allelically-skewed DNA methylation.

    PubMed

    Marzi, Sarah J; Meaburn, Emma L; Dempster, Emma L; Lunnon, Katie; Paya-Cano, Jose L; Smith, Rebecca G; Volta, Manuela; Troakes, Claire; Schalkwyk, Leonard C; Mill, Jonathan

    2016-01-01

    While DNA methylation is usually thought to be symmetrical across both alleles, there are some notable exceptions. Genomic imprinting and X chromosome inactivation are two well-studied sources of allele-specific methylation (ASM), but recent research has indicated a more complex pattern in which genotypic variation can be associated with allelically-skewed DNA methylation in cis. Given the known heterogeneity of DNA methylation across tissues and cell types we explored inter- and intra-individual variation in ASM across several regions of the human brain and whole blood from multiple individuals. Consistent with previous studies, we find widespread ASM with > 4% of the ∼220,000 loci interrogated showing evidence of allelically-skewed DNA methylation. We identify ASM flanking known imprinted regions, and show that ASM sites are enriched in DNase I hypersensitivity sites and often located in an extended genomic context of intermediate DNA methylation. We also detect examples of genotype-driven ASM, some of which are tissue-specific. These findings contribute to our understanding of the nature of differential DNA methylation across tissues and have important implications for genetic studies of complex disease. As a resource to the community, ASM patterns across each of the tissues studied are available in a searchable online database: http://epigenetics.essex.ac.uk/ASMBrainBlood.

  10. Distribution of forensic marker allelic frequencies in Pernambuco, Northestern Brazil.

    PubMed

    Santos, S M; Souza, C A; Rabelo, K C N; Souza, P R E; Moura, R R; Oliveira, T C; Crovella, S

    2015-04-30

    Pernambuco is one of the 27 federal units of Brazil, ranking seventh in the number of inhabitants. We examined the allele frequencies of 13 short tandem repeat loci (CFS1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, vWA, and TPOX), the minimum recommended by the Federal Bureau of Investigation and commonly used in forensic genetics laboratories in Brazil, in a sample of 609 unrelated individuals from all geographic regions of Pernambuco. The allele frequencies ranged from 5 to 47.2%. No significant differences for any loci analyzed were observed compared with other publications in other various regions of Brazil. Most of the markers observed were in Hardy-Weinberg equilibrium. The occurrence of the allele 47.2 (locus FGA) and alleles 35.1 and 39 (locus D21S11), also described in a single study of the Brazilian population, was observed. The other forensic parameters analyzed (matching probability, power of discrimination, polymorphic information content, paternity exclusion, complement factor I, observed heterozygosity, expected heterozygosity) indicated that the studied markers are very informative for human forensic identification purposes in the Pernambuco population.

  11. Allelism and Molecular Mapping of Soybean Necrotic Root Mutants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mutability of the w4 flower color locus in soybean [Glycine max (L.) Merr.] is conditioned by an allele designated w4-m. Germinal revertants recovered among self-pollinated progeny of mutable plants have been associated with the generation of necrotic root mutations, chlorophyll-deficiency mutation...

  12. A genotype probability index for multiple alleles and haplotypes.

    PubMed

    Percy, A; Kinghorn, B P

    2005-12-01

    We use linear algebra to calculate an index of information content in genotype probabilities which has previously been calculated using trigonometry. The new method can be generalized allowing the index to be calculated for loci with more than two alleles. Applications of this index include its use in genotyping strategies, strategies to manage genetic disorders and in estimation of genotype effects.

  13. Natural allelic variations in highly polyploidy Saccharum complex

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sugarcane (Saccharum spp.) as important sugar and biofuel crop are highly polypoid with complex genomes. A large amount of natural phenotypic variation exists in sugarcane germplasm. Understanding its allelic variance has been challenging but is a critical foundation for discovery of the genomic seq...

  14. Efficient nonmeiotic allele introgression in livestock using custom endonucleases

    PubMed Central

    Tan, Wenfang; Carlson, Daniel F.; Lancto, Cheryl A.; Garbe, John R.; Webster, Dennis A.; Hackett, Perry B.; Fahrenkrug, Scott C.

    2013-01-01

    We have expanded the livestock gene editing toolbox to include transcription activator-like (TAL) effector nuclease (TALEN)- and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-stimulated homology-directed repair (HDR) using plasmid, rAAV, and oligonucleotide templates. Toward the genetic dehorning of dairy cattle, we introgressed a bovine POLLED allele into horned bull fibroblasts. Single nucleotide alterations or small indels were introduced into 14 additional genes in pig, goat, and cattle fibroblasts using TALEN mRNA and oligonucleotide transfection with efficiencies of 10–50% in populations. Several of the chosen edits mimic naturally occurring performance-enhancing or disease- resistance alleles, including alteration of single base pairs. Up to 70% of the fibroblast colonies propagated without selection harbored the intended edits, of which more than one-half were homozygous. Edited fibroblasts were used to generate pigs with knockout alleles in the DAZL and APC genes to model infertility and colon cancer. Our methods enable unprecedented meiosis-free intraspecific and interspecific introgression of select alleles in livestock for agricultural and biomedical applications. PMID:24014591

  15. MHC class II DR allelic diversity in bighorn sheep

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We hypothesized that decreased diversity and/or unique polymorphisms in MHC class II alleles of bighorn sheep (BHS, Ovis canadensis) are responsible for lower titer of antibodies against Mannheimia haemolytica leukotoxin, in comparison to domestic sheep (DS, Ovis aries). To test this hypothesis, DRA...

  16. Tissue-specific patterns of allelically-skewed DNA methylation

    PubMed Central

    Marzi, Sarah J.; Meaburn, Emma L.; Dempster, Emma L.; Lunnon, Katie; Paya-Cano, Jose L.; Smith, Rebecca G.; Volta, Manuela; Troakes, Claire; Schalkwyk, Leonard C.; Mill, Jonathan

    2016-01-01

    ABSTRACT While DNA methylation is usually thought to be symmetrical across both alleles, there are some notable exceptions. Genomic imprinting and X chromosome inactivation are two well-studied sources of allele-specific methylation (ASM), but recent research has indicated a more complex pattern in which genotypic variation can be associated with allelically-skewed DNA methylation in cis. Given the known heterogeneity of DNA methylation across tissues and cell types we explored inter- and intra-individual variation in ASM across several regions of the human brain and whole blood from multiple individuals. Consistent with previous studies, we find widespread ASM with > 4% of the ∼220,000 loci interrogated showing evidence of allelically-skewed DNA methylation. We identify ASM flanking known imprinted regions, and show that ASM sites are enriched in DNase I hypersensitivity sites and often located in an extended genomic context of intermediate DNA methylation. We also detect examples of genotype-driven ASM, some of which are tissue-specific. These findings contribute to our understanding of the nature of differential DNA methylation across tissues and have important implications for genetic studies of complex disease. As a resource to the community, ASM patterns across each of the tissues studied are available in a searchable online database: http://epigenetics.essex.ac.uk/ASMBrainBlood. PMID:26786711

  17. Estimating the age of alleles by use of intraallelic variability

    SciTech Connect

    Slatkin, M.; Rannala, B.

    1997-02-01

    A method is presented for estimating the age of an allele by use of its frequency and the extent of variation among different copies. The method uses the joint distribution of the number of copies in a population sample and the coalescence times of the intraallelic gene genealogy conditioned on the number of copies. The linear birth-death process is used to approximate the dynamics of a rare allele in a finite population. A maximum-likelihood estimate of the age of the allele is obtained by Monte Carlo integration over the coalescence times. The method is applied to two alleles at the cystic fibrosis (CFTR) locus, {Delta}F508 and G542X, for which intraallelic variability at three intronic microsatellite loci has been examined. Our results indicate that G542X is somewhat older than {Delta}F508. Although absolute estimates depend on the mutation rates at the microsatellite loci, our results support the hypothesis that {Delta}F508 arose <500 generations ({approx}10,000 years) ago. 32 refs., 4 figs.

  18. Multifragment alleles in DNA fingerprints of the parrot, Amazona ventralis

    USGS Publications Warehouse

    Brock, M.K.; White, B.N.

    1991-01-01

    Human DNA probes that identify variable numbers of tandem repeat loci are being used to generate DNA fingerprints in many animal and plant species. In most species the majority of the sc rable autoradiographic bands of the DNA fingerprint represent alleles from numerous unlinked loci. This study was initiated to use DNA fingerprints to determine the amount of band-sharing among captive Hispaniolan parrots (Amazona ventralis) with known genetic relationships. This would form the data base to examine DNA fingerprints of the closely related and endangered Puerto Rican parrot (A. vittata) and to estimate the degree of inbreeding in the relic population. We found by segregation analysis of the bands scored in the DNA fingerprints of the Hispaniolan parrots that there may be as few as two to five loci identified by the human 33.15 probe. Furthermore, at one locus we identified seven alleles, one of which is represented by as many as 19 cosegregating bands. It is unknown how common multiband alleles might be in natural populations, and their existence will cause problems in the assessment of relatedness by band-sharing analysis. We believe, therefore, that a pedigree analysis should be included in all DNA fingerprinting studies, where possible, in order to estimate the number of loci identified by a minisatellite DNA probe and to examine the nature of their alleles.

  19. Registration of two allelic erect leaf mutants of sorghum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two allelic sorghum [Sorghum bicolor (L.) Moench] erect leaf (erl) mutants were isolated from an Annotated Individually-pedigreed Mutagenized Sorghum (AIMS) mutant library developed at the Plant Stress and Germplasm Development Unit, at Lubbock, Texas. The two mutants, erl1-1 and erl1-2, were isol...

  20. Substituting homemade fruit juice for sugar-sweetened beverages is associated with lower odds of metabolic syndrome among Hispanic adults.

    PubMed

    Mattei, Josiemer; Malik, Vasanti; Hu, Frank B; Campos, Hannia

    2012-06-01

    Consumption of sugar-sweetened beverages (SSB) has been associated with metabolic syndrome (MetS); however, studies conducted on Hispanic adults are scarce. To determine the association between beverages consumed by Hispanic adults and MetS and its components, data were analyzed in 1872 Costa Rican adults who served as controls of a population-based, case-control study of coronary heart disease. Multivariate-adjusted means were calculated for components of MetS by servings (never, ≤ 1/wk; 2-6/wk, ≥ 1/d) of 2 traditional fruit-based beverages ("fresco" and freshly-squeezed homemade fruit juice, separately) and 2 SSB (instant drinks and regular sodas, separately and combined). The prevalence ratio (PR) of MetS was calculated for each beverage and the OR was calculated by substituting one serving of homemade fruit juice or water for one of SSB. Significant positive trends were observed for increasing servings of instant drinks with plasma TG and waist circumference and for regular soda with waist circumference (all P-trend < 0.001). Increasing servings of homemade fruit juice were positively associated with HDL cholesterol (P-trend = 0.033). Consuming ≥1 serving/d of instant drinks was associated with a higher PR of MetS [1.42 (95% CI: 1.11, 1.83)] compared with no consumption. Substituting one serving of homemade fruit juice for instant drink was associated with 29% (95% CI: 7, 47%) lower odds of MetS and for regular soda with 30% (95% CI: 1, 50%) lower odds. Substituting water for combined SSB was marginally significant (OR = 0.86 (95% CI: 0.74, 1.00). In conclusion, reducing the consumption of SSB and substituting them with homemade fruit juices in moderation may be a culturally appropriate approach to lower MetS among Hispanic adults.

  1. Testing for Ancient Selection Using Cross-population Allele Frequency Differentiation

    PubMed Central

    Racimo, Fernando

    2016-01-01

    A powerful way to detect selection in a population is by modeling local allele frequency changes in a particular region of the genome under scenarios of selection and neutrality and finding which model is most compatible with the data. A previous method based on a cross-population composite likelihood ratio (XP-CLR) uses an outgroup population to detect departures from neutrality that could be compatible with hard or soft sweeps, at linked sites near a beneficial allele. However, this method is most sensitive to recent selection and may miss selective events that happened a long time ago. To overcome this, we developed an extension of XP-CLR that jointly models the behavior of a selected allele in a three-population tree. Our method - called “3-population composite likelihood ratio” (3P-CLR) - outperforms XP-CLR when testing for selection that occurred before two populations split from each other and can distinguish between those events and events that occurred specifically in each of the populations after the split. We applied our new test to population genomic data from the 1000 Genomes Project, to search for selective sweeps that occurred before the split of Yoruba and Eurasians, but after their split from Neanderthals, and that could have led to the spread of modern-human-specific phenotypes. We also searched for sweep events that occurred in East Asians, Europeans, and the ancestors of both populations, after their split from Yoruba. In both cases, we are able to confirm a number of regions identified by previous methods and find several new candidates for selection in recent and ancient times. For some of these, we also find suggestive functional mutations that may have driven the selective events. PMID:26596347

  2. Cryptic virulence and avirulence alleles revealed by controlled sexual recombination in pea aphids.

    PubMed

    Kanvil, Sadia; Collins, C Matilda; Powell, Glen; Turnbull, Colin G N

    2015-02-01

    Although aphids are worldwide crop pests, little is known about aphid effector genes underlying virulence and avirulence. Here we show that controlling the genetics of both aphid and host can reveal novel recombinant genotypes with previously undetected allelic variation in both virulence and avirulence functions. Clonal F1 progeny populations were derived from reciprocal crosses and self-matings between two parental genotypes of pea aphid (Acyrthosiphon pisum) differing in virulence on a Medicago truncatula host carrying the RAP1 and RAP2 resistance genes. These populations showed Mendelian segregation consistent with aphid performance being controlled largely by a dominant virulence allele derived from only one parent. Altered segregation ratios on near-isogenic host genotypes differing in the region carrying RAP1 were indicative of additional heritable functions likely related to avirulence genes originating from both parents. Unexpectedly, some virulent F1 progeny were recovered from selfing of an avirulent parent, suggesting a reservoir of cryptic alleles. Host chlorosis was associated with virulence, whereas necrotic hypersensitive-like response was not. No maternal inheritance was found for any of these characteristics, ruling out sex-linked, cytoplasmic, and endosymbiotic factors. Our results demonstrate the tractability of dissecting the genetic basis of pest-host resistance mechanisms and indicate that the annual sexual cycle in aphids may lead to frequent novel genotypes with both increased and decreased virulence. Availability of genomes for both pest and host can facilitate definition of cognate gene-for-gene relationships, potentially leading to selection of crop genotypes with multiple resistance traits.

  3. Allele Dependent Silencing of Collagen Type I Using Small Interfering RNAs Targeting 3'UTR Indels - a Novel Therapeutic Approach in Osteogenesis Imperfecta

    PubMed Central

    Lindahl, Katarina; Kindmark, Andreas; Laxman, Navya; Åström, Eva; Rubin, Carl-Johan; Ljunggren, Östen

    2013-01-01

    Osteogenesis imperfecta, also known as “brittle bone disease”, is a heterogeneous disorder of connective tissue generally caused by dominant mutations in the genes COL1A1 and COL1A2, encoding the α1 and α2 chains of type I (pro)collagen. Symptomatic patients are usually prescribed bisphosphonates, but this treatment is neither curative nor sufficient. A promising field is gene silencing through RNA interference. In this study small interfering RNAs (siRNAs) were designed to target each allele of 3'UTR insertion/deletion polymorphisms (indels) in COL1A1 (rs3840870) and COL1A2 (rs3917). For both indels, the frequency of heterozygous individuals was determined to be approximately 50% in Swedish cohorts of healthy controls as well as in patients with osteogenesis imperfecta. Cultures of primary human bone derived cells were transfected with siRNAs through magnet-assisted transfection. cDNA from transfected cells was sequenced in order to measure targeted allele/non-targeted allele ratios and the overall degree of silencing was assessed by quantitative PCR. Successful allele dependent silencing was observed, with promising results for siRNAs complementary to both the insertion and non-insertion harboring alleles. In COL1A1 cDNA the indel allele ratios were shifted from 1 to 0.09 and 0.19 for the insertion and non-insertion allele respectively while the equivalent resulting ratios for COL1A2 were 0.05 and 0.01. Reductions in mRNA abundance were also demonstrated; in cells treated with siRNAs targeting the COL1A1 alleles the average COL1A1 mRNA levels were reduced 65% and 78% compared to negative control levels and in cells treated with COL1A2 siRNAs the average COL1A2 mRNA levels were decreased 26% and 49% of those observed in the corresponding negative controls. In conclusion, allele dependent silencing of collagen type I utilizing 3'UTR indels common in the general population constitutes a promising mutation independent therapeutic approach for osteogenesis

  4. Ratio imaging instrumentation.

    PubMed

    Dunn, Kenneth; Maxfield, Frederick R

    2003-01-01

    Using ratio imaging to obtain quantitative information from microscope images is a powerful tool that has been used successfully in numerous studies. Although ratio imaging reduces the effects of many parameters that can interfere with accurate measurements, it is not a panacea. In designing a ratio imaging experiment, all of the potential problems discussed in this chapter must be considered. Undoubtedly, other problems that were not discussed can also interfere with accurate and meaningful measurements. Many of the problems discussed here were observed in the authors' laboratories. In our experience there are no standard routines or methods that can foresee every problem before it has been encountered. Good experimental design can minimize problems, but the investigator must continue to be alert. Progress in instrumentation continues to overcome some of the difficulties encountered in ratio imaging. CCD cameras with 12- to 14-bit pixel depth are being used more frequently, and several confocal microscope manufacturers are now also using 12-bit digitization. The dramatic increase in the use of confocal microscopes over the past decade is now causing microscope manufacturers to more critically evaluate the effect of axial chromatic aberration in objectives, and recent designs to minimize this problem are being implemented. Other developments such as the use of AOTFs to attenuate laser lines extend the applicability of ratio imaging. Ratio imaging is clearly applicable to a wide range of cell biological problems beyond its widespread use for measuring ion concentrations. Imaginative but careful use of this technique should continue to provide novel insights into the properties of cells.

  5. Male-offspring-specific, haplotype-dependent, nonrandom cosegregation of alleles at loci on two mouse chromosomes.

    PubMed Central

    Pardo-Manuel de Villena, F; de la Casa-Esperon, E; Briscoe, T L; Malette, J M; Sapienza, C

    2000-01-01

    F(1) backcrosses involving the DDK and C57BL/6 inbred mouse strains show transmission ratio distortion at loci on two different chromosomes, 11 and X. Transmission ratio distortion on chromosome X is restricted to female offspring while that on chromosome 11 is present in offspring of both sexes. In this article we investigate whether the inheritance of alleles at loci on one chromosome is independent of inheritance of alleles on the other. A strong nonrandom association between the inheritance of alleles at loci on both chromosomes is found among male offspring, while independent assortment occurs among female offspring. We also provide evidence that the mechanism by which this phenomenon occurs involves preferential cosegregation of nonparental chromatids of both chromosomes at the second meiotic division, after the ova has been fertilized by a C57BL/6 sperm bearing a Y chromosome. These observations confirm the influence of the sperm in the segregation of chromatids during female meiosis, and indicate that a locus or loci on the Y chromosome are involved in this instance of meiotic drive. PMID:10628994

  6. KIR2DL2/2DL3-E(35) alleles are functionally stronger than -Q(35) alleles.

    PubMed

    Bari, Rafijul; Thapa, Rajoo; Bao, Ju; Li, Ying; Zheng, Jie; Leung, Wing

    2016-03-31

    KIR2DL2 and KIR2DL3 segregate as alleles of a single locus in the centromeric motif of the killer cell immunoglobulin-like receptor (KIR) gene family. Although KIR2DL2/L3 polymorphism is known to be associated with many human diseases and is an important factor for donor selection in allogeneic hematopoietic stem cell transplantation, the molecular determinant of functional diversity among various alleles is unclear. In this study we found that KIR2DL2/L3 with glutamic acid at position 35 (E(35)) are functionally stronger than those with glutamine at the same position (Q(35)). Cytotoxicity assay showed that NK cells from HLA-C1 positive donors with KIR2DL2/L3-E(35) could kill more target cells lacking their ligands than NK cells with the weaker -Q(35) alleles, indicating better licensing of KIR2DL2/L3(+) NK cells with the stronger alleles. Molecular modeling analysis reveals that the glutamic acid, which is negatively charged, interacts with positively charged histidine located at position 55, thereby stabilizing KIR2DL2/L3 dimer and reducing entropy loss when KIR2DL2/3 binds to HLA-C ligand. The results of this study will be important for future studies of KIR2DL2/L3-associated diseases as well as for donor selection in allogeneic stem cell transplantation.

  7. KIR2DL2/2DL3-E35 alleles are functionally stronger than -Q35 alleles

    NASA Astrophysics Data System (ADS)

    Bari, Rafijul; Thapa, Rajoo; Bao, Ju; Li, Ying; Zheng, Jie; Leung, Wing

    2016-03-01

    KIR2DL2 and KIR2DL3 segregate as alleles of a single locus in the centromeric motif of the killer cell immunoglobulin-like receptor (KIR) gene family. Although KIR2DL2/L3 polymorphism is known to be associated with many human diseases and is an important factor for donor selection in allogeneic hematopoietic stem cell transplantation, the molecular determinant of functional diversity among various alleles is unclear. In this study we found that KIR2DL2/L3 with glutamic acid at position 35 (E35) are functionally stronger than those with glutamine at the same position (Q35). Cytotoxicity assay showed that NK cells from HLA-C1 positive donors with KIR2DL2/L3-E35 could kill more target cells lacking their ligands than NK cells with the weaker -Q35 alleles, indicating better licensing of KIR2DL2/L3+ NK cells with the stronger alleles. Molecular modeling analysis reveals that the glutamic acid, which is negatively charged, interacts with positively charged histidine located at position 55, thereby stabilizing KIR2DL2/L3 dimer and reducing entropy loss when KIR2DL2/3 binds to HLA-C ligand. The results of this study will be important for future studies of KIR2DL2/L3-associated diseases as well as for donor selection in allogeneic stem cell transplantation.

  8. Allelic divergence and cultivar-specific SSR alleles revealed by capillary electrophoresis using fluorescence-labeled SSR markers in sugarcane

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Though sugarcane cultivars (Saccharum spp. hybrids) are complex aneu-polyploid hybrids, genetic evaluation and tracking of clone- or cultivar-specific alleles become possible due to capillary electrophoregrams (CE) using fluorescence-labeled SSR primer pairs. Twenty-four sugarcane cultivars, 12 each...

  9. Why the Faulhaber Polynomials Are Sums of Even or Odd Powers of (n + 1/2)

    ERIC Educational Resources Information Center

    Hersh, Reuben

    2012-01-01

    By extending Faulhaber's polynomial to negative values of n, the sum of the p'th powers of the first n integers is seen to be an even or odd polynomial in (n + 1/2) and therefore expressible in terms of the sum of the first n integers.

  10. Perspectives on the Aetiology of ODD and CD: A Grounded Theory Approach

    ERIC Educational Resources Information Center

    McFarland, Patrick; Sanders, James; Hagen, Bradley

    2016-01-01

    Antisocial disorders, such as oppositional defiant disorder (ODD) and conduct disorder (CD), are common reasons for youth to be seen for clinical intervention. The intent of this constructivist grounded theory study was to evaluate clinicians' perspectives on the aetiology of antisocial disorders. Six professionals from various professional…

  11. Singular eigenstates in the even(odd) length Heisenberg spin chain

    NASA Astrophysics Data System (ADS)

    Ranjan Giri, Pulak; Deguchi, Tetsuo

    2015-05-01

    We study the implications of the regularization for the singular solutions on the even(odd) length spin-1/2 XXX chains in some specific down-spin sectors. In particular, the analytic expressions of the Bethe eigenstates for three down-spin sector have been obtained along with their numerical forms in some fixed length chains. For an even-length chain if the singular solutions \\{{{λ }α }\\} are invariant under the sign changes of their rapidities \\{{{λ }α }\\}=\\{-{{λ }α }\\}, then the Bethe ansatz equations are reduced to a system of (M-2)/2((M-3)/2) equations in an even (odd) down-spin sector. For an odd N length chain in the three down-spin sector, it has been analytically shown that there exist singular solutions in any finite length of the spin chain of the form N=3(2k+1) with k=1,2,3,\\cdots . It is also shown that there exist no singular solutions in the four down-spin sector for some odd-length spin-1/2 XXX chains.

  12. Building and Solving Odd-One-Out Classification Problems: A Systematic Approach

    ERIC Educational Resources Information Center

    Ruiz, Philippe E.

    2011-01-01

    Classification problems ("find the odd-one-out") are frequently used as tests of inductive reasoning to evaluate human or animal intelligence. This paper introduces a systematic method for building the set of all possible classification problems, followed by a simple algorithm for solving the problems of the R-ASCM, a psychometric test derived…

  13. Odd asymmetric factorization of Wiener-Hopf plus Hankel operators on variable exponent Lebesgue spaces

    NASA Astrophysics Data System (ADS)

    Castro, L. P.; Silva, A. S.

    2017-01-01

    The main goal of this paper is to obtain an invertibility criterion for Wiener-Hopf plus Hankel operators acting between variable exponent Lebesgue spaces on the real line. This is obtained by a so-called odd asymmetric factorization which is applied to the Fourier symbols of the operators under study.

  14. Delaware Middle Schools Beating the Odds. Technical Report Number T2010.4

    ERIC Educational Resources Information Center

    Grusenmeyer, Linda; Fifield, Steve; Murphy, Aideen; Nian, Qinghua; Qian, Xiaoyu

    2010-01-01

    The investigation identified Delaware public and charter middle schools across the state which outperformed other Delaware middle schools with similar student demographic profiles. Teachers and administrators at six of these "Beating the Odds" schools and at six comparison middle schools were surveyed regarding their schools…

  15. Improving the Odds for Adolescents: State Policies That Support Adolescent Health and Well-Being. Report

    ERIC Educational Resources Information Center

    Schwarz, Susan Wile; Aratani, Yumiko

    2011-01-01

    For policymakers, adolescence presents an invaluable opportunity to ensure that all young people can access the high-quality services and supports they need to improve their odds of becoming successful, healthy, productive adults. At an historic moment when the provisions and breadth of health care reform are under vigorous debate, it is important…

  16. Wellness Factors Decrease the Odds of Drinking and Driving among College Students

    ERIC Educational Resources Information Center

    Lewis, Todd F.; Myers, Jane E.

    2012-01-01

    The authors examined holistic wellness factors and drinking and driving behaviors among undergraduate students. Two factors of the Indivisible Self Wellness Model, the Coping Self and the Physical Self, decreased the odds of engaging in drinking and driving behavior. (Contains 2 tables and 1 figure.)

  17. Anger and Irritability Symptoms among Youth with ODD: Cross-Informant versus Source-Exclusive Syndromes

    ERIC Educational Resources Information Center

    Gadow, Kenneth D.; Drabick, Deborah A. G.

    2012-01-01

    We examined differences in co-occurring psychological symptoms and background characteristics among clinically referred youth with oppositional defiant disorder (ODD) with and without anger/irritability symptoms (AIS) according to either parent or teacher (source-exclusive) and both informants (cross-informant), youth with noncompliant symptoms…

  18. The numerology of gender: gendered perceptions of even and odd numbers

    PubMed Central

    Wilkie, James E. B.; Bodenhausen, Galen V.

    2015-01-01

    Do numbers have gender? Wilkie and Bodenhausen (2012) examined this issue in a series of experiments on perceived gender. They examined the perceived gender of baby faces and foreign names. Arbitrary numbers presented with these faces and names influenced their perceived gender. Specifically, odd numbers connoted masculinity, while even numbers connoted femininity. In two new studies (total N = 315), we further examined the gendering of numbers. The first study examined explicit ratings of 1-digit numbers. We confirmed that odd numbers seemed masculine while even numbers seemed feminine. Although both men and women showed this pattern, it was more pronounced among women. We also examined whether this pattern holds for automatic as well as deliberated reactions. Results of an Implicit Association Test showed that it did, but only among the women. The implicit and explicit patterns of numerical gender ascription were moderately correlated. The second study examined explicit perceptions of 2-digit numbers. Again, women viewed odd numbers as more masculine and less feminine than even numbers. However, men viewed 2-digit numbers as relatively masculine, regardless of whether they were even or odd. These results indicate that women and men impute gender to numbers in different ways and to different extents. We discuss possible implications for understanding how people relate to and are influenced by numbers in a variety of real-life contexts. PMID:26113839

  19. Changing the Odds: Informing Policy with Research on How Adult Learners Succeed

    ERIC Educational Resources Information Center

    Condelli, Larry; Kirshstein, Rita; Silver-Pacuilla, Heidi; Reder, Stephen; Wrigley, Heide Spruck

    2010-01-01

    Research has identified the barriers adult learners face in attaining their education and English proficiency goals, entering and advancing in employment, succeeding in postsecondary education and training, and navigating service systems. Most adult learners face long odds in trying to meet these goals. What would it take to address these barriers…

  20. Partial proportional odds model-an alternate choice for analyzing pedestrian crash injury severities.

    PubMed

    Sasidharan, Lekshmi; Menéndez, Mónica

    2014-11-01

    The conventional methods for crash injury severity analyses include either treating the severity data as ordered (e.g. ordered logit/probit models) or non-ordered (e.g. multinomial models). The ordered models require the data to meet proportional odds assumption, according to which the predictors can only have the same effect on different levels of the dependent variable, which is often not the case with crash injury severities. On the other hand, non-ordered analyses completely ignore the inherent hierarchical nature of crash injury severities. Therefore, treating the crash severity data as either ordered or non-ordered results in violating some of the key principles. To address these concerns, this paper explores the application of a partial proportional odds (PPO) model to bridge the gap between ordered and non-ordered severity modeling frameworks. The PPO model allows the covariates that meet the proportional odds assumption to affect different crash severity levels with the same magnitude; whereas the covariates that do not meet the proportional odds assumption can have different effects on different severity levels. This study is based on a five-year (2008-2012) national pedestrian safety dataset for Switzerland. A comparison between the application of PPO models, ordered logit models, and multinomial logit models for pedestrian injury severity evaluation is also included here. The study shows that PPO models outperform the other models considered based on different evaluation criteria. Hence, it is a viable method for analyzing pedestrian crash injury severities.

  1. Nodal lines and nodal loops in nonsymmorphic odd-parity superconductors

    NASA Astrophysics Data System (ADS)

    Micklitz, T.; Norman, M. R.

    2017-01-01

    We discuss the nodal structure of odd-parity superconductors in the presence of nonsymmorphic crystal symmetries, both with and without spin-orbit coupling, and with and without time-reversal symmetry. We comment on the relation of our work to previous work in the literature, and also the implications for unconventional superconductors such as UPt3.

  2. Even-odd spatial nonequivalence for atomic quantum gases with isotropic spin-orbit couplings

    NASA Astrophysics Data System (ADS)

    Singh, G. S.; Gupta, Reena

    2014-05-01

    A general expression for the density of states (DOS) of power-law trapped d-dimensional ideal quantum gases with isotropic spin-orbit couplings (SOCs) is derived and is found to bifurcate into even- dand odd- d classes. The expressions for the grand potential and hence for several thermodynamic quantities are then shown to be amenable to exact analytical forms provided d is an odd integer. Also, a condition γ < 2 d is obtained in case of odd- d for appearance of the Bose-Einstein condensation with γ as the power-law exponent. It is thus established that isotropic SOCs render even and odd dimensional spaces nonequivalent for uniform as well as trapped gases, and that the DOS of one-dimensional (1D) ideal gases, uniform or trapped, remains unaffected by the SOC. Furthermore, the analytical study of the transition temperature and the condensate fraction in a 3D Bose gas under combined presence of the harmonic trapping and the Weyl coupling shows that the condensation is favored by the former but disfavored by the latter. This countering behavior is discussed to be in conformity with the exchange-symmetry-induced statistical interactions resulting from these two entities as enunciated recently [Phys. Rev. A 88, 053607 (2013)].

  3. Empowerment Zone: Texas School Beats the Odds with a Shared Commitment to Student Learning

    ERIC Educational Resources Information Center

    Berkey, Timothy; Dow, Elizabeth

    2008-01-01

    The odds were stacked against the new elementary school from the beginning. In its favor, the school was a beautiful building with an established principal. Beyond that, anyone would predict that the first year would be tough. The staff consisted of new teachers and transfers from across the district. The students were reassigned from two…

  4. Mother-Teacher Agreement on Preschoolers' Symptoms of ODD and CD: Does Context Matter?

    ERIC Educational Resources Information Center

    Strickland, Jennifer; Hopkins, Joyce; Keenan, Kate

    2012-01-01

    The aims of this study were to examine mother-teacher agreement on oppositional defiant disorder (ODD) and conduct disorder (CD) symptoms and diagnoses in preschool children; to determine if context is a source of disagreement; and to explore if sex, referral status, and age moderated agreement rates. Participants included 158 male and 139 female…

  5. Learning in the Home and at School: How Working Class Children "Succeed against the Odds"

    ERIC Educational Resources Information Center

    Siraj-Blatchford, Iram

    2010-01-01

    This paper presents data collected in individual case studies that aimed to investigate children and their families who succeeded against the usual "odds" of disadvantage. Funded as an extension of EPPE 3-11 by the Cabinet Office for the Equalities Review, the study focused particularly closely upon the performance of disadvantaged…

  6. Teenage Parenthood among Child Welfare Clients: A Swedish National Cohort Study of Prevalence and Odds

    ERIC Educational Resources Information Center

    Vinnerljung, Bo; Franzen, Eva; Danielsson, Maria

    2007-01-01

    To assess prevalence and odds for teenage parenthood among former child welfare clients, we used national register data for all children born in Sweden 1972-1983 (n = 1,178,207), including 49,582 former child welfare clients with varying intervention experiences. Logistic regression models, adjusted for demographic, socio-economic and familial…

  7. Systematic study of α decay for odd-A nuclei within a two-potential approach

    NASA Astrophysics Data System (ADS)

    Sun, Xiao-Dong; Duan, Chao; Deng, Jun-Gang; Guo, Ping; Li, Xiao-Hua

    2017-01-01

    α decay is usually associated with both ground and low-lying isomeric states of heavy and superheavy nuclei, and the unpaired nucleon plays a key role in α decay. In this work, we systematically studied the α decay half-lives of odd-A nuclei, including both favored and unfavored α decay within the two-potential approach based on the isospin dependent nuclear potential. The α preformation probabilities are estimated by using an analytic formula taking into account the shell structure and proton-neutron correlation, and the parameters are obtained through the α decay half-lives data. The results indicate that, in general, the α preformation probabilities of even-Z , odd-N nuclei are slightly smaller than the odd-Z , even-N ones. We found that the odd-even staggering effect may play a more important role on spontaneous fission than α decay. The calculated half-lives can well reproduce the experimental data.

  8. Spontaneous topological transitions of electromagnetic fields in spatially inhomogeneous C P -odd domains

    NASA Astrophysics Data System (ADS)

    Tuchin, Kirill

    2016-12-01

    Metastable C P -odd domains of the hot QCD matter are coupled to QED via the chiral anomaly. The topology of electromagnetic field in these domains is characterized by magnetic helicity. It is argued, using the Maxwell-Chern-Simons model, that spatial inhomogeneity of the domains induces spontaneous transitions of electromagnetic field between the opposite magnetic helicity states.

  9. Tri-allelic pattern at the TPOX locus: a familial study.

    PubMed

    Picanço, Juliane Bentes; Raimann, Paulo Eduardo; Paskulin, Giorgio Adriano; Alvarez, Luís; Amorim, António; Batista Dos Santos, Sidney Emanuel; Alho, Clarice Sampaio

    2014-02-10

    Alleles at the TPOX STR locus have 6-14 different numbers of a four-nucleotide (AATG) repeat motif arranged in tandem. Although tri-allelic genotypes are generally rare, the TPOX tri-allelic pattern has a higher frequency, varying widely among populations. Despite this, there are few accurate reports to disclose the nature of the TPOX third allele. In this work we present data obtained from 45 individuals belonging to the same pedigree, in which there are cases of tri-allelic TPOX genotypes. The subjects were apparently healthy with a normal biological development. We noticed six tri-allelic cases in this family, and all of them were women. Karyotype analysis showed no occurrence of partial 2p trisomy. All the tri-allelic cases had the genotype 8-10-11, probably due to three copies of the TPOX STR sequence in all cells (Type 2 tri-allelic pattern). Based on previous data we assumed the allele 10 as the TPOX third allele. The pedigree analyses show evidences that the TPOX extra-allele was the allele10, it is placed far from the main TPOX locus, and that there is a potential linkage of the TPOX extra-allele-10 with Xq. This was the first study that included a large pedigree analysis in order to understand the nature TPOX tri-allelic pattern.

  10. Nonfrequent but well-documented, rare and very rare HLA alleles observed in the Croatian population.

    PubMed

    Grubic, Z; Burek Kamenaric, M; Maskalan, M; Stingl Jankovic, K; Zunec, R

    2014-12-01

    The aim of the study was to evaluate the presence of nonfrequent, rare and very rare alleles among Croats and to estimate whether they are associated with specific alleles at other human leukocyte antigen (HLA) loci. This retrospective study included the typing results from the last 10 years; total number of individuals included was approximately 45,000. Among 17 alleles so far observed only once in our population, 6 (A*24:41, B*07:02:28, B*35:03:03, B*39:40N, DRB1*13:23 and DRB1*14:111) belong to very rare alleles, 2 (B*44:16 and DRB1*01:31) belong to rare alleles according to the 'Rare Alleles Detector' tool ( www.allelefrequencies.net), while for the B*35:101:01 allele published data exist only in the IMGT/HLA database. The remaining eight HLA alleles observed only once among Croats are considered as frequent according to the 'Rare Alleles Detector'. Those 17 HLA alleles are not declared as common well defined (CWD) alleles in the CWD allele catalogue 2.0.0. Haplotype analysis of nonfrequent alleles detected in our sample supports the idea that different populations, although similar in some aspects regarding HLA allele and haplotype distribution, still have some unique characteristics. This is the case for A*01:02, B*39:10 and DRB1*13:32 which form haplotypes unreported to date among our subjects.

  11. Hindered Gamow-Teller decay to the odd-odd N=Z (62)Ga: absence of proton-neutron T=0 condensate in A=62.

    PubMed

    Grodner, E; Gadea, A; Sarriguren, P; Lenzi, S M; Grebosz, J; Valiente-Dobón, J J; Algora, A; Górska, M; Regan, P H; Rudolph, D; de Angelis, G; Agramunt, J; Alkhomashi, N; Amon Susam, L; Bazzacco, D; Benlliure, J; Benzoni, G; Boutachkov, P; Bracco, A; Caceres, L; Cakirli, R B; Crespi, F C L; Domingo-Pardo, C; Doncel, M; Dombrádi, Zs; Doornenbal, P; Farnea, E; Ganioğlu, E; Gelletly, W; Gerl, J; Gottardo, A; Hüyük, T; Kurz, N; Leoni, S; Mengoni, D; Molina, F; Morales, A I; Orlandi, R; Oktem, Y; Page, R D; Perez, D; Pietri, S; Podolyák, Zs; Poves, A; Quintana, B; Rinta-Antila, S; Rubio, B; Nara Singh, B S; Steer, A N; Verma, S; Wadsworth, R; Wieland, O; Wollersheim, H J

    2014-08-29

    Search for a new kind of superfluidity built on collective proton-neutron pairs with aligned spin is performed studying the Gamow-Teller decay of the T=1, J(π)=0+ ground state of (62)Ge into excited states of the odd-odd N=Z nucleus (62)Ga. The experiment is performed at GSI Helmholtzzentrum für Shwerionenforshung with the (62)Ge ions selected by the fragment separator and implanted in a stack of Si-strip detectors, surrounded by the RISING Ge array. A half-life of T1/2=82.9(14)  ms is measured for the (62)Ge ground state. Six excited states of (62)Ga, populated below 2.5 MeV through Gamow-Teller transitions, are identified. Individual Gamow-Teller transition strengths agree well with theoretical predictions of the interacting shell model and the quasiparticle random phase approximation. The absence of any sizable low-lying Gamow-Teller strength in the reported beta-decay experiment supports the hypothesis of a negligible role of coherent T=0 proton-neutron correlations in (62)Ga.

  12. Evaluating forensic DNA profiles using peak heights, allowing for multiple donors, allelic dropout and stutters.

    PubMed

    Puch-Solis, Roberto; Rodgers, Lauren; Mazumder, Anjali; Pope, Susan; Evett, Ian; Curran, James; Balding, David

    2013-09-01

    Increases in the sensitivity of DNA profiling technology now allow profiles to be obtained from smaller and more degraded DNA samples than was previously possible. The resulting profiles can be highly informative, but the subjective elements in the interpretation make it problematic to achieve the valid and efficient evaluation of evidential strength required in criminal cases. The problems arise from stochastic phenomena such as "dropout" (absence of an allele in the profile that is present in the underlying DNA) and experimental artefacts such as "stutter" that can generate peaks of ambiguous allelic status. Currently in the UK, evidential strength evaluation uses an approach in which the complex signals in the DNA profiles are interpreted in a semi-manual fashion by trained experts aided by a set of guidelines, but also relying substantially on professional judgment. We introduce a statistical model to calculate likelihood ratios for evaluating DNA evidence arising from multiple known and unknown contributors that allows for such stochastic phenomena by incorporating peak heights. Efficient use of peak heights allows for more crime scene profiles to be reported to courts than is currently possible. The model parameters are estimated from experimental data incorporating multiple sources of variability in the profiling system. We report and analyse experimental results from the SGMPlus system, run at 28 amplification cycles with no enhancements, currently used in the UK. Our methods are readily adapted to other DNA profiling systems provided that the experimental data for the parameter estimation is available.

  13. Impact of Human Leukocyte Antigen Allele Mismatch in Unrelated Bone Marrow Transplantation with Reduced-Intensity Conditioning Regimen.

    PubMed

    Yokoyama, Hisayuki; Kanda, Junya; Fuji, Shigeo; Kim, Sung-Won; Fukuda, Takahiro; Najima, Yuho; Ohno, Hitoshi; Uchida, Naoyuki; Ueda, Yasunori; Eto, Tetsuya; Iwato, Koji; Kobayashi, Hikaru; Ozawa, Yukiyasu; Kondo, Tadakazu; Ichinohe, Tatsuo; Atsuta, Yoshiko; Kanda, Yoshinobu

    2017-02-01

    The impact of HLA mismatch in hematopoietic stem cell transplantation with reduced-intensity conditioning (RIC) has not been fully examined. We analyzed a total of 1130 cases to examine the effects of HLA allele mismatch in unrelated bone marrow transplantation (BMT) with RIC in the Japan Marrow Donor Program registry cohort. Compared with HLA 8/8-allele match (n = 720, 8/8 match), both 1 (n = 295, 7/8 match) and 2 allele mismatches (n = 115, 6/8 match) were associated with significant reduction of overall survival (OS) (hazard ratio [HR],  1.34; P = .0024 and HR, 1.33; P = .035 for 7/8 and 6/8 match, respectively). The incidence of grades 2 to 4 acute graft-versus-host disease (aGVHD) increased with increasing number of mismatched alleles (HR, 1.36 and HR, 2.08 for 7/8 and 6/8 match, respectively). Nonrelapse mortality showed a similar tendency to aGVHD (HR, 1.35 for 7/8 and HR, 1.63 for 6/8). One-allele mismatches at the HLA-A or -B and HLA-C loci were significantly associated with inferior OS compared with 8/8 match (HR, 1.64 for A or B mismatch and HR, 1.41 for C mismatch), whereas HLA-DRB1 allele mismatch was not (HR, 1.16; P = .30). However, the effect of HLA-A or -B and -C mismatch on OS was not observed in those who received RIC BMT since 2010, in contrast to recipients before 2010. These results suggested that in unrelated RIC BMT, 1-allele mismatch is associated with poorer outcome, and the impact of HLA mismatch may differ depending on the HLA locus, although these HLA mismatch effects may be different in recent cases.

  14. Digit ratio in birds.

    PubMed

    Lombardo, Michael P; Thorpe, Patrick A; Brown, Barbara M; Sian, Katie

    2008-12-01

    The Homeobox (Hox) genes direct the development of tetrapod digits. The expression of Hox genes may be influenced by endogenous sex steroids during development. Manning (Digit ratio. New Brunswick, NJ: Rutgers University Press, 2002) predicted that the ratio between the lengths of digits 2 (2D) and 4 (4D) should be sexually dimorphic because prenatal exposure to estrogens and androgens positively influence the lengths of 2D and 4D, respectively. We measured digits and other morphological traits of birds from three orders (Passeriformes, house sparrow, Passer domesticus; tree swallow, Tachycineta bicolor; Pscittaciformes, budgerigar, Melopsittacus undulates; Galliformes, chicken, Gallus domesticus) to test this prediction. None were sexually dimorphic for 2D:4D and there were no associations between 2D:4D and other sexually dimorphic traits. When we pooled data from all four species after we averaged right and left side digits from each individual and z-transformed the resulting digit ratios, we found that males had significantly larger 2D:4D than did females. Tetrapods appear to be sexually dimorphic for 2D:4D with 2D:4D larger in males as in some birds and reptiles and 2D:4D smaller in males as in some mammals. The differences between the reptile and mammal lineages in the directionality of 2D:4D may be related to the differences between them in chromosomal sex determination. We suggest that (a) natural selection for a perching foot in the first birds may have overridden the effects of hormones on the development of digit ratio in this group of vertebrates and (b) caution be used in making inferences about prenatal exposure to hormones and digit ratio in birds.

  15. Characterization of 18 new BoLA-DRB3 alleles.

    PubMed

    Maillard, J C; Renard, C; Chardon, P; Chantal, I; Bensaid, A

    1999-06-01

    The second exon of the bovine MHC class II DRB3 gene was amplified by polymerase chain reaction (PCR) from DNA samples of 568 zebu Brahman cattle (Bos indicus) from Martinique (French West Indies). Cloning of these PCR products allowed the isolation of both alleles from each animal, which were characterized by the PCR-restriction fragment length polymorphism (RFLP) technique using the restriction enzymes RsaI, BstYI and HaeIII. Four new PCR-RFLP patterns were obtained by digestion with RsaI. These patterns were named 'v', 'w', 'x' and 'y' continuing the accepted nomenclature. Sequencing of each allele allowed the identification of 18 new BoLA-DRB3 exon 2 nucleotide sequences and their deduced amino acid sequences.

  16. Early allelic selection in maize as revealed by ancient DNA.

    PubMed

    Jaenicke-Després, Viviane; Buckler, Ed S; Smith, Bruce D; Gilbert, M Thomas P; Cooper, Alan; Doebley, John; Pääbo, Svante

    2003-11-14

    Maize was domesticated from teosinte, a wild grass, by approximately 6300 years ago in Mexico. After initial domestication, early farmers continued to select for advantageous morphological and biochemical traits in this important crop. However, the timing and sequence of character selection are, thus far, known only for morphological features discernible in corn cobs. We have analyzed three genes involved in the control of plant architecture, storage protein synthesis, and starch production from archaeological maize samples from Mexico and the southwestern United States. The results reveal that the alleles typical of contemporary maize were present in Mexican maize by 4400 years ago. However, as recently as 2000 years ago, allelic selection at one of the genes may not yet have been complete.

  17. Multi-ratio transmission

    SciTech Connect

    Polak, J.C.

    1987-07-14

    A preselected multi-ratio power transmission is described comprising: input means for transmitting drive forces; output means; first, second and third friction clutch means each selectively engageable with the input means for accepting drive forces. First input gear means drivingly connects with the first friction clutch means; second input gear means drivingly connects with the second friction clutch means; third input gear means drivingly connects with the third clutch means; first output gear means drivingly connects with the first input gear means; second output gear means drivingly connects with the first and second input gear means; third output means drivingly connects between the third input gear means and the output means; and one double-acting synchronizer clutch for selectively engaging the first output gear means with the output means and alternately the second output gear means with the output means. The first friction clutch means and the one double-acting synchronizer clutch cooperates during engagement to establish two forward drive ratios between the input and output means. The second friction clutch means and the one double-acting synchronizer clutch cooperates during engagement to establish two other forward drive ratios between the input and output means. The third friction clutch means is engageable to provide another forward drive ratio between the input means and the output means; and the one double-acting synchronizer clutch is relieved of transmitting drive forces during the engagement of the third friction clutch means and being manipulable for alternate connection with either the first output gear or the second output gear while the third friction clutch means is engaged.

  18. Natural Allelic Variations in Highly Polyploidy Saccharum Complex

    PubMed Central

    Song, Jian; Yang, Xiping; Resende, Marcio F. R.; Neves, Leandro G.; Todd, James; Zhang, Jisen; Comstock, Jack C.; Wang, Jianping

    2016-01-01

    Sugarcane (Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designed based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWA-mem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. The target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes. PMID:27375658

  19. Natural Allelic Variations in Highly Polyploidy Saccharum Complex.

    PubMed

    Song, Jian; Yang, Xiping; Resende, Marcio F R; Neves, Leandro G; Todd, James; Zhang, Jisen; Comstock, Jack C; Wang, Jianping

    2016-01-01

    Sugarcane (Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designed based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWA-mem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. The target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes.

  20. Allelic exchange in Mycobacterium tuberculosis with long linear recombination substrates.

    PubMed Central

    Balasubramanian, V; Pavelka, M S; Bardarov, S S; Martin, J; Weisbrod, T R; McAdam, R A; Bloom, B R; Jacobs, W R

    1996-01-01

    Genetic studies of Mycobacterium tuberculosis have been greatly hampered by the inability to introduce specific chromosomal mutations. Whereas the ability to perform allelic exchanges has provided a useful method of gene disruption in other organisms, in the clinically important species of mycobacteria, such as M. tuberculosis and Mycobacterium bovis, similar approaches have thus far been unsuccessful. In this communication, we report the development of a shuttle mutagenesis strategy that involves the use of long linear recombination substrates to reproducibly obtain recombinants by allelic exchange in M. tuberculosis. Long linear recombination substrates, approximately 40 to 50 kb in length, were generated by constructing libraries in the excisable cosmid vector pYUB328. The cosmid vector could be readily excised from the recombinant cosmids by digestion with PacI, a restriction endonuclease for which there exist few, if any, sites in mycobacterial genomes. A cosmid containing the mycobacterial leuD gene was isolated, and a selectable marker conferring resistance to kanamycin was inserted into the leuD gene in the recombinant cosmid by interplasmid recombination in Escherichia coli. A long linear recombination substrate containing the insertionally mutated leuD gene was generated by PacI digestion. Electroporation of this recombination substrate containing the insertionally mutated leuD allele resulted in the generation of leucine auxotrophic mutants by homologous recombination in 6% of the kanamycin-resistant transformants for both the Erdman and H37Rv strains of M. tuberculosis. The ability to perform allelic exchanges provides an important approach for investigating the biology of this pathogen as well as developing new live-cell M. tuberculosis-based vaccines. PMID:8550428

  1. Citrobacter spp. as a source of qnrB Alleles.

    PubMed

    Jacoby, George A; Griffin, Caitlin M; Hooper, David C

    2011-11-01

    qnrB is the most common of the five qnr families and has the greatest number of allelic variants. Almost two-thirds of the qnrB alleles have been reported in Citrobacter spp., and several were shown to be located on the chromosome. In this study, PCR was used to investigate the prevalence of plasmid-mediated quinolone resistance genes in 71 clinical isolates belonging to the Citrobacter freundii complex. Thirty-seven percent contained qnrB alleles, including 7 (qnrB32 to qnrB38) that were novel and 1 pseudogene, while none contained qnrA, qnrC, qnrD, qnrS, or aac(6')-Ib-cr. When the strains were arrayed by related 16S rRNA sequence and further separated into subspecies by biochemical criteria, clustering of qnrB-positive strains was evident. In only two strains with qnrB2 and qnrB4 was quinolone resistance transferable by conjugation, and only these strains contained the ISCR1 sequence that is often associated with qnrB on plasmids. Five of 26 qnrB-positive strains contained integrase genes, but these included the strains with qnrB2 and qnrB4 as well as two strains with other transmissible plasmids. In a fully sequenced genome of Citrobacter youngae, a member of the C. freundii complex, another novel qnrB allele, qnrB39, occurs in a sequence of genes that is 90% identical to sequence surrounding integron-associated qnrB4 incorporated into plasmids. The chromosome of Citrobacter is the likely source of plasmid-mediated qnrB.

  2. Fast spatial ancestry via flexible allele frequency surfaces

    PubMed Central

    Rañola, John Michael; Novembre, John; Lange, Kenneth

    2014-01-01

    Motivation: Unique modeling and computational challenges arise in locating the geographic origin of individuals based on their genetic backgrounds. Single-nucleotide polymorphisms (SNPs) vary widely in informativeness, allele frequencies change non-linearly with geography and reliable localization requires evidence to be integrated across a multitude of SNPs. These problems become even more acute for individuals of mixed ancestry. It is hardly surprising that matching genetic models to computational constraints has limited the development of methods for estimating geographic origins. We attack these related problems by borrowing ideas from image processing and optimization theory. Our proposed model divides the region of interest into pixels and operates SNP by SNP. We estimate allele frequencies across the landscape by maximizing a product of binomial likelihoods penalized by nearest neighbor interactions. Penalization smooths allele frequency estimates and promotes estimation at pixels with no data. Maximization is accomplished by a minorize–maximize (MM) algorithm. Once allele frequency surfaces are available, one can apply Bayes’ rule to compute the posterior probability that each pixel is the pixel of origin of a given person. Placement of admixed individuals on the landscape is more complicated and requires estimation of the fractional contribution of each pixel to a person’s genome. This estimation problem also succumbs to a penalized MM algorithm. Results: We applied the model to the Population Reference Sample (POPRES) data. The model gives better localization for both unmixed and admixed individuals than existing methods despite using just a small fraction of the available SNPs. Computing times are comparable with the best competing software. Availability and implementation: Software will be freely available as the OriGen package in R. Contact: ranolaj@uw.edu or klange@ucla.edu Supplementary information: Supplementary data are available at

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

    PubMed Central

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

    2016-01-01

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

  4. Pollution-tolerant allele in fingernail clams (Musculium transversum).

    PubMed

    Sloss, B L; Romano, M A; Anderson, R V

    1998-08-01

    For nearly 50 years, the fingernail clam (Musculium transversum) was believed to be virtually eliminated from the Illinois River. In 1991, workers began finding substantial populations of M. transversum in the Illinois River including several beds in and around the highly polluted Chicago Sanitary District. In order to determine if populations of M. transversum from polluted sites exhibited any genetic response to the high levels of toxins and to examine the genetic structure of several populations of M. transversum for any changes due to the population crash, starch-gel electrophoresis was performed on M. transversum from three Illinois River localities and four Mississippi River basin locations. The sampled populations produced an inbreeding coefficient (FIS) of 0.929, indicating that the populations were highly inbred. The results of a suspected founder effect due to a bottleneck was suggested by an FST = 0.442. The isozyme Glucose-6-phosphate isomerase-2 (Gpi-2) produced allelic frequency patterns that were consistent with expected patterns of a pollution-tolerant allele. Polluted sites exhibited elevated frequencies of Gpi-2(100) whereas nonpolluted sites exhibited elevated frequencies of Gpi-2(74). This frequency pattern suggested that natural selection was occurring in populations under severe toxic pressures, leading to an increase in the frequency of the allele Gpi-2(100). Therefore, Gpi-2(100) is a possible pollution-tolerant mutation in M. transversum.

  5. RNA-FISH to analyze allele-specific expression.

    PubMed

    Braidotti, G

    2001-01-01

    One of the difficulties associated with the analysis of imprinted gene expression is the need to distinguish RNA synthesis occurring at the maternal vs the paternally inherited copy of the gene. Most of the techniques used to examine allele-specific expression exploit naturally occurring polymorphisms and measure steady-state levels of RNA isolated from a pool of cells. Hence, a restriction fragment length polymorphism (RFLP) an be exploited in a heterozygote, by a reverse transcriptase polymerase chain reaction (RT-PCR)- based procedure, to analyze maternal vs paternal gene expression. The human IGF2R gene was analyzed in this way. Smrzka et al. (1) were thus able to show that the IGF2R gene possesses a hemimethylated, intronic CpG island analogous to the mouse imprinting box. However, IGF2R mRNA was detected that possessed the RFLP from both the maternal and paternal alleles in all but one of the 70 lymphoblastoid samples. (The one monoallelic sample reactivated its paternal allele with continued cell culturing.) It was concluded that monoallelic expression of the human gene is a polymorphic trait occurring in a small minority of all tested samples (reviewed in refs. 2,3). Although this is a sound conclusion, the question remains: Is the human IGF2R gene imprinted?

  6. Tracing pastoralist migrations to southern Africa with lactase persistence alleles.

    PubMed

    Macholdt, Enrico; Lede, Vera; Barbieri, Chiara; Mpoloka, Sununguko W; Chen, Hua; Slatkin, Montgomery; Pakendorf, Brigitte; Stoneking, Mark

    2014-04-14

    Although southern African Khoisan populations are often assumed to have remained largely isolated during prehistory, there is growing evidence for a migration of pastoralists from eastern Africa some 2,000 years ago, prior to the arrival of Bantu-speaking populations in southern Africa. Eastern Africa harbors distinctive lactase persistence (LP) alleles, and therefore LP alleles in southern African populations may be derived from this eastern African pastoralist migration. We sequenced the lactase enhancer region in 457 individuals from 18 Khoisan and seven Bantu-speaking groups from Botswana, Namibia, and Zambia and additionally genotyped four short tandem repeat (STR) loci that flank the lactase enhancer region. We found nine single-nucleotide polymorphisms, of which the most frequent is -14010(∗)C, which was previously found to be associated with LP in Kenya and Tanzania and to exhibit a strong signal of positive selection. This allele occurs in significantly higher frequency in pastoralist groups and in Khoe-speaking groups in our study, supporting the hypothesis of a migration of eastern African pastoralists that was primarily associated with Khoe speakers. Moreover, we find a signal of ongoing positive selection in all three pastoralist groups in our study, as well as (surprisingly) in two foraging groups.

  7. A survey of FRAXE allele sizes in three populations

    SciTech Connect

    Zhong, N.; Ju, W.; Curley, D.

    1996-08-09

    FRAXE is a fragile site located at Xq27-8, which contains polymorphic triplet GCC repeats associated with a CpG island. Similar to FRAXA, expansion of the GCC repeats results in an abnormal methylation of the CpG island and is associated with a mild mental retardation syndrome (FRAXE-MR). We surveyed the GCC repeat alleles of FRAXE from 3 populations. A total of 665 X chromosomes including 416 from a New York Euro-American sample (259 normal and 157 with FRAXA mutations), 157 from a Chinese sample (144 normal and 13 FRAXA), and 92 from a Finnish sample (56 normal and 36 FRAXA) were analyzed by polymerase chain reaction. Twenty-seven alleles, ranging from 4 to 39 GCC repeats, were observed. The modal repeat number was 16 in the New York and Finnish samples and accounted for 24% of all the chromosomes tested (162/665). The modal repeat number in the Chinese sample was 18. A founder effect for FRAXA was suggested among the Finnish FRAXA samples in that 75% had the FRAXE 16 repeat allele versus only 30% of controls. Sequencing of the FRAXE region showed no imperfections within the GCC repeat region, such as those commonly seen in FRAXA. The smaller size and limited range of repeats and the lack of imperfections suggests the molecular mechanisms underlying FRAXE triplet mutations may be different from those underlying FRAXA. 27 refs., 4 figs., 1 tab.

  8. Mutant power: using mutant allele collections for yeast functional genomics.

    PubMed

    Norman, Kaitlyn L; Kumar, Anuj

    2016-03-01

    The budding yeast has long served as a model eukaryote for the functional genomic analysis of highly conserved signaling pathways, cellular processes and mechanisms underlying human disease. The collection of reagents available for genomics in yeast is extensive, encompassing a growing diversity of mutant collections beyond gene deletion sets in the standard wild-type S288C genetic background. We review here three main types of mutant allele collections: transposon mutagen collections, essential gene collections and overexpression libraries. Each collection provides unique and identifiable alleles that can be utilized in genome-wide, high-throughput studies. These genomic reagents are particularly informative in identifying synthetic phenotypes and functions associated with essential genes, including those modeled most effectively in complex genetic backgrounds. Several examples of genomic studies in filamentous/pseudohyphal backgrounds are provided here to illustrate this point. Additionally, the limitations of each approach are examined. Collectively, these mutant allele collections in Saccharomyces cerevisiae and the related pathogenic yeast Candida albicans promise insights toward an advanced understanding of eukaryotic molecular and cellular biology.

  9. Computer simulation for the growing probability of additional offspring with an advantageous reversal allele in the decoupled continuous-time mutation-selection model

    NASA Astrophysics Data System (ADS)

    Gill, Wonpyong

    2016-01-01

    This study calculated the growing probability of additional offspring with the advantageous reversal allele in an asymmetric sharply-peaked landscape using the decoupled continuous-time mutation-selection model. The growing probability was calculated for various population sizes, N, sequence lengths, L, selective advantages, s, fitness parameters, k and measuring parameters, C. The saturated growing probability in the stochastic region was approximately the effective selective advantage, s*, when C≫1/Ns* and s*≪1. The present study suggests that the growing probability in the stochastic region in the decoupled continuous-time mutation-selection model can be described using the theoretical formula for the growing probability in the Moran two-allele model. The selective advantage ratio, which represents the ratio of the effective selective advantage to the selective advantage, does not depend on the population size, selective advantage, measuring parameter and fitness parameter; instead the selective advantage ratio decreases with the increasing sequence length.

  10. Negative BOLD response and serotonin concentration within rostral subgenual portion of the anterior cingulate cortex for long-allele carriers during perceptual processing of emotional tasks

    NASA Astrophysics Data System (ADS)

    Hadi, Shamil M.; Siadat, Mohamad R.; Babajani-Feremi, Abbas

    2012-03-01

    We investigated the effect of synaptic serotonin concentration on hemodynamic responses. The stimuli paradigm involved the presentation of fearful and threatening facial expressions to a set of 24 subjects who were either5HTTLPR long- or short-allele carriers (12 of each type in each group). The BOLD signals of the rACC from subjects of each group were averaged to increase the signal-to-noise ratio. We used a Bayesian approach to estimate the parameters of the underlying hemodynamic model. Our results, during this perceptual processing of emotional task, showed a negative BOLD signal in the rACC in the subjects with long-alleles. In contrast, the subjects with short-alleles showed positive BOLD signals in the rACC. These results suggest that high synaptic serotonin concentration in the rACC inhibits neuronal activity in a fashion similar to GABA, and a consequent negative BOLD signal ensues.

  11. Observation of the {pi}h{sub 11/2}x{nu}i{sub 13/2} band in odd-odd {sup 170}Re

    SciTech Connect

    Wang, H.L.; Zhang, Y.H.; Zhou, X.H.; Guo, Y.X.; Lei, X.G.; Liu, M.L.; Peng, L.; Xie, C.Y.; Song, L.T.; Yu, H.P.; Zheng, Y.; Guo, W.T.; Ndontchueng, M. Moyo; Wen, S.X.; Zhu, L.H.; Wu, X.G.; Xu, F.R.

    2004-12-01

    High-spin states in doubly odd {sup 170}Re have been populated via the {sup 142}Nd({sup 32}S,p3n{gamma}) reaction at beam energies of 155 and 166 MeV. K X-{gamma} and {gamma}-{gamma} coincidences have been measured using a detector array consisting of 12 high-purity germanium detectors with BGO suppressors. A rotational band is identified and assigned to {sup 170}Re for the first time. This band is proposed to be built on the {pi}h{sub 11/2}x{nu}i{sub 13/2} two-quasiparticle configuration by comparing the band properties with known bands in neighboring nuclei and the cranked-shell model calculations.

  12. Conditional Allele Mouse Planner (CAMP): software to facilitate the planning and design of breeding strategies involving mice with conditional alleles.

    PubMed

    Hoffert, Jason D; Pisitkun, Trairak; Miller, R Lance

    2012-06-01

    Transgenic and conditional knockout mouse models play an important role in biomedical research and their use has grown exponentially in the last 5-10 years. Generating conditional knockouts often requires breeding multiple alleles onto the background of a single mouse or group of mice. Breeding these mice depends on parental genotype, litter size, transmission frequency, and the number of breeding rounds. Therefore, a well planned breeding strategy is critical for keeping costs to a minimum. However, designing a viable breeding strategy can be challenging. With so many different variables this would be an ideal task for a computer program. To facilitate this process, we created a Java-based program called Conditional Allele Mouse Planner (CAMP). CAMP is designed to provide an estimate of the number of breeders, amount of time, and costs associated with generating mice of a particular genotype. We provide a description of CAMP, how to use it, and offer it freely as an application.

  13. Time reversal odd fragmentation functions in semi-inclusive deep inelastic lepton-hadron scattering

    SciTech Connect

    Mulders, P.J.; Levelt, J.

    1994-04-01

    In semi-inclusive scattering of polarized leptons from unpolarized hadrons, one can measure a time reversal odd structure function. It shows up as a sin({phi}) asymmetry of the produced hadrons. This asymmetry can be expressed as the product of a twist-three {open_quotes}hadron {r_arrow} quark{close_quotes} profile function and a time reversal odd twist-two {open_quotes}quark {r_arrow} hadron{close_quotes} fragmentation function. This fragmentation function can only be measured for nonzero transverse momenta of the produced hadron. Its appearance is a consequence of final state interactions between the produced hadron and the rest of the final state.

  14. Nonadiabatic quasiparticle approach for rotation-particle coupling in triaxial odd-A nuclei

    NASA Astrophysics Data System (ADS)

    Modi, Swati; Patial, M.; Arumugam, P.; Maglione, E.; Ferreira, L. S.

    2017-02-01

    We discuss the formulation of a nonadiabatic approach to study the rotational states in triaxially deformed odd-A nuclei. The rotation-particle coupling is treated microscopically by coupling the triaxial rotor states of the even-even core with the states of the valence particle in order to obtain the matrix elements of the odd-A system. We arrive at a nonadiabatic quasiparticle approach where the rotational states can have contributions from various quasiparticle states near the Fermi level. We bring out the advantages of this approach over the conventional particle rotor model with a fixed or variable moment of inertia. One clear evidence favoring our approach is the rotation alignment phenomenon which is demonstrated in the case of 137Pm. We discuss our results for 136Nd and 137Pm, and justify that this approach is suitable also for studying nuclei away from stability.

  15. Signature of magnetic-dependent gapless odd frequency states at superconductor/ferromagnet interfaces

    PubMed Central

    Di Bernardo, A.; Diesch, S.; Gu, Y.; Linder, J.; Divitini, G.; Ducati, C.; Scheer, E.; Blamire, M.G.; Robinson, J.W.A.

    2015-01-01

    The theory of superconductivity developed by Bardeen, Cooper and Schrieffer (BCS) explains the stabilization of electron pairs into a spin-singlet, even frequency, state by the formation of an energy gap within which the density of states is zero. At a superconductor interface with an inhomogeneous ferromagnet, a gapless odd frequency superconducting state is predicted, in which the Cooper pairs are in a spin-triplet state. Although indirect evidence for such a state has been obtained, the gap structure and pairing symmetry have not so far been determined. Here we report scanning tunnelling spectroscopy of Nb superconducting films proximity coupled to epitaxial Ho. These measurements reveal pronounced changes to the Nb subgap superconducting density of states on driving the Ho through a metamagnetic transition from a helical antiferromagnetic to a homogeneous ferromagnetic state for which a BCS-like gap is recovered. The results prove odd frequency spin-triplet superconductivity at superconductor/inhomogeneous magnet interfaces. PMID:26329811

  16. Signature of magnetic-dependent gapless odd frequency states at superconductor/ferromagnet interfaces.

    PubMed

    Di Bernardo, A; Diesch, S; Gu, Y; Linder, J; Divitini, G; Ducati, C; Scheer, E; Blamire, M G; Robinson, J W A

    2015-09-02

    The theory of superconductivity developed by Bardeen, Cooper and Schrieffer (BCS) explains the stabilization of electron pairs into a spin-singlet, even frequency, state by the formation of an energy gap within which the density of states is zero. At a superconductor interface with an inhomogeneous ferromagnet, a gapless odd frequency superconducting state is predicted, in which the Cooper pairs are in a spin-triplet state. Although indirect evidence for such a state has been obtained, the gap structure and pairing symmetry have not so far been determined. Here we report scanning tunnelling spectroscopy of Nb superconducting films proximity coupled to epitaxial Ho. These measurements reveal pronounced changes to the Nb subgap superconducting density of states on driving the Ho through a metamagnetic transition from a helical antiferromagnetic to a homogeneous ferromagnetic state for which a BCS-like gap is recovered. The results prove odd frequency spin-triplet superconductivity at superconductor/inhomogeneous magnet interfaces.

  17. Odd-parity topological superconductors: theory and application to CuxBi2Se3.

    PubMed

    Fu, Liang; Berg, Erez

    2010-08-27

    Topological superconductors have a full pairing gap in the bulk and gapless surface Andreev bound states. In this Letter, we provide a sufficient criterion for realizing time-reversal-invariant topological superconductors in centrosymmetric superconductors with odd-parity pairing. We next study the pairing symmetry of the newly discovered superconductor CuxBi2Se3 within a two-orbital model, and find that a novel spin-triplet pairing with odd parity is favored by strong spin-orbit coupling. Based on our criterion, we propose that CuxBi2Se3 is a good candidate for a topological superconductor. We close by discussing experimental signatures of this new topological phase.

  18. T-odd asymmetry in W + jet events at the LHC.

    PubMed

    Frederix, Rikkert; Hagiwara, Kaoru; Yamada, Toshifumi; Yokoya, Hiroshi

    2014-10-10

    W bosons produced at high transverse momentum in hadron collisions can have polarization along the direction perpendicular to the production plane, which is odd under naïve T reversal where both the three-momenta and angular momenta are reversed. Perturbative QCD predicts nonzero polarization at the one-loop level, which can be measured as parity-odd components in the angular distribution of charged leptons from the decay of W bosons. We perform a detector-level simulation with the generator MadGraph5_aMC@NLO, and demonstrate that the asymmetry can be observed at the 8 TeV LHC with 20 fb(-1) of data. If confirmed, it will be the first experimental measurement of the sign of the imaginary part of one-loop QCD amplitudes.

  19. Rotational structure of the odd-proton nuclide 171Tm: A projected shell model study

    NASA Astrophysics Data System (ADS)

    Liu, YanXin; Chen, FangQi; Yu, ShaoYing; Sun, Yang

    2015-05-01

    Deformed odd-mass nuclei are ideal examples where the interplay between single-particle and collective degrees of freedom can be studied. Inspired by the recent experimental high-spin data in the odd-proton nuclide 171Tm, we perform projected shell model (PSM) calculations to investigate structure of the ground band and other bands based on isomeric states. In addition to the usual quadrupole-quadrupole force in the Hamiltonian, we employ the hexadecapole-hexadecapole ( HH) interaction, in a self-consistent way with the hexadecapole deformation of the deformed basis. It is found that the known experimental data can be well described by the PSM calculation. The effect of the HH force on the quasiparticle isomeric states is discussed.

  20. Odd-Parity Pairing and Topological Superconductivity in a Strongly Spin-Orbit Coupled Semiconductor

    NASA Astrophysics Data System (ADS)

    Sasaki, Satoshi; Ren, Zhi; Taskin, A. A.; Segawa, Kouji; Fu, Liang; Ando, Yoichi

    2012-11-01

    The existence of topological superconductors preserving time-reversal symmetry was recently predicted, and they are expected to provide a solid-state realization of itinerant massless Majorana fermions and a route to topological quantum computation. Their first likely example, CuxBi2Se3, was discovered last year, but the search for new materials has so far been hindered by the lack of a guiding principle. Here, we report point-contact spectroscopy experiments suggesting that the low-carrier-density superconductor Sn1-xInxTe is accompanied by surface Andreev bound states which, with the help of theoretical analysis, would give evidence for odd-parity pairing and topological superconductivity. The present and previous finding of possible topological superconductivity in Sn1-xInxTe and CuxBi2Se3 suggests that odd-parity pairing favored by strong spin-orbit coupling is likely to be a common underlying mechanism for materializing topological superconductivity.