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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. [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.

  3. 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

  4. 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.

  5. Limits on Log Odds Ratios for Unidimensional Item Response Theory Models

    ERIC Educational Resources Information Center

    Haberman, Shelby J.; Holland, Paul W.; Sinharay, Sandip

    2007-01-01

    Bounds are established for log odds ratios (log cross-product ratios) involving pairs of items for item response models. First, expressions for bounds on log odds ratios are provided for one-dimensional item response models in general. Then, explicit bounds are obtained for the Rasch model and the two-parameter logistic (2PL) model. Results are…

  6. 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.

  7. 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.

  8. 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.

  9. 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. PMID:26231012

  10. Constant Latent Odds-Ratios Models and the Mantel-Haenszel Null Hypothesis

    ERIC Educational Resources Information Center

    Hessen, David J.

    2005-01-01

    In the present paper, a new family of item response theory (IRT) models for dichotomous item scores is proposed. Two basic assumptions define the most general model of this family. The first assumption is local independence of the item scores given a unidimensional latent trait. The second assumption is that the odds-ratios for all item-pairs are…

  11. 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…

  12. 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

  13. Asymptotic stabilisation for a class of feedforward input-delay systems with ratios of odd integers

    NASA Astrophysics Data System (ADS)

    Wu, Jian; Chen, Weisheng; Miao, Qiguang

    2013-11-01

    This article addresses the stabilisation problem by state-feedback for a class of feedforward input-delay nonlinear systems with ratios of odd integer powers. The designed controller achieves the global asymptotic stability. Based on the appropriate state transformation of time-delay systems and the Lyapunov method, the problem of controller design can be converted into the problem of finding a parameter which can be obtained by appraising the nonlinear terms of the systems. Finally, three simulation examples are given to illustrate the effectiveness of the control algorithm proposed in this article.

  14. Risk Factors of End Stage Renal Disease in Peshawar, Pakistan: Odds Ratio Analysis

    PubMed Central

    Khan, Salahuddin; Hussain, Tariq; Salahuddin, Najma; Mehreen, Salahuddin

    2016-01-01

    AIM: The basic aim of this study was to discover the association of End Stage Renal Disease (ESRD) with various risk factors. End Stage Renal Failure is the last stage of the chronic renal failure in which kidneys become completely fail to function. MATERIALS AND METHODS: The data were collected from the patients of renal diseases from three major hospitals in Peshawar, Pakistan. Odds ratio analysis was performed to examine the relationship of ESRD (a binary response variable) with various risk factors: Gender, Diabetic, Hypertension, Glomerulonephritis, Obstructive Nephropathy, Polycystic kidney disease, Myeloma, SLE Nephritis, Heredity, Hepatitis, Excess use of Drugs, heart problem and Anemia. RESULTS: Using odds ratio analysis, the authors found that the ESRD in diabetic patients was 11.04 times more than non-diabetic patients and the ESRD were 7.29 times less in non-hypertensive patients as compared to hypertensive patients. Similarly, glomerulonephritis patients had 3.115 times more risk of having ESRD than non-glomerulonephritis. Other risk factors may also, to some extent, were causes of ESRD but turned out insignificant due to stochastic sample. CONCLUSION: The authors concluded that there is a strong association between ESRD and three risk factors, namely diabetes, hypertension and glomerulonephritis. PMID:27703559

  15. Changes in Obesity Odds Ratio among Iranian Adults, since 2000: Quadratic Inference Functions Method

    PubMed Central

    Etemad, Koorosh; Seifi, Behjat; Mohammad, Kazem; Biglarian, Akbar; Koohpayehzadeh, Jalil

    2016-01-01

    Background. Monitoring changes in obesity prevalence by risk factors is relevant to public health programs that focus on reducing or preventing obesity. The purpose of this paper was to study trends in obesity odds ratios (ORs) for individuals aged 20 years and older in Iran by using a new statistical methodology. Methods. Data collected by the National Surveys in Iran, from 2000 through 2011. Since responses of the member of each cluster are correlated, the quadratic inference functions (QIF) method was used to model the relationship between the odds of obesity and risk factors. Results. During the study period, the prevalence rate of obesity increased from 12% to 22%. By using QIF method and a model selection criterion for performing stepwise regression analysis, we found that while obesity prevalence generally increased in both sexes, all ages, all employment, residence, and smoking levels, it seems to have changes in obesity ORs since 2000. Conclusions. Because obesity is one of the main risk factors for many diseases, awareness of the differences by factors allows development of targets for prevention and early intervention. PMID:27803729

  16. Multiple Imputation for Missing Values Through Conditional Semiparametric Odds Ratio Models

    PubMed Central

    Chen, Hua Yun; Xie, Hui; Qian, Yi

    2010-01-01

    Summary Multiple imputation is a practically useful approach to handling incompletely observed data in statistical analysis. Parameter estimation and inference based on imputed full data have been made easy by Rubin's rule for result combination. However, creating proper imputation that accommodates flexible models for statistical analysis in practice can be very challenging. We propose an imputation framework that uses conditional semiparametric odds ratio models to impute the missing values. The proposed imputation framework is more flexible and robust than the imputation approach based on the normal model. It is a compatible framework in comparison to the approach based on fully conditionally specified models. The proposed algorithms for multiple imputation through the Monte Carlo Markov Chain sampling approach can be straightforwardly carried out. Simulation studies demonstrate that the proposed approach performs better than existing, commonly used imputation approaches. The proposed approach is applied to imputing missing values in bone fracture data. PMID:21210771

  17. Relationships among three popular measures of differential risks: relative risk, risk difference, and odds ratio.

    PubMed

    Feng, Changyong; Wang, Hongyue; Wang, Bokai; Lu, Xiang; Sun, Hao; Tu, Xin M

    2016-02-25

    The relative risk, risk difference, and odds ratio are the three most commonly used measures for comparing the risk of disease between different groups. Although widely popular in biomedical and psychosocial research, the relationship among the three measures has not been clarified in the literature. Many researchers incorrectly assume a monotonic relationship, such that higher (or lower) values in one measure are associated with higher (or lower) values in the other measures. In this paper we discuss three theorems and provide examples demonstrating that this is not the case; there is no logical relationship between any of these measures. Researchers must be very cautious when implying a relationship between the different measures or when combining results of studies that use different measures of risk. PMID:27688647

  18. Relationships among three popular measures of differential risks: relative risk, risk difference, and odds ratio

    PubMed Central

    FENG, Changyong; WANG, Hongyue; WANG, Bokai; LU, Xiang; SUN, Hao; TU, Xin M.

    2016-01-01

    The relative risk, risk difference, and odds ratio are the three most commonly used measures for comparing the risk of disease between different groups. Although widely popular in biomedical and psychosocial research, the relationship among the three measures has not been clarified in the literature. Many researchers incorrectly assume a monotonic relationship, such that higher (or lower) values in one measure are associated with higher (or lower) values in the other measures. In this paper we discuss three theorems and provide examples demonstrating that this is not the case; there is no logical relationship between any of these measures. Researchers must be very cautious when implying a relationship between the different measures or when combining results of studies that use different measures of risk. PMID:27688647

  19. Notes on interval estimation of the generalized odds ratio under stratified random sampling.

    PubMed

    Lui, Kung-Jong; Chang, Kuang-Chao

    2013-05-01

    It is not rare to encounter the patient response on the ordinal scale in a randomized clinical trial (RCT). Under the assumption that the generalized odds ratio (GOR) is homogeneous across strata, we consider four asymptotic interval estimators for the GOR under stratified random sampling. These include the interval estimator using the weighted-least-squares (WLS) approach with the logarithmic transformation (WLSL), the interval estimator using the Mantel-Haenszel (MH) type of estimator with the logarithmic transformation (MHL), the interval estimator using Fieller's theorem with the MH weights (FTMH) and the interval estimator using Fieller's theorem with the WLS weights (FTWLS). We employ Monte Carlo simulation to evaluate the performance of these interval estimators by calculating the coverage probability and the average length. To study the bias of these interval estimators, we also calculate and compare the noncoverage probabilities in the two tails of the resulting confidence intervals. We find that WLSL and MHL can generally perform well, while FTMH and FTWLS can lose either precision or accuracy. We further find that MHL is likely the least biased. Finally, we use the data taken from a study of smoking status and breathing test among workers in certain industrial plants in Houston, Texas, during 1974 to 1975 to illustrate the use of these interval estimators.

  20. Estimation of Odds Ratios of Genetic Variants for the Secondary Phenotypes Associated with Primary Diseases

    PubMed Central

    Wang, Jian; Shete, Sanjay

    2011-01-01

    Genetic association studies for binary diseases are designed as case-control studies: the cases are those affected with the primary disease and the controls are free of the disease. At the time of case-control collection, information about secondary phenotypes is also collected. Association studies of secondary phenotype and genetic variants have received a great deal of interest recently. To study the secondary phenotypes, investigators use standard regression approaches, where individuals with secondary phenotypes are coded as cases and those without secondary phenotypes are coded as controls. However, using the secondary phenotype as an outcome variable in a case-control study might lead to a biased estimate of odds ratios (ORs) for genetic variants. The secondary phenotype is associated with the primary disease; therefore, individuals with and without the secondary phenotype are not sampled following the principles of a case-control study. In this article, we demonstrate that such analyses will lead to a biased estimate of OR and propose new approaches to provide more accurate OR estimates of genetic variants associated with the secondary phenotype for both unmatched and frequency-matched (with respect to the secondary phenotype) case-control studies. We also propose a bootstrapping method to estimate the empirical confidence intervals for the corrected ORs. Using simulation studies and analysis of lung cancer data for single-nucleotide polymorphism associated with smoking quantity, we compared our new approaches to standard logistic regression and to an extended version of the inverse-probability-of-sampling-weighted regression. The proposed approaches provide more accurate estimation of the true OR. PMID:21308766

  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. 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.

  3. 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. PMID:25126485

  4. Likelihood ratio and score tests to test the non-inferiority (or equivalence) of the odds ratio in a crossover study with binary outcomes.

    PubMed

    Li, Xiaochun; Li, Huilin; Jin, Man; D Goldberg, Judith

    2016-09-10

    We consider the non-inferiority (or equivalence) test of the odds ratio (OR) in a crossover study with binary outcomes to evaluate the treatment effects of two drugs. To solve this problem, Lui and Chang (2011) proposed both an asymptotic method and a conditional method based on a random effects logit model. Kenward and Jones (1987) proposed a likelihood ratio test (LRTM ) based on a log linear model. These existing methods are all subject to model misspecification. In this paper, we propose a likelihood ratio test (LRT) and a score test that are independent of model specification. Monte Carlo simulation studies show that, in scenarios considered in this paper, both the LRT and the score test have higher power than the asymptotic and conditional methods for the non-inferiority test; the LRT, score, and asymptotic methods have similar power, and they all have higher power than the conditional method for the equivalence test. When data can be well described by a log linear model, the LRTM has the highest power among all the five methods (LRTM , LRT, score, asymptotic, and conditional) for both non-inferiority and equivalence tests. However, in scenarios for which a log linear model does not describe the data well, the LRTM has the lowest power for the non-inferiority test and has inflated type I error rates for the equivalence test. We provide an example from a clinical trial that illustrates our methods. Copyright © 2016 John Wiley & Sons, Ltd. PMID:27095359

  5. Likelihood ratio and score tests to test the non-inferiority (or equivalence) of the odds ratio in a crossover study with binary outcomes.

    PubMed

    Li, Xiaochun; Li, Huilin; Jin, Man; D Goldberg, Judith

    2016-09-10

    We consider the non-inferiority (or equivalence) test of the odds ratio (OR) in a crossover study with binary outcomes to evaluate the treatment effects of two drugs. To solve this problem, Lui and Chang (2011) proposed both an asymptotic method and a conditional method based on a random effects logit model. Kenward and Jones (1987) proposed a likelihood ratio test (LRTM ) based on a log linear model. These existing methods are all subject to model misspecification. In this paper, we propose a likelihood ratio test (LRT) and a score test that are independent of model specification. Monte Carlo simulation studies show that, in scenarios considered in this paper, both the LRT and the score test have higher power than the asymptotic and conditional methods for the non-inferiority test; the LRT, score, and asymptotic methods have similar power, and they all have higher power than the conditional method for the equivalence test. When data can be well described by a log linear model, the LRTM has the highest power among all the five methods (LRTM , LRT, score, asymptotic, and conditional) for both non-inferiority and equivalence tests. However, in scenarios for which a log linear model does not describe the data well, the LRTM has the lowest power for the non-inferiority test and has inflated type I error rates for the equivalence test. We provide an example from a clinical trial that illustrates our methods. Copyright © 2016 John Wiley & Sons, Ltd.

  6. Increased mortality odds ratio of male liver cancer in a community contaminated by chlorinated hydrocarbons in groundwater

    PubMed Central

    Lee, L; Chung, C; Ma, Y; Wang, G; Chen, P; Hwang, Y; Wang, J

    2003-01-01

    Aims: To investigate the association between cancer mortality risk and exposure to chlorinated hydrocarbons in groundwater of a downstream community near a contaminated site. Methods: Death certificates inclusive for the years 1966–97 were collected from two villages in the vicinity of an electronics factory operated between 1970 and 1992. These two villages were classified into the downstream (exposed) village and the upstream (unexposed) according to groundwater flow direction. Exposure classification was validated by the contaminant levels in 49 residential wells measured with gas chromatography/mass spectrometry. Mortality odds ratios (MORs) for cancer were calculated with cardiovascular-cerebrovascular diseases as the reference diseases. Multiple logistic regressions were performed to estimate the effects of exposure and period after adjustment for age. Results: Increased MORs were observed among males for all cancer, and liver cancer for the periods after 10 years of latency, namely, 1980–89, and 1990–97. Adjusted MOR for male liver cancer was 2.57 (95% confidence interval 1.21 to 5.46) with a significant linear trend for the period effect. Conclusion: The results suggest a link between exposure to chlorinated hydrocarbons and male liver cancer risk. However, the conclusion is limited by lack of individual information on groundwater exposure and potential confounding factors. PMID:12709523

  7. Signal detection for Thai traditional medicine: examination of national pharmacovigilance data using reporting odds ratio and reported population attributable risk.

    PubMed

    Wechwithan, Sareeya; Suwankesawong, Wimon; Sornsrivichai, Vorasith; McNeil, Edward B; Jiraphongsa, Chuleeporn; Chongsuvivatwong, Virasakdi

    2014-10-01

    Herbal containing medicine consumption has increased while the awareness of adverse drug reaction (ADR) was less than conventional medicine. Early detection of unexpected numbers of ADRs from herbal medicines' reports which are abnormal from the whole database needs quantification. Disproportionality analysis has been performed for signal detection by using reporting odds ratio (ROR) as measurement. The impact of having medicine as exposures in each ADR should be measured by using reported population attributable risks (RPAR). This study aimed to quantify the contribution of Thai traditional medicine (TTM) to ADR reports and to assess the association between TTMs and serious adverse drug reactions. Data were retrieved from the adverse drug reaction surveillance database, Thai-Food and Drug Administration from 2002 to 2013. Crude and adjusted RORs for each drug-ADR pair and RPARs were computed. TTM contributed only 0.001% of all serious ADRs reported. Out of 4208 TTM-ADR pairs were examined, three had the statistically significant RORs, namely Andrographis paniculata and anaphylactic shock (ROR 2.32, 95% CI 1.03, 5.21); green traditional medicine and Stevens-Johnson syndrome (ROR 13.04, 95% CI 5.4-31.51) and Derris scandens Benth and angioedema (ROR 2.71, 95% CI 1.05-6.95). Their RPARs ranged from 0.05% to 0.16%. We conclude that TTMs need more intensive surveillance. PMID:24945744

  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. 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

  12. Enhanced ratio of signals enables digital mutation scanning for rare allele detection.

    PubMed

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

    2015-05-01

    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.

  13. A graphic display for the presentation of site-wise odds ratios for score transitions to augment the traditional findings from clinical studies employing dental indexes.

    PubMed

    Proskin, H M; Kleber, C J; Sharma, N C; Nelson, B J

    2001-07-01

    Many of the parameters used in clinical dental research involve the assessment of a condition at each of a number of sites within the mouth. Traditionally, such measurements are averaged over all sites within the mouth (or over all sites of a specified type) for each study participant before statistical analysis. However, a consideration of the original, site-wise scores may provide some additional insights into the performance of therapeutic modalities that might not be made evident through an application of the traditional, means-based approach. A method based on the calculation of site-wise odds ratios of certain types of baseline-to-final examination score transitions was applied to the modified gingival index data from two clinical studies performed to investigate the effect of the daily chewing of a commercially available chewing gum relative to a mint control. A graphical display of these site-specific findings was prepared, which indicated that the chewing gum regimen tended to be associated with a higher frequency of occurrence of favorable score transitions than was the mint control at several measurement sites throughout the mouth. PMID:11913305

  14. Transmission-ratio distortion and allele sharing in affected sib pairs: a new linkage statistic with reduced bias, with application to chromosome 6q25.3.

    PubMed

    Lemire, Mathieu; Roslin, Nicole M; Laprise, Catherine; Hudson, Thomas J; Morgan, Kenneth

    2004-10-01

    We studied the effect of transmission-ratio distortion (TRD) on tests of linkage based on allele sharing in affected sib pairs. We developed and implemented a discrete-trait allele-sharing test statistic, Sad, analogous to the Spairs test statistic of Whittemore and Halpern, that evaluates an excess sharing of alleles at autosomal loci in pairs of affected siblings, as well as a lack of sharing in phenotypically discordant relative pairs, where available. Under the null hypothesis of no linkage, nuclear families with at least two affected siblings and one unaffected sibling have a contribution to Sad that is unbiased, with respect to the effects of TRD independent of the disease under study. If more distantly related unaffected individuals are studied, the bias of Sad is generally reduced compared with that of Spairs, but not completely. Moreover, Sad has higher power, in some circumstances, because of the availability of unaffected relatives, who are ignored in affected-only analyses. We discuss situations in which it may be an efficient use of resources to genotype unaffected relatives, which would give insights for promising study designs. The method is applied to a sample of pedigrees ascertained for asthma in a chromosomal region in which TRD has been reported. Results are consistent with the presence of transmission distortion in that region. PMID:15322985

  15. Reconstructing 2 X 2 Contingency Tables from Odds Ratios Using the Di Pietrantonj Method: Difficulties, Constraints and Impact in Meta-Analysis Results

    ERIC Educational Resources Information Center

    Veroniki, Areti Angeliki; Pavlides, Marios; Patsopoulos, Nikolaos A.; Salanti, Georgia

    2013-01-01

    A problem that is frequently encountered during the systematic review process is when studies that meet the inclusion criteria do not provide the appropriate numerical estimates to include in a meta-analysis. For dichotomous outcomes, a method has been suggested by Di Pietrantonj for reconstructing the 2 × 2 table when the Odds Ratio…

  16. Aberrations Involving Chromosome 1 as a Possible Predictor of Odds Ratio for Colon Cancer - Results from the Krakow Case-Control Study

    PubMed Central

    Galas, Aleksander; Miszczyk, Justyna

    2016-01-01

    Background There is still an open question how to predict colorectal cancer risk before any morphological changes appear in the colon. Objective The purpose was to investigate aberrations in chromosomes 1, 2 and 4 in peripheral blood lymphocytes analyzed by fluorescence in situ hybridization technique as a tool to assess the likelihood of colorectal cancer. Methods A hospital-based case-control study included 20 colon cancer patients and 18 hospital-based controls. Information about potential covariates was collected by interview. The frequency of stable and unstable chromosome aberrations in chromosome 1, 2 and 4 was assessed by fluorescence in situ hybridization technique. Results Colorectal cancer patients, as compared to controls, had a relatively higher frequency of chromosome 1 translocations (median: 3.5 versus 1.0 /1000 cells, p = 0.006), stable aberrations (3.8 versus 1.0 /1000 cells, p = 0.007) and total aberrations (p = 0.009). There were no differences observed for chromosomes 2 and 4. Our results showed an increase in the odds of having colon cancer by about 50–80% associated with an increase by 1/1000 cells in the number of chromosome 1 aberrations. Conclusions The results revealed that the frequency of chromosomal aberrations, especially translocations in chromosome 1, seems to be a promising method to show a colon cancer risk. Additionally, our study suggests the reasonableness of use of biomarkers such as chromosome 1 aberrations in peripheral blood lymphocytes in screening prevention programs for individuals at higher colon cancer risk to identify those who are at increased risk and require more frequent investigations, e.g. by sigmoidoscopy. PMID:26824604

  17. No effect of the α1-antichymotrypsin A allele in Alzheimer's disease

    PubMed Central

    Didierjean, O; Martinez, M; Campion, D; Hannequin, D; Dubois, B; Martin, C; Puel, M; Anterion, C; Pasquier, F; Moreau, O; Babron, M; Penet, C; Agid, Y; Clerget-Darpoux, F; Frebourg, T; Brice, A

    1997-01-01

    The apolipoprotein E (ApoE)-ε4 allele is associated in a dose dependent manner to an increased risk for Alzheimer's disease. However, the ApoE-ε4 allele effect does not account for all patients with Alzheimer's disease, and the existence of other genetic risk factors has been postulated. Kamboh et al reported an association between Alzheimer's disease and the A allele of α1-antichymotrypsin (Aact) gene, which was not confirmed in a larger series more recently analysed. The ApoE and Aact genotypes were analysed in 314 patients with Alzheimer's disease and 173 healthy controls, confirming the dose dependent effect of the ApoE-ε4 allele. Nevertheless, even using odds ratios adjusted for age and sex, there was no significant effect of the Aact genotype on Alzheimer's disease or on the ApoE-ε4 allele associated risk for Alzheimer's disease.

 PMID:9221977

  18. Heterogeneity of dN/dS Ratios at the Classical HLA Class I Genes over Divergence Time and Across the Allelic Phylogeny.

    PubMed

    Bitarello, Bárbara Domingues; Francisco, Rodrigo dos Santos; Meyer, Diogo

    2016-01-01

    The classical class I HLA loci of humans show an excess of nonsynonymous with respect to synonymous substitutions at codons of the antigen recognition site (ARS), a hallmark of adaptive evolution. Additionally, high polymporphism, linkage disequilibrium, and disease associations suggest that one or more balancing selection regimes have acted upon these genes. However, several questions about these selective regimes remain open. First, it is unclear if stronger evidence for selection on deep timescales is due to changes in the intensity of selection over time or to a lack of power of most methods to detect selection on recent timescales. Another question concerns the functional entities which define the selected phenotype. While most analyses focus on selection acting on individual alleles, it is also plausible that phylogenetically defined groups of alleles ("lineages") are targets of selection. To address these questions, we analyzed how dN/dS (ω) varies with respect to divergence times between alleles and phylogenetic placement (position of branches). We find that ω for ARS codons of class I HLA genes increases with divergence time and is higher for inter-lineage branches. Throughout our analyses, we used non-selected codons to control for possible effects of inflation of ω associated to intra-specific analysis, and showed that our results are not artifactual. Our findings indicate the importance of considering the timescale effect when analysing ω over a wide spectrum of divergences. Finally, our results support the divergent allele advantage model, whereby heterozygotes with more divergent alleles have higher fitness than those carrying similar alleles.

  19. 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.

  20. 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, though…

  1. Major histocompatibility complex class I chain related (MIC) A gene, TNFa microsatellite alleles and TNFB alleles in juvenile idiopathic arthritis patients from Latvia.

    PubMed

    Nikitina Zake, Liene; Cimdina, Ija; Rumba, Ingrida; Dabadghao, Preethi; Sanjeevi, Carani B

    2002-05-01

    In order to analyze involvement of major histocompatibility complex class I chain-related gene A (MICA) and tumor necrosis factor a (TNFa) microsatellite polymorphisms as well as TNFB gene in juvenile idiopathic arthritis (JIA), we studied 128 patients divided into groups according to clinical features [monoarthritis (n = 14), oligoarthritis (n = 58), polyarthritis (n = 50), and systemic (n = 6)], and 114 age- and sex-matched healthy controls from Latvia. DNA samples were amplified with specific primers and used for genotyping of MICA and TNFa microsatellite. Typing for a biallelic NcoI polymerase chain reaction RFLP polymorphism located at the first intron of TNFB gene was done as follows: restriction digests generated fragments of 555bp and 185bp for TNFB*1 allele, and 740bp for TNFB*2 allele. The results were compared between cases and controls. We found significant increase of MICA allele A4 (p = 0.009; odds ratio [OR] = 2.3) and allele TNFa2 (p = 0.0001; OR = 4.4) in patients compared with controls. The frequency of allele TNFa9 was significantly decreased (p = 0.0001; OR = 0.1) in patients with JIA. No significant differences of TNFB allele frequency were found. Our data suggest that MICA and TNFa microsatellite polymorphisms may be used as markers for determination of susceptibility and protection from JIA.

  2. 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

  3. Confirmation of association between the e4 allele of apolipoprotein E and Alzheimer's disease.

    PubMed

    Liddell, M; Williams, J; Bayer, A; Kaiser, F; Owen, M

    1994-03-01

    The Apo E genotype of 86 patients with Alzheimer's disease (AD) and 77 age matched controls was determined by digestion of Apo E PCR products with the restriction enzyme CfoI. The frequency of the e4 allele was significantly increased in the patient group (0.33) as compared with controls (0.12). This effect was seen in patients with a family history and in sporadic cases. The odds ratio in homozygotes for the e4 allele was 11.24 (95% confidence interval 2.45-51.50). There was no relationship between age of onset and Apo E genotype. There was no linkage disequilibrium between the apolipoprotein E locus and a TaqI polymorphism at the Apo CII locus, and no allelic association between Apo CII and AD.

  4. Is the Universe odd?

    SciTech Connect

    Land, Kate; Magueijo, Joao

    2005-11-15

    We investigate the point-parity and mirror-parity handedness of the large angle anisotropy in the cosmic microwave background (CMB). In particular we consider whether the observed low CMB quadrupole could more generally signal odd point-parity, i.e., suppression of even multipoles. Even though this feature is 'visually' present in most renditions of the WMAP dataset we find that it never supports parity preference beyond the meagre 95% confidence level. This is fortunate as point-parity handedness implies almost certainly a high level of galactic contamination. Mirror reflection parity, on the contrary, is related to the emergence of a preferred axis, defining the symmetry plane. We use this technique to make contact with recent claims for an anisotropic Universe, showing that the detected preferred axis is associated with positive (even) mirror parity. This feature may be an important clue in identifying the culprit for this unexpected signal.

  5. 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

  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. Survey of odd-odd deformed nuclear spectroscopy

    SciTech Connect

    Hoff, R.W.

    1993-09-14

    In this paper, we survey the current experimental data that support assignment of rotational bands in odd-odd deformed nuclear in the rare earth and actinide regions. We present the results of a new study of {sup 170}Mt nuclear structure. In a comparing experimental and calculated Gallagher-Moszkowski matrix elements for rare earth-region nuclei, we have developed a new approach to the systematics of these matrix elements.

  8. A study of the association of childhood asthma with HLA alleles in the population of Siliguri, West Bengal, India.

    PubMed

    Lama, M; Chatterjee, M; Chaudhuri, T K

    2014-09-01

    Asthma is a heterogeneous disease for which a strong genetic basis is firmly established. It is a complex disorder influenced by gene-environment interaction. Human leukocyte antigen (HLA) genes have been shown to be consistently associated with asthma and its related phenotypes in various populations. The aim of this study was to determine the frequency of the selected HLA classes I and II allelic groups in asthmatic and control groups. HLA typing was performed using polymerase chain reaction-sequence-specific typing (PCR-SSP) method. The allele frequency was estimated by direct counting. Frequency of each HLA allelic group was compared between asthmatic group and control group using χ(2) test. P-value was corrected by multiplying with the number of the allelic groups studied. Odds ratio (OR) and its corresponding 95% confidence interval (CI) for each allelic group were calculated using graphpad instat 3.10. The results of this study showed a significantly higher frequency of HLA-DRB1*03 in asthmatics than in controls (11.43% vs 3.64%, OR = 3.78, 95% CI = 1.61-8.85, P = 0.0025, Pcorr  < 0.05). Analysis of HLA alleles in low and high total serum immunoglobulin E (IgE) level in asthmatics revealed no significant association. HLA-DRB1*03 may be implicated in the susceptibility to asthma in the pediatric population.

  9. 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.

  10. 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.

  11. 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.

  12. Helicobacter pylori hopQ alleles (type I and II) in gastric cancer

    PubMed Central

    LEYLABADLO, HAMED EBRAHIMZADEH; YEKANI, MINA; GHOTASLOU, REZA

    2016-01-01

    The Helicobacter pylori (H. pylori) outer membrane protein (HopQ) of is one of the proteins involved in bacterial adherence to gastric mucosa and has been suggested to have a role in the virulence of H. pylori. The aim of the present study was to determine the association between H. pylori virulence types I and II hopQ genotypes and patients with different gastrointestinal diseases. A polymerase chain reaction-based assay was used to determine the presence of type I and type II hopQ genes in 88 H. pylori strains isolated from H. pylori-infected patients. Of the total 88 H. pylori isolates, type I and type II hopQ alleles were detected in 52 (59.1%) and 36 (40.9%), respectively. A significant association was found between type I hopQ gene and gastric cancer [odds ratio, 2.3; 95% confidence interval (CI), 1.3–4.1] and gastric ulcers (odds ratio, 2.5; 95% CI, 1.4–4.3). A significant association was also identified between the type II hopQ gene and gastric cancer (odds ratio, 2.4; 95% CI, 1.1–3.0). The association between hopQ type I and hopQ type II genotypes and clinical status suggest that these genes may be helpful in the universal prediction of specific disease risks. PMID:27123254

  13. Association of MICA and MICB alleles with symptomatic dengue infection.

    PubMed

    García, Gissel; del Puerto, Florencia; Pérez, Ana B; Sierra, Beatriz; Aguirre, Eglys; Kikuchi, Mihoko; Sánchez, Lizet; Hirayama, Kenji; Guzmán, María G

    2011-10-01

    Dengue viruses (DV) are one of the most important arthropod-borne viral diseases in the developing world. DV can cause syndromes that are either self-limiting or severe. Allelic variants of human leukocyte antigen (HLA) genes have been demonstrated to be associated with disease susceptibility. Here we report the association of nonclassical HLA class I MICA-MICB genes with disease outcome during DV infection. A sequencing-based typing method and genotyping of MICA and MICB in a well-characterized group of Cuban individuals with dengue hemorrhagic fever (DHF), dengue fever (DF), or asymptomatic dengue infection (ADI) was performed. Statistical analysis revealed a tendency for MICA*008 and MICB*008 to associate with susceptibility to illness when symptomatic versus asymptomatic cases (odds ratio [OR] = 2.1, p(v) = 0.03, and OR = 10.4, p = 0.0096, respectively) were compared. Surprisingly, a stronger association of both allelic forms was observed for the DF patients compared with the ADI group (MICA*008, OR = 5.2, p = 0.0001; and MICB*008, OR = 13.2, p = 0.0025) rather than the severe cases. Major histocompatibility class I-related gene-related natural killer cells and/or γδ and αβ T-cell activation might regulate the development of symptomatic DF and DHF.

  14. 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.

  15. Frequency of the apolipoprotein E epsilon 4 allele in a case-control study of early onset Parkinson's disease.

    PubMed Central

    Whitehead, A S; Bertrandy, S; Finnan, F; Butler, A; Smith, G D; Ben-Shlomo, Y

    1996-01-01

    OBJECTIVES: It has been suggested that Parkinson's disease and Alzheimer's disease may share a common or at least overlapping aetiology. The prevalence of dementia among cases of Parkinson's disease is known to be greater than expected in the general population. The frequency of the apolipoprotein epsilon 4 allele in a large case-control study of early onset Parkinson's disease has been examined. METHODS: 215 patients and 212 population based controls were recruited from the Republic of Ireland between 1992 and 1994. Cases had to have disease onset at 55 years or younger and be born after 1925. RESULTS: The frequency of the epsilon 4 allele was almost identical between cases of Parkinson's disease (14.6%) and healthy controls (13.3%). There was no relation between epsilon 4 status and disease onset, disease duration, Hoehn and Yahr score, and disease progression. The frequency of the epsilon 4 allele was not increased among 10 patients with Parkinson's disease with dementia (10.0%) compared with the other patients without dementia (14.8%). There was no association between epsilon 4 allele status and either a history of smoking, family history of dementia, or Parkinson's disease, or being born in a rural area. The odds ratio for the ApoE epsilon 4 allele associated with Parkinson's disease was 1.10 (95% confidence interval (95% CI) 0.68-1.79), adjusting for age group, sex, and residential status. The pooled odds ratio from a meta-analysis of six studies of ApoE epsilon 4 status and Parkinson's disease was 0.94 (95% CI 0.69-1.27). CONCLUSIONS: The results from our study as well as the pooled meta-analysis exclude any important role for ApoE epsilon 4 status in the development of Parkinson's disease. Our results similarly do not support its role either in dementia associated with Parkinson's disease or disease prognosis. PMID:8890771

  16. 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.

  17. 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.

  18. HLA Allele Frequencies in 5802 Koreans: Varied Allele Types Associated with SJS/TEN According to Culprit Drugs

    PubMed Central

    Park, Hye Jung; Kim, Young Joo; Kim, Dong Hyun; Kim, Junho; Park, Kyung Hee; Park, Jung-Won

    2016-01-01

    Purpose Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) are very serious forms of drug-induced cutaneous adverse reaction. SJS/TEN induced by certain drug is well known to be associated with some human leukocyte antigen (HLA) gene type. We aimed to explore HLA allele frequencies and their association with SJS/TEN according to culprit drugs in Korea. Materials and Methods We enrolled 5802 subjects who had results of HLA typing test from August 2005 to July 2014. Total 28 SJS/TEN patients were categorized based on culprit drugs (allopurinol, lamotrigine, carbamazepine) and identified the presence of HLA-B*58:01, HLA-B*44:03, HLA-B*15:02, and HLA-A*31:01. Results HLA-A*24:02 (20.5%), HLA-B*44:03 (10.0%), and HLA-Cw*01:02 (17.1%) were the most frequent type in HLA-A, -B, and -C genes, respectively. Allele frequencies of HLA-B*58:01, HLA-B*44:03, HLA-A*31:01, and HLA-B*15:02 were 7.0%, 10.0%, 5.0%, and 0.3%, respectively. In 958 allopurinol users, 9 subjects (0.9%) were diagnosed with SJS/TEN. Among them, 8 subjects possessed HLA-B*58:01 allele. SJS/TEN induced by allopurinol was more frequently developed in subjects with HLA-B*58:01 than in subjects without it [odds ratio: 57.4; confidence interval (CI) 7.12-463.50; p<0.001]. Allopurinol treatment, based on screening by HLA-B*58:01 genotyping, could be more cost-effective than that not based on screening. HLA-B*44:03 may be associated with lamotrigine-induced SJS/TEN (odds ratio: 12.75; CI 1.03-157.14; p=0.053). Among carbamazepine users, only two patients experienced SJS/TEN and possessed neither HLA-B*15:02 nor HLA-A*31:03. Conclusion HLA gene frequencies varied in Korea. Screening of HLA-B*58:01 before the use of allopurinol might be needed to anticipate probability of SJS/TEN. PMID:26632391

  19. Human Leukocyte Antigen Class I and II Alleles and Cervical Adenocarcinoma

    PubMed Central

    Safaeian, Mahboobeh; Johnson, Lisa G.; Yu, Kai; Wang, Sophia S.; Gravitt, Patti E.; Hansen, John A.; Carrington, Mary; Schwartz, Stephen M.; Gao, Xiaojiang; Hildesheim, Allan; Madeleine, Margaret M.

    2014-01-01

    Background: Associations between human leukocyte antigens (HLA) alleles and cervical cancer are largely representative of squamous cell carcinoma (SCC), the major histologic subtype. We evaluated the association between HLA class I (A, B, and C) and class II (DRB1 and DQB1) loci and risk of cervical adenocarcinoma (ADC), a less common but aggressive histologic subtype. Methods: We pooled data from the Eastern and Western US Cervical Cancer studies, and evaluated the association between individual alleles and allele combinations and ADC (n = 630 ADC; n = 775 controls). Risk estimates were calculated for 11 a priori (based on known associations with cervical cancer regardless of histologic type) and 38 non a priori common alleles, as odds ratios (OR) and 95% confidence intervals (CI), adjusted for age and study. In exploratory analysis, we compared the risk associations between subgroups with HPV16 or HPV18 DNA in ADC tumor tissues in the Western US study cases and controls. Results: Three of the a priori alleles were significantly associated with decreased risk of ADC [DRB1*13:01 (OR = 0.61; 95% CI: 0.41–0.93), DRB1*13:02 (OR = 0.49; 95% CI: 0.31–0.77), and DQB1*06:03 (OR = 0.64; 95% CI: 0.42–0.95)]; one was associated with increased risk [B*07:02 (OR = 1.39; 95% CI: 1.07–1.79)]. Among alleles not previously reported, DQB1*06:04 (OR = 0.46; 95% CI: 0.27–0.78) was associated with decreased risk of ADC and remained significant after correction for multiple comparisons, and C*07:02 (OR = 1.41; 95% CI: 1.09–1.81) was associated with increased risk. We did not observe a difference by histologic subtype. ADC was most strongly associated with increased risk with B*07:02/C*07:02 alleles (OR = 1.33; 95% CI: 1.01–1.76) and decreased risk with DRB1*13:02/DQB1*06:04 (OR = 0.41; 95% CI: 0.21–0.80). Conclusion: Results suggest that HLA allele associations with cervical ADC are similar to those for cervical SCC. An intriguing

  20. Odd nitrogen production by meteoroids

    NASA Technical Reports Server (NTRS)

    Park, C.; Menees, G. P.

    1978-01-01

    The process by which odd nitrogen species (atomic nitrogen and nitric oxide) are formed during atmospheric entry of meteoroids is analyzed theoretically. An ablating meteoroid is assumed to be a point source of mass with a continuum regime evolving in its wake. The amounts of odd nitrogen species, produced by high-temperature reactions of air in the continuum wake, are calculated by numerical integration of chemical rate equations. Flow properties are assumed to be uniform across the wake, and 29 reactions involving five neutral species and five singly ionized species are considered, as well as vibrational and electron temperature nonequilibrium phenomena. The results, when they are summed over the observed mass, velocity, and entry-angle distribution of meteoroids, provide odd-nitrogen-species annual global production rates as functions of altitude. The peak production of nitric oxide is found to occur at an altitude of about 85 km; atomic nitrogen production peaks at about 95 km. The total annual rate for nitric oxide is 40 million kg; for atomic nitrogen it is 170 million kg.

  1. Level structures in odd-odd deformed nucleus 184Ta

    NASA Astrophysics Data System (ADS)

    Gowrishankar, R.; Sood, P. C.

    2016-02-01

    A detailed low-energy level scheme of the odd-odd n-rich nucleus 184 73Ta111 is constructed using the well tested Two-Quasiparticle Rotor Model (TQRM) for calculating the bandhead energies of physically admissible 2qp configurations with the inclusion of residual n-p interaction contribution. The presently available data on this level scheme from 184Hf decay are shown to be in agreement with these calculations. Our analysis concludes that 184Hf ( Q_{β}=1340(30) keV) decay admits of 7 additional (to the 3 presently reported) β-branches to 184Ta with J = 0 or 1 and 8 more physically admissible weak ( 1fu β-branches populating J^{π}=2- levels in 184Ta. Further, a close examination of our level scheme clearly indicates the existence of a low-lying ( Ex = 260(40) keV) high-spin ( J^{π}=10-) long-lived isomer in this nucleus.

  2. 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.

  3. Chiral Bands in Odd-Odd Triaxially Deformed Nuclei

    NASA Astrophysics Data System (ADS)

    Starosta, K.

    2001-10-01

    In rotational bands built on high-j single-particle orbitals in odd-odd nuclei having triaxial shapes, the angular momenta of the valence proton, the valence neutron, and the collective rotation tend to align along the perpendicular axes of the triaxial core. This occurs when the Fermi level is low within the proton (neutron) subshell, but high within the neutron (proton) subshell resulting in their angular momenta oriented along the short and long axes, respectively. The core angular momentum is oriented along the intermediate axis because it has the largest moment of inertia according to the model of irrotational flow. These three mutually perpendicular vectors can be arranged to form two systems which differ by intrinsic chirality, a left- and a right-handed system; the two systems cannot be transformed into each other by rotation or space inversion, but are related by an operator, which involves time reversal. Chirality resulting from orthogonal coupling of angular momenta is unique to rotational bands in atomic nuclei since these are the only systems where a significant part of the total spin results from single-particle contributions. In relation to time reversal, chirality is a novel example of spontaneous symmetry breaking, on the same level as octupole deformation in relation to space inversion. The main experimental fingerprint of chirality in nuclear rotation is the doubling of states in rotational bands. Δ I=1 doublet-band structures with remarkably similar experimental characteristics, recently observed for N=75 and N=73 isotones in the A ~130 region, have been interpreted as chiral-band partners built on the πh_11/2νh_11/2 configuration. Additional transition rate information is being investigated both experimentally and theoretically. The description of the chiral partner bands based on the microscopic Tilted Axis Cranking approach in the intrinsic, body-fixed reference frame and phenomenological core-particle coupling in the laboratory reference

  4. 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

  5. Use of prior odds for missing persons identifications.

    PubMed

    Budowle, Bruce; Ge, Jianye; Chakraborty, Ranajit; Gill-King, Harrell

    2011-06-27

    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.

  6. The longitudinal effect of the aldehyde dehydrogenase 2*2 allele on the risk for nonalcoholic fatty liver disease

    PubMed Central

    Oniki, K; Morita, K; Watanabe, T; Kajiwara, A; Otake, K; Nakagawa, K; Sasaki, Y; Ogata, Y; Saruwatari, J

    2016-01-01

    Aldehyde dehydrogenase 2 (ALDH2) detoxifies toxic aldehydes and has a key role in protecting the liver. An elevated gamma-glutamyl transferase (GGT) level is related to oxidative stress and nonalcoholic fatty liver disease (NAFLD). We herein investigated the association between inactive ALDH2*2 allele (rs671) and the risk of NAFLD, including the relationship to the GGT level. A retrospective follow-up study (mean 5.4±1.1 years) was conducted among 341 Japanese health screening program participants. The receiver operating characteristic curve indicated that the GGT level predicted the development of NAFLD (area under the curve: 0.65, P<0.05) with a cutoff value of 25.5 IUl−1. The longitudinal risk of NAFLD was higher in the ALDH2*2 allele carriers than in the noncarriers (odds ratio (OR): 2.30, 95% confidence interval (CI): 1.21–4.40), and the risk was further increased among the *2 allele carriers with GGT values ⩾25.5 IUl−1 (OR: 4.28, 95% CI: 1.80–10.19). On the other hand, there were no significant changes in the subjects' body weight and body mass index during observation period. The ALDH2*2 allele, in relation to the GGT level, may potentially be a novel risk factor for NAFLD. PMID:27214654

  7. 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.

  8. Association of HLA-DQA1 and -DQB1 alleles with type I diabetes in Arabs: a meta-analyses.

    PubMed

    Hamzeh, A R; Nair, P; Al-Khaja, N; Al Ali, M T

    2015-07-01

    This study aimed at assessing the nature and significance of associations between various alleles of HLA-DQA1, HLA-DQB1, and type I diabetes (T1D) in Arab populations. Evidence from literature (published before 20 April 2015) was amassed and analysed through multiple meta-analyses, which yielded effect summary odds ratios and 95% confidence intervals for 24 alleles and 4 haplotypes. A total of 1273 cases and 1747 controls from 16 studies were analysed. High levels of significance were obtained to support higher T1D risk when harbouring DQA1*03:01. The alleles DQB1*02:01 and *03:02 and the haplotypes DR3 and DR4 were significant risk factors, albeit with high publication heterogeneity. The protective effects of DQA1*01:01, DQB1*05:03, *06:02, *06:03, and *06:04 were robustly suggested by all indicators of meta-analyses. The haplotypes DR7 and DR11 were strongly suggested to be protective in Arabs. A relatively small number of studies have emerged from Arab countries, mostly with inadequate power on an individual basis. This study fills the gap by providing significant size effect of human leukocyte antigen (HLA) alleles and completes the continuum of global ethnic differences in this context.

  9. The longitudinal effect of the aldehyde dehydrogenase 2*2 allele on the risk for nonalcoholic fatty liver disease.

    PubMed

    Oniki, K; Morita, K; Watanabe, T; Kajiwara, A; Otake, K; Nakagawa, K; Sasaki, Y; Ogata, Y; Saruwatari, J

    2016-05-23

    Aldehyde dehydrogenase 2 (ALDH2) detoxifies toxic aldehydes and has a key role in protecting the liver. An elevated gamma-glutamyl transferase (GGT) level is related to oxidative stress and nonalcoholic fatty liver disease (NAFLD). We herein investigated the association between inactive ALDH2*2 allele (rs671) and the risk of NAFLD, including the relationship to the GGT level. A retrospective follow-up study (mean 5.4±1.1 years) was conducted among 341 Japanese health screening program participants. The receiver operating characteristic curve indicated that the GGT level predicted the development of NAFLD (area under the curve: 0.65, P<0.05) with a cutoff value of 25.5 IUl(-1). The longitudinal risk of NAFLD was higher in the ALDH2*2 allele carriers than in the noncarriers (odds ratio (OR): 2.30, 95% confidence interval (CI): 1.21-4.40), and the risk was further increased among the *2 allele carriers with GGT values ⩾25.5 IUl(-1) (OR: 4.28, 95% CI: 1.80-10.19). On the other hand, there were no significant changes in the subjects' body weight and body mass index during observation period. The ALDH2*2 allele, in relation to the GGT level, may potentially be a novel risk factor for NAFLD.

  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. PMID:26818120

  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. 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.

  13. Protective Effect of the HLA-DRB1*13:02 Allele in Japanese Rheumatoid Arthritis Patients

    PubMed Central

    Oka, Shomi; Furukawa, Hiroshi; Kawasaki, Aya; Shimada, Kota; Sugii, Shoji; Hashimoto, Atsushi; Komiya, Akiko; Fukui, Naoshi; Ito, Satoshi; Nakamura, Tadashi; Saisho, Koichiro; Katayama, Masao; Tsunoda, Shinichiro; Sano, Hajime; Migita, Kiyoshi; Suda, Akiko; Nagaoka, Shouhei

    2014-01-01

    Rheumatoid arthritis (RA) is a chronic systemic inflammatory disease. Certain HLA-DRB1 “shared-epitope” alleles are reported to be positively associated with increased RA susceptibility, whereas some of the other alleles may be negatively associated. However, studies on the latter are rare. Here, we focus on the protective effects of DRB1 alleles in Japanese RA patients in an association study. Relative predispositional effects (RPE) were analyzed by sequential elimination of carriers of each allele with the strongest association. The protective effects of DRB1 alleles were investigated in patients stratified according to whether they possessed anti-citrullinated peptide antibodies (ACPA). The DRB1*13:02 allele was found to be negatively associated with RA (P = 4.59×10−10, corrected P (Pc) = 1.42×10−8, odds ratio [OR] 0.42, 95% CI 0.32–0.55, P [RPE] = 1.27×10−6); the genotypes DRB1*04:05/*13:02 and *09:01/*13:02 were also negatively associated with RA. The protective effect of *13:02 was also present in ACPA-positive patients (P = 3.95×10−8, Pc = 1.22×10−6, OR 0.42, 95%CI 0.31–0.58) whereas *15:02 was negatively associated only with ACPA-negative RA (P = 8.87×10−5, Pc = 0.0026, OR 0.26, 95%CI 0.12–0.56). Thus, this study identified a negative association of DRB1*13:02 with Japanese RA; our findings support the protective role of DRB1*13:02 in the pathogenesis of ACPA-positive RA. PMID:24911054

  14. 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.

  15. 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.

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

    PubMed Central

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

    2013-01-01

    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. PMID:23710940

  17. BOOK REVIEW: The Odd Quantum

    NASA Astrophysics Data System (ADS)

    Reynolds, Helen

    2000-03-01

    The Odd Quantum is aiming to be odd. Falling between being a quantum mechanics textbook and a `popular' science book, it aims to convey something of the substance of quantum mechanics without being overly technical or professional. It does not shy away from the mathematics of the subject or resort solely to analogy and metaphor, as so often is the case. Books aimed at the lay reader tend to take on a particular aspect of quantum mechanics, for example, wave-particle duality, and can do little more than hint at the complexity of the subject. This book is more than a textbook on quantum mechanics; it gives the reader a comprehensive account of history and an appreciation of the nature of quantum mechanics. The introductory chapters deal with the earlier part of the century and the thinking of that time. The approach is familiar, as are the stories that Treiman tells, but he also manages to convey the speed with which ideas changed and the excitement this brought to the physics community. Classical ideas of force and energy are dealt with succinctly but with sufficient depth to set up the reader for what is to come; Maxwell's equations and a brief glimpse at relativity are included. This is followed by a brief description of what the author terms the `old' quantum mechanics, in effect a highly readable tour around black body radiation and spectroscopy and the models of the atom that emerged from them. The `new' quantum mechanics begins about a third of the way through the book, and in a chapter entitled `Foundations' starts gently but rapidly moves into a detailed mathematical treatment. This section, of necessity, relapses into the style of a textbook and covers a lot of ground quickly. It is at this point that the non-specialist popular science readers for whom Treiman has written this book may become a little bemused. Concepts such as non-degeneracy and operators come thick and fast. It is difficult to imagine an educated non-physicist with little mathematical

  18. [Polymorphism of human HLA-DRB1 leukocyte antigen alleles and its association to juvenile rheumatoid arthritis in a sample of Colombian mestizo children].

    PubMed

    Garavito, Gloria; Malagón, Clara; Ramírez, Luis A; De La Cruz, Oscar F; Uribe, Oscar; Navarro, Edgar; Iglesias, Antonio; Martínez, Paz; Jaraquemada, Dolores; Egea, Eduardo

    2003-09-01

    Oligotypes of the human leukocyte antigen HLA Class II, DRB1 alleles were characterized at the molecular level in a group of Colombian children suffering juvenile rheumatoid arthritis (JRA). The distribution of these alleles was examined in a group of Colombian mestizo children (genetic admixture of Amerindians, Europeans and Africans) suffering from clinically distinct JRA subsets in order to detect HLA allele frequency differences in patients with different JRA subsets. A group of 65 patients with JRA and 65 controls were characterized for the subtypes of the HLA-DRB1 alleles using polymerase chain reaction with sequence-specific oligonucleotide probes (PCR-SSOP). The oligotyping protocol recommended by the 12th International Histocompatibility Workshop held in St. Malo, Paris, in 1996, was used. Subtype HLA-DRB1*1104 was the allele most strongly associated with susceptibility to JRA (Fisher's p = 0.013, odds ratio (OR) = 16.79, etiologic fraction (EF) = 0.93). HLA-DRB1*1602 was also associated with susceptibility to a lesser degree (Fisher's p = 0.016, OR = 8.98, EF = 0.88). HLA-DRB1 alleles participating in JRA protection were HLA-DRB1*1501 (preventive fraction (PF) = 0.466, p = 0.005) and HLA DRB1*1402 (PF = 0.49, p = 0.009). The relationship between some HLA-DRB1 alleles and clinical features was also compared. The presence of rheumatic factor was associated with the alleles HLA-DRB1*0407 (p = 0.05, OR = 11.2, EF = 0.45) and HLA-DRB1*1302 (p = 0.02, OR = 22.8, EF = 0.63). There was also an association between HLA-DRB1*0701 (p = 0.001, OR = 58, EF = 0.73) with expressing ANA +. We found that in the oligoarticular subset, the allele HLA-DRB1*1104 (p = 0.0034, OR = 41.53, EF = 0.97) was the one expressed most commonly. In the poliarticular group, the alleles most frequently expressed were HLA-DRB1*0404 (Fisher's p = 0.012, OR = 8.75, EF = 0.88). In patients with systemic JRA, the HLA-DRB1*1602 allele (p = 0.005, OR = 21.33, EF = 0.95) was most frequent. These

  19. Improving the Odds of Surviving Sepsis

    MedlinePlus

    ... Improving the Odds of Surviving Sepsis Inside Life Science View All Articles | Inside Life Science Home Page Improving the Odds of Surviving Sepsis ... Threatening Bacterial Infection Remains Mysterious This Inside Life Science article also appears on LiveScience . Learn about related ...

  20. The nuclear structure of deformed odd-odd nuclei: Experimental and theoretical investigations

    SciTech Connect

    Hoff, R.W.; Jain, A.K.; Sood, P.C.; Sheline, R.K.

    1988-06-06

    Previous surveys of experimental level structure in deformed odd-odd nuclei have been updated with recent results for the lanthanide and actinide regions. The relative strengths of the effective neutron-proton interaction derived from these data are compared. The predictive power of a semi-empirical model for level structure in deformed odd-odd nuclei is demonstrated. Comparison is made with recent Hartree-Fock calculations of selected nuclei.

  1. Social Adjustment among Taiwanese Children with Symptoms of ADHD, ODD, and ADHD Comorbid with ODD

    ERIC Educational Resources Information Center

    Tseng, Wan-Ling; Kawabata, Yoshito; Gau, Susan Shur-Fen

    2011-01-01

    This study examined social problems at school and relationships with peers, siblings, mothers, and fathers among children with ADHD only (n = 41), ODD only (n = 14), ADHD + ODD (n = 47), and normal controls (n = 204) from a school-based sample of 2,463 first to ninth graders in Taiwan. ADHD and ODD symptoms were determined by teacher and mother…

  2. Variant ABO Blood Group Alleles, Secretor Status and Risk of Pancreatic Cancer: Results from the Pancreatic Cancer Cohort Consortium

    PubMed Central

    Wolpin, Brian M.; Kraft, Peter; Xu, Mousheng; Steplowski, Emily; Olsson, Martin L.; Arslan, Alan A.; Bueno-de-Mesquita, H. Bas; Gross, Myron; Helzlsouer, Kathy; Jacobs, Eric J.; LaCroix, Andrea; Petersen, Gloria; Stolzenberg-Solomon, Rachael Z.; Zheng, Wei; Albanes, Demetrius; Allen, Naomi E.; Amundadottir, Laufey; Austin, Melissa A.; Boutron-Ruault, Marie-Christine; Buring, Julie E.; Canzian, Federico; Chanock, Stephen J.; Gaziano, J. Michael; Giovannucci, Edward L.; Hallmans, Göran; Hankinson, Susan E.; Hoover, Robert N.; Hunter, David J.; Hutchinson, Amy; Jacobs, Kevin B.; Kooperberg, Charles; Mendelsohn, Julie B.; Michaud, Dominique S.; Overvad, Kim; Patel, Alpa V.; Sanchéz, Maria-José; Sansbury, Leah; Shu, Xiao-Ou; Slimani, Nadia; Tobias, Geoffrey S.; Trichopoulos, Dimitrios; Vineis, Paolo; Visvanathan, Kala; Virtamo, Jarmo; Wactawski-Wende, Jean; Watters, Joanne; Yu, Kai; Zeleniuch-Jacquotte, Anne; Hartge, Patricia; Fuchs, Charles S.

    2010-01-01

    Background Subjects with non-O ABO blood group alleles have increased risk of pancreatic cancer. Glycosyltransferase activity is greater for the A1 versus A2 variant, while O01 and O02 variants are nonfunctioning. We hypothesized: (1) A1 allele would confer greater risk than A2 allele, (2) protective effect of the O allele would be equivalent for O01 and O02 variants, (3) secretor phenotype would modify the association with risk. Methods We determined ABO variants and secretor phenotype from single nucleotide polymorphisms in ABO and FUT2 genes in 1533 cases and 1582 controls from 12 prospective cohort studies. Adjusted odds ratios (ORs) for pancreatic cancer were calculated using logistic regression. Results An increased risk was observed in participants with A1, but not A2 alleles. Compared to subjects with genotype O/O, genotypes A2/O, A2/A1, A1/O, and A1/A1 had ORs of 0.96 (95% confidence interval [CI], 0.72–1.26), 1.46 (95%CI, 0.98–2.17), 1.48 (95%CI, 1.23–1.78), and 1.71 (95%CI, 1.18–2.47). Risk was similar for O01 and O02 variant O alleles. Compared to O01/O01, the ORs for each additional allele of O02, A1, and A2 were 1.00 (95%CI, 0.87–1.14), 1.38 (95%CI, 1.20–1.58), and 0.96 (95%CI, 0.77–1.20); P-value, O01 versus O02=0.94, A1 versus A2=0.004. Secretor phenotype was not an effect modifier (P-interaction=0.63). Conclusions Among participants in a large prospective cohort consortium, ABO allele subtypes corresponding to increased glycosyltransferase activity were associated with increased pancreatic cancer risk. Impact These data support the hypothesis that ABO glycosyltransferase activity influences pancreatic cancer risk, rather than actions of other nearby genes on chromosome 9q34. PMID:20971884

  3. 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

  4. Allelic loss in colorectal carcinoma

    SciTech Connect

    Kern, S.E.; Fearon, E.R.; Tersmette, K.W.F.; Enterline, J.P.; Vogelstein, B.; Hamilton, S.R. ); Leppert, M.; Nakamura, Yusuke; White, R. )

    1989-06-02

    Clinical and pathological associations with molecular genetic alterations were studied in colorectal carcinomas from 83 patients. Fractional allelic loss, a measure of allelic deletions throughout the genome, and allelic deletions of specific chromosomal arms (the short arm of 17 and long arm of 18) each provided independent prognostic information by multivariate analysis when considered individually with Dukes' classification. Distant metastasis was significantly associated with high fractional allelic loss and with deletions of 17p and 18q. Mutations of ras proto-oncogenes and deletions of 5q had no prognostic importance. Statistically significant associations were also found between allelic losses and a family history of cancer, left-sided tumor location, and absence of extracellular tumor mucin. Allelic deletion analysis thus identified subsets of colorectal carcinoma with increased predilection for distant metastasis and cancer-related death. Further studies may define a subset of genetic alterations that can be used clinically to help assess prognosis.

  5. Individual risk alleles of susceptibility to schizophrenia are associated with poor clinical and social outcomes.

    PubMed

    Sakamoto, Shinji; Takaki, Manabu; Okahisa, Yuko; Mizuki, Yutaka; Inagaki, Masatoshi; Ujike, Hiroshi; Mitsuhashi, Toshiharu; Takao, Soshi; Ikeda, Masashi; Uchitomi, Yosuke; Iwata, Nakao; Yamada, Norihito

    2016-04-01

    Many patients with schizophrenia have poor clinical and social outcomes. Some risk alleles closely related to the onset of schizophrenia have been reported to be associated with their clinical phenotypes, but the direct relationship between genetic vulnerability to schizophrenia and clinical/social outcomes of schizophrenia, as evaluated by both practical clinical scales and 'real-world' function, has not been investigated. We evaluated the clinical and social outcomes of 455 Japanese patients with schizophrenia by severity of illness according to the Clinical Global Impression-Severity Scale (CGI-S) and social outcomes by social adjustment/maladjustment at 5 years after the first visit. We examined whether 46 single nucleotide polymorphisms (SNPs) selected from a Japanese genome-wide association study of susceptibility to schizophrenia were associated with clinical and social outcomes. We also investigated the polygenic risk scores of 46 SNPs. Allele-wise association analysis detected three SNPs, including rs2623659 in the CUB and Sushi multiple domains-1 (CSMD1) gene, associated with severity of illness at end point. The severity of illness at end point was associated with treatment response, but not with the severity of illness at baseline. Three SNPs, including rs2294424 in the C6orf105 gene, were associated with social outcomes. Point estimates of odds ratios showed positive relationships between polygenic risk scores and clinical/social outcomes; however, the results were not statistically significant. Because these results are exploratory, we need to replicate them with a larger sample in a future study. PMID:26674612

  6. The TGFBR1*6A allele is not associated with susceptibility to colorectal cancer in a Spanish population: a case-control study

    PubMed Central

    2009-01-01

    Background TGF-β receptor type I is a mediator of growth inhibitory signals. TGFBR1*6A (rs11466445) is a common polymorphic variant of the TGF-β receptor I gene and has been associated with tumour susceptibility. Nevertheless, the role of this polymorphism as a risk factor for colorectal cancer is controversial. The aim of this study was to assess the association between TGFBR1*6A and colorectal cancer, age, sex, tumour location and tumour stage in a Spanish population. Methods The case-control study involved 800 Spanish subjects: 400 sporadic colorectal cancer patients and 400 age-, sex-, and ethnic-matched controls. The odds ratio (OR) and 95% confidence interval (95% CI) for the TGFBR1*6A polymorphism were calculated using unconditional logistic regression adjusted for age and sex. Analysis of somatic mutations at the GCG repeat of TGFBR1 exon 1 and germline allele-specific expression were also conducted to obtain further information on the contribution of the TGFBR1*6A allele to CRC susceptibility. Results There was no statistically significant association between the TGFBR1*6A allele and CRC (p > 0.05). The OR was 1.147 (95% CI: 0.799–1.647) for carriers of the TGFBR1*6A allele and 0.878 (95% CI: 0.306–2.520) for homozygous TGFBR1*6A individuals compared with the reference. The frequency of the polymorphism was not affected by age, sex or tumour stage. The TGFBR1*6A allele was more prevalent among colon tumour patients than among rectal tumour patients. Tumour somatic mutations were found in only two of 69 cases (2.9%). Both cases involved a GCG deletion that changed genotype 9A/9A in normal DNA to genotype 9A/8A. Interestingly, these two tumours were positive for microsatellite instability, suggesting that these mutations originated because of a deficient DNA mismatch repair system. Allele-specific expression of the 9A allele was detected in seven of the 14 heterozygous 9A/6A tumour cases. This could have been caused by linkage disequilibrium of the

  7. 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.

  8. Biased Allelic Expression in Human Primary Fibroblast Single Cells

    PubMed Central

    Borel, Christelle; Ferreira, Pedro G.; Santoni, Federico; Delaneau, Olivier; Fort, Alexandre; Popadin, Konstantin Y.; Garieri, Marco; Falconnet, Emilie; Ribaux, Pascale; Guipponi, Michel; Padioleau, Ismael; Carninci, Piero; Dermitzakis, Emmanouil T.; Antonarakis, Stylianos E.

    2015-01-01

    The study of gene expression in mammalian single cells via genomic technologies now provides the possibility to investigate the patterns of allelic gene expression. We used single-cell RNA sequencing to detect the allele-specific mRNA level in 203 single human primary fibroblasts over 133,633 unique heterozygous single-nucleotide variants (hetSNVs). We observed that at the snapshot of analyses, each cell contained mostly transcripts from one allele from the majority of genes; indeed, 76.4% of the hetSNVs displayed stochastic monoallelic expression in single cells. Remarkably, adjacent hetSNVs exhibited a haplotype-consistent allelic ratio; in contrast, distant sites located in two different genes were independent of the haplotype structure. Moreover, the allele-specific expression in single cells correlated with the abundance of the cellular transcript. We observed that genes expressing both alleles in the majority of the single cells at a given time point were rare and enriched with highly expressed genes. The relative abundance of each allele in a cell was controlled by some regulatory mechanisms given that we observed related single-cell allelic profiles according to genes. Overall, these results have direct implications in cellular phenotypic variability. PMID:25557783

  9. 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

  10. Reward Region Responsivity Predicts Future Weight Gain and Moderating Effects of the TaqIA Allele

    PubMed Central

    Burger, Kyle S.; Yokum, Sonja

    2015-01-01

    Because no large prospective study has investigated neural vulnerability factors that predict future weight gain, we tested whether neural response to receipt and anticipated receipt of palatable food and monetary reward predicted body fat gain over a 3-year follow-up in healthy-weight adolescent humans and whether the TaqIA polymorphism moderates these relations. A total of 153 adolescents completed fMRI paradigms assessing response to these events; body fat was assessed annually over follow-up. Elevated orbitofrontal cortex response to cues signaling impending milkshake receipt predicted future body fat gain (r = 0.32), which is a novel finding that provides support for the incentive sensitization theory of obesity. Neural response to receipt and anticipated receipt of monetary reward did not predict body fat gain, which has not been tested previously. Replicating an earlier finding (Stice et al., 2008a), elevated caudate response to milkshake receipt predicted body fat gain for adolescents with a genetic propensity for greater dopamine signaling by virtue of possessing the TaqIA A2/A2 allele, but lower caudate response predicted body fat gain for adolescents with a genetic propensity for less dopamine signaling by virtue of possessing a TaqIA A1 allele, though this interaction was only marginal [p-value <0.05 corrected using voxel-level familywise error rate (pFWE) = 0.06]. Parental obesity, which correlated with TaqIA allele status (odds ratio = 2.7), similarly moderated the relation of caudate response to milkshake receipt to future body fat gain, which is another novel finding. The former interaction implies that too much or too little dopamine signaling and reward region responsivity increases risk for overeating, suggesting qualitatively distinct reward surfeit and reward deficit pathways to obesity. SIGNIFICANCE STATEMENT Because no large prospective study has investigated neural vulnerability factors that predict future weight gain we tested whether

  11. Tilted excitation implies odd periodic resonances

    NASA Astrophysics Data System (ADS)

    Depetri, G. I.; Sartorelli, J. C.; Marin, B.; Baptista, M. S.

    2016-07-01

    Our aim is to unveil how resonances of parametric systems are affected when symmetry is broken. We showed numerically and experimentally that odd resonances indeed come about when the pendulum is excited along a tilted direction. Applying the Melnikov subharmonic function, we not only determined analytically the loci of saddle-node bifurcations delimiting resonance regions in parameter space but also explained these observations by demonstrating that, under the Melnikov method point of view, odd resonances arise due to an extra torque that appears in the asymmetric case.

  12. CPT-Odd resonances in neutrino oscillations

    PubMed

    Barger; Pakvasa; Weiler; Whisnant

    2000-12-11

    We consider the consequences for future neutrino factory experiments of small CPT-odd interactions in neutrino oscillations. The nu(&mgr;)-->nu(&mgr;) and nu;(&mgr;)-->nu;(&mgr;) survival probabilities at a baseline L = 732 km can test for CPT-odd contributions at orders of magnitude better sensitivity than present neutrino sector limits. Interference between the CPT-violating interaction and CPT-even mass terms in the Lagrangian can lead to a resonant enhancement of the oscillation amplitude. For oscillations in matter, a simultaneous enhancement of both neutrino and antineutrino oscillation amplitudes is possible.

  13. Tilted excitation implies odd periodic resonances.

    PubMed

    Depetri, G I; Sartorelli, J C; Marin, B; Baptista, M S

    2016-07-01

    Our aim is to unveil how resonances of parametric systems are affected when symmetry is broken. We showed numerically and experimentally that odd resonances indeed come about when the pendulum is excited along a tilted direction. Applying the Melnikov subharmonic function, we not only determined analytically the loci of saddle-node bifurcations delimiting resonance regions in parameter space but also explained these observations by demonstrating that, under the Melnikov method point of view, odd resonances arise due to an extra torque that appears in the asymmetric case. PMID:27575118

  14. 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.

  15. 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.

  16. 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

  17. Allelic association between marker loci.

    PubMed

    Lonjou, C; Collins, A; Morton, N E

    1999-02-16

    Allelic association has proven useful to refine the location of major genes prior to positional cloning, but it is of uncertain value for genome scans in complex inheritance. We have extended kinship theory to give information content for linkage and allelic association. Application to pairs of closely linked markers as a surrogate for marker x oligogene pairs indicates that association is largely determined by regional founders, with little effect of subsequent demography. Sub-Saharan Africa has the least allelic association, consistent with settlement of other regions by small numbers of founders. Recent speculation about substantial advantages of isolates over large populations, of constant size over expansion, and of F1 hybrids over incrosses is not supported by theory or data. On the contrary, fewer affected cases, less opportunity for replication, and more stochastic variation tend to make isolates less informative for allelic association, as they are for linkage.

  18. 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)

  19. 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.

  20. 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…

  1. The Alleged Oddness of Ethical Egoism

    ERIC Educational Resources Information Center

    Marietta, Don E., Jr.

    1977-01-01

    There are some critics of ethical egoism who treat it seriously as an ethical doctrine, but consider it an odd approach. Examines this doctrine and suggests that if we are to have the benefit of egoism as a sound ethical approach, or rightly assess its inadequacies, we must first see it fairly. (Author/RK)

  2. (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.

  3. 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.

  4. Delimiting Allelic Imbalance of TYMS by Allele-Specific Analysis

    PubMed Central

    Balboa-Beltrán, Emilia; Cruz, Raquel; Carracedo, Angel; Barros, Francisco

    2015-01-01

    Abstract Allelic imbalance of thymidylate synthase (TYMS) is attributed to polymorphisms in the 5′- and 3′-untranslated region (UTR). These polymorphisms have been related to the risk of suffering different cancers, for example leukemia, breast or gastric cancer, and response to different drugs, among which are methotrexate glutamates, stavudine, and specifically 5-fluorouracil (5-FU), as TYMS is its direct target. A vast literature has been published in relation to 5-FU, even suggesting the sole use of these polymorphisms to effectively manage 5-FU dosage. Estimates of the extent to which these polymorphisms influence in TYMS expression have in the past been based on functional analysis by luciferase assays and quantification of TYMS mRNA, but both these studies, as the association studies with cancer risk or with toxicity or response to 5-FU, are very contradictory. Regarding functional assays, the artificial genetic environment created in luciferase assay and the problems derived from quantitative polymerase chain reactions (qPCRs), for example the use of a reference gene, may have distorted the results. To avoid these sources of interference, we have analyzed the allelic imbalance of TYMS by allelic-specific analysis in peripheral blood mononuclear cells (PBMCs) from patients. Allelic imbalance in PBMCs, taken from 40 patients with suspected myeloproliferative haematological diseases, was determined by fluorescent fragment analysis (for the 3′-UTR polymorphism), Sanger sequencing and allelic-specific qPCR in multiplex (for the 5′-UTR polymorphisms). For neither the 3′- nor the 5′-UTR polymorphisms did the observed allelic imbalance exceed 1.5 fold. None of the TYMS polymorphisms is statistically associated with allelic imbalance. The results acquired allow us to deny the previously established assertion of an influence of 2 to 4 fold of the rs45445694 and rs2853542 polymorphisms in the expression of TYMS and narrow its allelic imbalance to 1.5 fold

  5. Analysis of bla(SHV) codon 238 and 240 allele mixtures using Sybr green high-resolution melting analysis.

    PubMed

    Andersson, Patiyan; Harris, Tegan; Tong, Steven Y C; Giffard, Philip M

    2009-06-01

    Klebsiella pneumoniae isolates frequently contain complex mixtures of bla(SHV) alleles. A high-resolution melting-based method for interrogating the extended-spectrum activity conferring codon 238 and 240 polymorphisms was developed. This detects minority extended-spectrum beta-lactamase-encoding alleles, allows estimation of allele ratios, and discriminates between single and double mutants.

  6. 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.

  7. Correlation Between HLA-A, B and DRB1 Alleles and Severe Fever with Thrombocytopenia Syndrome

    PubMed Central

    Zhang, Xiao-mei; Jiang, Xiao-lin; Pang, Bo; Song, Yong-hong; Wang, Jian-xing; Pei, Yao-wen; Zhu, Chuan-fu; Wang, Xian-jun; Yu, Xue-jie

    2016-01-01

    Objective Severe fever with thrombocytopenia syndrome (SFTS) is an emerging hemorrhagic fever caused by a tick-borne bunyavirus (SFTSV) in East Asian countries. The role of human leukocyte antigen (HLA) in resistance and susceptibility to SFTSV is not known. We investigated the correlation of HLA locus A, B and DRB1 alleles with the occurrence of SFTS. Methods A total of 84 confirmed SFTS patients (patient group) and 501 unrelated non-SFTS patients (healthy individuals as control group) from Shandong Province were genotyped by PCR-sequence specific oligonucleotide probe (PCR-SSOP) for HLA-A, B and DRB1 loci.Allele frequency was calculated and compared using χ2 test or the Fisher's exact test. A corrected P value was calculated with a bonferronis correction. Odds Ratio (OR) and 95% confidence intervals (CI) were calculated by Woolf’s method. Results A total of 11 HLA-A, 23 HLA-B and 12 HLA-DRB1 alleles were identified in the patient group, whereas 15 HLA-A, 30 HLA-B and 13 HLA-DRB1 alleles were detected in the control group. The frequencies of A*30 and B*13 in the SFTS patient group were lower than that in the control group (P = 0.0341 and 0.0085, Pc = 0.5115 and 0.252). The ORs of A*30 and B*13 in the SFTS patient group were 0.54 and 0.49, respectively. The frequency of two-locus haplotype A*30-B*13 was lower in the patient group than in the control group(5.59% versus 12.27%, P = 0.037,OR = 0.41, 95%CI = 0.18–0.96) without significance(Pc>0.05). A*30-B*13-DRB1*07 and A*02-B*15-DRB1*04 had strong associations with SFTS resistance and susceptibility respectively (Pc = 0.0412 and 0.0001,OR = 0.43 and 5.07). Conclusion The host HLA class I polymorphism might play an important role with the occurrence of SFTS. Negative associations were observed with HLA-A*30, HLA-B*13 and Haplotype A*30-B*13, although the associations were not statistically significant. A*30-B*13-DRB1*07 had negative correlation with the occurrence of SFTS; in contrast, haplotype A*02-B*15-DRB1

  8. 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.

  9. Study of Even-Even/Odd-Even/Odd-Odd Nuclei in Zn-Ga-Ge Region in the Proton-Neutron IBM/IBFM/IBFFM

    SciTech Connect

    Yoshida, N.; Brant, S.; Zuffi, L.

    2009-08-26

    We study the even-even, odd-even and odd-odd nuclei in the region including Zn-Ga-Ge in the proton-neutron IBM and the models derived from it: IBM2, IBFM2, IBFFM2. We describe {sup 67}Ga, {sup 65}Zn, and {sup 68}Ga by coupling odd particles to a boson core {sup 66}Zn. We also calculate the beta{sup +}-decay rates among {sup 68}Ge, {sup 68}Ga and {sup 68}Zn.

  10. 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.

  11. Association of HLA-DQ alleles with the presence of an anti-β2-glycoprotein I antibody in patients with recurrent miscarriage.

    PubMed

    Chen, X; Liang, P-Y; Li, G-G; Diao, L-H; Liu, C-C; Huang, C-Y; Wu, T-H; Xu, J; Zeng, Y

    2016-01-01

    Immunogenetic studies have suggested that autoantibody production is commonly associated with particular human leukocyte antigens (HLA) class II genotypes in certain autoimmune diseases. The objective of this study was to investigate whether the production of anti-β2-glycoprotein I antibody (aβ2GPI) was associated with particular HLA-DQ alleles in patients with recurrent miscarriage (RM). The HLA-DQ genotypes in 126 patients with RM were determined using the polymerase chain reaction-sequence-specific primer method. Both the IgG and IgM isotypes of aβ2GPI were measured via enzyme-linked immunosorbent assay. Positive results for either IgG or IgM on two occasions within an interval of 12 weeks were defined as antiphospholipid antibody-positive. The frequencies of the HLA-DQA1*01:02 [odds ratio (OR) 3.4, 95% confidence interval (CI) 1.6-7.0, Pc = 0.018] and HLA-DQB1*02:01 alleles (OR 4.6, 95% CI 2.1-10.2, Pc = 9.18 × 10(-4)) were significantly increased in aβ2GPI-positive RM patients compared with aβ2GPI-negative RM patients. These results suggest that the HLA-DQA1*0102 and HLA-DQB1*0201 alleles may be involved in the production of aβ2GPI in RM patients.

  12. 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.

  13. 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}

  14. Dissecting Allele Architecture of Early Onset IBD Using High-Density Genotyping

    PubMed Central

    Prahalad, Sampath; Walters, Thomas; Guthery, Stephen L.; Dubinsky, Marla; Baldassano, Robert; Crandall, Wallace V.; Rosh, Joel; Markowitz, James; Stephens, Michael; Kellermayer, Richard; Pfefferkorn, Marian; Heyman, Melvin B.; LeLeiko, Neal; Mack, David; Moulton, Dedrick; Kappelman, Michael D.; Kumar, Archana; Prince, Jarod; Bose, Promita; Mondal, Kajari; Ramachandran, Dhanya; Bohnsack, John F.; Griffiths, Anne M.; Haberman, Yael; Essers, Jonah; Thompson, Susan D.; Aronow, Bruce; Keljo, David J.; Hyams, Jeffrey S.; Denson, Lee A.; Kugathasan, Subra

    2015-01-01

    Background The inflammatory bowel diseases (IBD) are common, complex disorders in which genetic and environmental factors are believed to interact leading to chronic inflammatory responses against the gut microbiota. Earlier genetic studies performed in mostly adult population of European descent identified 163 loci affecting IBD risk, but most have relatively modest effect sizes, and altogether explain only ~20% of the genetic susceptibility. Pediatric onset represents about 25% of overall incident cases in IBD, characterized by distinct disease physiology, course and risks. The goal of this study is to compare the allelic architecture of early onset IBD with adult onset in population of European descent. Methods We performed a fine mapping association study of early onset IBD using high-density Immunochip genotyping on 1008 pediatric-onset IBD cases (801 Crohn’s disease; 121 ulcerative colitis and 86 IBD undetermined) and 1633 healthy controls. Of the 158 SNP genotypes obtained (out of the 163 identified in adult onset), this study replicated 4% (5 SNPs out of 136) of the SNPs identified in the Crohn’s disease (CD) cases and 0.8% (1 SNP out of 128) in the ulcerative colitis (UC) cases. Replicated SNPs implicated the well known NOD2 and IL23R. The point estimate for the odds ratio (ORs) for NOD2 was above and outside the confidence intervals reported in adult onset. A polygenic liability score weakly predicted the age of onset for a larger collection of CD cases (p< 0.03, R2= 0.007), but not for the smaller number of UC cases. Conclusions The allelic architecture of common susceptibility variants for early onset IBD is similar to that of adult onset. This immunochip genotyping study failed to identify additional common variants that may explain the distinct phenotype that characterize early onset IBD. A comprehensive dissection of genetic loci is necessary to further characterize the genetic architecture of early onset IBD. PMID:26098103

  15. Comparative study of Gamow-Teller strength distributions in the odd-odd nucleus {sup 50}V and its impact on electron capture rates in astrophysical environments

    SciTech Connect

    Nabi, Jameel-Un; Sajjad, Muhammad

    2007-11-15

    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 {sup 50}V by using the pn-QRPA theory. At present {sup 50}V 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 {sup 50}V(d, {sup 2}He){sup 50}Ti 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 {sup 50}V. SNe Ia model calculations performed using FFN rates result in overproduction of {sup 50}Ti, 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.

  16. 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.

  17. 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.

  18. Soil clay content underlies prion infection odds

    PubMed Central

    David Walter, W.; Walsh, Daniel P.; Farnsworth, Matthew L.; Winkelman, Dana L.; Miller, Michael 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. PMID:21326232

  19. 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.

  20. 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.

  1. Comparison of model results transporting the odd nitrogen family with results transporting separate odd nitrogen species

    NASA Technical Reports Server (NTRS)

    Douglass, Anne R.; Jackman, Charles H.; Stolarski, Richard S.

    1989-01-01

    A fast two-dimensional residual circulation stratospheric family transport model, designed to minimize computer requirements, is developed. The model was used to calculate the ambient and perturbed atmospheres in which odd nitrogen species are transported as a family, and the results were compared with calculations in which HNO3, N2O5, ClONO2, and HO2NO2 are transported separately. It was found that ozone distributions computed by the two models for a present-day atmosphere are nearly identical. Good agreement was also found between calculated species concentrations and the ozone response, indicating the general applicability of the odd-nitrogen family approximations.

  2. 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.

  3. A cis-eQTL of HLA-DRB1 and a frameshift mutation of MICA contribute to the pattern of association of HLA alleles with cervical cancer.

    PubMed

    Chen, Dan; Gyllensten, Ulf

    2014-04-01

    The association of classic human leukocyte antigen (HLA) alleles with risk of cervical cancer has been extensively studied, and a protective effect has consistently been found for DRB1*1301, DQA1*0103, and/or DQB1*0603 (these three alleles are in perfect linkage disequilibrium [LD] and often occur on the same haplotype in Europeans), while reports have differed widely with respect to the effect of HLA-B*07, DRB1*1501, and/or DQB1*0602 (the last two alleles are also in perfect LD in Europeans). It is not clear whether the reported HLA alleles are responsible for the differences in cervical cancer susceptibility, or if functional variants at other locations within the major histocompatibility complex (MHC) region may explain the effect. In order to assess the relative contribution of both classic HLA alleles and single-nucleotide polymorphisms (SNPs) within the MHC region to cervical cancer susceptibility, we have imputed classic HLA alleles in 1034 cervical cancer patients and 3948 controls in a Swedish population for an integrated analysis. We found that the protective haplotype DRB1*1301-DQA1*0103-DQB1*0603 has a direct effect on cervical cancer and always occurs together with the C allele of a HLA-DRB1 cis-eQTL (rs9272143), which increases the expression of HLA-DRB1. The haplotype rs9272143C-DRB1*1301-DQA1*0103-DQB1*0603 conferred the strongest protection against cervical cancer (odds ratio [OR] = 0.41, 95% confidence interval [CI] = 0.32-0.52, P = 6.2 × 10(-13)). On the other hand, the associations with HLA-B*0702 and DRB1*1501-DQB1*0602 are attributable to the joint effects of both the HLA-DRB1 cis-eQTL (rs9272143) and a frameshift mutation (G inserion of rs67841474, also known as A5.1) of the MHC class I polypeptide-related sequence A gene (MICA). Variation in LD between the classic HLA loci, rs9272143 and rs67841474 between populations may explain the different associations of HLA-B*07 and DRB1*1501-DQB1*0602 with cervical cancer between studies. The

  4. Effect of odd hydrogen on ozone depletion by chlorine reactions

    NASA Technical Reports Server (NTRS)

    Donahue, T. M.; Cicerone, R. J.; Liu, S. C.; Chameides, W. L.

    1976-01-01

    The present paper discusses how the shape of the ozone layer changes under the influence of injected ClX for several choices of two key HOx reaction rates. The two HOx reactions are: OH + HO2 yields H2O + O2 and O + HO2 yields OH + O2. Results of calculations are presented which show that the two reaction rates determine the stratospheric concentrations of OH and HO2, and that these concentrations regulate the amount by which the stratospheric ozone column can be reduced due to injections of odd chlorine. It is concluded that the amount of ozone reduction by a given mixing ratio of ClX will remain very uncertain until the significance of several possible feedback effects involving HOx in a chlorine-polluted atmosphere are determined and measurements of the reaction rates and HOx concentrations are made at the relevant temperatures.

  5. 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

  6. The HLA-DRB1 allele polymorphisms and nasopharyngeal carcinoma.

    PubMed

    Yang, Huimin; Yu, Kaihui; Zhang, Ruoheng; Li, Jiatong; Wei, Xiaomou; Zhang, Yuening; Zhang, Chengdong; Xiao, Feifan; Zhao, Dong; Lin, Xuandong; Wu, Huayu; Yang, Xiaoli

    2016-06-01

    Human leukocyte antigen (HLA)-DRB1 has been reported to influence individual's susceptibility to nasopharyngeal carcinoma (NPC) by many studies in recent years; however, these studies provided controversial results. The meta-analysis was thus conducted here to estimate the relationship between HLA-DRB1 polymorphisms and NPC. After an extensive review of journals from various databases (PubMed, the Web of Science, Embase, China National Knowledge Internet (CNKI), and Wanfang Database), 8 out of 69 case-control studies, including 778 cases and 1148 controls, were extracted. The results showed that 4 of 13 polymorphisms allele are statistically significantly associated with NPC, among them, HLA-DRB1*3, HLA-DRB1*9, and HLA-DRB1*10 may increase the risk of NPC while HLA-DRB1*01 has the opposite effect. The pooled odds ratio and 95 % confidence interval (CI) were 1.702 [95 % CI (1.047, 2.765)], 1.363 [95 % CI (1.029, 1.806)], 1.989 [95 % CI (1.042, 3.799)], and 0.461 [95 % CI (0.315, 0.676)], respectively. In a further ethnicity-based subgroup analysis, HLA-DRB1*08, HLA-DRB1*11, and HLA-DRB1*16 were found to be linked with NPC in Asian, Tunisian, and Caucasian, respectively. In Asian, HLA-DRB1*03, 08, and 10 may elevate the risk whereas HLA-DRB1*09 could lower it. In Tunisian, HLA-DRB1*01 and 11 are the protective factors while HLA-DRB1*03 is the only risk factor. In Caucasian, HLA-DRB1*01 and 03 increase the risk and HLA-DRB1*16 lowers it. The most frequent statistically associated gene is found to be HLA-DRB1*03 which has protective influence on Asian and Tunisian. In conclusion, HLA-DRB1*01, DRB1*03, DRB1*09, and DRB1*10 are related with NPC susceptibility, and the association of HLA-DRB1*08, DRB1*11, and DRB1*16 with NPC risk are significantly different in different ethnicities. PMID:27059731

  7. FMR1 Gray Zone Alleles: Association with Parkinson Disease in Women?

    PubMed Central

    Hall, Deborah A; Berry-Kravis, Elizabeth; Zhang, Wenting; Tassone, Flora; Spector, Elaine; Zerbe, Gary; Hagerman, Paul J; Ouyang, Bichun; Leehey, Maureen A

    2014-01-01

    Purpose Carriers of fragile X mental retardation 1 (FMR1) repeat expansions in the premutation range (55–200 CGG repeats), especially males, often develop tremor, ataxia, and parkinsonism.1–2 These neurological signs are believed to be due to elevated levels of expanded CGG repeat FMR1 mRNA. The purpose of this study was to determine the prevalence of FMR1 repeat expansions in a movement disorder population, comprised of all types of tremor, ataxia or parkinsonism subjects. Methods We screened 335 consecutive movement disorders patients with tremor, ataxia, or parkinsonism and 273 controls confirmed to have no movement disorders. Results There was no difference in FMR1 premutation size expansions in the cases compared to controls. Eleven percent of the women with Parkinson disease (PD) had FMR1 gray zone expansions compared to 4.4% of female controls, odds ratio of 3.2 (95% CI 1.2–8.7). Gray zone expansions in patients with other phenotypes were not overrepresented in comparison with controls. Conclusions FMR1 premutation range expansions are not more common in a mixed movement disorder population compared to controls. Our results, however, suggest that FMR1 gray zone alleles may be associated with PD in women. PMID:21567456

  8. 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

  9. 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.

  10. Airborne measurements of total reactive odd nitrogen (NO(y))

    NASA Technical Reports Server (NTRS)

    Huebler, G.; Fahey, D. W.; Ridley, B. A.; Gregory, G. L.; Fehsenfeld, F. C.

    1992-01-01

    Airborne total reactive odd nitrogen measurements were made during August and September 1986 over the continental United States and off the west coast over the Pacific Ocean during NASA's Global Tropospheric Experiment/Chemical Instrumentation Test and Evaluation 2 program. Measurements were made in the marine and continental boundary layer and the free troposphere up to 6.1 km altitude. NO(y) mixing ratios between 24 pptv and more than 1 ppbv were found, with median values of 101 pptv in the marine boundary layer, 298 pptv in the marine free troposphere, and 288 pptv in the continental free troposphere, respectively. The marine troposphere exhibited layered structure which was also seen in the simultaneously measured ozone mixing ratio and dew point temperature. The averaged vertical NO(y) profile over the ocean does not show a distinct gradient. The NO(y) mixing ratio over the continent decreases with increasing altitude. The latter is consistent with our understanding that the continents are the major source region for these gases.

  11. ODD, ADHD, versus ODD+ADHD in Clinic and Community Adults

    ERIC Educational Resources Information Center

    Gadow, Kenneth D.; Sprafkin, Joyce; Schneider, Jayne; Nolan, Edith E.; Schwartz, Joseph; Weiss, Margaret D.

    2007-01-01

    Objective: To seek evidence for the validity of oppositional defiant disorder (ODD) as a behavioral syndrome in adults. Method: Two samples of adults, mental health outpatient clinic referrals (N = 490) and community controls (N = 900), completed a "Diagnostic and Statistic Manual of Mental Disorders"--referenced rating scale and a brief…

  12. Invasive Allele Spread under Preemptive Competition

    NASA Astrophysics Data System (ADS)

    Yasi, J. A.; Korniss, G.; Caraco, T.

    We study a discrete spatial model for invasive allele spread in which two alleles compete preemptively, initially only the "residents" (weaker competitors) being present. We find that the spread of the advantageous mutation is well described by homogeneous nucleation; in particular, in large systems the time-dependent global density of the resident allele is well approximated by Avrami's law.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. Isospin and deformation studies in the odd-odd N=Z nucleus {sup 54}Co

    SciTech Connect

    Rudolph, D.; Andersson, L.-L.; Ekman, J.; Erten, O.; Fahlander, C.; Johansson, E. K.; Andreoiu, C.; Bengtsson, R.; Ragnarsson, I.; Bentley, M. A.; Williams, S. J.; Carpenter, M. P.; Seweryniak, D.; Charity, R. J.; Reviol, W.; Sarantites, D. G.; Clark, R. M.; Fallon, P.; Macchiavelli, A. O.; Svensson, C. E.

    2010-11-15

    High-spin states in the odd-odd N=Z nucleus {sup 54}Co have been investigated by the fusion-evaporation reaction {sup 28}Si({sup 32}S,1{alpha}1p1n){sup 54}Co. Gamma-ray information gathered with the Ge detector array Gammasphere was correlated with evaporated particles detected in the charged particle detector system Microball and a 1{pi} neutron detector array. A significantly extended excitation scheme of {sup 54}Co is presented, which includes a candidate for the isospin T=1, 6{sup +} state of the 1f{sub 7/2}{sup -2} multiplet. The results are compared to large-scale shell-model calculations in the fp shell. Effective interactions with and without isospin-breaking terms have been used to probe isospin symmetry and isospin mixing. A quest for deformed high-spin rotational cascades proved negative. This feature is discussed by means of cranking calculations.

  18. Meeting report for "OddPols" 2014: the odds invite an even.

    PubMed

    Roy-Engel, Astrid M

    2015-02-01

    The Ninth International Biennial Conference on RNA Polymerases I and III (the "OddPols") was held on June 19-21, 2014 at the University of Michigan, Ann Arbor, USA. Sponsored by New England Biolabs, the Cayman Chemical Company, the Rackham Graduate School and the University of Michigan Health System, and organized by David Engelke, Craig Pikaard, Lawrence Rothblum, Andrzej Wierzbicki and Astrid Engel. This year at the conference, the "odds" were increased by expanding the usual topics on the advances in RNA polymerases I and III research to include presentations on RNA polymerase IV and V. The keynote speaker, Craig Pikaard, opened the meeting with his presentation entitled "Five nuclear multisubunit RNA polymerases". The meeting drew attendees from fourteen countries that shared their research discoveries through oral and poster presentations. The talks were organized into 11 sessions covering seven distinct topics. Here we present some of the highlights from the meeting using summaries provided by the participants.

  19. 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.

  20. 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.

  1. Alleles that increase risk for type 2 diabetes mellitus are not associated with increased risk for Alzheimer's disease.

    PubMed

    Proitsi, Petroula; Lupton, Michelle K; Velayudhan, Latha; Hunter, Gillian; Newhouse, Stephen; Lin, Kuang; Fogh, Isabella; Tsolaki, Magda; Daniilidou, Makrina; Pritchard, Megan; Craig, David; Todd, Stephen; Johnston, Janet A; McGuinness, Bernadette; Kloszewska, Iwona; Soininen, Hilkka; Mecocci, Patrizia; Vellas, Bruno; Passmore, Peter A; Sims, Rebecca; Williams, Julie; Brayne, Carol; Stewart, Robert; Sham, Pak; Lovestone, Simon; Powell, John F

    2014-12-01

    Although epidemiological studies suggest that type 2 diabetes mellitus (T2DM) increases the risk of late-onset Alzheimer's disease (LOAD), the biological basis of this relationship is not well understood. The aim of this study was to examine the genetic comorbidity between the 2 disorders and to investigate whether genetic liability to T2DM, estimated by a genotype risk scores based on T2DM associated loci, is associated with increased risk of LOAD. This study was performed in 2 stages. In stage 1, we combined genotypes for the top 15 T2DM-associated polymorphisms drawn from approximately 3000 individuals (1349 cases and 1351 control subjects) with extracted and/or imputed data from 6 genome-wide studies (>10,000 individuals; 4507 cases, 2183 controls, 4989 population controls) to form a genotype risk score and examined if this was associated with increased LOAD risk in a combined meta-analysis. In stage 2, we investigated the association of LOAD with an expanded T2DM score made of 45 well-established variants drawn from the 6 genome-wide studies. Results were combined in a meta-analysis. Both stage 1 and stage 2 T2DM risk scores were not associated with LOAD risk (odds ratio = 0.988; 95% confidence interval, 0.972-1.004; p = 0.144 and odds ratio = 0.993; 95% confidence interval, 0.983-1.003; p = 0.149 per allele, respectively). Contrary to expectation, genotype risk scores based on established T2DM candidates were not associated with increased risk of LOAD. The observed epidemiological associations between T2DM and LOAD could therefore be a consequence of secondary disease processes, pleiotropic mechanisms, and/or common environmental risk factors. Future work should focus on well-characterized longitudinal cohorts with extensive phenotypic and genetic data relevant to both LOAD and T2DM.

  2. Redistribution of reactive odd nitrogen in the lower arctic stratosphere

    NASA Technical Reports Server (NTRS)

    Huebler, G.; Fahey, D. W.; Kelly, K. K.; Montzka, D. D.; Carroll, M. A.; Tuck, A. F.; Heidt, L. E.; Pollock, W. H.; Gregory, G. L.; Vedder, J. F.

    1990-01-01

    In-situ measurements of total reactive odd nitrogen NO(y), were made from the NASA DC-8 aircraft in the lower arctic stratosphere during the 1989 Airborne Arctic Stratospheric Expedition. Throughout January and February, NO(y) mixing ratios were typically between 0.5 and 3 parts per billion by volume (ppbv) at altitudes between 10 and 12.5 km. During several flights late in the mission, events of unusually light NO(y) occurred with mixing ratios up to 12 ppbv at these altitudes. Simultaneous measurements of N2O, O3, and H2O during these events suggest that large changes in NO(y) are not expected. The elevated NO(y) values are interpreted as a vertical redistribution of NO(y) in the lower stratosphere resulting from gravitational sedimentation of aerosol particles containing HNO3. No evidence of the redistribution of H2O is noted, consistent with observations of denitrification without dehydration higher in the stratosphere.

  3. Photon scattering experiments on the quasistable, odd-odd mass nucleus Lu176

    NASA Astrophysics Data System (ADS)

    Walter, S.; Stedile, F.; Carroll, J. J.; Fransen, C.; Friessner, G.; Hollmann, N.; von Garrel, H.; Jolie, J.; Karg, O.; Käppeler, F.; Kneissl, U.; Kohstall, C.; von Neumann-Cosel, P.; Linnemann, A.; Mücher, D.; Pietralla, N.; Pitz, H. H.; Rusev, G.; Scheck, M.; Scholl, C.; Schwengner, R.; Werner, V.; Wisshak, K.

    2007-03-01

    The quasistable odd-odd-mass nucleus Lu176 is of special interest in nuclear structure physics and, above all, in nuclear astrophysics. Systematic photon scattering experiments have been performed at the bremsstrahlung facility of the 4.3-MV Stuttgart Dynamitron accelerator with bremsstrahlung end-point energies of 2.3 and 3.1 MeV to determine the low-energy dipole strength distribution in the s-only isotope Lu176. The main goal was to pin down possible intermediate states (IS) for the photoactivation of the short-lived 123-keV isomer, which is the key process determining the effective lifetime of Lu176 in a stellar photon bath and hence for the use of this isotope as a stellar chronometer. Using an enriched sample, 29 transitions ascribed to Lu176 were detected below 2.9-MeV excitation energy. The corresponding excitation strengths were determined. For the previously proposed lowest IS at 839 keV, an upper limit for the excitation strength corresponding to a lifetime of τ⩾ 1.5 ps can be given. Astrophysical consequences, also in view of new Stuttgart photoactivation experiments, are discussed. The fragmentation of the dipole strength is compared to those in neighboring even-even and odd-even nuclei.

  4. 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

  5. Association between rs2431697 T allele on 5q33.3 and systemic lupus erythematosus: case-control study and meta-analysis.

    PubMed

    Tang, Zhao-Ming; Wang, Ping; Chang, Pan-Pan; Hasahya, Tony; Xing, Hui; Wang, Jin-Ping; Hu, Li-Hua

    2015-11-01

    rs2431697 is located on 5q33.3, between pituitary tumor-transforming gene 1 and miR-146a. Several studies have estimated the association between rs2431697 and systemic lupus erythematosus risk. However, the results were inconsistent. A case-control study was carried out to explore the association between rs2431697 and systemic lupus erythematosus risk in a central Chinese population. Meta-analyses combining present with previous studies were conducted to further explore the association. Our case-control study included 322 cases and 353 controls. rs2431697 T allele was associated with increased risk of systemic lupus erythematosus (odds ratios (ORs) = 1.461, 95% confidence intervals (CI) 1.091-1.957, P = 0.011). The association was stronger between T allele and the risk of anti-double-stranded DNA (dsDNA)-positive systemic lupus erythematosus (OR = 2.510, 95% CI 1.545-4.077, P < 0.001). The meta-analyses included 8648 systemic lupus erythematosus patients and 10947 controls. rs2431697 T allele had an overall OR of 1.262 (95% CI 1.205-1.323, P < 0.001) under fixed-effects model. After stratified by ethnicity, I (2) reduced from 24.3 to 0 %. T allele had an OR of 1.213 (95% CI 1.145-1.284, P < 0.001) in European descendant and 1.365 (95% CI 1.259-1.480, P < 0.001) in Asian under fixed-effects model. Data on women were also extracted, and T allele had an OR of 1.337 (95% CI 1.162-1.539, P < 0.001) under random-effects model. The pooled ORs were not influenced by each study in sensitivity analyses. There were no publication biases observed in these analyses. The results from our case-control study and the meta-analyses indicate that rs2431697 T allele significantly associates with the increased risk of systemic lupus erythematosus.

  6. RHD allele distribution in Africans of Mali

    PubMed Central

    Wagner, Franz F; Moulds, Joann M; Tounkara, Anatole; Kouriba, Bourema; Flegel, Willy A

    2003-01-01

    Background Aberrant and non-functional RHD alleles are much more frequent in Africans than in Europeans. The DAU cluster of RHD alleles exemplifies that the alleles frequent in Africans have evaded recognition until recently. A comprehensive survey of RHD alleles in any African population was lacking. Results We surveyed the molecular structure and frequency of RHD alleles in Mali (West Africa) by evaluating 116 haplotypes. Only 69% could be attributed to standard RHD (55%) or the RHD deletion (14%). The aberrant RHD allele DAU-0 was predicted for 19%, RHDΨ for 7% and Ccdes for 4% of all haplotypes. DAU-3 and the new RHD allele RHD(L207F), dubbed DMA, were found in one haplotype each. A PCR-RFLP for the detection of the hybrid Rhesus box diagnostic for the RHD deletion in Europeans was false positive in 9 individuals, including all carriers of RHDΨ . Including two silent mutations and the RHD deletion, a total of 9 alleles could be differentiated. Conclusion Besides standard RHD and the RHD deletion, DAU-0, RHDΨ and Ccdes are major alleles in Mali. Our survey proved that the most frequent alleles of West Africans have been recognized allowing to devise reliable genotyping and phenotyping strategies. PMID:14505497

  7. Large odd{endash}even effect in RbC{sup {minus}}{sub {ital n}} cluster size distributions

    SciTech Connect

    Vandenbosch, R.; Will, D.I.

    1996-04-01

    RbC{sub {ital n}} cluster anions have been produced by Rb sputtering of graphite. The intensity ratio of clusters with an even number of carbon atoms to those with an odd number of carbons is much larger for RbC{sup {minus}}{sub {ital n}} clusters than for C{sup {minus}}{sub {ital n}} clusters. {ital Ab} {ital initio} quantum mechanical calculations suggest that this arises from RbC{sub {ital n}} electron affinities that are close to zero or negative for odd {ital n}, rather than from an enhanced odd{endash}even alternation in the affinities. {copyright} {ital 1996 American Institute of Physics.}

  8. Quantum Phase Transitions in Odd-Mass Nuclei

    NASA Astrophysics Data System (ADS)

    Leviatan, A.; Petrellis, D.; Iachello, F.

    2013-03-01

    Quantum shape-phase transitions in odd-even nuclei are investigated in the framework of the interacting boson-fermion model. Classical and quantum analysis show that the presence of the odd fermion strongly influences the location and nature of the phase transition, especially near the critical point. Experimental evidence for the occurrence of spherical to axially-deformed transitions in odd-proton nuclei Pm, Eu and Tb (Z=61, 63, 65) is presented.

  9. Reduced Height (Rht) Alleles Affect Wheat Grain Quality.

    PubMed

    Casebow, Richard; Hadley, Caroline; Uppal, Rajneet; Addisu, Molla; Loddo, Stefano; Kowalski, Ania; Griffiths, Simon; Gooding, Mike

    2016-01-01

    The effects of dwarfing alleles (reduced height, Rht) in near isogenic lines on wheat grain quality are characterised in field experiments and related to effects on crop height, grain yield and GA-sensitivity. Alleles included those that conferred GA-insensitivity (Rht-B1b, Rht-B1c, Rht-D1b, Rht-D1c) as well as those that retained GA-sensitivity (rht(tall), Rht8, Rht8 + Ppd-D1a, Rht12). Full characterisation was facilitated by including factors with which the effects of Rht alleles are known to interact for grain yield (i.e. system, [conventional or organic]; tillage intensity [plough-based, minimum or zero]; nitrogen fertilizer level [0-450 kg N/ha]; and genetic backgrounds varying in height [cvs Maris Huntsman, Maris Widgeon, and Mercia]. Allele effects on mean grain weight and grain specific weight were positively associated with final crop height: dwarfing reduced these quality criteria irrespective of crop management or GA-sensitivity. In all but two experiments the effects of dwarfing alleles on grain nitrogen and sulphur concentrations were closely and negatively related to effects on grain yield, e.g. a quadratic relationship between grain yield and crop height manipulated by the GA-insensitive alleles was mirrored by quadratic relationships for nitrogen and sulphur concentrations: the highest yields and most dilute concentrations occurred around 80cm. In one of the two exceptional experiments the GA-insensitive Rht-B1b and Rht-B1c significantly (P<0.05) reduced grain nitrogen concentration in the absence of an effect on yield, and in the remaining experiment the GA-sensitive Rht8 significantly reduced both grain yield and grain nitrogen concentration simultaneously. When Rht alleles diluted grain nitrogen concentration, N:S ratios and SDS-sedimentation volumes were often improved. Hagberg falling number (HFN) was negatively related to crop height but benefits from dwarfing were only seen for GA-insensitive alleles. For HFN, therefore, there was the

  10. Reduced Height (Rht) Alleles Affect Wheat Grain Quality

    PubMed Central

    Casebow, Richard; Hadley, Caroline; Uppal, Rajneet; Addisu, Molla; Loddo, Stefano; Kowalski, Ania; Griffiths, Simon; Gooding, Mike

    2016-01-01

    The effects of dwarfing alleles (reduced height, Rht) in near isogenic lines on wheat grain quality are characterised in field experiments and related to effects on crop height, grain yield and GA-sensitivity. Alleles included those that conferred GA-insensitivity (Rht-B1b, Rht-B1c, Rht-D1b, Rht-D1c) as well as those that retained GA-sensitivity (rht(tall), Rht8, Rht8 + Ppd-D1a, Rht12). Full characterisation was facilitated by including factors with which the effects of Rht alleles are known to interact for grain yield (i.e. system, [conventional or organic]; tillage intensity [plough-based, minimum or zero]; nitrogen fertilizer level [0–450 kg N/ha]; and genetic backgrounds varying in height [cvs Maris Huntsman, Maris Widgeon, and Mercia]. Allele effects on mean grain weight and grain specific weight were positively associated with final crop height: dwarfing reduced these quality criteria irrespective of crop management or GA-sensitivity. In all but two experiments the effects of dwarfing alleles on grain nitrogen and sulphur concentrations were closely and negatively related to effects on grain yield, e.g. a quadratic relationship between grain yield and crop height manipulated by the GA-insensitive alleles was mirrored by quadratic relationships for nitrogen and sulphur concentrations: the highest yields and most dilute concentrations occurred around 80cm. In one of the two exceptional experiments the GA-insensitive Rht-B1b and Rht-B1c significantly (P<0.05) reduced grain nitrogen concentration in the absence of an effect on yield, and in the remaining experiment the GA-sensitive Rht8 significantly reduced both grain yield and grain nitrogen concentration simultaneously. When Rht alleles diluted grain nitrogen concentration, N:S ratios and SDS-sedimentation volumes were often improved. Hagberg falling number (HFN) was negatively related to crop height but benefits from dwarfing were only seen for GA-insensitive alleles. For HFN, therefore, there was the

  11. Coulomb excitation of the odd-odd isotopes 106, 108In

    NASA Astrophysics Data System (ADS)

    Ekström, A.; Cederkäll, J.; Fahlander, C.; Hjorth-Jensen, M.; Engeland, T.; Blazhev, A.; Butler, P. A.; Davinson, T.; Eberth, J.; Finke, F.; Görgen, A.; Górska, M.; Hurst, A. M.; Ivanov, O.; Iwanicki, J.; Köster, U.; Marsh, B. A.; Mierzejewski, J.; Reiter, P.; Siem, S.; Sletten, G.; Stefanescu, I.; Tveten, G. M.; van de Walle, J.; Voulot, D.; Warr, N.; Weisshaar, D.; Wenander, F.; Zielińska, M.

    2010-06-01

    The low-lying states in the odd-odd and unstable isotopes 106, 108In have been Coulomb excited from the ground state and the first excited isomeric state at the REX-ISOLDE facility at CERN. With the additional data provided here the π g 9/2 -1 ⊗ ν d 5/2 and π g 9/2 -1 ⊗ ν g 7/2 multiplets have been re-analyzed and are modified compared to previous results. The observed γ -ray de-excitation patterns were interpreted within a shell model calculation based on a realistic effective interaction. The agreement between theory and experiment is satisfactory and the calculations reproduce the observed differences in the excitation pattern of the two isotopes. The calculations exclude a 6+ ground state in 106In . This is in agreement with the conclusions drawn using other techniques. Furthermore, based on the experimental results, it is also concluded that the ordering of the isomeric and ground state in 108In is inverted compared to the shell model prediction. Limits on B( E2) values have been extracted where possible. A previously unknown low-lying state at 367keV in 106In is also reported.

  12. 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.

  13. Spectroscopy of the odd-odd fp-shell nucleus {sup 52}Sc from secondary fragmentation

    SciTech Connect

    Gade, A.; Bazin, D.; Mueller, W.F.; Janssens, R.V.F.; Carpenter, M.P.; Zhu, S.; Brown, B.A.; Campbell, C.M.; Cook, J.M.; Dinca, D.-C.; Glasmacher, T.; Terry, J.R.; Deacon, A.N.; Freeman, S.J.; Kay, B.P.; Mantica, P.F.

    2006-03-15

    The odd-odd fp-shell nucleus {sup 52}Sc was investigated using in-beam {gamma}-ray spectroscopy following secondary fragmentation of a {sup 55}V and {sup 57}Cr cocktail beam. Aside from the known {gamma}-ray transition at 674(5) keV, a new decay at E{sub {gamma}}=212(3) keV was observed. It is attributed to the depopulation of a low-lying excited level. This new state is discussed in the framework of shell-model calculations with the GXPF1, GXPF1A, and KB3G effective interactions. These calculations are found to be fairly robust for the low-lying level scheme of {sup 52}Sc irrespective of the choice of the effective interaction. In addition, the frequency of spin values predicted by the shell model is successfully modeled by a spin distribution formulated in a statistical approach with an empirical, energy-independent spin-cutoff parameter.

  14. 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.

  15. 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

  16. Allelic variations in the CYBA gene of NADPH oxidase and risk of kidney complications in patients with type 1 diabetes.

    PubMed

    Patente, Thiago A; Mohammedi, Kamel; Bellili-Muñoz, Naïma; Driss, Fathi; Sanchez, Manuel; Fumeron, Frédéric; Roussel, Ronan; Hadjadj, Samy; Corrêa-Giannella, Maria Lúcia; Marre, Michel; Velho, Gilberto

    2015-09-01

    Oxidative stress plays a pivotal role in the pathophysiology of diabetic nephropathy, and the nicotinamide adenine dinucleotide phosphate (NADPH) oxidase system is an important source of reactive oxygen species in hyperglycemic conditions in the kidney. Plasma concentration of advanced oxidation protein products (AOPP), a marker of oxidative stress, is increased in patients with diabetic nephropathy. We investigated associations of variants in the CYBA gene, encoding the regulatory subunit p22(phox) of NADPH oxidase, with diabetic nephropathy and plasma AOPP and myeloperoxidase (MPO) concentrations in type 1 diabetic patients. Seven SNPs in the CYBA region were analyzed in 1357 Caucasian subjects with type 1 diabetes from the SURGENE (n=340), GENEDIAB (n=444), and GENESIS (n=573) cohorts. Duration of follow-up was 10, 9, and 6 years, respectively. Cox proportional hazards and logistic regression analyses were used to estimate hazard ratios (HR) or odds ratios (OR) for incidence and prevalence of diabetic nephropathy. The major G-allele of rs9932581 was associated with the incidence of renal events defined as new cases of microalbuminuria or the progression to a more severe stage of nephropathy during follow-up (HR 1.59, 95% CI 1.17-2.18, P=0.003) in SURGENE. The same allele was associated with established/advanced nephropathy (OR 1.52, 95% CI 1.22-1.92, P=0.0001) and with the incidence of end-stage renal disease (ESRD) (HR 2.01, 95% CI 1.30-3.24, P=0.001) in GENEDIAB/GENESIS pooled studies. The risk allele was also associated with higher plasma AOPP concentration in subsets of SURGENE and GENEDIAB, with higher plasma MPO concentration in a subset of GENEDIAB, and with lower estimated glomerular filtration rate (eGFR) in the three cohorts. In conclusion, a functional variant in the promoter of the CYBA gene was associated with lower eGFR and with prevalence and incidence of diabetic nephropathy and ESRD in type 1 diabetic patients. These results are consistent with

  17. Allelic variations in the CYBA gene of NADPH oxidase and risk of kidney complications in patients with type 1 diabetes.

    PubMed

    Patente, Thiago A; Mohammedi, Kamel; Bellili-Muñoz, Naïma; Driss, Fathi; Sanchez, Manuel; Fumeron, Frédéric; Roussel, Ronan; Hadjadj, Samy; Corrêa-Giannella, Maria Lúcia; Marre, Michel; Velho, Gilberto

    2015-09-01

    Oxidative stress plays a pivotal role in the pathophysiology of diabetic nephropathy, and the nicotinamide adenine dinucleotide phosphate (NADPH) oxidase system is an important source of reactive oxygen species in hyperglycemic conditions in the kidney. Plasma concentration of advanced oxidation protein products (AOPP), a marker of oxidative stress, is increased in patients with diabetic nephropathy. We investigated associations of variants in the CYBA gene, encoding the regulatory subunit p22(phox) of NADPH oxidase, with diabetic nephropathy and plasma AOPP and myeloperoxidase (MPO) concentrations in type 1 diabetic patients. Seven SNPs in the CYBA region were analyzed in 1357 Caucasian subjects with type 1 diabetes from the SURGENE (n=340), GENEDIAB (n=444), and GENESIS (n=573) cohorts. Duration of follow-up was 10, 9, and 6 years, respectively. Cox proportional hazards and logistic regression analyses were used to estimate hazard ratios (HR) or odds ratios (OR) for incidence and prevalence of diabetic nephropathy. The major G-allele of rs9932581 was associated with the incidence of renal events defined as new cases of microalbuminuria or the progression to a more severe stage of nephropathy during follow-up (HR 1.59, 95% CI 1.17-2.18, P=0.003) in SURGENE. The same allele was associated with established/advanced nephropathy (OR 1.52, 95% CI 1.22-1.92, P=0.0001) and with the incidence of end-stage renal disease (ESRD) (HR 2.01, 95% CI 1.30-3.24, P=0.001) in GENEDIAB/GENESIS pooled studies. The risk allele was also associated with higher plasma AOPP concentration in subsets of SURGENE and GENEDIAB, with higher plasma MPO concentration in a subset of GENEDIAB, and with lower estimated glomerular filtration rate (eGFR) in the three cohorts. In conclusion, a functional variant in the promoter of the CYBA gene was associated with lower eGFR and with prevalence and incidence of diabetic nephropathy and ESRD in type 1 diabetic patients. These results are consistent with

  18. Asymptotically Unbiased Estimation of Exposure Odds Ratios in Complete Records Logistic Regression

    PubMed Central

    Bartlett, Jonathan W.; Harel, Ofer; Carpenter, James R.

    2015-01-01

    Missing data are a commonly occurring threat to the validity and efficiency of epidemiologic studies. Perhaps the most common approach to handling missing data is to simply drop those records with 1 or more missing values, in so-called “complete records” or “complete case” analysis. In this paper, we bring together earlier-derived yet perhaps now somewhat neglected results which show that a logistic regression complete records analysis can provide asymptotically unbiased estimates of the association of an exposure of interest with an outcome, adjusted for a number of confounders, under a surprisingly wide range of missing-data assumptions. We give detailed guidance describing how the observed data can be used to judge the plausibility of these assumptions. The results mean that in large epidemiologic studies which are affected by missing data and analyzed by logistic regression, exposure associations may be estimated without bias in a number of settings where researchers might otherwise assume that bias would occur. PMID:26429998

  19. Asymptotically Unbiased Estimation of Exposure Odds Ratios in Complete Records Logistic Regression.

    PubMed

    Bartlett, Jonathan W; Harel, Ofer; Carpenter, James R

    2015-10-15

    Missing data are a commonly occurring threat to the validity and efficiency of epidemiologic studies. Perhaps the most common approach to handling missing data is to simply drop those records with 1 or more missing values, in so-called "complete records" or "complete case" analysis. In this paper, we bring together earlier-derived yet perhaps now somewhat neglected results which show that a logistic regression complete records analysis can provide asymptotically unbiased estimates of the association of an exposure of interest with an outcome, adjusted for a number of confounders, under a surprisingly wide range of missing-data assumptions. We give detailed guidance describing how the observed data can be used to judge the plausibility of these assumptions. The results mean that in large epidemiologic studies which are affected by missing data and analyzed by logistic regression, exposure associations may be estimated without bias in a number of settings where researchers might otherwise assume that bias would occur. PMID:26429998

  20. Asymptotically Unbiased Estimation of Exposure Odds Ratios in Complete Records Logistic Regression.

    PubMed

    Bartlett, Jonathan W; Harel, Ofer; Carpenter, James R

    2015-10-15

    Missing data are a commonly occurring threat to the validity and efficiency of epidemiologic studies. Perhaps the most common approach to handling missing data is to simply drop those records with 1 or more missing values, in so-called "complete records" or "complete case" analysis. In this paper, we bring together earlier-derived yet perhaps now somewhat neglected results which show that a logistic regression complete records analysis can provide asymptotically unbiased estimates of the association of an exposure of interest with an outcome, adjusted for a number of confounders, under a surprisingly wide range of missing-data assumptions. We give detailed guidance describing how the observed data can be used to judge the plausibility of these assumptions. The results mean that in large epidemiologic studies which are affected by missing data and analyzed by logistic regression, exposure associations may be estimated without bias in a number of settings where researchers might otherwise assume that bias would occur.

  1. Could Weight-Loss Surgery Boost Odds of Preemie Birth?

    MedlinePlus

    ... https://medlineplus.gov/news/fullstory_160596.html Could Weight-Loss Surgery Boost Odds of Preemie Birth? Monitoring is ... HealthDay News) -- Mothers-to-be who've had weight-loss surgery may have increased odds for premature delivery, ...

  2. 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.

  3. Efficient genotype elimination via adaptive allele consolidation.

    PubMed

    De Francesco, Nicoletta; Lettieri, Giuseppe; Martini, Luca

    2012-01-01

    We propose the technique of Adaptive Allele Consolidation, that greatly improves the performance of the Lange-Goradia algorithm for genotype elimination in pedigrees, while still producing equivalent output. Genotype elimination consists in removing from a pedigree those genotypes that are impossible according to the Mendelian law of inheritance. This is used to find errors in genetic data and is useful as a preprocessing step in other analyses (such as linkage analysis or haplotype imputation). The problem of genotype elimination is intrinsically combinatorial, and Allele Consolidation is an existing technique where several alleles are replaced by a single “lumped” allele in order to reduce the number of combinations of genotypes that have to be considered, possibly at the expense of precision. In existing Allele Consolidation techniques, alleles are lumped once and for all before performing genotype elimination. The idea of Adaptive Allele Consolidation is to dynamically change the set of alleles that are lumped together during the execution of the Lange-Goradia algorithm, so that both high performance and precision are achieved. We have implemented the technique in a tool called Celer and evaluated it on a large set of scenarios, with good results.

  4. Segregation of male-sterility alleles across a species boundary.

    PubMed

    Weller, S G; Sakai, A K; Culley, T M; Duong, L; Danielson, R E

    2014-02-01

    Hybrid zones may serve as bridges permitting gene flow between species, including alleles influencing the evolution of breeding systems. Using greenhouse crosses, we assessed the likelihood that a hybrid zone could serve as a conduit for transfer of nuclear male-sterility alleles between a gynodioecious species and a hermaphroditic species with very rare females in some populations. Segregation patterns in progeny of crosses between rare females of hermaphroditic Schiedea menziesii and hermaphroditic plants of gynodioecious Schiedea salicaria heterozygous at the male-sterility locus, and between female S. salicaria and hermaphroditic plants from the hybrid zone, were used to determine whether male-sterility was controlled at the same locus in the parental species and the hybrid zone. Segregations of females and hermaphrodites in approximately equal ratios from many of the crosses indicate that the same nuclear male-sterility allele occurs in the parent species and the hybrid zone. These rare male-sterility alleles in S. menziesii may result from gene flow from S. salicaria through the hybrid zone, presumably facilitated by wind pollination in S. salicaria. Alternatively, rare male-sterility alleles might result from a reversal from gynodioecy to hermaphroditism in S. menziesii, or possibly de novo evolution of male sterility. Phylogenetic analysis indicates that some species of Schiedea have probably evolved separate sexes independently, but not in the lineage containing S. salicaria and S. menziesii. High levels of selfing and expression of strong inbreeding depression in S. menziesii, which together should favour females in populations, argue against a reversal from gynodioecy to hermaphroditism in S. menziesii.

  5. 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

    2016-01-01

    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

  6. Low-lying excitations in the odd-odd nucleus154Eu

    NASA Astrophysics Data System (ADS)

    Katajanheimo, R.; Jäderholm, R.; Siivola, A.; Julin, R.; Liukkonen, E.

    1988-03-01

    The doubly odd nucleus154Eu was produced during in-beam bombardments of a154Sm target with3He and deuteron beams at 27 and 10 MeV. The resulting gamma-rays were investigated using prompt and delayed gamma-gamma-coincidence equipment. The half-life of the isomeric 2+ level was determined as 2.2±0.1 μs. The partial level scheme, including numerous previously unidentified excitations, can be divided into two separate groups of levels. The results provide evidence for the existence of a very regular ground band and two rather regular K=3 level structures, whose configurations are closely related to it. In addition, several rotational sequences built on the band heads with other K values have been deduced. Our interpretation of the level scheme disagrees with the previous conclusion that the N=91 nucleus154Eu might have a stable deformation only in its ground state configuration.

  7. 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.

  8. 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

  9. Human Leukocyte Antigen and Systemic Sclerosis in Japanese: The Sign of the Four Independent Protective Alleles, DRB1*13:02, DRB1*14:06, DQB1*03:01, and DPB1*02:01

    PubMed Central

    Furukawa, Hiroshi; Oka, Shomi; Kawasaki, Aya; Shimada, Kota; Sugii, Shoji; Matsushita, Takashi; Hashimoto, Atsushi; Komiya, Akiko; Fukui, Naoshi; Kobayashi, Kouji; Osada, Atsumu; Ihata, Atsushi; Kondo, Yuya; Nagai, Tatsuo; Setoguchi, Keigo; Okamoto, Akiko; Okamoto, Akira; Chiba, Noriyuki; Suematsu, Eiichi; Kono, Hajime; Katayama, Masao; Hirohata, Shunsei; Sumida, Takayuki; Migita, Kiyoshi; Hasegawa, Minoru; Fujimoto, Manabu; Sato, Shinichi; Nagaoka, Shouhei; Takehara, Kazuhiko

    2016-01-01

    Objective Several studies on associations between human leukocyte antigen (HLA) allele frequencies and susceptibility to systemic sclerosis (SSc) have been reported. Anti-centromere antibodies (ACA) and anti-topoisomerase I antibodies (ATA) are found in SSc patients. Here, we sought to identify HLA alleles associated with SSc in Japanese, and explored their associations with SSc phenotypes including the presence of autoantibodies. Methods Associations of HLA-DRB1, DQB1, and DPB1 were analyzed in 463 Japanese SSc patients and 413 controls. Results We found that DRB1*13:02 (P = 0.0011, Pc = 0.0319, odds ratio [OR] 0.46, 95% confidence interval [CI] 0.29–0.73), DRB1*14:06 (P = 6.60X10-5, Pc = 0.0020, OR 0.05, 95%CI 0.01–0.41), DQB1*03:01 (P = 0.0009, Pc = 0.0150, OR 0.56, 95%CI 0.40–0.79), and DPB1*02:01 (P = 5.16X10-6, Pc = 8.77X10-5, OR 0.52, 95%CI 0.39–0.69) were protectively associated with SSc. In addition, these four alleles seemed to be independently associated with the protection against the susceptibility of SSc. On the other hand, we could not find predisposing alleles for overall SSc. With respect to SSc subsets, a tendency for these four alleles to be protectively associated was observed. However, there was a significant association between DRB1*01:01, DRB1*10:01, DQB1*05:01, and DPB1*04:02 and the susceptibility to SSc with ACA. On the other hand, the presence of DRB1*15:02, DQB1*06:01, DPB1*03:01, and DPB1*09:01 was associated with SSc with ATA. Conclusion Thus, the present study has identified protective associations of the four HLA class II alleles with overall Japanese SSc and predisposing associations of HLA class II alleles with Japanese SSc subsets. PMID:27116456

  10. Nuclear spin of odd-odd α emitters based on the behavior of α -particle preformation probability

    NASA Astrophysics Data System (ADS)

    Ismail, M.; Adel, A.; Botros, M. M.

    2016-05-01

    The preformation probabilities of an α cluster inside radioactive parent nuclei for both odd-even and odd-odd nuclei are investigated. The calculations cover the isotopic chains from Ir to Ac in the mass regions 166 ≤A ≤215 and 77 ≤Z ≤89 . The calculations are employed in the framework of the density-dependent cluster model. A realistic density-dependent nucleon-nucleon (N N ) interaction with a finite-range exchange part is used to calculate the microscopic α -nucleus potential in the well-established double-folding model. The main effect of antisymmetrization under exchange of nucleons between the α and daughter nuclei has been included in the folding model through the finite-range exchange part of the N N interaction. The calculated potential is then implemented to find both the assault frequency and the penetration probability of the α particle by means of the Wentzel-Kramers-Brillouin approximation in combination with the Bohr-Sommerfeld quantization condition. The correlation of the α -particle preformation probability and the neutron and proton level sequences of the parent nucleus as obtained in our previous work is extended to odd-even and odd-odd nuclei to determine the nuclear spin and parities. Two spin coupling rules are used, namely, strong and weak rules to determine the nuclear spin for odd-odd isotopes. This work can be a useful reference for theoretical calculation of undetermined nuclear spin of odd-odd nuclei in the future.

  11. Association of Human Leukocyte Antigen Alleles and Nevirapine Hypersensitivity in a Malawian HIV-Infected Population

    PubMed Central

    Carr, Daniel F.; Chaponda, Mas; Jorgensen, Andrea L.; Castro, Elena Cornejo; van Oosterhout, Joep J.; Khoo, Saye H.; Lalloo, David G.; Heyderman, Robert S.; Alfirevic, Ana; Pirmohamed, Munir

    2013-01-01

    Background. The nonnucleoside reverse transcriptase inhibitor nevirapine is the cornerstone of treatment for human immunodeficiency virus (HIV) in many sub-Saharan African countries. However, nevirapine is associated with a 6%–10% risk of developing a hypersensitivity reaction, with different phenotypes, including the blistering conditions Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN). Our aim was to identify predictive human leukocyte antigen (HLA) markers that are associated with nevirapine hypersensitivity. Methods. We identified 117 HIV-infected Malawian adults with nevirapine hypersensitivity (15 drug-induced liver injury [DILI], 33 SJS/TEN, 20 hypersensitivity syndrome, and 46 nevirapine-induced rash plus 3 with both DILI and SJS phenotype) and 155 age-, sex- and ethnicity-matched nevirapine-exposed controls. HLA typing for 5 loci (A, B, C, DRB1, and DQB1) was undertaken using a sequence-based high-resolution protocol. Logistic regression analysis included CD4+ cell count as a covariate. Results. HLA-C*04:01 was found to markedly increase the risk for SJS (odds ratio [OR] = 17.52; 95% confidence interval, 3.31–92.80) and all hypersensitivity phenotypes (OR = 2.64; 95% CI, 1.13–6.18) when compared to the baseline rare allele group in a binary logistic regression model. The OR for absolute risk of SJS/TEN associated with carriage of HLA-C*04:01 was 5.17 (95% CI, 2.39–11.18). Positive predictive value was 2.6% and negative predictive value was 99.2%. In addition, a number of alleles within the HLA-DQB1 loci protected against nevirapine-induced hypersensitivity phenotypes. Conclusions. Our study has identified HLA-C*04:01 carriage as a risk factor for nevirapine-induced SJS/TEN in a Malawian HIV cohort. Validation of these findings in a larger cohort of patients and mechanistic investigation of the pathogenesis are required. PMID:23362284

  12. Properties of the {pi}i{sub 13/2}x{nu}i{sub 13/2} band in odd-odd {sup 184}Au

    SciTech Connect

    Zhang, Y.H.; Fang, Y.D.; Wang, H.L.; Zhou, X.H.; Guo, W.T.; Liu, M.L.; Guo, Y.X.; Lei, X.G.; De Angelis, G.; Marginean, N.; Gadea, A.; Napoli, D.R.; Axiotis, M.; Rusu, C.; Martinez, T.; Oshima, M.; Toh, Y.

    2004-11-01

    High-spin level structure in {sup 184}Au has been reinvestigated using the multidetector array of GASP via the {sup 159}Tb({sup 29}Si,4n{gamma}){sup 184}Au reaction at a beam energy of 140 MeV. The ground-state band and the excited {pi}i{sub 13/2}x{nu}i{sub 13/2} 2-qp band have been extended up to lower and higher spin states. An upbend has been observed in the excited band at ({Dirac_h}/2{pi}){omega}{approx}0.25 MeV and is interpreted as resulting from a pair of {pi}h{sub 9/2} alignment. This low-frequency ({pi}h{sub 9/2}){sup 2} alignment is supported by the measured B(M1)/B(E2) ratios and alignment properties in neighboring odd-A nuclei. The linking transitions between the two bands and to the ground state have been established leading to a firm spin-and-parity assignment for the {pi}i{sub 13/2}x{nu}i{sub 13/2} band in {sup 184}Au. This result provides strong evidence for the low-spin signature inversion in the {pi}i{sub 13/2}x{nu}i{sub 13/2} bands of odd-odd nuclei in the A{approx}180 mass region.

  13. Burden of risk alleles for Hypertension Increases Risk of Intracerebral Hemorrhage

    PubMed Central

    Falcone, Guido J.; Biffi, Alessandro; Devan, William; Jagiella, Jeremiasz M.; Schmidt, Helena; Kissela, Brett; Hansen, Björn M.; Jimenez-Conde, Jordi; Giralt-Steinhauer, Eva; Elosua, Roberto; Cuadrado-Godia, Elisa; Soriano, Carolina; Ayres, Alison M.; Schwab, Kristin; Pera, Joanna; Urbanik, Andrzej; Rost, Natalia S.; Goldstein, Joshua N.; Viswanathan, Anand; Pichler, Alexander; Enzinger, Christian; Norrving, Bo; Tirschwell, David L.; Selim, Magdy; Brown, Devin L.; Silliman, Scott L.; Worrall, Bradford B.; Meschia, James F.; Kidwell, Chelsea S.; Montaner, Joan; Fernandez-Cadenas, Israel; Delgado, Pilar; Broderick, Joseph P.; Greenberg, Steven M.; Roquer, Jaume; Lindgren, Arne; Slowik, Agnieszka; Schmidt, Reinhold; Flaherty, Matthew L.; Kleindorfer, Dawn O.; Langefeld, Carl D.; Woo, Daniel; Rosand, Jonathan

    2012-01-01

    SUMMARY Background and Purpose Genetic variation influences risk of intracerebral hemorrhage (ICH). Hypertension (HTN) is a potent risk factor for ICH and several common genetic variants (SNPs) associated with blood pressure (BP) levels have been identified. We sought to determine whether the cumulative burden of BP-related SNPs is associated with risk of ICH and pre-ICH diagnosis of HTN. Methods Prospective multicenter case-control study in 2272 subjects of European descent (1025 cases and 1247 controls). Thirty-nine SNPs reported to be associated with BP levels were identified from the National Human Genome Research Institute GWAS catalog. Single-SNP association analyses were performed for the outcomes ICH and pre-ICH HTN. Subsequently, weighted and unweighted genetic risk scores were constructed using these SNPs and entered as the independent variable in logistic regression models with ICH and pre-ICH HTN as the dependent variables. Results No single SNP was associated with either ICH or pre-ICH HTN. The BP-based unweighted genetic risk score was associated with risk of ICH (odds ratio [OR] = 1.11, 95% confidence interval [CI] 1.02–1.21, p=0.01) and the subset of ICH in deep regions (OR=1.18, 95%CI 1.07–1.30, p=0.001), but not with the subset of lobar ICH. The score was associated with a history of HTN among controls (OR=1.17, 95%CI 1.04–1.31, p=0.009) and ICH cases (OR=1.15, 95%CI 1.01–1.31, p=0.04). Similar results were obtained when using a weighted score. Conclusion Increasing numbers of high blood pressure-related alleles are associated with increased risk of deep ICH as well as with clinically identified HTN. PMID:22933587

  14. The relationships between HLA class II alleles and antigens with gestational diabetes mellitus: A meta-analysis

    PubMed Central

    Guo, Cong-cong; Jin, Yi-mei; Lee, Kenneth Ka Ho; Yang, Guang; Jing, Chun-xia; Yang, Xuesong

    2016-01-01

    Gestational diabetes mellitus (GDM) is defined as glucose intolerance with onset or first recognition during pregnancy. It is associated with an increased risk of pregnancy complications. Susceptibility to GDM is partly determined by genetics and linked with type 1 diabetes-associated high risk HLA class II genes. However, the evidence for this relationship is still highly controversial. In this study, we assessed the relationship between HLA class II variants and GDM. We performed meta-analysis on all of literatures available in PubMed, Embase, Web of Science and China National Knowledge Infrastructure databases. The odds ratio and 95% confidence interval of each variant were estimated. All statistical analyses were conducted using the Comprehensive Meta Analysis 2.2.064 software. At the allelic analysis, DQB1*02, DQB1*0203, DQB1*0402, DQB1*0602, DRB1*03, DRB1*0301 and DRB1*1302 reached a nominal level of significance, and only DQB1*02, DQB1*0602 and DRB1*1302 were statistically significant after Bonferroni correction. At the serological analysis, none of DQ2, DQ6, DR13 and DR17 was statistically significant following Bonferroni correction although they reached a nominal level of significance. In sum, our meta-analysis demonstrated that there were the associations between HLA class II variants and GDM but more studies are required to elucidate how these variants contribute to GDM susceptibility. PMID:27721507

  15. 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.

  16. 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.

  17. Preschool enrollment is associated with lower odds of childhood obesity among WIC participants in LA County.

    PubMed

    Koleilat, Maria; Harrison, Gail G; Whaley, Shannon; McGregor, Samar; Jenks, Eloise; Afifi, Abdelmonem

    2012-04-01

    The prevalence of obesity among children in the United States has increased rapidly during the past few decades. Research into social and behavioral determinants of obesity could lead to innovative strategies for prevention. The objective of the present study was to examine the association between childhood obesity and preschool enrollment and number of hours in child care among low-income preschool-aged children who were participants in the Special Supplemental Nutrition Program for Women, Infants and Children (WIC). We conducted a case-control study including 556 3- to 4-year-old children who were either obese (BMI > 95th percentile of reference standard) or normal-weight (BMI 25-75th percentile). The population was largely (96%) Hispanic, an ethnic group that has one of the highest rates of overweight and obesity in adults and children in the US. In multiple logistic regression analysis, controlling for a variety of psychosocial and cognitive home environment variables, key demographics and maternal variables, the odds ratio of being obese was 0.61 for children who attended preschool more than 4 days a week (95% CI: 0.41-0.90). Watching television or videos for an hour or more on a typical day (odds ratio 1.71 (95% CI 1.07-2.75)), and higher maternal BMI (odds ratio 1.08 (95% CI 1.05-1.11)) were independently related to odds of obesity. The impact of preschool attendance and TV viewing are potentially instructive in terms of preventive interventions for children at this age.

  18. 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.

  19. 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.

  20. New description of the doublet bands in doubly odd nuclei

    SciTech Connect

    Ganev, H. G.; Georgieva, A. I.; Brant, S.; Ventura, A.

    2009-04-15

    The experimentally observed {delta}I=1 doublet bands in some odd-odd nuclei are analyzed within the orthosymplectic extension of the interacting vector boson model (IVBM). A new, purely collective interpretation of these bands is given on the basis of the obtained boson-fermion dynamical symmetry of the model. It is illustrated by its application to three odd-odd nuclei from the A{approx}130 region, namely {sup 126}Pr, {sup 134}Pr, and {sup 132}La. The theoretical predictions for the energy levels of the doublet bands as well as E2 and M1 transition probabilities between the states of the yrast band in the last two nuclei are compared with experiment and the results of other theoretical approaches. The obtained results reveal the applicability of the orthosymplectic extension of the IVBM.

  1. Veterans' Painkiller Abuse Can Raise Odds for Heroin Use

    MedlinePlus

    ... html Veterans' Painkiller Abuse Can Raise Odds for Heroin Use 3 of 4 who tried the illicit ... narcotic painkillers may be at high risk for heroin use, a new study cautions. The research included ...

  2. 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.

  3. 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.

  4. 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

    2015-06-01

    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.

  5. 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.

  6. 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

  7. An African ancestry-specific allele of CTLA4 confers protection against rheumatoid arthritis in African Americans.

    PubMed

    Kelley, James M; Hughes, Laura B; Faggard, Jeffrey D; Danila, Maria I; Crawford, Monica H; Edberg, Yuanqing; Padilla, Miguel A; Tiwari, Hemant K; Westfall, Andrew O; Alarcón, Graciela S; Conn, Doyt L; Jonas, Beth L; Callahan, Leigh F; Smith, Edwin A; Brasington, Richard D; Allison, David B; Kimberly, Robert P; Moreland, Larry W; Edberg, Jeffrey C; Bridges, S Louis

    2009-03-01

    Cytotoxic T-lymphocyte associated protein 4 (CTLA4) is a negative regulator of T-cell proliferation. Polymorphisms in CTLA4 have been inconsistently associated with susceptibility to rheumatoid arthritis (RA) in populations of European ancestry but have not been examined in African Americans. The prevalence of RA in most populations of European and Asian ancestry is approximately 1.0%; RA is purportedly less common in black Africans, with little known about its prevalence in African Americans. We sought to determine if CTLA4 polymorphisms are associated with RA in African Americans. We performed a 2-stage analysis of 12 haplotype tagging single nucleotide polymorphisms (SNPs) across CTLA4 in a total of 505 African American RA patients and 712 African American controls using Illumina and TaqMan platforms. The minor allele (G) of the rs231778 SNP was 0.054 in RA patients, compared to 0.209 in controls (4.462 x 10(-26), Fisher's exact). The presence of the G allele was associated with a substantially reduced odds ratio (OR) of having RA (AG+GG genotypes vs. AA genotype, OR 0.19, 95% CI: 0.13-0.26, p = 2.4 x 10(-28), Fisher's exact), suggesting a protective effect. This SNP is polymorphic in the African population (minor allele frequency [MAF] 0.09 in the Yoruba population), but is very rare in other groups (MAF = 0.002 in 530 Caucasians genotyped for this study). Markers associated with RA in populations of European ancestry (rs3087243 [+60C/T] and rs231775 [+49A/G]) were not replicated in African Americans. We found no confounding of association for rs231778 after stratifying for the HLA-DRB1 shared epitope, presence of anti-cyclic citrullinated peptide antibody, or degree of admixture from the European population. An African ancestry-specific genetic variant of CTLA4 appears to be associated with protection from RA in African Americans. This finding may explain, in part, the relatively low prevalence of RA in black African populations.

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. Allele Workbench: Transcriptome Pipeline and Interactive Graphics for Allele-Specific Expression

    PubMed Central

    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

  13. APOL1 Kidney Risk Alleles: Population Genetics and Disease Associations

    PubMed Central

    Limou, Sophie; Nelson, George W.; Kopp, Jeffrey B.; Winkler, Cheryl A.

    2014-01-01

    APOL1 kidney disease is a unique case in the field of the genetics of common disease: 2 variants (termed G1 and G2) with high population frequency have been repeatedly associated with nondiabetic CKDs, with very strong effect size (odds ratios 3–29) in populations of sub-Saharan African descent. This review provides an update on the spectrum of APOL1 kidney disease and on the worldwide distribution of these kidney risk variants. We also summarize the proper way to run a recessive analysis on joint and independent effects of APOL1 G1 and G2 kidney risk variants. PMID:25168832

  14. 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.

  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. 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. PMID:25030454

  17. Excited states of deformable odd {sup 157,159}Tb nuclei: Nonconservation of the angular momentum of external nucleon

    SciTech Connect

    Sharipov, Sh.; Ermamatov, M. J.

    2009-01-15

    The previously developed rotationally single-particle and vibrational model of the triaxial deformable odd nuclei is extended to the case where the total angular momentum of an external nucleon is not conserved. The calculated ratios of the excitation energies of the {sup 157,159}Tb nuclei are compared with the existing experimental data. The ratios of E2-transition probabilities and those of quadrupole moments of the above nuclei are calculated using parameters determined from the spectra of these nuclei.

  18. Multicomponent fluids of hard hyperspheres in odd dimensions.

    PubMed

    Rohrmann, René D; Santos, Andrés

    2011-01-01

    Mixtures of hard hyperspheres in odd-space dimensionalities are studied with an analytical approximation method. This technique is based on the so-called rational function approximation and provides a procedure for evaluating equations of state, structure factors, radial distribution functions, and direct correlation functions of additive mixtures of hard hyperspheres with any number of components and in arbitrary odd-dimension space. The method gives the exact solution of the Ornstein-Zernike equation coupled with the Percus-Yevick closure, thus, extending the solution for hard-sphere mixtures [J. L. Lebowitz, Phys. Rev. 133, A895 (1964)] to arbitrary odd dimensions. Explicit evaluations for binary mixtures in five dimensions are performed. The results are compared with computer simulations, and a good agreement is found.

  19. Effect of time-odd fields on odd-even mass differences of semi-magic nuclei

    NASA Astrophysics Data System (ADS)

    Yu, Kun; Zhou, XianRong; Cui, JiWei; Sagawa, H.

    2016-05-01

    The effect of time-odd fields of Skyrme interaction on neutron odd-even mass differences is studied in the framework of axially deformed Skyrme Hartree-Fock (DSHF)+BCS model. To this end, we take into account both the time-even and time-odd fields to calculate the one-neutron and two-neutron separation energies and pairing gaps of semi-magic Ca, Ni, and Sn isotopic chains. In the calculations, a surface-type pairing interaction (IS pairing) and an isospin dependent contact pairing interaction (IS+IV pairing) are adopted on top of Skyrme interactions SLy4, SLy6 and SkM*, respectively. We find that the time-odd fields have in general small effects on pairing gaps, but achieve better agreement with experimental data using SLy4 and Sly6 interactions, respectively. It is also shown that the calculations with IS+IV pairing reproduce the one-neutron separation energies of Sn isotopes better than those with the IS pairing interaction when the contributions of the time-odd fields are included.

  20. 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).

  1. Three allele combinations associated with Multiple Sclerosis

    PubMed Central

    Favorova, Olga O; Favorov, Alexander V; Boiko, Alexey N; Andreewski, Timofey V; Sudomoina, Marina A; Alekseenkov, Alexey D; Kulakova, Olga G; Gusev, Eugenyi I; Parmigiani, Giovanni; Ochs, Michael F

    2006-01-01

    Background Multiple sclerosis (MS) is an immune-mediated disease of polygenic etiology. Dissection of its genetic background is a complex problem, because of the combinatorial possibilities of gene-gene interactions. As genotyping methods improve throughput, approaches that can explore multigene interactions appropriately should lead to improved understanding of MS. Methods 286 unrelated patients with definite MS and 362 unrelated healthy controls of Russian descent were genotyped at polymorphic loci (including SNPs, repeat polymorphisms, and an insertion/deletion) of the DRB1, TNF, LT, TGFβ1, CCR5 and CTLA4 genes and TNFa and TNFb microsatellites. Each allele carriership in patients and controls was compared by Fisher's exact test, and disease-associated combinations of alleles in the data set were sought using a Bayesian Markov chain Monte Carlo-based method recently developed by our group. Results We identified two previously unknown MS-associated tri-allelic combinations: -509TGFβ1*C, DRB1*18(3), CTLA4*G and -238TNF*B1,-308TNF*A2, CTLA4*G, which perfectly separate MS cases from controls, at least in the present sample. The previously described DRB1*15(2) allele, the microsatellite TNFa9 allele and the biallelic combination CCR5Δ32, DRB1*04 were also reidentified as MS-associated. Conclusion These results represent an independent validation of MS association with DRB1*15(2) and TNFa9 in Russians and are the first to find the interplay of three loci in conferring susceptibility to MS. They demonstrate the efficacy of our approach for the identification of complex-disease-associated combinations of alleles. PMID:16872485

  2. Effect of core polarization on magnetic dipole moments in deformed odd-mass nuclei

    NASA Astrophysics Data System (ADS)

    Bonneau, L.; Minkov, N.; Duc, Dao Duy; Quentin, P.; Bartel, J.

    2015-05-01

    Magnetic properties of deformed odd-mass nuclei are studied within a nonrelativistic mean-field-plus-pairing approach, namely the Skyrme-Hartree-Fock-BCS approach with self-consistent blocking. For an odd number of nucleons these approaches lead to the breaking of the time-reversal invariance. The deviation from the Schmidt values of the isoscalar magnetic dipole moment is known to result from a subtle balance between core-polarization effects and meson-exchange current effects. However, the former are usually calculated in the random phase approximation without time-reversal symmetry breaking at the mean-field level. In this work we show that if one takes into account this symmetry breaking already in the mean-field solution, the correction from core polarization yields a significant contribution to the empirical quenching of the spin gyromagnetic ratios as compared to the free values in deformed odd-mass nuclei. Moreover, we calculate magnetic dipole moments in the Bohr and Mottelson unified-model description with self-consistent blocked mean-field intrinsic states. The obtained results in the A ˜100 and A ˜180 mass regions as well as for three actinide nuclei compare favorably with experimental data.

  3. Time-resolved dynamics of odd and even harmonic emission from oriented asymmetric molecules

    NASA Astrophysics Data System (ADS)

    Zhang, Bing; Yu, Shujuan; Chen, Yanjun; Jiang, Xiangqian; Sun, Xiudong

    2015-11-01

    We study the time-resolved dynamics of high-order harmonic generation (HHG) from oriented asymmetric molecules in intense laser fields theoretically. Previous studies have shown that the odd-even HHG spectra of asymmetric molecules don't show the striking two-center-interference-induced minimum, as the symmetric molecules do, due to the symmetry breaking. Surprisingly, with considering only the short-trajectory contribution, an apparent groove with small amplitudes is observed in the HHG time-frequency distribution, which implies that the harmonic emission is strongly suppressed in a specific time-frequency region. The position of this groove is sensitive to the molecular parameters and the orientation. Our analyses on this origin of the groove reveal different time-frequency properties of odd versus even signals, where the interplay of intramolecular interference and the permanent-dipole effect plays an important role. We show that the even-odd ratio often used in high-harmonic spectroscopy can be influenced significantly by the interference effect.

  4. 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.

  5. 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.

  6. 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 anti-evolutionists…

  7. Quantum description of T-odd correlations in ternary fission

    SciTech Connect

    Bunakov, V. E.; Kadmensky, S. G.

    2008-07-15

    A quantum version of a unified description of two T-odd effects recently observed in the ternary fission of nuclei that is induced by polarized neutrons is considered. These effects are explained by the effect of the Coriolis interaction of the rotating fissile system on the angular distributions of light charged particles in the interior and exterior regions of the nucleus.

  8. Against the Odds: Disadvantaged Students Who Succeed in School

    ERIC Educational Resources Information Center

    OECD Publishing (NJ1), 2011

    2011-01-01

    This report explores the factors and conditions that could help more students succeed at school despite challenging socio-economic backgrounds. It does this by studying resilient students and what sets them apart from their less successful peers. Understanding how educational systems can support disadvantaged students and help them "beat the odds"…

  9. 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…

  10. CP-odd phase correlations and electric dipole moments

    SciTech Connect

    Olive, Keith A.; Pospelov, Maxim; Ritz, Adam; Santoso, Yudi

    2005-10-01

    We revisit the constraints imposed by electric dipole moments (EDMs) of nucleons and heavy atoms on new CP-violating sources within supersymmetric theories. We point out that certain two-loop renormalization group corrections induce significant mixing between the basis-invariant CP-odd phases. In the framework of the constrained minimal supersymmetric standard model, the CP-odd invariant related to the soft trilinear A-phase at the grand unified theory (GUT) scale, {theta}{sub A}, induces nontrivial and distinct CP-odd phases for the three gaugino masses at the weak scale. The latter give one-loop contributions to EDMs enhanced by tan{beta}, and can provide the dominant contribution to the electron EDM induced by {theta}{sub A}. We perform a detailed analysis of the EDM constraints within the constrained minimal supersymmetric standard model, exhibiting the reach, in terms of sparticle spectra, which may be obtained assuming generic phases, as well as the limits on the CP-odd phases for some specific parameter points where detailed phenomenological studies are available. We also illustrate how this reach will expand with results from the next generation of experiments which are currently in development.

  11. 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.

  12. Co-selection and replacement of resistance alleles to Lysinibacillus sphaericus in a Culex quinquefasciatus colony.

    PubMed

    Chalegre, Karlos Diogo de Melo; Tavares, Daniella A; Romão, Tatiany P; de Menezes, Heverly Suzany G; Nascimento, Nathaly A; de Oliveira, Cláudia Maria F; de-Melo-Neto, Osvaldo P; Silva-Filha, Maria Helena N L

    2015-09-01

    The Cqm1 α-glucosidase, expressed within the midgut of Culex quinquefasciatus mosquito larvae, is the receptor for the Binary toxin (Bin) from the entomopathogen Lysinibacillus sphaericus. Mutations of the Cqm1 α-glucosidase gene cause high resistance levels to this bacterium in both field and laboratory populations, and a previously described allele, cqm1REC, was found to be associated with a laboratory-resistant colony (R2362). This study described the identification of a novel resistance allele, cqm1REC-2, that was co-selected with cqm1REC within the R2362 colony. The two alleles display distinct mutations but both generate premature stop codons that prevent the expression of midgut-bound Cqm1 proteins. Using a PCR-based assay to monitor the frequency of each allele during long-term maintenance of the resistant colony, cqm1REC was found to predominate early on but later was replaced by cqm1REC-2 as the most abundant resistance allele. Homozygous larvae for each allele were then generated that displayed similar high-resistance phenotypes with equivalent low levels of transcript and lack of protein expression for both cqm1REC and cqm1REC-2. In progeny from a cross of homozygous individuals for each allele at a 1 : 1 ratio, analyzed for ten subsequent generations, cqm1REC showed a higher frequency than cqm1REC-2. The replacement of cqm1REC by cqm1REC -2 observed in the R2362 colony, kept for 210 generations, indicates changes in fitness related to traits that are unknown but linked to these two alleles, and constitutes a unique example of evolution of resistance within a controlled laboratory environment. PMID:26131741

  13. 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.

  14. 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. PMID:25773521

  15. 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.

  16. When is an odd number not odd? Influence of task rule on the MARC effect for numeric classification.

    PubMed

    Cho, Yang Seok; Proctor, Robert W

    2007-09-01

    When classifying numbers as odd or even with left-right keypresses, performance is better with the mapping even-right/odd-left than with the opposite mapping. This linguistic markedness association of response codes (MARC) effect has been attributed to compatibility between the linguistic markedness of stimulus and response codes. In 2 experiments participants made keypresses to the Arabic numerals or number words 3, 4, 8, and 9 using the odd-even parity rule or a multiple-of-3 rule, which yield the same keypress response for each stimulus. For both stimulus modes, the MARC effect was obtained with the odd-even rule, but tended to reverse with the multiple-of-3 rule. The reversal was complete for the right response, but task rule had little influence on the left response. The results are consistent with the view that the MARC effect and its reversal are caused by correspondence of the stimulus code designated as positive by the task rule with the positive-polarity right response code.

  17. Executive Functioning in Children: A Comparison of Hospitalised ODD and ODD/ADHD Children and Normal Controls

    ERIC Educational Resources Information Center

    Van Goozen, Stephanie H. M.; Cohen-Kettenis, Peggy T.; Snoek, Heddeke; Matthys, Walter; Swaab-Barneveld, Hanna; Van Engeland, Herman

    2004-01-01

    Background: Deficits in executive functioning are supposed to have a predisposing influence on impulsive or aggressive behaviour. We tested the hypothesis that oppositional-defiant disorder (ODD) children with or without attention deficit hyperactivity disorder (ADHD) have problems in executive functioning. Method: Seventy-seven 7- to 12-year-old…

  18. Maternal dietary patterns during early pregnancy and the odds of childhood germ cell tumors: A Children's Oncology Group study.

    PubMed

    Musselman, Jessica R B; Jurek, Anne M; Johnson, Kimberly J; Linabery, Amy M; Robison, Leslie L; Shu, Xiao-Ou; Ross, Julie A

    2011-02-01

    Maternal diet during pregnancy may be associated with cancer in offspring. Intake of individual foods, as well as dietary patterns, can be used when examining these relations. Here, the authors examined associations between maternal dietary intake patterns and pediatric germ cell tumors (GCTs) using principal components analysis and logistic regression. Mothers of 222 GCT cases aged less than 15 years who were diagnosed at a Children's Oncology Group institution between 1993 and 2001 and those of 336 frequency-matched controls completed a self-administered food frequency questionnaire of diet during early pregnancy. Four dietary patterns were identified: "Western," "fruits and vegetables," "protein," and "healthful." With adjustment for birth weight, parity, and vitamin use, the fruits and vegetables pattern was significantly associated with a lower odds for GCTs (odds ratio (OR) = 0.83, 95% confidence interval (CI): 0.69, 0.99; 2 sided). Upon stratification, the fruits and vegetables pattern was significantly associated with a lower odds in males (OR = 0.66, 95% CI: 0.47, 0.92) but not females (OR = 0.91, 95% CI: 0.72, 1.14). A quantitative assessment of assumed nondifferential reporting error indicated no notable deviations from unadjusted odds ratio estimates. Results of this exploratory analysis suggest that maternal prenatal dietary patterns could be considered in future studies of GCTs in offspring. PMID:21098631

  19. 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.

  20. 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.

  1. 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.

  2. Predator fitness increases with selectivity for odd prey.

    PubMed

    Rutz, Christian

    2012-05-01

    The fundamental currency of normative models of animal decision making is Darwinian fitness. In foraging ecology, empirical studies typically assess foraging strategies by recording energy intake rates rather than realized reproductive performance. This study provides a rare empirical link, in a vertebrate predator-prey system, between a predator's foraging behavior and direct measures of its reproductive fitness. Goshawks Accipiter gentilis selectively kill rare color variants of their principal prey, the feral pigeon Columba livia, presumably because targeting odd-looking birds in large uniform flocks helps them overcome confusion effects and enhances attack success. Reproductive performance of individual hawks increases significantly with their selectivity for odd-colored pigeons, even after controlling for confounding age effects. Older hawks exhibit more pronounced dietary preferences, suggesting that hunting performance improves with experience. Intriguingly, although negative frequency-dependent predation by hawks exerts strong selection against rare pigeon phenotypes, pigeon color polymorphism is maintained through negative assortative mating. PMID:22503502

  3. 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.

  4. 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.

  5. 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.

  6. Chiral-odd TMDs in Drell-Yan processes

    NASA Astrophysics Data System (ADS)

    Lu, Zhun

    2014-01-01

    We calculate the Boer-Mulders function of the pion by applying the MIT bag model, and compare the result with that from the spectator model. We then study the azimuthal asymmetries contributed by the chiral-odd transverse momentum distributions in pion-nucleon Drell-Yan process at COMPASS and in proton-proton Drell-Yan process at RHIC, J-PARC, E906 and NICA.

  7. 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

  8. Mitochondrial data support an odd-nosed colobine clade.

    PubMed

    Sterner, Kirstin N; Raaum, Ryan L; Zhang, Ya-Ping; Stewart, Caro-Beth; Disotell, Todd R

    2006-07-01

    To obtain a more complete understanding of the evolutionary history of the leaf-eating monkeys we have examined the mitochondrial genome sequence of two African and six Asian colobines. Although taxonomists have proposed grouping the "odd-nosed" colobines (proboscis monkey, douc langur, and the snub-nosed monkey) together, phylogenetic support for such a clade has not been tested using molecular data. Phylogenetic analyses using parsimony, maximum likelihood, and Bayesian methods support a monophyletic clade of odd-nosed colobines consisting of Nasalis, Pygathrix, and Rhinopithecus, with tentative support for Nasalis occupying a basal position within this clade. The African and Asian colobine lineages are inferred to have diverged by 10.8 million years ago (mya or Ma). Within the Asian colobines the odd-nosed clade began to diversify by 6.7 Ma. These results augment our understanding of colobine evolution, particularly the nature and timing of the colobine expansion into Asia. This phylogenetic information will aid those developing conservation strategies for these highly endangered, diverse, and unique primates. PMID:16500120

  9. 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.

  10. Do Heliconius butterfly species exchange mimicry alleles?

    PubMed

    Smith, Joel; Kronforst, Marcus R

    2013-08-23

    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.

  11. Allelic variation at the interleukin 1β gene is associated with decreased bone mass in patients with inflammatory bowel diseases

    PubMed Central

    Nemetz, A; Toth, M; Garcia-Gonzalez, M; Zagoni, T; Feher, J; Pena, A; Tulassay, Z

    2001-01-01

    BACKGROUND—Interleukin 1β (IL-1β) and its natural antagonist have been implicated in the pathogenesis of inflammatory bowel disease (IBD). Both cytokines influence bone formation. IL-1β stimulates osteoclast activity while interleukin 1 receptor antagonist (IL-1ra) enhances bone formation.
AIMS—To determine whether the decreased bone mass in IBD is related to gene polymorphisms coding for IL-1β and IL-1ra, and thus identify patients with an increased risk.
METHODS—Bone mineral densitometry was performed at the femoral neck, lumbar spine, and the distal third of the radius in 75 IBD patients (34 men/41 women; 40.3 (1.6) years) and in 58 healthy controls (HC; 28 men/30 women; 32.4 (1.2) years). Values were correlated with the TaqI and AvaI gene polymorphisms in the IL1B and the variable number of tandem repeats gene polymorphism in the IL1RN gene.
RESULTS—In IBD patients, but not in HC, carriers of allele 2 at the AvaI gene polymorphism (IL1B-511*2) had significantly lower Z scores at the lumbar spine (−0.82 (0.13) v −0.29 (0.21) p=0.03) and the femoral neck (−0.59 (0.14) v 0.15 (0.19); p=0.003) than non-carriers. These patients also had a higher risk for osteopenia or osteoporosis at the femoral neck (odds ratio 3.63 (95% confidence interval 0.95-13.93)). No association was found between bone mass and the other gene polymorphisms analysed in IBD patients or in HC.
CONCLUSIONS—Our results suggest that genetic variability may be a major determinant of bone loss in IBD. Carriers of IL1B-511*2, who are hypersecretors of IL-1β, have a higher risk of presenting with low bone mass in IBD. Screening for this allele may contribute to determination of the risk of bone loss at the time of disease onset.


Keywords: inflammatory bowel diseases; ulcerative colitis; Crohn's disease; osteoporosis; bone density; genetic polymorphisms; interleukin 1 PMID:11600466

  12. Allelic variation contributes to bacterial host specificity.

    PubMed

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

    2015-01-01

    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. Together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts. PMID:26515720

  13. 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.

  14. Allelic variation contributes to bacterial host specificity

    DOE PAGES

    Yue, Min; Han, Xiangan; Masi, Leon De; Zhu, Chunhong; Ma, Xun; Zhang, Junjie; Wu, Renwei; Schmieder, Robert; Kaushik, Radhey S.; Fraser, George P.; et al

    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

  15. Allelic variation contributes to bacterial host specificity

    PubMed Central

    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.

    2015-01-01

    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. Together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts. PMID:26515720

  16. 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

  17. 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.

  18. 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

  19. Evidence for yrast positive-parity high-spin states in odd-odd {sup 72}As

    SciTech Connect

    Doering, J.; Tekyi-Mensah, O.J.; Tabor, S.L.; Doering, J.; Pantelica, D.; Petrovici, A.; Pantelica, D.; Petrovici, A.; Babu, B.R.; Hamilton, J.H.; Kormicki, J.; Lu, Q.H.; Ramayya, A.V.; Petrovici, A.

    1998-01-01

    The parities of high-spin bands in the odd-odd nucleus {sup 72}As have been established by measurements of the angular distributions and linear polarizations of the decay {gamma} rays via the {sup 62}Ni({sup 13}C,p2n) reaction at a beam energy of 48.5 MeV. In particular, the parity change determined between the 8{sup +} and 7{sup {minus}} states leads to positive parity for the yrast high-spin band. This band and the electromagnetic transition strengths within it are interpreted based on microscopic calculations using the VAMPIR model as arising from the intruder ({pi}g{sub 9/2}{circle_times}{nu}g{sub 9/2}) configuration. {copyright} {ital 1998} {ital The American Physical Society}

  20. Increased TNFA*2, but not TNFB*1, allele frequency in Spanish atopic patients.

    PubMed

    Castro, J; Tellería, J J; Linares, P; Blanco-Quirós, A

    2000-01-01

    Tumor necrosis factor (TNF) is a potent proinflammatory cytokine involved in asthma and atopy. Increased TNF-alpha levels have been found in airway biopsies and bronchoalveolar lavage fluids from asthmatic patients. Constitutional variations in the TNF-alpha secretion levels in vitro are associated with molecular polymorphisms located within and around the TNF loci. Our study objective was to investigate the association between atopy and two described di-allelic polymorphisms in the TNF locus: a G to A transition at position -308 in the 5'-promoter region of the TNFA gene (TNFA*1 and TNFA*2 alleles) and an Ncol restriction fragment length polymorphism (RFLP) in the first intron of the TNFB gene (TNFB*1 and TNFB*2 alleles). The genetic study was performed in 65 unrelated atopic patients and 60 healthy controls. The regions of interest were amplified from genomic DNA using specific primers and polymerase chain reaction. SSP-PCR analysis for TNFA -308 polymorphism genotyping and endonuclease digestion analysis for the TNFB Ncol RFLP were used. The frequency of the TNFA*2 allele was significantly higher in atopic subjects compared to the control group (38.5% vs. 10.5%; chi2 = 32.06; p <0.0001). The TNFA*2 allele is associated with a higher risk for the development of atopy (risk ratio = 9.44; EF = 0.65; chi2 = 30.06 p <0.0005). On the other hand, no significant association between the TNFB alleles and atopy was found. In conclusion, the TNFA*2 allele could be also a genetic risk marker for the predisposition to atopy in our population, as has been reported in other studies. Either the TNFA gene itself or a linked gene on chromosome region 6p21, which has yet to be identified, is a candidate gene for susceptibility to atopy. PMID:10923589

  1. A novel fluorescent quadruplex STR typing system and the allele frequency distributions in a Thai population.

    PubMed

    Yoshimoto, Takashi; Yamamoto, Toshimichi; Mizutani, Masaki; Uchihi, Rieko; Ohtaki, Hiroyuki; Katsumata, Yoshinao; Waiyawuth, Worawee; Songsivilai, Sirirurg

    2003-01-01

    We have previously reported a new triplex amplification and typing system by silver staining for three short tandem repeat (STR) loci, 9q2h2 (D2S3020), D15S233, and D14S299 without "microvariant" alleles such as .1, .2, and, .3 alleles in the Japanese population. In the present study, we established a new quadruplex system with an additional locus D7S809 using primer sets labeled with fluorescent multi-color dyes. Using this system, we genotyped 183 Thai people, found only one "microvariant" allele (allele 20.2) at D7S809, and calculated allele frequencies and some statistical properties at these four STR loci. From these allele frequencies at four STR loci, we performed three statistical analyses including a homozygosity test, a likelihood ratio test, and an exact test for Hardy-Weinberg equilibrium (HWE). Deviations from HWE (p < 0.05) were observed only in the two tests at the locus D7S809. In the present study, we compared the allele frequencies at these four loci in the Thai population to those in the Japanese population described previously. Consequently, all observed heterozygosities and power of discrimination (PD) at those loci in the Thai population were higher than 0.8 and 0.9, respectively, and all statistical values for discriminating power in the Thai population were slightly higher than those in the Japanese population. The combined paternity exclusion rate (combined PE) in the Thai population (0.978) was almost the same as that in the Japanese population (0.971). Therefore, this novel PCR amplification and typing system for four STR loci would be a convenient and informative DNA profiling system in the forensic field. PMID:12570210

  2. Solar Cycle Dependence Of Temperature, Odd-Oxygen, Odd-Hydrogen, And Airglow In The Mesopause Region Observed By SABER

    NASA Astrophysics Data System (ADS)

    Mlynczak, M. G.; Hunt, L. A.; Mertens, C. J.; Marshall, T.; Russell, J. M.; Thompson, R. E.; Gordley, L. L.

    2013-12-01

    We present the first consistent, global set of temperature, pressure, odd-oxygen, odd-hydrogen and airglow measurements in the mesopause region spanning a complete solar cycle. The measurements are derived from the Sounding of the Atmosphere using Broadband Emission Radiometry (SABER) instrument on the NASA TIMED satellite. These data clearly indicate the influence of solar variability on the atmosphere structure and composition. In general, the values of most parameters decrease with decreasing solar activity. However, odd-hydrogen is observed to increase with decreasing solar activity. While the data indicate a direct relation between solar activity and atmospheric response, the role of dynamical variability in modulating the direct solar response has not yet been investigated, particularly on regional scales (e.g.,tropical, mid-latitude, or polar). We describe the SABER observations in detail and discuss how they can be used with general circulation models to assess the coupled role of dynamics and solar variability in determining the overall atmospheric response.

  3. 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.

  4. 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.

  5. 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...

  6. 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.

  7. 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.

  8. 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.

  9. Radiative lifetimes of odd-parity levels in Nb I

    NASA Astrophysics Data System (ADS)

    Mukund, Sheo; Bhattacharyya, Soumen; Yarlagadda, Suresh; Nakhate, S. G.

    2015-11-01

    Radiative lifetimes are reported for 37 odd-parity energy levels of neutral niobium (Nb I), out of which 33 have been measured for the first time. The levels belong to electronic configurations 4d35s5p and 4d45p between 18,790 and 35,730 cm-1. The time-resolved laser-induced fluorescence spectroscopy technique was employed. The Nb atoms were generated in a free-jet by laser vaporization of niobium metal. Lifetime values reported in this work fall in the range 12-340 ns and are accurate to ±10%.

  10. Dimension-5 C P -odd operators: QCD mixing and renormalization

    NASA Astrophysics Data System (ADS)

    Bhattacharya, Tanmoy; Cirigliano, Vincenzo; Gupta, Rajan; Mereghetti, Emanuele; Yoon, Boram

    2015-12-01

    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. We present the renormalization matrix to one loop in the 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 MS ¯ scheme to one loop in perturbation theory, using both the naïve dimensional regularization and 't Hooft-Veltman prescriptions for γ5.

  11. DLA Class II Alleles and Haplotypes Are Associated with Risk for and Protection from Chronic Hepatitis in the English Springer Spaniel

    PubMed Central

    Bexfield, Nicholas H.; Watson, Penny J.; Aguirre-Hernandez, Jesús; Sargan, David R.; Tiley, Laurence; Heeney, Jonathan L.; Kennedy, Lorna J.

    2012-01-01

    Chronic hepatitis (CH) is common in dogs in the United Kingdom. An increased prevalence of the disease is seen in the English Springer spaniel (ESS), and this breed suffer from a severe form with young to middle aged female dogs being predisposed. The disease shares histological features with those of human viral hepatitis, although the specific aetiological agent has not yet been identified. The aim of the current study was to investigate whether dog leucocyte antigen (DLA) class II alleles and haplotypes are associated with susceptibility/resistance to CH in the ESS. Sequence-based genotyping of the polymorphic exon 2 from DLA-DRB1, -DQA1 and -DQB1 class II loci were performed in 66 ESSs with CH and 84 healthy controls. There was a significant difference in the distribution of the protective alleles DRB1*00501 (3.0% vs. 12.0%, odds ratio [OR] = 0.23, 95% confidence interval [CI] = 0.06–0.74) and DQB1*00501 (3.8% vs. 12.0%, OR = 0.29, 95% CI = 0.09–0.85) between cases and controls. The haplotype DLA-DRB1*00501/DQA1*00301/DQB1*00501 was present in 11.9% of controls and 3.0% of cases and was significantly associated with protection against disease development (OR = 0.26, 95% CI = 0.08–0.80). There was a significant difference in the distribution of the risk alleles DRB1*00601 (14.4% vs. 6.5%, OR = 2.40, 95% CI = 1.10–5.63) and DQB1*00701 (14.4% vs. 6.5%, OR = 2.40, 95% CI = 1.10–5.63) between cases and controls. A risk haplotype (DLA-DRB1*00601/DQA1*005011/DQB1*00701) was present in 14.4% of cases and 6.5% of controls and conferred an elevated risk of developing CH with an OR of 3.13 (95% CI = 1.20–8.26). These results demonstrate that DLA class II is significantly associated with risk and protection from developing CH in ESSs. PMID:22870335

  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. Determination of DQB1 alleles using PCR amplification and allele-specific primers.

    PubMed

    Lepage, V; Ivanova, R; Loste, M N; Mallet, C; Douay, C; Naoumova, E; Charron, D

    1995-10-01

    Molecular genotyping of HLA class II genes is commonly carried out using polymerase chain reaction (PCR) in combination with sequence-specific oligotyping (PCR-SSO) or a combination of the PCR and restriction fragment length polymorphism methods (PCR-RFLP). However, the identification of the DQB1 type by PCR-SSO and PCR-RFLP is very time-consuming which is disadvantageous for the typing of cadaveric organ donors. We have developed a DQB1 typing method using PCR in combination with allele-specific amplification (PCR-ASA), which allows the identification of the 17 most frequent alleles in one step using seven amplification mixtures. PCR allele-specific amplification HLA-DQB1 typing is easy to perform, and the results are easy to interpret in routine clinical practice. The PCR-ASA method is therefore better suited to DQB1 typing for organ transplantation than other methods.

  15. Borrowed alleles and convergence in serpentine adaptation.

    PubMed

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

    2016-07-19

    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

  16. 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

  17. Borrowed alleles and convergence in serpentine adaptation.

    PubMed

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

    2016-07-19

    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.

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

    PubMed

    Lachance, Joseph; Tishkoff, Sarah A

    2014-10-01

    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.

  19. Characterizing allelic association in the genome era

    PubMed Central

    WEIR, B. S.; LAURIE, C. C.

    2015-01-01

    Summary Whole genome data are allowing the estimation of population genetic parameters with an accuracy not imagined 50 years ago. Variation in these parameters along the genome is being found empirically where once only approximate theoretical values were available. Along with increased information, however, has come the issue of multiple testing and the realization that high values of the coefficients of variation of quantities such as relatedness measures may make it difficult to draw inferences. This review concentrates on measures of allelic association within and between individuals and within and between populations. PMID:21429275

  20. The odds of wrong-way crashes and resulting fatalities: A comprehensive analysis.

    PubMed

    Ponnaluri, Raj V

    2016-03-01

    The United States of America and other nations are grappling with the incidence of wrong-way driving (WWD). The issue is as important today (NTSB, 2012) as it was a half-century ago (Hulbert and Beers, 1966). In the absence of a comprehensive analysis, any effort to implement WWD countermeasures can be counterproductive. Hence, this effort began with the express intent to identify the factors that cause WWD crashes and fatalities. This work is sizeable in that it evaluated one million complete crash records from Florida. The methodology comprised (a) administering a survey on the perceptions about WWD; (b) developing binomial logistic models for computing the odds of WWD crashes, and of fatal crashes within the WWD space; (c) analyzing the contributing variables; and (d) comparing perceptions with crash analysis results. The study parameters included driver's age, gender, licensing state, physical defect, blood alcohol concentration, vehicle use, seatbelt compliance, day and time of crash, roadway lighting, facility type, weather conditions, road geometrics, and traffic volumes. Individual variable analysis of 23 parameters and the model development process included the determination of odds ratios and statistical tests for the predictive power and goodness-of-fit. The results of this work are generally consistent with expectation, yet surprising at times. This work concludes with decision-making inputs to the scientist, policy-maker and practitioner on the need for effectively engineering the roads, actively educating people about wrong-way driving, and strictly enforcing traffic laws, rules and regulations.

  1. Light Charged and CP-odd Higgses in MSSM-like Models

    SciTech Connect

    Dermisek, Radovan

    2008-11-23

    We study the Higgs sector of supersymmetric models containing two Higgs doublets with a light MSSM-like CP odd Higgs, m{sub A} < or approx. 10 GeV, and tan{beta} < or approx. 2.5. In this scenario all Higgses resulting from two Higgs doublets: light and heavy CP even Higgses, h and H, the CP odd Higgs, A, and the charged Higgs, H{sup {+-}}, could have been produced at LEP or the Tevatron, but would have escaped detection because they decay in modes that have not been searched for or the experiments are not sensitive to. Especially H{yields}ZA and H{sup {+-}}{yields}W{sup {+-}}*A with A{yields}cc-bar, {tau}{sup +}{tau}{sup -} present an opportunity to discover some of the Higgses at LEP, the Tevatron and also at B factories. In addition, the 2.8{sigma} excess of the branching ratio W{yields}{tau}v with respect to the other leptons measured at LEP correlates well with the existence of the charged Higgs with properties typical for this scenario. Dominant {tau}- and c-rich decay products of all Higgses require modified strategies for their discovery at the LHC.

  2. Structure of hard-hypersphere fluids in odd dimensions

    NASA Astrophysics Data System (ADS)

    Rohrmann, René D.; Santos, Andrés

    2007-11-01

    The structural properties of single component fluids of hard hyperspheres in odd space dimensionalities d are studied with an analytical approximation method that generalizes the rational function approximation earlier introduced in the study of hard-sphere fluids [S. B. Yuste and A. Santos, Phys. Rev. A 43, 5418 (1991)]. The theory makes use of the exact form of the radial distribution function to first order in density and extends it to finite density by assuming a rational form for a function defined in Laplace space, the coefficients being determined by simple physical requirements. Fourier transform in terms of reverse Bessel polynomials constitute the mathematical framework of this approximation, from which an analytical expression for the static structure factor is obtained. In its most elementary form, the method recovers the solution of the Percus-Yevick closure to the Ornstein-Zernike equation for hyperspheres at odd dimensions. The present formalism allows one to go beyond by yielding solutions with thermodynamic consistency between the virial and compressibility routes to any desired equation of state. Excellent agreement with available computer simulation data at d=5 and d=7 is obtained.

  3. Odd-even staggering in neutron drip line nuclei

    NASA Astrophysics Data System (ADS)

    Changizi, S. A.; Qi, Chong

    2016-07-01

    We have done systematic Hartree-Fock-Bogoliubov calculations in coordinate space on the one-quasi-particle energies and binding energy odd-even staggering (OES) in semi-magic nuclei with the zero-range volume, mixed and surface pairing forces in order to explore the influence of their density dependence. The odd-N isotopes are calculated within the blocking scheme. The strengths for the pairing forces are determined in two schemes by fitting locally to reproduce pairing gap in 120Sn and globally to all available data on the OES of semi-magic nuclei with Z ≥ 8. In the former calculations, there is a noticeable difference between the neutron mean gaps in neutron-rich O, Ca, Ni and Sn isotopes calculated with the surface pairing and those with the mixed and volume pairing. The difference gets much smaller if the globally optimized pairing strengths are employed. The heavier Pb isotopes show the opposite trend. Moreover, large differences between the mean gap and the OES may be expected in both calculations when one goes towards the neutron drip line.

  4. Isomer ratio calculations using modeled discrete levels

    SciTech Connect

    Gardner, M.A.; Gardner, D.G.; Hoff, R.W.

    1984-10-16

    Isomer ratio calculations were made for the reactions: /sup 175/Lu(n,..gamma..)/sup 176m,g/Lu, /sup 175/Lu(n,2n)/sup 174m,g/Lu, /sup 237/Np(n,2n)/sup 236m,g/Np, /sup 241/Am(n,..gamma..)/sup 242m,g/Am, and /sup 243/Am(n,..gamma..)/sup 244m,g/Am using modeled level structures in the deformed, odd-odd product nuclei. The hundreds of discrete levels and their gamma-ray branching ratios provided by the modeling are necessary to achieve agreement with experiment. Many rotational bands must be included in order to obtain a sufficiently representative selection of K quantum numbers. The levels of each band must be extended to appropriately high values of angular momentum.

  5. Assessment of allele-specific gene silencing by RNA interference with mutant and wild-type reporter alleles.

    PubMed

    Ohnishi, Yusuke; Tokunaga, Katsushi; Kaneko, Kiyotoshi; Hohjoh, Hirohiko

    2006-02-28

    Allele-specific gene silencing by RNA interference (RNAi) is therapeutically useful for specifically suppressing the expression of alleles associated with disease. To realize such allele-specific RNAi (ASPRNAi), the design and assessment of small interfering RNA (siRNA) duplexes conferring ASP-RNAi is vital, but is also difficult. Here, we show ASP-RNAi against the Swedish- and London-type amyloid precursor protein (APP) variants related to familial Alzheimer's disease using two reporter alleles encoding the Photinus and Renilla luciferase genes and carrying mutant and wild-type allelic sequences in their 3'-untranslated regions. We examined the effects of siRNA duplexes against the mutant alleles in allele-specific gene silencing and off-target silencing against the wild-type allele under heterozygous conditions, which were generated by cotransfecting the reporter alleles and siRNA duplexes into cultured human cells. Consistently, the siRNA duplexes determined to confer ASP-RNAi also inhibited the expression of the bona fide mutant APP and the production of either amyloid beta 40- or 42-peptide in Cos-7 cells expressing both the full-length Swedish- and wild-type APP alleles. The present data suggest that the system with reporter alleles may permit the preclinical assessment of siRNA duplexes conferring ASP-RNAi, and thus contribute to the design and selection of the most suitable of such siRNA duplexes.

  6. Sensitivity of calculated odd nitrogen distributions to the diabatic wind fields

    NASA Technical Reports Server (NTRS)

    Boughner, R. E.; Callis, L. B., Jr.; Natarajan, M.

    1991-01-01

    This paper compares atmospheric total odd nitrogen and ozone computed with two different advective wind fields, one using climatological averages of ozone and temperature to obtain monthly averaged horizontal and vertical winds and the other using measurements from the LIMS instrument. Calculations using the former data show stronger poleward and downward motion in the winter season compared to those using the LIMS data. This leads to NO(y) mixing ratios in the lower stratosphere that are about 20 percent larger in the polar regions of both hemispheres and about 40 percent higher in the equatorial region for climatological transport fields compared to those derived from LIMS data. Consequently, the NO(y) distributions calculated with the LIMS advective field show worse agreement with the NO(y) values inferred from the LIMS measurements than similar results obtained with the climatological wind field.

  7. Mixed symmetry states and {beta} decays of odd-A Xe to I isotopes

    SciTech Connect

    Al-Khudair, Falih H.

    2009-07-15

    The energy spectra of the parent and daughter nuclei in the {beta} decays ({sup 121-127}Xe,{beta}{sup +121-127}I) are considered in the interacting boson fermion model (IBFM-2) with the g{sub 7/2},d{sub 5/2},d{sub 3/2},s{sub 1/2}, and h{sub 11/2} single-particle orbitals. Electromagnetic transition probabilities and branching ratios in odd {sup 121-127}I isotopes are investigated. Special attention is given to the occurrence of mixed symmetry states, and the F-spin structures of the wave functions are analyzed. The log{sub 10}ft values of the allowed {beta} decay transitions are calculated. It is found that the IBFM-2 results agree with the experimental data quite well.

  8. 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.

  9. 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.

  10. Allelic disequilibrium and allele frequency distribution as a function of social and demographic history.

    PubMed Central

    Thompson, E A; Neel, J V

    1997-01-01

    Allelic disequilibrium between closely linked genes is a common observation in human populations and often gives rise to speculation concerning the role of selective forces. In a previous treatment, we have developed a population model of the expected distribution of rare variants (including private polymorphisms) in Amerindians and have argued that, because of the great expansion of Amerindian numbers with the advent of agriculture, most of these rare variants are of relatively recent origin. Many other populations have similar histories of striking recent expansions. In this treatment, we demonstrate that, in consequence of this fact, a high degree of linkage disequilibrium between two nonhomologous alleles <0.5 cM apart is the "normal" expectation, even in the absence of selection. This expectation is enhanced by the previous subdivision of human populations into relatively isolated tribes characterized by a high level of endogamy and inbreeding. We also demonstrate that the alleles associated with a recessive disease phenotype are expected to exist in a population in very variable frequencies: there is no need to postulate positive selection with respect to the more common disease-associated alleles for such entities as phenylketonuria or cystic fibrosis. PMID:8981963

  11. DQB1*06:02 allele specific expression varies by allelic dosage, not narcolepsy status

    PubMed Central

    lachmi, Karin Weiner; Lin, Ling; Kornum, Birgitte Rahbek; Rico, Tom; Lo, Betty; Aran, Adi; Mignot, Emmanuel

    2012-01-01

    The association of narcolepsy-cataplexy, a sleep disorder caused by the loss of hypocretin/orexin neurons in the hypothalamus, with DQA1*01:02-DQB1*06:02 is one of the tightest known single allele HLA associations. In this study, we explored genome wide expression in peripheral white blood cells of 50 narcolepsy versus 47 controls (half of whom were DQB1*06:02 positive) and found the largest differences between the groups to be in the signal from HLA probes. Further studies of HLA-DQ expression (mRNA and protein in a subset) in 125 controls and 147 narcolepsy cases did not reveal any difference, a result we explain by the lack of proper control of allelic diversity in Affymetrix HLA probes. Rather, a clear effect of DQB1*06:02 allelic dosage on DQB1*06:02 mRNA levels (1.65 fold) and protein (1.59 fold) could be demonstrated independent of the disease status. These results indicate that allelic dosage is transmitted into changes in heterodimer availability, a phenomenon that may explain increased risk for narcolepsy in DQB1*06:02 homozygotes versus heterozygotes. PMID:22326585

  12. DQB1*06:02 allele-specific expression varies by allelic dosage, not narcolepsy status.

    PubMed

    Weiner Lachmi, Karin; Lin, Ling; Kornum, Birgitte Rahbek; Rico, Tom; Lo, Betty; Aran, Adi; Mignot, Emmanuel

    2012-04-01

    The association of narcolepsy-cataplexy, a sleep disorder caused by the loss of hypocretin/orexin neurons in the hypothalamus, with DQA1*01:02-DQB1*06:02 is one of the tightest known single-allele human leukocyte antigen (HLA) associations. In this study, we explored genome-wide expression in peripheral white blood cells of 50 narcolepsy versus 47 controls (half of whom were DQB1*06:02 positive) and observed the largest differences between the groups in the signal from HLA probes. Further studies of HLA-DQ expression (mRNA and protein in a subset) in 125 controls and 147 narcolepsy cases did not reveal any difference, a result we explain by the lack of proper control of allelic diversity in Affymetrix HLA probes. Rather, a clear effect of DQB1*06:02 allelic dosage on DQB1*06:02 mRNA levels (1.65-fold) and protein (1.59-fold) could be demonstrated independent of disease status. These results indicate that allelic dosage is transmitted into changes in heterodimer availability, a phenomenon that may explain the increased risk for narcolepsy in DQB1*06:02 homozygotes versus heterozygotes.

  13. 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. PMID:27480981

  14. 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.

  15. The Euler current and relativistic parity odd transport

    NASA Astrophysics Data System (ADS)

    Golkar, Siavash; Roberts, Matthew M.; Son, Dam T.

    2015-04-01

    For a spacetime of odd dimensions endowed with a unit vector field, we introduce a new topological current that is identically conserved and whose charge is equal to the Euler character of the even dimensional spacelike foliations. The existence of this current allows us to introduce new Chern-Simons-type terms in the effective field theories describing relativistic quantum Hall states and (2 + 1) dimensional superfluids. Using effective field theory, we calculate various correlation functions and identify transport coefficients. In the quantum Hall case, this current provides the natural relativistic generalization of the Wen-Zee term, required to characterize the shift and Hall viscosity in quantum Hall systems. For the superfluid case this term is required to have nonzero Hall viscosity and to describe superfluids with non s-wave pairing.

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

    DOE PAGES

    Bhattacharya, Tanmoy; Cirigliano, Vincenzo; Gupta, Rajan; Mereghetti, Emanuele; Yoon, Boram

    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

  17. 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

  18. 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.

  19. 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.

  20. Systematic study of the fragmentation of low-lying dipole strength in odd-A rare earth nuclei investigated in nuclear resonance fluorescence experiments

    NASA Astrophysics Data System (ADS)

    Nord, A.; Schiller, A.; Eckert, T.; Beck, O.; Besserer, J.; von Brentano, P.; Fischer, R.; Herzberg, R.-D.; Jäger, D.; Kneissl, U.; Margraf, J.; Maser, H.; Pietralla, N.; Pitz, H. H.; Rittner, M.; Zilges, A.

    1996-11-01

    Nuclear resonance fluorescence experiments were performed on the rare earth nuclei 155Gd and 159Tb to study the fragmentation of the M1 scissors mode in odd deformed nuclei and to establish a kind of systematics. Using the bremsstrahlung photon beam of the Stuttgart Dynamitron (end point energy 4.1 MeV) and high resolution Ge-γ spectrometers detailed information was obtained on excitation energies, decay widths, transition probabilities, and branching ratios. The results are compared to those observed recently for the neighboring odd nuclei 161,163Dy and 157Gd. Whereas in the odd Dy isotopes the dipole strength is rather concentrated, both Gd isotopes show a strong fragmentation of the strength into about 25 (155Gd) and 90 transitions (157Gd) in the energy range 2-4 MeV. The nucleus 159Tb linking the odd Dy and Gd isotopes exhibits an intermediate strength fragmentation. In general the observed total strength in the odd nuclei is reduced by a factor of 2-3 as compared to their neighboring even-even isotopes. The different fragmentation behavior of the dipole strengths in the odd Dy and Gd isotopes is unexplained up to now.

  1. Pentadecanoic and Heptadecanoic Acids: Multifaceted Odd-Chain Fatty Acids.

    PubMed

    Pfeuffer, Maria; Jaudszus, Anke

    2016-07-01

    The odd-chain fatty acids (OCFAs) pentadecanoic acid (15:0) and heptadecanoic acid (17:0), which account for only a small proportion of total saturated fatty acids in milk fat and ruminant meat, are accepted biomarkers of dairy fat intake. However, they can also be synthesized endogenously, for example, from gut-derived propionic acid (3:0). A number of studies have shown an inverse association between OCFA concentrations in human plasma phospholipids or RBCs and risk of type 2 diabetes and cardiovascular disease. We propose a possible involvement in metabolic regulation from the assumption that there is a link between 15:0 and 17:0 and the metabolism of other short-chain, medium-chain, and longer-chain OCFAs. The OCFAs 15:0 and 17:0 can be elongated to very-long-chain FAs (VLCFAs) such as tricosanoic acid (23:0) and pentacosanoic acid (25:0) in glycosphingolipids, particularly found in brain tissue, or can be derived from these VLCFAs. Their chains can be shortened, yielding propionyl-coenzyme A (CoA). Propionyl-CoA, by succinyl-CoA, can replenish the citric acid cycle (CAC) with anaplerotic intermediates and, thus, improve mitochondrial energy metabolism. Mitochondrial function is compromised in a number of disorders and may be impaired with increasing age. Optimizing anaplerotic intermediate availability for the CAC may help to cope with demands in times of increased metabolic stress and with aging. OCFAs may serve as substrates for synthesis of both odd-numbered VLCFAs and propionyl-CoA or store away excess propionic acid. PMID:27422507

  2. 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.

  3. Pentadecanoic and Heptadecanoic Acids: Multifaceted Odd-Chain Fatty Acids.

    PubMed

    Pfeuffer, Maria; Jaudszus, Anke

    2016-07-01

    The odd-chain fatty acids (OCFAs) pentadecanoic acid (15:0) and heptadecanoic acid (17:0), which account for only a small proportion of total saturated fatty acids in milk fat and ruminant meat, are accepted biomarkers of dairy fat intake. However, they can also be synthesized endogenously, for example, from gut-derived propionic acid (3:0). A number of studies have shown an inverse association between OCFA concentrations in human plasma phospholipids or RBCs and risk of type 2 diabetes and cardiovascular disease. We propose a possible involvement in metabolic regulation from the assumption that there is a link between 15:0 and 17:0 and the metabolism of other short-chain, medium-chain, and longer-chain OCFAs. The OCFAs 15:0 and 17:0 can be elongated to very-long-chain FAs (VLCFAs) such as tricosanoic acid (23:0) and pentacosanoic acid (25:0) in glycosphingolipids, particularly found in brain tissue, or can be derived from these VLCFAs. Their chains can be shortened, yielding propionyl-coenzyme A (CoA). Propionyl-CoA, by succinyl-CoA, can replenish the citric acid cycle (CAC) with anaplerotic intermediates and, thus, improve mitochondrial energy metabolism. Mitochondrial function is compromised in a number of disorders and may be impaired with increasing age. Optimizing anaplerotic intermediate availability for the CAC may help to cope with demands in times of increased metabolic stress and with aging. OCFAs may serve as substrates for synthesis of both odd-numbered VLCFAs and propionyl-CoA or store away excess propionic acid.

  4. The A Allele of the rs1990760 Polymorphism in the IFIH1 Gene Is Associated with Protection for Arterial Hypertension in Type 1 Diabetic Patients and with Expression of This Gene in Human Mononuclear Cells

    PubMed Central

    Bouças, Ana P.; Brondani, Letícia A.; Souza, Bianca M.; Lemos, Natália E.; de Oliveira, Fernanda S.; Canani, Luis H.; Crispim, Daisy

    2013-01-01

    Background The rs1990760 polymorphism of interferon induced with helicase C domain 1 (IFIH1) has been associated with type 1 diabetes mellitus (T1DM). Here, we investigated whether this polymorphism is associated with T1DM or its clinical characteristics in a Brazilian population, and if IFIH1 gene expression in mononuclear cells from T1DM patients differs according to the genotypes of this polymorphism. A meta-analysis was also conducted to evaluate if the rs1990760 polymorphism is associated with T1DM. Methods Frequencies of the rs1990760 polymorphism were analyzed in 527 T1DM patients and in 517 healthy subjects. IFIH1 gene expressions according to genotypes were measured in a sub-sample of 26 T1DM patients by quantitative real-time PCR. Results Our data show the association of the A allele with risk to T1DM under a dominant model of inheritance [odds ratio (OR) = 1.421, P = 0.037], adjusting for ethnicity. The meta-analysis revealed significant association between the rs199760A allele and risk for T1DM for all analyzed inheritance models. Surprisingly, T1DM patients carrying the A allele showed lower levels of systolic (P = 0.001) and diastolic (P = 1×10−10) blood pressures as compared to G/G carriers. Furthermore, the A/A genotype seems to be associated with protection to arterial hypertension (AH) after adjustment for covariates (OR = 0.339, P = 0.019). IFIH1 gene expression in mononuclear cells from 26 T1DM patients did not differ among genotypes (P = 0.274). Nevertheless, IFIH1 gene expression was increased in mononuclear cells from T1DM patients with AH as compared with T1DM patients without AH [6.7 (1.7–2.0) vs. 1.8 (1.3–7.1) arbitrary units; P = 0.036]. The association with blood pressures and AH was not observed in patients with type 2 diabetes mellitus. Conclusions Our results indicate that the rs1990760 polymorphism is associated with T1DM. Interestingly, the rs1990760 A allele seems to be associated with

  5. Four novel PEPD alleles causing prolidase deficiency

    SciTech Connect

    Ledoux, P.; Scriver, C.; Hechtman, P. )

    1994-06-01

    Mutations at the PEPD locus cause prolidase (an enzyme specific for proline- and hydroxyproline-terminated dipeptides) deficiency (McKusick 170100), a rare autosomal recessive disorder characterized by iminodipeptiduria, skin ulcers, mental retardation, and recurrent infections. Four PEPD mutations from five severely affected individuals were characterized by analysis of reverse-transcribed, PCR-amplified (RT-PCR) cDNA. The authors used SSCP analysis on four overlapping cDNA fragments covering the entire coding region of the PEPD gene and detected abnormal SSCP bands for the fragments spanning all or part of exons 13-15 in three of the probands. Direct sequencing of the mutant cDNAs showed a G[yields]A, 1342 substitution (G448R) in two patients and a 3-bp deletion ([Delta]E452 or [Delta]E453) in another. In the other two probands the amplified products were of reduced size. Direct sequencing of these mutant cDNAs revealed a deletion of exon 5 in one patient and of exon 7 in the other. Intronic sequences flanking exons 5 and 7 were identified using inverse PCR followed by direct sequencing. Conventional PCR and direct sequencing then established the intron-exon borders of the mutant genomic DNA revealing two splice acceptor mutations: a G[yields]C substitution at position -1 of intron 4 and an A[yields]G substitution at position -2 of intron 6. The results indicate that the severe form of prolidase deficiency is caused by multiple PEPD alleles. In this report the authors attempt to begin the process of describing these alleles and cataloging their phenotype expression. 31 refs., 8 figs., 2 tabs.

  6. A novel HLA-A allele: A*0257.

    PubMed

    García-Ortiz, J E; Cox, S T; Sandoval-Ramirez, L; Little, A M; Marsh, S G E; Madrigal, J A; Argüello, J R

    2004-01-01

    A novel human leucocyte antigen-A*02 (HLA-A*02) allele was detected by reference strand-mediated conformation analysis (RSCA) of a DNA sample from a Tarahumara individual. Direct sequencing of HLA-A locus polymerase chain reaction products identified a mutation in one of the alleles. Cloning and sequencing confirmed the presence of a new allele, A*0257 which differed from A*0206 by two nucleotides at positions 355 and 362, inducing changes in residues 95 and 97, respectively, within the peptide-binding site. Those changes suggest that allele A*0257 may have resulted from an intralocus recombination event.

  7. 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.

  8. Nomenclature for human CYP2D6 alleles.

    PubMed

    Daly, A K; Brockmöller, J; Broly, F; Eichelbaum, M; Evans, W E; Gonzalez, F J; Huang, J D; Idle, J R; Ingelman-Sundberg, M; Ishizaki, T; Jacqz-Aigrain, E; Meyer, U A; Nebert, D W; Steen, V M; Wolf, C R; Zanger, U M

    1996-06-01

    To standardize CYP2D6 allele nomenclature, and to conform with international human gene nomenclature guidelines, an alternative to the current arbitrary system is described. Based on recommendations for human genome nomenclature, we propose that alleles be designated by CYP2D6 followed by an asterisk and a combination of roman letters and arabic numerals distinct for each allele with the number specifying the key mutation and, where appropriate, a letter specifying additional mutations. Criteria for classification as a separate allele and protein nomenclature are also presented. PMID:8807658

  9. A noncomplementation screen for quantitative trait alleles in saccharomyces cerevisiae.

    PubMed

    Kim, Hyun Seok; Huh, Juyoung; Riles, Linda; Reyes, Alejandro; Fay, Justin C

    2012-07-01

    Both linkage and linkage disequilibrium mapping provide well-defined approaches to mapping quantitative trait alleles. However, alleles of small effect are particularly difficult to refine to individual genes and causative mutations. Quantitative noncomplementation provides a means of directly testing individual genes for quantitative trait alleles in a fixed genetic background. Here, we implement a genome-wide noncomplementation screen for quantitative trait alleles that affect colony color or size by using the yeast deletion collection. As proof of principle, we find a previously known allele of CYS4 that affects colony color and a novel allele of CTT1 that affects resistance to hydrogen peroxide. To screen nearly 4700 genes in nine diverse yeast strains, we developed a high-throughput robotic plating assay to quantify colony color and size. Although we found hundreds of candidate alleles, reciprocal hemizygosity analysis of a select subset revealed that many of the candidates were false positives, in part the result of background-dependent haploinsufficiency or second-site mutations within the yeast deletion collection. Our results highlight the difficulty of identifying small-effect alleles but support the use of noncomplementation as a rapid means of identifying quantitative trait alleles of large effect. PMID:22870398

  10. 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.

  11. Ultra-deep Illumina sequencing accurately identifies MHC class IIb alleles and provides evidence for copy number variation in the guppy (Poecilia reticulata).

    PubMed

    Lighten, Jackie; van Oosterhout, Cock; Paterson, Ian G; McMullan, Mark; Bentzen, Paul

    2014-07-01

    We address the bioinformatic issue of accurately separating amplified genes of the major histocompatibility complex (MHC) from artefacts generated during high-throughput sequencing workflows. We fit observed ultra-deep sequencing depths (hundreds to thousands of sequences per amplicon) of allelic variants to expectations from genetic models of copy number variation (CNV). We provide a simple, accurate and repeatable method for genotyping multigene families, evaluating our method via analyses of 209 b of MHC class IIb exon 2 in guppies (Poecilia reticulata). Genotype repeatability for resequenced individuals (N = 49) was high (100%) within the same sequencing run. However, repeatability dropped to 83.7% between independent runs, either because of lower mean amplicon sequencing depth in the initial run or random PCR effects. This highlights the importance of fully independent replicates. Significant improvements in genotyping accuracy were made by greatly reducing type I genotyping error (i.e. accepting an artefact as a true allele), which may occur when using low-depth allele validation thresholds used by previous methods. Only a small amount (4.9%) of type II error (i.e. rejecting a genuine allele as an artefact) was detected through fully independent sequencing runs. We observed 1-6 alleles per individual, and evidence of sharing of alleles across loci. Variation in the total number of MHC class II loci among individuals, both among and within populations was also observed, and some genotypes appeared to be partially hemizygous; total allelic dosage added up to an odd number of allelic copies. Collectively, observations provide evidence of MHC CNV and its complex basis in natural populations.

  12. Causal inference for bivariate longitudinal quality of life data in presence of death by using global odds ratios.

    PubMed

    Lee, Keunbaik; Daniels, Michael J

    2013-10-30

    In longitudinal clinical trials, if a subject drops out due to death, certain responses, such as those measuring quality of life (QoL), will not be defined after the time of death. Thus, standard missing data analyses, e.g., under ignorable dropout, are problematic because these approaches implicitly 'impute' values of the response after death. In this paper we define a new survivor average causal effect for a bivariate response in a longitudinal quality of life study that had a high dropout rate with the dropout often due to death (or tumor progression). We show how principal stratification, with a few sensitivity parameters, can be used to draw causal inferences about the joint distribution of these two ordinal quality of life measures.

  13. 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.

  14. Nonsyntenic Genes Drive Tissue-Specific Dynamics of Differential, Nonadditive, and Allelic Expression Patterns in Maize Hybrids1[OPEN

    PubMed Central

    2016-01-01

    Distantly related maize (Zea mays) inbred lines display an exceptional degree of genomic diversity. F1 progeny of such inbred lines are often more vigorous than their parents, a phenomenon known as heterosis. In this study, we investigated how the genetic divergence of the maize inbred lines B73 and Mo17 and their F1 hybrid progeny is reflected in differential, nonadditive, and allelic expression patterns in primary root tissues. In pairwise comparisons of the four genotypes, the number of differentially expressed genes between the two parental inbred lines significantly exceeded those of parent versus hybrid comparisons in all four tissues under analysis. No differentially expressed genes were detected between reciprocal hybrids, which share the same nuclear genome. Moreover, hundreds of nonadditive and allelic expression ratios that were different from the expression ratios of the parents were observed in the reciprocal hybrids. The overlap of both nonadditive and allelic expression patterns in the reciprocal hybrids significantly exceeded the expected values. For all studied types of expression - differential, nonadditive, and allelic - substantial tissue-specific plasticity was observed. Significantly, nonsyntenic genes that evolved after the last whole genome duplication of a maize progenitor from genes with synteny to sorghum (Sorghum bicolor) were highly overrepresented among differential, nonadditive, and allelic expression patterns compared with the fraction of these genes among all expressed genes. This observation underscores the role of nonsyntenic genes in shaping the transcriptomic landscape of maize hybrids during the early developmental manifestation of heterosis in root tissues of maize hybrids. PMID:27208302

  15. 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.

  16. 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. PMID:25549886

  17. Strain-induced time-reversal odd superconductivity in graphene

    NASA Astrophysics Data System (ADS)

    Juricic, Vladimir; Roy, Bitan

    2014-03-01

    I will discuss the possibility of realizing a time-reversal-symmetry breaking superconducting state that exhibits an f + is pairing symmetry in strained graphene. Although the underlying attractive interactions need to be sufficiently strong and comparable in pristine graphene to support such pairing state, I will argue that strain can be conducive for its formation even for weak interactions. I will show that quantum-critical behavior near the transition is controlled by a fermionic multicritical point, characterized by various critical exponents computed in the framework of an ɛ-expansion near four spacetime dimensions. I will then discuss the scaling of the superconducting gap with the strain-induced axial pseudo-magnetic field. Furthermore, a vortex in this mixed superconducting state hosts a pair of Majorana fermions supporting a quartet of insulating and superconducting orders, among which quantum spin Hall topological insulator. Finally, I will mention some experimental signatures of this f + is time-reversal odd superconductor. These findings suggest that strained graphene could provide a platform for the realization of exotic superconducting states of Dirac fermions. VJ is supported by the Netherlands Organization for Scientific Research (NWO).

  18. 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

  19. Succinate esters: odd-even effects in melting points.

    PubMed

    Joseph, Sumy; Sathishkumar, Ranganathan

    2014-10-01

    Dialkyl succinates show a pattern of alternating behavior in their melting points, as the number of C atoms in the alkane side chain increases, unlike in the dialkyl oxalates [Joseph et al. (2011). Acta Cryst. B67, 525-534]. Dialkyl succinates with odd numbers of C atoms in the alkyl side chain show higher melting points than the immediately adjacent analogues with even numbers. The crystal structures and their molecular packing have been analyzed for a series of dialkyl succinates with 1-4 C atoms in the alkyl side chain. The energy difference (ΔE) between the optimized and observed molecular conformations, density, Kitaigorodskii packing index (KPI) and C-H...O interactions are considered to rationalize this behavior. In contrast to the dialkyl oxalates where a larger number of moderately strong C-H...O interactions were characteristic of oxalates with elevated melting points, here the molecular packing and the density play a major role in raising the melting point. On moving from oxalate to succinate esters the introduction of the C2 spacer adds two activated H atoms to the asymmetric unit, resulting in the formation of stronger C-H...O hydrogen bonds in all succinates. As a result the crystallinity of long-chain alkyl substituted esters improves enormously in the presence of hydrogen bonds from activated donors.

  20. Comparative in vivo expression of beta(+)-thalassemia alleles.

    PubMed

    Marwan, M M; Scerri, C A; Zarroag, S O; Cao, A; Kyrri, A; Kalogirou, E; Kleanthous, M; Ioannou, P; Angastiniotis, M; Felice, A E

    1999-08-01

    Double heterozygotes who inherit one abnormal though stable beta-globin variant in association with a molecularly identified beta(+)-thalassaemia allele provide unique opportunities to quantify the in vivo expression of particular beta(+)-thalassemia alleles. The globin products of the two alleles can be separated, quantified and the output of the beta(+)-thalassaemia allele expressed as the MCH-beta(A) in pg beta(A)-globin/beta(+)-thalassemia allele/RBC = 0.5 MCH x Hb A%. In this communication we provide new quantitative data on the expression of five mutations as follows: the beta(+)-87 (C-->G) = 3.8 pg beta(A)-globin/beta(+)-thalassemia allele/RBC (n = 1); the beta(+) IVS-I-1 (G-->A) = 0.2 pg beta(A)-globin/beta(+)-thalassemia allele/RBC (n = 1); the beta(+) IVS-I-6 (T-->C) = 2.9 pg beta(A)-globin/beta(+)-thalassemia allele/RBC (n = 7); the beta(+) IVS-I-110 (G-->A) = 1.1 pg beta(A)-globin/beta(+)-thalassemia allele/RBC (n = 13), and the beta(+) IVS-II-745 (C-->G) = 1.74 pg beta(A)-globin/beta(+)-thalassemia allele/RBC (n = 2). The values obtained are compared with those of other beta(+)-thalassemia alleles from the literature. It can be seen that the MCH-beta(A) value may be a correct index of thalassemia severity useful for the correlation of genotype with phenotype, and for understanding the effects of mutations in beta-globin genes on pathophysiologically meaningful beta-globin gene expression. PMID:10490134

  1. 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

  2. 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. PMID:26368021

  3. 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.

  4. Trans allele methylation and paramutation-like effects in mice

    PubMed Central

    Herman, Herry; Lu, Michael; Anggraini, Melly; Sikora, Aimee; Chang, Yanjie; Yoon, Bong June; Soloway, Paul D

    2009-01-01

    In mammals, imprinted genes have parent-of-origin–specific patterns of DNA methylation that cause allele-specific expression. At Rasgrf1 (encoding RAS protein-specific guanine nucleotide-releasing factor 1), a repeated DNA element is needed to establish methylation and expression of the active paternal allele1. At Igf2r (encoding insulin-like growth factor 2 receptor), a sequence called region 2 is needed for methylation of the active maternal allele2,3. Here we show that replacing the Rasgrf1 repeats on the paternal allele with region 2 allows both methylation and expression of the paternal copy of Rasgrf1, indicating that sequences that control methylation can function ectopically. Paternal transmission of the mutated allele also induced methylation and expression in trans of the normally unmethylated and silent wild-type maternal allele. Once activated, the wild-type maternal Rasgrf1 allele maintained its activated state in the next generation independently of the paternal allele. These results recapitulate in mice several features in common with paramutation described in plants4. PMID:12740578

  5. Rescue of Progeria in Trichothiodystrophy by Homozygous Lethal Xpd Alleles

    PubMed Central

    Andressoo, Jaan-Olle; Jans, Judith; de Wit, Jan; Coin, Frederic; Hoogstraten, Deborah; van de Ven, Marieke; Toussaint, Wendy; Huijmans, Jan; Thio, H. Bing; van Leeuwen, Wibeke J; de Boer, Jan; Egly, Jean-Marc; Hoeijmakers, Jan H. J; van der Horst, Gijsbertus T. J; Mitchell, James R

    2006-01-01

    Although compound heterozygosity, or the presence of two different mutant alleles of the same gene, is common in human recessive disease, its potential to impact disease outcome has not been well documented. This is most likely because of the inherent difficulty in distinguishing specific biallelic effects from differences in environment or genetic background. We addressed the potential of different recessive alleles to contribute to the enigmatic pleiotropy associated with XPD recessive disorders in compound heterozygous mouse models. Alterations in this essential helicase, with functions in both DNA repair and basal transcription, result in diverse pathologies ranging from elevated UV sensitivity and cancer predisposition to accelerated segmental progeria. We report a variety of biallelic effects on organismal phenotype attributable to combinations of recessive Xpd alleles, including the following: (i) the ability of homozygous lethal Xpd alleles to ameliorate a variety of disease symptoms when their essential basal transcription function is supplied by a different disease-causing allele, (ii) differential developmental and tissue-specific functions of distinct Xpd allele products, and (iii) interallelic complementation, a phenomenon rarely reported at clinically relevant loci in mammals. Our data suggest a re-evaluation of the contribution of “null” alleles to XPD disorders and highlight the potential of combinations of recessive alleles to affect both normal and pathological phenotypic plasticity in mammals. PMID:17020410

  6. CYP2D6: novel genomic structures and alleles

    PubMed Central

    Kramer, Whitney E.; Walker, Denise L.; O’Kane, Dennis J.; Mrazek, David A.; Fisher, Pamela K.; Dukek, Brian A.; Bruflat, Jamie K.; Black, John L.

    2010-01-01

    Objective CYP2D6 is a polymorphic gene. It has been observed to be deleted, to be duplicated and to undergo recombination events involving the CYP2D7 pseudogene and surrounding sequences. The objective of this study was to discover the genomic structure of CYP2D6 recombinants that interfere with clinical genotyping platforms that are available today. Methods Clinical samples containing rare homozygous CYP2D6 alleles, ambiguous readouts, and those with duplication signals and two different alleles were analyzed by long-range PCR amplification of individual genes, PCR fragment analysis, allele-specific primer extension assay, and DNA sequencing to characterize alleles and genomic structure. Results Novel alleles, genomic structures, and the DNA sequence of these structures are described. Interestingly, in 49 of 50 DNA samples that had CYP2D6 gene duplications or multiplications where two alleles were detected, the chromosome containing the duplication or multiplication had identical tandem alleles. Conclusion Several new CYP2D6 alleles and genomic structures are described which will be useful for CYP2D6 genotyping. The findings suggest that the recombination events responsible for CYP2D6 duplications and multiplications are because of mechanisms other than interchromosomal crossover during meiosis. PMID:19741566

  7. 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.

  8. Frequency of CCR5Δ32 allele in healthy Bosniak population.

    PubMed

    Adler, Grażyna; Valjevac, Amina; Skonieczna-Żydecka, Karolina; Mackic-Djurovic, Mirela; Parczewski, Miłosz; Urbańska, Anna; Salkic, Nermin Nusret

    2014-08-28

    Recent evidence has demonstrated the role of CCR5Δ32 in a variety of human diseases: from infectious and inflammatory diseases to cancer. Several studies have confirmed that genetic variants in chemokine receptor CCR5 gene are correlated with susceptibility and resistance to HIV infection. A 32-nucleotide deletion within the CCR5 reading frame is associated with decreased susceptibility to HIV acquisition and a slower progression to AIDS. Mean frequency of CCR5Δ32 allele in Europe is approximately 10%. The highest allele frequency is observed among Nordic populations (about 12%) and lower in the regions of Southeast Mediterranean (about 5%). Although the frequency of CCR5Δ32 was determined in numerous European populations, there is a lack of studies on this variant in the Bosnia and Hercegovina population. Therefore, the aim of our study was to assess the frequency of CCR5Δ32 allele in the cohort of Bosniaks and compare the results with European reports. CCR5Δ32 was detected by sequence-specific PCR in a sample of 100 healthy subjects from Bosnia and Herzegovina (DNA collected 2011-2013). Mean age of the cohort being 58.8 (± 10.7) years, with 82% of women. We identified 17 heterozygotes and one mutant homozygote in study group, with mean ∆32 allele frequency of 9.5%. CCR5∆32 allele frequency among Bosniaks is comparable to that found in Caucasian populations and follows the pattern of the north-southern gradient observed for Europe. Further studies on larger cohorts with adequate female-to-male ratio are necessary.

  9. Frequency of CCR5Δ32 allele in healthy Bosniak population

    PubMed Central

    Adler, Grażyna; Valjevac, Amina; Skonieczna-Żydecka, Karolina; Mackic-Djurovic, Mirela; Parczewski, Miłosz; Urbańska, Anna; Salkic, Nermin N

    2014-01-01

    Recent evidence has demonstrated the role of CCR5Δ32 in a variety of human diseases: from infectious and inflammatory diseases to cancer. Several studies have confirmed that genetic variants in chemokine receptor CCR5 gene are correlated with susceptibility and resistance to HIV infection. A 32-nucleotide deletion within the CCR5 reading frame is associated with decreased susceptibility to HIV acquisition and a slower progression to AIDS. Mean frequency of CCR5Δ32 allele in Europe is approximately 10%. The highest allele frequency is observed among Nordic populations (about 12%) and the lowest in the regions of Southeast Mediterranean (about 5%). Although the frequency of CCR5Δ32 was determined in numerous European populations, there is a lack of studies on this variant in the Bosnia and Herzegovina population. Therefore, the aim of our study was to assess the frequency of CCR5Δ32 allele in the cohort of Bosniaks and compare the results with European reports. CCR5Δ32 was detected by sequence-specific PCR in a sample of 100 healthy Bosniaks (DNA collected 2011-2013). Mean age of the cohort being 58.8 (±10.7) years, with 82% of women. We identified 17 heterozygotes and one mutant homozygote in study group, with mean ∆32 allele frequency of 9.5%. CCR5∆32 allele frequency among Bosniaks is comparable to that found in Caucasian populations and follows the pattern of the north-southern gradient observed for Europe. Further studies on larger cohorts with adequate female-to-male ratio are necessary. PMID:25172974

  10. Statistical Studies on Protein Polymorphism in Natural Populations. III. Distribution of Allele Frequencies and the Number of Alleles per Locus

    PubMed Central

    Chakraborty, Ranajit; Fuerst, Paul A.; Nei, Masatoshi

    1980-01-01

    With the aim of understanding the mechanism of maintenance of protein polymorphism, we have studied the properties of allele frequency distribution and the number of alleles per locus, using gene-frequency data from a wide range of organisms (mammals, birds, reptiles, amphibians, Drosophila and non-Drosophila invertebrates) in which 20 or more loci with at least 100 genes were sampled. The observed distribution of allele frequencies was U-shaped in all of the 138 populations (mostly species or subspecies) examined and generally agreed with the theoretical distribution expected under the mutation-drift hypothesis, though there was a significant excess of rare alleles (gene frequency, 0 ∼ 0.05) in about a quarter of the populations. The agreement between the mutation-drift theory and observed data was quite satisfactory for the numbers of polymorphic (gene frequency, 0.05 ∼ 0.95) and monomorphic (0.95 ∼ 1.0) alleles.—The observed pattern of allele-frequency distribution was incompatible with the prediction from the overdominance hypothesis. The observed correlations of the numbers of rare alleles, polymorphic alleles and monomorphic alleles with heterozygosity were of the order of magnitude that was expected under the mutation-drift hypothesis. Our results did not support the view that intracistronic recombination is an important source of genetic variation. The total number of alleles per locus was positively correlated with molecular weight in most of the species examined, and the magnitude of the correlation was consistent with the theoretical prediction from mutation-drift hypothesis. The correlation between molecular weight and the number of alleles was generally higher than the correlation between molecular weight and heterozygosity, as expected. PMID:17249018

  11. Fission barriers for the emission of odd-numbered fragments from multicharged C{sub 60} prepared in Ar{sup 8+}-C{sub 60} collisions

    SciTech Connect

    Martin, S.; Chen, L.; Bernard, J.; Buchet-Poulizac, M. C.; Wei, B.; Bredy, R.

    2006-01-15

    We report on measurements of the branching ratios of emission of small C{sub n}{sup +} fragments in asymmetrical fission of highly charged C{sub 60}{sup r+} ions (r=4-6). For the channels corresponding to the emission of one fragment, only small fragments with an even number of carbon atoms are observed. For the channels with the emission of two fragments, successive emission of small fragments with an odd number of carbon atoms has been observed with a surprisingly high branching ratio (30%). In order to reproduce the experimental branching ratios in the framework of a statistical evaporation model, the height of fission barriers for the emission of one odd numbered fragment has to be reduced at higher temperature in order to allow the opening of these channels that are forbidden at lower temperature.

  12. ALFRED: an allele frequency resource for research and teaching

    PubMed Central

    Rajeevan, Haseena; Soundararajan, Usha; Kidd, Judith R.; Pakstis, Andrew J.; Kidd, Kenneth K.

    2012-01-01

    ALFRED (http://alfred.med.yale.edu) is a free, web accessible, curated compilation of allele frequency data on DNA sequence polymorphisms in anthropologically defined human populations. Currently, ALFRED has allele frequency tables on over 663 400 polymorphic sites; 170 of them have frequency tables for more than 100 different population samples. In ALFRED, a population may have multiple samples with each ‘sample’ consisting of many individuals on which an allele frequency is based. There are 3566 population samples from 710 different populations with allele frequency tables on at least one polymorphism. Fifty of those population samples have allele frequency data for over 650 000 polymorphisms. Records also have active links to relevant resources (dbSNP, PharmGKB, OMIM, Ethnologue, etc.). The flexible search options and data display and download capabilities available through the web interface allow easy access to the large quantity of high-quality data in ALFRED. PMID:22039151

  13. 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.

  14. The frequency of HLA alleles in the Romanian population.

    PubMed

    Constantinescu, Ileana; Boșcaiu, Voicu; Cianga, Petru; Dinu, Andrei-Antoniu; Gai, Elena; Melinte, Mihaela; Moise, Ana

    2016-03-01

    Knowledge of human leukocyte antigen (HLA) allele frequencies is essential for bone marrow and kidney donor searches. The Romanian Caucasian population is heterogeneous and information on HLA polymorphism has not been well studied. We characterized the HLA genetic profile and allele frequencies of regional populations in Romania. HLA-A, B and DRB1 alleles were examined in 8252 individuals, belonging to the four main regions of Romania. The most common alleles found in the Romanian population are the following: HLA-A*01, A*02, A*03, A*11, A*24; HLA-B*18, B*35, B*44, B*51 and HLA-DRB1*01, DRB1*03, DRB1*07, DRB1*11, DRB1*13, DRB1*15, DRB1*16. More than half of the alleles are non-homogeneously spread in Romania. These results provide a starting point for future analyses of genetic heterogeneity in Romania.

  15. The frequency of HLA alleles in the Romanian population.

    PubMed

    Constantinescu, Ileana; Boșcaiu, Voicu; Cianga, Petru; Dinu, Andrei-Antoniu; Gai, Elena; Melinte, Mihaela; Moise, Ana

    2016-03-01

    Knowledge of human leukocyte antigen (HLA) allele frequencies is essential for bone marrow and kidney donor searches. The Romanian Caucasian population is heterogeneous and information on HLA polymorphism has not been well studied. We characterized the HLA genetic profile and allele frequencies of regional populations in Romania. HLA-A, B and DRB1 alleles were examined in 8252 individuals, belonging to the four main regions of Romania. The most common alleles found in the Romanian population are the following: HLA-A*01, A*02, A*03, A*11, A*24; HLA-B*18, B*35, B*44, B*51 and HLA-DRB1*01, DRB1*03, DRB1*07, DRB1*11, DRB1*13, DRB1*15, DRB1*16. More than half of the alleles are non-homogeneously spread in Romania. These results provide a starting point for future analyses of genetic heterogeneity in Romania. PMID:26711124

  16. 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.

  17. 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.

  18. 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.

  19. 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. PMID:26850319

  20. A Risk Allele for Nicotine Dependence in CHRNA5 Is a Protective Allele for Cocaine Dependence

    PubMed Central

    Grucza, Richard A; Wang, Jen C.; Stitzel, Jerry A.; Hinrichs, Anthony L.; Saccone, Scott F.; Saccone, Nancy L.; Bucholz, Kathleen K.; Cloninger, C. Robert; Neuman, Rosalind J.; Budde, John P.; Fox, Louis; Bertelsen, Sarah; Kramer, John; Hesselbrock, Victor; Tischfield, Jay; Nurnberger, John. I.; Almasy, Laura; Porjesz, Bernice; Kuperman, Samuel; Schuckit, Marc A.; Edenberg, Howard J.; Rice, John P.; Goate, Alison M.; Bierut, Laura J.

    2008-01-01

    Background A non-synonymous coding polymorphism, rs16969968, of the CHRNA5 gene which encodes the alpha-5 subunit of the nicotinic acetylcholine receptor (nAChR) has been found to be associated with nicotine dependence (20). The goal of the present study is to examine the association of this variant with cocaine dependence. Methods Genetic association analysis in two, independent samples of unrelated cases and controls; 1.) 504 European-American participating in the Family Study on Cocaine Dependence (FSCD); 2.) 814 European Americans participating in the Collaborative Study on the Genetics of Alcoholsim (COGA). Results In the FSCD, there was a significant association between the CHRNA5 variant and cocaine dependence (OR = 0.67 per allele, p = 0.0045, assuming an additive genetic model), but in the reverse direction compared to that previously observed for nicotine dependence. In multivariate analyses that controlled for the effects of nicotine dependence, both the protective effect for cocaine dependence and the previously documented risk effect for nicotine dependence were statistically significant. The protective effect for cocaine dependence was replicated in the COGA sample. In COGA, effect sizes for habitual smoking, a proxy phenotype for nicotine dependence, were consistent with those observed in FSCD. Conclusion The minor (A) allele of rs16969968, relative to the major G allele, appears to be both a risk factor for nicotine dependence and a protective factor for cocaine dependence. The biological plausibility of such a bidirectional association stems from the involvement of nAChRs with both excitatory and inhibitory modulation of dopamine-mediated reward pathways. PMID:18519132

  1. Ethical guideposts for allelic variation databases.

    PubMed

    Knoppers, B M; Laberge, C M

    2000-01-01

    Basically, a mutation database (MDB) is a repository where allelic variations are described and assigned within a specific gene locus. The purposes of an MDB may vary greatly and have different content and structure. The curator of an electronic and computer-based MDB will provide expert feedback (clinical and research). This requires ethical guideposts. Going to direct on-line public access for the content of an MDB or to interactive communication also raises other considerations. Currently, HUGO's MDI (Mutation Database Initiative) is the only integrated effort supporting and guiding the coordinated deployment of MDBs devoted to genetic diversity. Thus, HUGO's ethical "Statements" are applicable. Among the ethical principles, the obligation of preserving the confidentiality of information transferred by a collaborator to the curator is particularly important. Thus, anonymization of such data prior to transmission is essential. The 1997 Universal Declaration on the Human Genome and Human Rights of UNESCO addresses the participation of vulnerable persons. Researchers in charge of MDBs should ensure that information received on the testing of children or incompetent adults is subject to ethical review and approval in the country of origin. Caution should be taken against the involuntary consequences of public disclosure of results without complete explanation. Clear and enforceable regulations must be developed to protect the public against misuse of genetic databanks. Interaction with a databank could be seen as creating a "virtual" physician-patient relationship. However, interactive public MDBs should not give medical advice. We have identified new social ethical principles to govern different levels of complexity of genetic information. They are: reciprocity, mutuality, solidarity, and universality. Finally, precaution and prudence at this early stage of the MDI may not only avoid ethically inextricable conundrums but also provide for the respect for the rights

  2. 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.

  3. 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.

  4. 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.

  5. 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. PMID:24190013

  6. 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

  7. Maternal-fetal interactions and birth order influence insulin variable number of tandem repeats allele class associations with head size at birth and childhood weight gain.

    PubMed

    Ong, Ken K; Petry, Clive J; Barratt, Bryan J; Ring, Susan; Cordell, Heather J; Wingate, Diane L; Pembrey, Marcus E; Todd, John A; Dunger, David B

    2004-04-01

    Polymorphism of the insulin gene (INS) variable number of tandem repeats (VNTR; class I or class III alleles) locus has been associated with adult diseases and with birth size. Therefore, this variant is a potential contributory factor to the reported fetal origins of adult disease. In the population-based Avon Longitudinal Study of Pregnancy and Childhood birth cohort, we have confirmed in the present study the association between the INS VNTR III/III genotype and larger head circumference at birth (odds ratio [OR] 1.92, 95% CI 1.23-3.07; P = 0.004) and identified an association with higher cord blood IGF-II levels (P = 0.05 to 0.0001). The genotype association with head circumference was influenced by maternal parity (birth order): the III/III OR for larger head circumference was stronger in second and subsequent pregnancies (OR 5.0, 95% CI 2.2-11.5; P = 0.00003) than in first pregnancies (1.2, 0.6-2.2; P = 0.8; interaction with birth order, P = 0.02). During childhood, the III/III genotype remained associated with larger head circumference (P = 0.004) and was also associated with greater BMI (P = 0.03), waist circumference (P = 0.03), and higher fasting insulin levels in girls (P = 0.02). In addition, there were interactions between INS VNTR genotype and early postnatal weight gain in determining childhood BMI (P = 0.001 for interaction), weight (P = 0.005), and waist circumference (P = 0.0005), such that in the approximately 25% of children (n = 286) with rapid early postnatal weight gain, class III genotype-negative children among this group gained weight more rapidly. Our results indicate that complex prenatal and postnatal gene-maternal/fetal interactions influence size at birth and childhood risk factors for adult disease. PMID:15047631

  8. Allelic interactions at the nivea locus of Antirrhinum.

    PubMed Central

    Bollmann, J; Carpenter, R; Coen, E S

    1991-01-01

    Most null alleles at the nivea (niv) locus are recessive to Niv+ and, when homozygous, give white flowers rather than the red of the wild type. In contrast, the niv-571 allele is semidominant; although it gives white flowers when homozygous, very pale flowers result when this allele is heterozygous with NIV+. We showed that in heterozygotes, niv-571 acts in trans to inhibit expression of its Niv+ homology 25-fold to 50-fold. The inhibition is reversible after meiosis and partially reversible somatically. The niv-571 allele carries a transposable element Tam3 insertion and three truncated copies of the niv gene, one copy being in inverse orientation. Analysis of two further niv alleles, niv-572 and niv-527, showed that excision of Tam3 from niv-571 does not affect the ability of the allele to repress Niv+ and that one truncated niv copy alone is insufficient to confer semidominance. The detailed structures of various semidominant niv alleles suggest that their effects in trans are not readily explained by production of antisense RNA but are more easily reconciled with a direct recognition/interaction between homologous genes, reminiscent of cosuppression and transvection phenomena described in other systems. PMID:1840900

  9. Allele frequencies at microsatellite loci: The stepwise mutation model revisited

    SciTech Connect

    Valdes, A.M.; Slatkin, M. ); Freimer, N.B. )

    1993-03-01

    The authors 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. They 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. It is also shown 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. 39 refs., 6 figs., 4 tabs.

  10. Common alleles contribute to schizophrenia in CNV carriers

    PubMed Central

    Tansey, K E; Rees, E; Linden, D E; Ripke, S; Chambert, K D; Moran, J L; McCarroll, S A; Holmans, P; Kirov, G; Walters, J; Owen, M J; O'Donovan, M C

    2016-01-01

    The genetic architecture of schizophrenia is complex, involving risk alleles ranging from common alleles of weak effect to rare alleles of large effect, the best exemplar of the latter being large copy number variants (CNVs). It is currently unknown whether pathophysiology in those with defined rare mutations overlaps with that in other individuals with the disorder who do not share the same rare mutation. Under an extreme heterogeneity model, carriers of specific high-penetrance mutations form distinct subgroups. In contrast, under a polygenic threshold model, high-penetrance rare allele carriers possess many risk factors, of which the rare allele is the only one, albeit an important, factor. Under the latter model, cases with rare mutations can be expected to share some common risk alleles, and therefore pathophysiological mechanisms, with cases without the same mutation. Here we show that, compared with controls, individuals with schizophrenia who have known pathogenic CNVs carry an excess burden of common risk alleles (P=2.25 × 10−17) defined from a genome-wide association study largely based on individuals without known CNVs. Our finding is not consistent with an extreme heterogeneity model for CNV carriers, but does offer support for the polygenic threshold model of schizophrenia. That this is so provides support for the notion that studies aiming to model the effects of rare variation may uncover pathophysiological mechanisms of relevance to those with the disorder more widely. PMID:26390827

  11. Allelic Diversity and Its Implications for the Rate of Adaptation

    PubMed Central

    Caballero, Armando; García-Dorado, Aurora

    2013-01-01

    Genetic variation is usually estimated empirically from statistics based on population gene frequencies, but alternative statistics based on allelic diversity (number of allelic types) can provide complementary information. There is a lack of knowledge, however, on the evolutionary implications attached to allelic-diversity measures, particularly in structured populations. In this article we simulated multiple scenarios of single and structured populations in which a quantitative trait subject to stabilizing selection is adapted to different fitness optima. By forcing a global change in the optima we evaluated which diversity variables are more strongly correlated with both short- and long-term adaptation to the new optima. We found that quantitative genetic variance components for the trait and gene-frequency-diversity measures are generally more strongly correlated with short-term response to selection, whereas allelic-diversity measures are more correlated with long-term and total response to selection. Thus, allelic-diversity variables are better predictors of long-term adaptation than gene-frequency variables. This observation is also extended to unlinked neutral markers as a result of the information they convey on the demographic population history. Diffusion approximations for the allelic-diversity measures in a finite island model under the infinite-allele neutral mutation model are also provided. PMID:24121776

  12. Measurements of odd nitrogen compounds in the stratosphere by the ATMOS experiment on Spacelab 3

    NASA Technical Reports Server (NTRS)

    Russell, J. M., III; Rinsland, C. P.; Farmer, C. B.; Froidevaux, L.; Toon, G. C.; Zander, R.

    1988-01-01

    Spacelab 3's Atmospheric Trace Molecule Spectroscopy (ATMOS) experiment has obtained 30 deg N and 48 deg S vertical profiles of reservoir gases, source gases, and other trace molecules that are important in the middle atmosphere's odd nitrogen, odd chlorine, and odd hydrogen chemical families. The abundances of individual gases and total odd nitrogen levels measured by ATMOS have been compared with prior results obtained from balloon and satellite platforms. The lower-limit profile agrees with ATMOS data to within 16 percent up to 42 km altitude.

  13. 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.

  14. Identification of multiple interacting alleles conferring low glycerol and high ethanol yield in Saccharomyces cerevisiae ethanolic fermentation

    PubMed Central

    2013-01-01

    Background Genetic engineering of industrial microorganisms often suffers from undesirable side effects on essential functions. Reverse engineering is an alternative strategy to improve multifactorial traits like low glycerol/high ethanol yield in yeast fermentation. Previous rational engineering of this trait always affected essential functions like growth and stress tolerance. We have screened Saccharomyces cerevisiae biodiversity for specific alleles causing lower glycerol/higher ethanol yield, assuming higher compatibility with normal cellular functionality. Previous work identified ssk1E330N…K356N as causative allele in strain CBS6412, which displayed the lowest glycerol/ethanol ratio. Results We have now identified a unique segregant, 26B, that shows similar low glycerol/high ethanol production as the superior parent, but lacks the ssk1E330N…K356N allele. Using segregants from the backcross of 26B with the inferior parent strain, we applied pooled-segregant whole-genome sequence analysis and identified three minor quantitative trait loci (QTLs) linked to low glycerol/high ethanol production. Within these QTLs, we identified three novel alleles of known regulatory and structural genes of glycerol metabolism, smp1R110Q,P269Q, hot1P107S,H274Y and gpd1L164P as causative genes. All three genes separately caused a significant drop in the glycerol/ethanol production ratio, while gpd1L164P appeared to be epistatically suppressed by other alleles in the superior parent. The order of potency in reducing the glycerol/ethanol ratio of the three alleles was: gpd1L164P > hot1P107S,H274Y ≥ smp1R110Q,P269Q. Conclusions Our results show that natural yeast strains harbor multiple specific alleles of genes controlling essential functions, that are apparently compatible with survival in the natural environment. These newly identified alleles can be used as gene tools for engineering industrial yeast strains with multiple subtle changes, minimizing the risk of

  15. Allelic imbalance of tissue-type plasminogen activator (t-PA) gene expression in human brain tissue.

    PubMed

    Tjarnlund-Wolf, A; Hultman, K; Curtis, M A; Faull, R L M; Medcalf, R L; Jern, C

    2011-06-01

    We have identified a single-nucleotide polymorphism (SNP) in the t-PA enhancer (-7351C>T), which is associated with endothelial t-PA release in vivo. In vitro studies demonstrated that this SNP is functional at the level of transcription. In the brain, t-PA has been implicated in both physiologic and pathophysiologic processes. The aim of the present study was to examine the effect of the t-PA -7351C>T SNP on t-PA gene expression in human brain tissue. Allelic mRNA expression was measured in heterozygous post-mortem brain tissues using quantitative TaqMan genotyping assay. Protein-DNA interactions were assessed using electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP). Significantly higher levels of t-PA mRNA were generated from chromosomes that harboured the wild-type -7351C allele, as compared to those generated from the mutant T allele (for the hippocampus, C to T allelic ratio of ~1.3, p=0.010, n=12; and for the cortex, C to T allelic ratio of ~1.2, p=0.017, n=12). EMSA showed reduced neuronal and astrocytic nuclear protein binding affinity to the T allele, and identified Sp1 and Sp3 as the major transcription factors that bound to the -7351 site. ChIP analyses confirmed that Sp1 recognises this site in intact cells. In conclusion, the t-PA -7351C>T SNP affects t-PA gene expression in human brain tissue. This finding might have clinical implications for neurological conditions associated with enhanced t-PA levels, such as in the acute phase of cerebral ischaemia, and also for stroke recovery.

  16. 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.

  17. 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

  18. Low-lying dipole excitations in the heavy, odd-mass nucleus 181Ta

    NASA Astrophysics Data System (ADS)

    Wolpert, A.; Beck, O.; Belic, D.; Besserer, J.; von Brentano, P.; Eckert, T.; Fransen, C.; Herzberg, R.-D.; Kneissl, U.; Margraf, J.; Maser, H.; Nord, A.; Pietralla, N.; Pitz, H. H.

    1998-08-01

    The strength distribution of low-lying dipole excitations in the heavy odd-mass nucleus 181Ta was studied in nuclear resonance fluorescence experiments performed at the bremsstrahlung beam of the Stuttgart 4.3 MV Dynamitron accelerator. To increase the detection sensitivity in the whole range of excitation energies between 1.8 and 4 MeV two measurements were carried out at different bremsstrahlung end-point energies of 2.7 and 4.1 MeV using two large-volume HPGe detectors of a relative efficiency of 100%. Detailed information on excitation energies, decay widths, transition probabilities, and branching ratios of 37 new low-lying states in the energy range 1.8-3.5 MeV have been obtained. The observed dipole strength is rather fragmented, apart from a strong excitation at 2.297 MeV. The total strength in the investigated range of excitation energies (1.8-4 MeV) is reduced by a factor of ~3.5 as compared to the neighboring even-even nucleus 180Hf.

  19. 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.

  20. 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. PMID:26761207

  1. 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

  2. Allelic exclusion of immunoglobulin genes: models and mechanisms.

    PubMed

    Vettermann, Christian; Schlissel, Mark S

    2010-09-01

    The allelic exclusion of immunoglobulin (Ig) genes is one of the most evolutionarily conserved features of the adaptive immune system and underlies the monospecificity of B cells. While much has been learned about how Ig allelic exclusion is established during B-cell development, the relevance of monospecificity to B-cell function remains enigmatic. Here, we review the theoretical models that have been proposed to explain the establishment of Ig allelic exclusion and focus on the molecular mechanisms utilized by developing B cells to ensure the monoallelic expression of Ig kappa and Ig lambda light chain genes. We also discuss the physiological consequences of Ig allelic exclusion and speculate on the importance of monospecificity of B cells for immune recognition.

  3. Inheritance and allelism of morphological traits in eastern redbud (Cercis canadensis L.).

    PubMed

    Roberts, David J; Werner, Dennis J; Wadl, Phillip A; Trigiano, Robert N

    2015-01-01

    Inheritance of purple, gold, and variegated foliage types, weeping architecture, and double flower was explored in F1, F2, and backcross families resulting from controlled hybridization of eastern redbud (Cercis canadensis L.). Potential allelic relationships were explored when possible. Inheritance analysis in families derived from controlled hybridization of 'Covey' (green leaf) and 'Forest Pansy' (purple leaf) suggest that purple leaf color and weeping architecture are both controlled by single recessive genes, for which the symbols pl1 and wp1 are proposed, respectively. Inheritance of gold leaf was explored in families of 'Covey' (green leaf) × 'Hearts of Gold' (gold leaf). Interpretation of inheritance of gold leaf in these families was confounded by the recovery of a leaf color phenotype in the F2 family unlike either parent. However, data suggested the action of a single locus controlling gold leaf color in 'Hearts of Gold', and that instability of gold leaf expression may be based on transposable element activity. Segregation of gold leaf in the F2 families of 'Texas White' [green leaf (C. canadensis var. texensis)] × 'JN2' [gold leaf (The Rising Sun)] did not fit a Mendelian ratio. Analysis of progeny of 'Silver Cloud' and 'Floating Clouds' (both showing white/green leaf variegation) with non-variegated cultivars demonstrated that variegation in 'Silver Cloud' is controlled by a single recessive nuclear gene, while variegation in 'Floating Clouds' is controlled by cytoplasmic factors. The symbol var1 is proposed for the gene controlling variegation in 'Silver Cloud'. Double flower in progeny derived from 'Flame' (double flower) suggested that double flower is dominant to single flower, and that 'Flame' is heterozygous at the double-flower locus, for which the symbol Df1 is proposed. Allelism studies showed that the gene controlling purple leaf in 'Forest Pansy' is allelic to the purple leaf gene in 'Greswan' and that the gene controlling weeping

  4. Inheritance and allelism of morphological traits in eastern redbud (Cercis canadensis L.).

    PubMed

    Roberts, David J; Werner, Dennis J; Wadl, Phillip A; Trigiano, Robert N

    2015-01-01

    Inheritance of purple, gold, and variegated foliage types, weeping architecture, and double flower was explored in F1, F2, and backcross families resulting from controlled hybridization of eastern redbud (Cercis canadensis L.). Potential allelic relationships were explored when possible. Inheritance analysis in families derived from controlled hybridization of 'Covey' (green leaf) and 'Forest Pansy' (purple leaf) suggest that purple leaf color and weeping architecture are both controlled by single recessive genes, for which the symbols pl1 and wp1 are proposed, respectively. Inheritance of gold leaf was explored in families of 'Covey' (green leaf) × 'Hearts of Gold' (gold leaf). Interpretation of inheritance of gold leaf in these families was confounded by the recovery of a leaf color phenotype in the F2 family unlike either parent. However, data suggested the action of a single locus controlling gold leaf color in 'Hearts of Gold', and that instability of gold leaf expression may be based on transposable element activity. Segregation of gold leaf in the F2 families of 'Texas White' [green leaf (C. canadensis var. texensis)] × 'JN2' [gold leaf (The Rising Sun)] did not fit a Mendelian ratio. Analysis of progeny of 'Silver Cloud' and 'Floating Clouds' (both showing white/green leaf variegation) with non-variegated cultivars demonstrated that variegation in 'Silver Cloud' is controlled by a single recessive nuclear gene, while variegation in 'Floating Clouds' is controlled by cytoplasmic factors. The symbol var1 is proposed for the gene controlling variegation in 'Silver Cloud'. Double flower in progeny derived from 'Flame' (double flower) suggested that double flower is dominant to single flower, and that 'Flame' is heterozygous at the double-flower locus, for which the symbol Df1 is proposed. Allelism studies showed that the gene controlling purple leaf in 'Forest Pansy' is allelic to the purple leaf gene in 'Greswan' and that the gene controlling weeping

  5. 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…

  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. 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…

  8. 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…

  9. 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,…

  10. 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...

  11. 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…

  12. 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…

  13. 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.

  14. Identification of incompatibility alleles in the tetraploid species sour cherry.

    PubMed

    Tobutt, K R; Bosković, R; Cerović, R; Sonneveld, T; Ruzić, D

    2004-03-01

    The incompatibility genetics of sour cherry ( Prunus cerasus), an allotetraploid species thought to be derived from sweet cherry (diploid) and ground cherry (tetraploid), were investigated by test crossing and by analysis of stylar ribonucleases which are known to be the products of incompatibility alleles in sweet cherry. Stylar extracts of 36 accessions of sour cherry were separated electrophoretically and stained for ribonuclease activity. The zymograms of most accessions showed three bands, some two or four. Of the ten bands seen, six co-migrated with bands that in sweet cherry are attributed to the incompatibility alleles S(1), S(3), S(4), S(6, ) S(9) and S(13). 'Cacanski Rubin', 'Erdi Botermo B', 'Koros' and 'Ujfehertoi Furtos', which showed bands apparently corresponding to S(1) and S(4), were test pollinated with the sweet cherry 'Merton Late' ( S(1) S(4)). Monitoring pollen tube growth, and, in one case, fruit set, showed that these crosses were incompatible and that the four sour cherries indeed have the alleles S(1) and S(4). Likewise, test pollination of 'Marasca Piemonte', 'Marasca Savena' and 'Morello, Dutch' with 'Noble' ( S(6) S(13)) showed that these three sour cherries have the alleles S(6) and S(13). S(13) was very frequent in sour cherry cultivars, but is rare in sweet cherry cultivars, whereas with S(3) the situation is reversed. It was suggested that the other four bands are derived from ground cherry and one of these, provisionally attributed to S(B), occurred frequently in a small set of ground cherry accessions surveyed. Analysing some progenies from sour by sweet crosses by S allele-specific PCR and monitoring the success of some sweet by sour crosses were informative. They indicated mostly disomic inheritance, with sweet cherry S alleles belonging to one locus and, presumably, the ground cherry alleles to the other, and helped clarify the genomic arrangement of the alleles and the interactions in heteroallelic pollen. PMID:14689184

  15. 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. PMID:23821598

  16. Robust Identification of Local Adaptation from Allele Frequencies

    PubMed Central

    Günther, Torsten; Coop, Graham

    2013-01-01

    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. PMID:23821598

  17. Nonrandom duplication of the chromosome bearing a mutated Ha-ras-1 allele in mouse skin tumors

    SciTech Connect

    Bianchi, A.B.; Aldaz, C.M.; Conti, C.J. )

    1990-09-01

    The authors analyzed the normal/mutated allelic ratio of the Ha-ras-1 gene in mouse skin squamous cell carcinomas induced by initation 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 alelotypic 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 9. 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 their previous cytogenetic studies, indicating that trisomy of chromosome 7 is present in themajority of these tumors show that nonrandom duplication of the chromosome carrying the mutated Ha-ras-1 allel appears to be a major mechanism by which the mutated gene is overrepresented.

  18. 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.

  19. 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

  20. Deformed ODD-ODD nuclei: Matrix elements for the residual n-p interaction and patterns of alternating perturbations in level spacings

    SciTech Connect

    Hoff, R.W.; Jain, A.K.; Kvasil, J.; Sood, P.C.; Sheline, R.K.; Florida State Univ., Tallahassee, FL )

    1989-09-01

    The application of a simple semi-empirical model is discussed in terms of interpreting experimental nuclear structure data for twelve of the best characterized odd-odd deformed nuclei. An essential part of this modeling is to calculate values for the Gallagher-Moszkowski splittings and Newby shifts, the observables that arise from the n-p residual interaction in odd-odd nuclei. Assumptions regarding the form for this n-p force are traced historically. The predictive power of a favored form of the n-p force, one that includes a central force with short and long-range components, a tensor force, and some effects of core polarization, is examined in light of experimental data obtained since its formulation. A data set of 42 experimentally determined Newby shifts has been reviewed as to the reliability of each entry. Exceptions to a recently proposed rule for the a priori determination of the sign of Newby shift are discussed. Evidence is presented for the existence of an odd-even staggering or signature effect in the rotational spacings of many K{sup {minus}} bands (with K > 0). By use of Coriolis-coupling calculations, it has been possible to reproduce the staggering observed in some of the K{sup {minus}} rotational bands of {sup 156}Tb, {sup 168}Tm, {sup 176}Lu, {sup 182}Ta, and {sup 182}Re. 27 refs., 3 figs., 3 tabs.

  1. 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.

  2. High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus

    DOE PAGES

    Muchero, Wellington; Guo, Jianjun; Difazio, Stephen P.; Chen, Jay; Ranjan, Priya; Slavov, Gancho; Gunter, Lee E.; Jawdy, Sara; Bryan, Anthony C.; Sykes, Robert; et al

    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

  3. Polymorphisms in MHC-DRA and -DRB alleles of water buffalo (Bubalus bubalis) reveal different features from cattle DR alleles.

    PubMed

    Sena, L; Schneider, M P C; Brenig, B; Honeycutt, R L; Womack, J E; Skow, L C

    2003-02-01

    Seventy-five individuals of Bubalus bubalis belonging to four different breeds, three of river buffalo and one of swamp buffalo, were studied for polymorphism in MHC DRB (Bubu-DRB) and DRA (Bubu-DRA) loci. Eight alleles of Bubu-DRB were found, and all alleles in the swamp type were shared with the three river breeds. All alleles sampled from the breed of European origin (Mediterranean) were present in breeds sampled in Brazil, thus variability of this locus may have been preserved to a great extent in the more recently founded Brazilian population. Bubu-DRB alleles contained higher proportions of synonymous vs. non-synonymous substitutions in the non-peptide-binding sites (PBS) region, in contrast to the pattern of variation found in BoLA-DRB3, the orthologous locus in cattle. This indicated that either the first domain exon (exon 2) of Bubu-DRB has not undergone as much recombination and/or gene conversion as in cattle alleles, or Bubu-DRB may be more ancient than BoLA-DRB3 alleles. Phylogenetic analysis of DRB alleles from Bubalus, Syncerus c. caffer, the Cape buffalo, and domestic cattle demonstrated transspecies polymorphism. Water buffalo contained two alleles of DRA that differed from each other in two amino acid positions, including one in the PBS (alpha22) that was also shared with Anoa depressicornis, the anoa. Discovery of variation in DRA was surprising as the first domain of DRA is a highly conserved polypeptide in mammals in general and especially in ruminants, where no other substitution in PBS was seen.

  4. 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.

  5. 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.

  6. 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.

  7. Distribution of HLA-B alleles in Mexican Amerindian populations.

    PubMed

    Vargas-Alarcón, Gilberto; Hernández-Pacheco, Guadalupe; Zuñiga, Joaquín; Rodríguez-Pérez, José Manuel; Pérez-Hernández, Nonanzit; Rangel, Carlos; Villarreal-Garza, Cynthia; Martínez-Laso, Jorge; Granados, Julio; Arnaiz-Villena, Antonio

    2003-02-01

    In the present study we analyzed by PCR-SSO technique the HLA-B gene frequencies in 281 healthy individuals from four Mexican Amerindian populations (66 Mayos, 90 Mazatecans, 72 Nahuas and 53 Teenek). The most frequent alleles in all studied populations were HLA-B35, HLA-B39, and HLA-B40; however, some differences were observed between populations. The HLA-B35 allele was the most frequent in three of the four populations studied (Mayos, Nahuas and Teenek), whereas in Mazatecans the most frequent allele was HLA-B39. HLA-B40 presented frequencies higher than 10% in all groups. On the other hand, only Mayos presented an HLA-B51 gene frequency higher than 10%. When comparisons were made, important differences between groups were observed. The Teenek group presented an increased frequency of HLA-B35 when compared to Mazatecans and the HLA-B52 allele was increased in Nahuas and Teenek when compared to Mayos. An increased frequency of HLA-B39 was observed in Mazatecans when compared to Nahuas, Mayos and Teenek. Also, an increased frequency of HLA-B51 was observed in Mayos when compared to Mazatecans and Nahuas. These data corroborate the restricted polymorphism of HLA-B alleles and the high frequency of HLA-B35, HLA-B39 and HLA-B40 alleles in autochthonous American populations. In spite of the restriction in this polymorphism, differences in frequencies of HLA-B alleles could be helpful in distinguishing each of these populations.

  8. 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…

  9. Laboratory Search for a Long-Range T-Odd, P-Odd Interaction from Axionlike Particles Using Dual-Species Nuclear Magnetic Resonance with Polarized Xe129 and Xe131 Gas

    NASA Astrophysics Data System (ADS)

    Bulatowicz, M.; Griffith, R.; Larsen, M.; Mirijanian, J.; Fu, C. B.; Smith, E.; Snow, W. M.; Yan, H.; Walker, T. G.

    2013-09-01

    Various theories beyond the standard model predict new particles with masses in the sub-eV range with very weak couplings to ordinary matter. A new P-odd and T-odd interaction between polarized and unpolarized nucleons proportional to K→·r→ is one such possibility, where r→ is the distance between the nucleons and K→ is the spin of the polarized nucleon. Such an interaction involving a scalar coupling gs at one vertex and a pseudoscalar coupling gp at the polarized nucleon vertex can be induced by the exchange of spin-0 bosons. We used the NMR cell test station at Northrop Grumman Corporation to search for NMR frequency shifts in polarized Xe129 and Xe131 when a nonmagnetic zirconia rod is moved near the NMR cell. Long (T2˜20s) spin-relaxation times allow precision measurements of the NMR frequency ratios, which are insensitive to magnetic field fluctuations. Combined with existing theoretical calculations of the neutron spin contribution to the nuclear angular momentum in xenon nuclei, the measurements improve the laboratory upper bound on the product gsgpn by 2 orders of magnitude for distances near 1 mm. The sensitivity of this technique can be increased by at least two more orders of magnitude.

  10. Laboratory search for a long-range T-odd, P-odd interaction from axionlike particles using dual-species nuclear magnetic resonance with polarized 129Xe and 131Xe gas.

    PubMed

    Bulatowicz, M; Griffith, R; Larsen, M; Mirijanian, J; Fu, C B; Smith, E; Snow, W M; Yan, H; Walker, T G

    2013-09-01

    Various theories beyond the standard model predict new particles with masses in the sub-eV range with very weak couplings to ordinary matter. A new P-odd and T-odd interaction between polarized and unpolarized nucleons proportional to K·r is one such possibility, where r is the distance between the nucleons and K is the spin of the polarized nucleon. Such an interaction involving a scalar coupling gs at one vertex and a pseudoscalar coupling gp at the polarized nucleon vertex can be induced by the exchange of spin-0 bosons. We used the NMR cell test station at Northrop Grumman Corporation to search for NMR frequency shifts in polarized 129Xe and 131Xe when a nonmagnetic zirconia rod is moved near the NMR cell. Long (T2∼20  s) spin-relaxation times allow precision measurements of the NMR frequency ratios, which are insensitive to magnetic field fluctuations. Combined with existing theoretical calculations of the neutron spin contribution to the nuclear angular momentum in xenon nuclei, the measurements improve the laboratory upper bound on the product gsgp(n) by 2 orders of magnitude for distances near 1 mm. The sensitivity of this technique can be increased by at least two more orders of magnitude.

  11. 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. PMID:27200022

  12. 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

  13. Detection of an allele conferring resistance to Bacillus sphaericus binary toxin in Culex quinquefasciatus populations by molecular screening.

    PubMed

    Chalegre, Karlos Diogo de Melo; Romão, Tatiany Patrícia; Amorim, Liliane Barbosa; Anastacio, Daniela Bandeira; de Barros, Rosineide Arruda; de Oliveira, Cláudia Maria Fontes; Regis, Lêda; de-Melo-Neto, Osvaldo Pompílio; Silva-Filha, Maria Helena Neves Lobo

    2009-02-01

    The activity of the Bacillus sphaericus binary (Bin) toxin on Culex quinquefasciatus larvae depends on its specific binding to the Cqm1 receptor, a midgut membrane-bound alpha-glucosidase. A 19-nucleotide deletion in the cqm1 gene (cqm1(REC)) mediates high-level resistance to Bin toxin. Here, resistance in nontreated and B. sphaericus-treated field populations of C. quinquefasciatus was assessed through bioassays as well as a specific PCR assay designed to detect the cqm1(REC) allele in individual larvae. Resistance ratios at 90% lethal concentration, gathered through bioassays, were close to 1 and indicate that the selected populations had similar levels of susceptibility to B. sphaericus, comparable to that of a laboratory colony. A diagnostic PCR assay detected the cqm1(REC) allele in all populations investigated, and its frequency in two nontreated areas was 0.006 and 0.003, while the frequency in the B. sphaericus-treated population was significantly higher. Values of 0.053 and 0.055 were detected for two distinct sets of samples, and homozygote resistant larvae were found. Evaluation of Cqm1 expression in individual larvae through alpha-glucosidase assays corroborated the allelic frequency revealed by PCR. The data from this study indicate that the cqm1(REC) allele was present at a detectable frequency in nontreated populations, while the higher frequency in samples from the treated area is, perhaps, correlated with the exposure to B. sphaericus. This is the first report of the molecular detection of a biolarvicide resistance allele in mosquito populations, and it confirms that the PCR-based approach is suitable to track such alleles in target populations. PMID:19098223

  14. 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. PMID:26596347

  15. Odd Viscosity in the Quantum Critical Region of a Holographic Weyl Semimetal

    NASA Astrophysics Data System (ADS)

    Landsteiner, Karl; Liu, Yan; Sun, Ya-Wen

    2016-08-01

    We study odd viscosity in a holographic model of a Weyl semimetal. The model is characterized by a quantum phase transition from a topological semimetal to a trivial semimetal state. Since the model is axisymmetric in three spatial dimensions there are two independent odd viscosities. Both odd viscosity coefficients are nonvanishing in the quantum critical region and nonzero only due to the mixed axial gravitational anomaly. It is therefore a novel example in which the mixed axial gravitational anomaly gives rise to a transport coefficient at first order in derivatives at finite temperature. In the quantum critical region, the physics of viscosities as well as conductivities is governed by the quantum critical point.

  16. 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. PMID:27391743

  17. Even-odd effect in spontaneously coherent bilayer quantum Hall droplets.

    PubMed

    Park, K; Scarola, V W; Das Sarma, S

    2003-07-11

    Using exact diagonalization in the disk geometry we predict a novel even-odd effect in the Coulomb-blockade spectra of vertically coupled double quantum dots under an external magnetic field. The even-odd effect in the tunneling conductance is a direct manifestation of spontaneous interlayer phase coherence, and is similar to the even-odd resonance in the Cooper pair box problem in mesoscopic superconducting grains. Coherent fluctuations in the number of Cooper pairs in superconductors are analogous to the fluctuations in the relative number difference between the two layers in quantum Hall droplets.

  18. 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.

  19. 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. PMID:26197946

  20. 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.

  1. 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.

  2. 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

  3. 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

  4. Allele-dependent barley grain beta-amylase activity.

    PubMed

    Erkkilä, M J; Leah, R; Ahokas, H; Cameron-Mills, V

    1998-06-01

    The wild ancestor of cultivated barley, Hordeum vulgare subsp. spontaneum (K. Koch) A. & Gr. (H. spontaneum), is a source of wide genetic diversity, including traits that are important for malting quality. A high beta-amylase trait was previously identified in H. spontaneum strains from Israel, and transferred into the backcross progeny of a cross with the domesticated barley cv Adorra. We have used Southern-blot analysis and beta-amy1 gene characterization to demonstrate that the high beta-amylase trait in the backcross line is co-inherited with the beta-amy1 gene from the H. spontaneum parent. We have analyzed the beta-amy1 gene organization in various domesticated and wild-type barley strains and identified three distinct beta-amy1 alleles. Two of these beta-amy1 alleles were present in modern barley, one of which was specifically found in good malting barley cultivars. The third allele, linked with high grain beta-amylase activity, was found only in a H. spontaneum strain from the Judean foothills in Israel. The sequences of three isolated beta-amy1 alleles are compared. The involvement of specific intron III sequences, in particular a 126-bp palindromic insertion, in the allele-dependent expression of beta-amylase activity in barley grain is proposed.

  5. Allele-Dependent Barley Grain β-Amylase Activity1

    PubMed Central

    Erkkilä, Maria J.; Leah, Robert; Ahokas, Hannu; Cameron-Mills, Verena

    1998-01-01

    The wild ancestor of cultivated barley, Hordeum vulgare subsp. spontaneum (K. Koch) A. & Gr. (H. spontaneum), is a source of wide genetic diversity, including traits that are important for malting quality. A high β-amylase trait was previously identified in H. spontaneum strains from Israel, and transferred into the backcross progeny of a cross with the domesticated barley cv Adorra. We have used Southern-blot analysis and β-amy1 gene characterization to demonstrate that the high β-amylase trait in the backcross line is co-inherited with the β-amy1 gene from the H. spontaneum parent. We have analyzed the β-amy1 gene organization in various domesticated and wild-type barley strains and identified three distinct β-amy1 alleles. Two of these β-amy1 alleles were present in modern barley, one of which was specifically found in good malting barley cultivars. The third allele, linked with high grain β-amylase activity, was found only in a H. spontaneum strain from the Judean foothills in Israel. The sequences of three isolated β-amy1 alleles are compared. The involvement of specific intron III sequences, in particular a 126-bp palindromic insertion, in the allele-dependent expression of β-amylase activity in barley grain is proposed. PMID:9625721

  6. 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

  7. 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

  8. Higgs boson mass constraint and the C P even-C P odd Higgs boson mixing in an MSSM extension

    NASA Astrophysics Data System (ADS)

    Ibrahim, Tarek; Nath, Pran; Zorik, Anas

    2016-08-01

    One-loop contributions to the C P even-C P odd Higgs boson mixings arising from contributions due to exchange of a vectorlike multiplet are computed under the Higgs boson mass constraint. The vectorlike multiplet consists of a fourth generation of quarks and a mirror generation. This sector brings in new C P phases which can be large consistent with the electric dipole moment constraints. In this work we compute the contributions from the exchange of quarks and mirror quarks t4 L,t4 R,TL,TR, and their scalar partners, the squarks, and the mirror squarks. The effect of their contributions to the Higgs boson masses and mixings are computed and analyzed. The possibility of measuring the effects of mixing of C P even and C P odd Higgs in experiment is discussed. It is shown that the branching ratios of the Higgs bosons into fermion pairs are sensitive to new physics and specifically to C P phases.

  9. 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.

  10. 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…

  11. 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

  12. 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

  13. 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. PMID:27307400

  14. Sequence analysis of two novel HLA-DMA alleles

    SciTech Connect

    Carrington, M.; Harding, A.

    1994-12-31

    Several novel genes have been mapped recently in the HLA class II region between DQ and DP. Two of these genes, DMA and DMB, are predicted to encode a protein which has a structure similar to that of the DR, DQ, and DP molecules. The function of the DM molecule, however, is unlikely to mimic precisely that of the other class II molecules, since they share a low level of similarity and both DMA and DMB have limited polymorphism. Based on sequences from the third exon, four alleles of DMB and two alleles of DMA were previously characterized. Single-strand conformation polymorphism (SSCP) patterns of amplified DMA exon 3 products indicated the existence of two additional DMA alleles, which were subsequently sequenced and are now reported here. 4 refs., 2 figs.

  15. Allele-Specific DNA Methylation Detection by Pyrosequencing®.

    PubMed

    Kristensen, Lasse Sommer; Johansen, Jens Vilstrup; Grønbæk, Kirsten

    2015-01-01

    DNA methylation is an epigenetic modification that plays important roles in healthy as well as diseased cells, by influencing the transcription of genes. In spite the fact that human somatic cells are diploid, most of the currently available methods for the study of DNA methylation do not provide information on the methylation status of individual alleles of genes. This information may be of importance in many situations. In particular, in cancer both alleles of tumour suppressor genes generally need to be inactivated for a phenotypic effect to be observed. Here, we present a simple and cost-effective protocol for allele-specific DNA methylation detection based on Pyrosequencing(®) of methylation-specific PCR (MSP) products including a single nucleotide polymorphism (SNP) within the amplicon. PMID:26103906

  16. Apolipoprotein E alleles in women with severe pre-eclampsia.

    PubMed Central

    Nagy, B; Rigó, J; Fintor, L; Karádi, I; Tóth, T

    1998-01-01

    This study investigated the frequency of apolipoprotein E (apoE) alleles among women with severe pre-eclampsia. The presence of the three most common apoE alleles (epsilon 2, epsilon 3, epsilon 4) was determined by polymerase chain reaction-restriction fragment length polymorphism in three groups of white women: non-pregnant healthy (n = 101), pregnant healthy (n = 52), and pregnant with a diagnosis of severe pre-eclampsia (n = 54). The frequency of apo epsilon 2 was highest among women with severe pre-eclampsia (16.6%) followed by non-pregnant women (12.9%), and those experiencing a healthy pregnancy (10.6%). The higher frequency of the apo epsilon 2 allele detected among women with severe pre-eclampsia suggests that apoE may play a role in the development of pre-eclampsia. PMID:9659248

  17. Sudden Drops in Blood Pressure Tied to Higher Odds for Dementia

    MedlinePlus

    ... news/fullstory_161422.html Sudden Drops in Blood Pressure Tied to Higher Odds for Dementia Dizziness, faintness ... be an association between sudden drops in blood pressure upon standing up -- a condition called orthostatic hypotension -- ...

  18. 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

  19. Strong odd-frequency correlations in fully gapped Zeeman-split superconductors.

    PubMed

    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

  20. Conductance of Disordered Wires with Symplectic Symmetry: Comparison between Odd- and Even-Channel Cases

    NASA Astrophysics Data System (ADS)

    Takane, Yositake

    2004-09-01

    The conductance of disordered wires with symplectic symmetry is studied by numerical simulations on the basis of a tight-binding model on a square lattice consisting of M lattice sites in the transverse direction. If the potential range of scatterers is much larger than the lattice constant, the number N of conducting channels becomes odd (even) when M is odd (even). The average dimensionless conductance < g > is calculated as a function of system length L. It is shown that when N is odd, the conductance behaves as < g > \\to 1 with increasing L. This indicates the absence of Anderson localization. In the even-channel case, the ordinary localization behavior arises and < g > decays exponentially with increasing L. It is also shown that the decay of < g > is much faster in the odd-channel case than in the even-channel case. These numerical results are in qualitative agreement with existing analytic theories.

  1. 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

  2. The odd-even effect in multiplication: parity rule or familiarity with even numbers?

    PubMed

    Lochy, A; Seron, X; Delazer, M; Butterworth, B

    2000-04-01

    This study questions the evidence that a parity rule is used during the verification of multiplication. Previous studies reported that products are rejected faster when they violate the expected parity, which was attributed to the use of a rule (Krueger, 1986; Lemaire & Fayol, 1995). This experiment tested an alternative explanation of this effect: the familiarity hypothesis. Fifty subjects participated in a verification task with contrasting types of problems (even x even, odd x odd, mixed). Some aspects of our results constitute evidence against the use of the parity rule: False even answers were rejected slowly, even when the two operands were odd. We suggest that the odd-even effect in verification of multiplication could not be due to the use of the parity rule, but rather to a familiarity with even numbers (three quarters of products are indeed even). PMID:10881553

  3. 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.

  4. 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.

  5. Allele-specific DNA methylation reinforces PEAR1 enhancer activity.

    PubMed

    Izzi, Benedetta; Pistoni, Mariaelena; Cludts, Katrien; Akkor, Pinar; Lambrechts, Diether; Verfaillie, Catherine; Verhamme, Peter; Freson, Kathleen; Hoylaerts, Marc F

    2016-08-18

    Genetic variation in the PEAR1 locus is linked to platelet reactivity and cardiovascular disease. The major G allele of rs12041331, an intronic cytosine guanine dinucleotide-single-nucleotide polymorphism (CpG-SNP), is associated with higher PEAR1 expression in platelets and endothelial cells than the minor A allele. The molecular mechanism underlying this difference remains elusive. We have characterized the histone modification profiles of the intronic region surrounding rs12041331 and identified H3K4Me1 enhancer-specific enrichment for the region that covers the CpG-SNP. Interestingly, methylation studies revealed that the CpG site is fully methylated in leukocytes of GG carriers. Nuclear protein extracts from megakaryocytes, endothelial cells, vs control HEK-293 cells show a 3-fold higher affinity for the methylated G allele compared with nonmethylated G or A alleles in a gel electrophoretic mobility shift assay. To understand the positive relationship between methylation and gene expression, we studied DNA methylation at 4 different loci of PEAR1 during in vitro megakaryopoiesis. During differentiation, the CpG-SNP remained fully methylated, while we observed rapid methylation increases at the CpG-island overlapping the first 5'-untranslated region exon, paralleling the increased PEAR1 expression. In the same region, A-allele carriers of rs12041331 showed significantly lower DNA methylation at CGI1 compared with GG homozygote. This CpG-island contains binding sites for the methylation-sensitive transcription factor CTCF, whose binding is known to play a role in enhancer activation and/or repression. In conclusion, we report the molecular characterization of the first platelet function-related CpG-SNP, a genetic predisposition that reinforces PEAR1 enhancer activity through allele-specific DNA methylation. PMID:27313330

  6. 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.

  7. 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.

  8. Silencing of genes and alleles by RNAi in Anopheles gambiae.

    PubMed

    Lamacchia, Marina; Clayton, John R; Wang-Sattler, Rui; Steinmetz, Lars M; Levashina, Elena A; Blandin, Stéphanie A

    2013-01-01

    Anopheles gambiae mosquitoes are the major vectors of human malaria parasites. However, mosquitoes are not passive hosts for parasites, actively limiting their development in vivo. Our current understanding of the mosquito antiparasitic response is mostly based on the phenotypic analysis of gene knockdowns obtained by RNA interference (RNAi), through the injection or transfection of long dsRNAs in adult mosquitoes or cultured cells, respectively. Recently, RNAi has been extended to silence specifically one allele of a given gene in a heterozygous context, thus allowing to compare the contribution of different alleles to a phenotype in the same genetic background. PMID:22990777

  9. Data-adaptive algorithms for calling alleles in repeat polymorphisms.

    PubMed

    Stoughton, R; Bumgarner, R; Frederick, W J; McIndoe, R A

    1997-01-01

    Data-adaptive algorithms are presented for separating overlapping signatures of heterozygotic allele pairs in electrophoresis data. Application is demonstrated for human microsatellite CA-repeat polymorphisms in LiCor 4000 and ABI 373 data. The algorithms allow overlapping alleles to be called correctly in almost every case where a trained observer could do so, and provide a fast automated objective alternative to human reading of the gels. The algorithm also supplies an indication of confidence level which can be used to flag marginal cases for verification by eye, or as input to later stages of statistical analysis. PMID:9059812

  10. Simultaneous inference of haplotypes and alleles at a causal gene.

    PubMed

    Larribe, Fabrice; Dupont, Mathieu J; Boucher, Gabrielle

    2015-01-01

    We present a methodology which jointly infers haplotypes and the causal alleles at a gene influencing a given trait. Often in human genetic studies, the available data consists of genotypes (series of genetic markers along the chromosomes) and a phenotype. However, for many genetic analyses, one needs haplotypes instead of genotypes. Our methodology is not only able to estimate haplotypes conditionally on the disease status, but is also able to infer the alleles at the unknown disease locus. Some applications of our methodology are in genetic mapping and in genetic counseling.

  11. 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.

  12. Bottomonium Spectroscopy with Mixing of eta{sub b} States and a Light CP-Odd Higgs Boson

    SciTech Connect

    Domingo, Florian; Ellwanger, Ulrich; Sanchis-Lozano, Miguel-Angel

    2009-09-11

    The mass of the eta{sub b}(1S), measured recently by the BABAR Collaboration, is significantly lower than expected from QCD predictions for the UPSILON(1S)-eta{sub b}(1S) hyperfine splitting. We suggest that the observed eta{sub b}(1S) mass is shifted downwards due to a mixing with a CP-odd Higgs boson A with a mass m{sub A} in the range 9.4-10.5 GeV compatible with LEP, CLEO, and BABAR constraints. We determine the resulting predictions for the spectrum of the eta{sub b}(nS)-A system and the branching ratios into tau{sup +}tau{sup -} as functions of m{sub A}.

  13. Swimming at low Reynolds number in fluids with odd, or Hall, viscosity

    NASA Astrophysics Data System (ADS)

    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.

  14. 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. PMID:24827344

  15. 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.

  16. 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.

  17. Time-odd mean fields in covariant density functional theory: Rotating systems

    SciTech Connect

    Afanasjev, A. V.; Abusara, H.

    2010-09-15

    Time-odd mean fields (nuclear magnetism) and their impact on physical observables in rotating nuclei are studied in the framework of covariant density functional theory (CDFT). It is shown that they have profound effect on the dynamic and kinematic moments of inertia. Particle number, configuration, and rotational frequency dependencies of their impact on the moments of inertia have been analyzed in a systematic way. Nuclear magnetism can also considerably modify the band crossing features such as crossing frequencies and the properties of the kinematic and dynamic moments of inertia in the band crossing region. The impact of time-odd mean fields on the moments of inertia in the regions away from band crossing only weakly depends on the relativistic mean-field parametrization, reflecting good localization of the properties of time-odd mean fields in CDFT. The moments of inertia of normal-deformed nuclei considerably deviate from the rigid-body value. On the contrary, superdeformed and hyperdeformed nuclei have the moments of inertia which are close to rigid-body value. The structure of the currents in rotating frame, their microscopic origin, and the relations to the moments of inertia have been systematically analyzed. The phenomenon of signature separation in odd-odd nuclei, induced by time-odd mean fields, has been analyzed in detail.

  18. 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.

  19. Genome-wide identification of allele-specific expression in response to Streptococcus suis 2 infection in two differentially susceptible pig breeds.

    PubMed

    Wu, Huayu; Gaur, Uma; Mekchay, Supamit; Peng, Xianwen; Li, Lianghua; Sun, Hua; Song, Zhongxu; Dong, Binke; Li, Mingbo; Wimmers, Klaus; Ponsuksili, Siriluck; Li, Kui; Mei, Shuqi; Liu, Guisheng

    2015-11-01

    Although allele expression imbalance has been recognized in many species, and strongly linked to diseases, no whole transcriptome allele imbalance has been detected in pigs during pathogen infections. The pathogen Streptococcus suis 2 (SS2) causes serious zoonotic disease. Different pig breeds show differential susceptibility/resistance to pathogen infection, but the biological insight is little known. Here we analyzed allele-specific expression (ASE) using the spleen transcriptome of four pigs belonging to two phenotypically different breeds after SS2 infection. The comparative analysis of allele specific SNPs between control and infected animals revealed 882 and 1096 statistically significant differentially expressed allele SNPs (criteria: ratio ≧ 2 or ≦ 0.5) in Landrace and Enshi black pig, respectively. Twenty nine allelically imbalanced SNPs were further verified by Sanger sequencing, and later six SNPs were quantified by pyrosequencing assay. The pyrosequencing results are in agreement with the RNA-seq results, except two SNPs. Looking at the role of ASE in predisposition to diseases, the discovery of causative variants by ASE analysis might help the pig industry in long term to design breeding programs for improving SS2 resistance.

  20. Study of HLA-DQA1 alleles in celiac children.

    PubMed

    Nieto, A; Blanco Quirós, A; Arranz, E; Alonso Franch, M; Garrote, J A; Calvo, C

    1995-01-01

    The familial incidence of celiac disease (CD) confirms its genetic basis, although acquired factors are also involved. Many authors have reported a linkage between celiac disease and HLA antigens, but there are differences which depend on geographical areas, and nowadays the study must be done at the genetic level. Thirty-eight celiac children and 52 normal controls were included in this study. All individuals were chosen from the Castilla and Leon area. We used the reverse ¿dot block¿ technique, using sequence-specific oligonucleotide DNA probes (Cetus, USA) to determine the HLA-DQA1 alleles in DNA samples previously amplified by PCR (polymerase chain reaction). The different frequency of alleles in patients and controls was assessed by 3 statistical tests: chi square (chi(2)), relative risk (RR) and etiologic fraction (EF). A very high frequency of DQA1*0201 (chi(2):p <0.0001) and DQA1*0501 (chi(2): p <0.0001) alleles was observed in patients; all but one (97%) had the DQA1*0501 allele vs. 40% of controls (RR: 37.00; EF: 0.955). The DQA1*0201 allele also had a high prevalence in celiacs (58%)(RR: 1.375: EF:0.438). The DQA1*01 allele was only found in 10.5% of patients compared to 79% of controls (chi(2): p <0.0001) and the DQA1*03 allele was also decreased in celiacs. There was only one celiac girl without the DQA1*0501 allele. She had no other clinical or serological differences, as compared to the other patients. In the study of allele subtypes, among the DQA1*01 allele, 50% of patients were positive for DQA1*101 and the remaining 50% had DQA1*0102, but none of the individuals were positive for DQA1*0103. Among normal controls, 32 individuals (61.5%) expressed the DQA1*0102 subtype, 15 (28.9%) the DQA1*0101 subtype and 5 (9.6%) the DQA1*0103 subtype. All positive cases for DQA1-*05 belong to the DQA1* 0501 subtype, in both celiac and control groups. There were 10 possible combinations of HLA-DQA1 genes, but we found a very unequal distribution in both celiacs

  1. 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…

  2. Molecular analysis of HLA-B35 alleles and their relationship to HLA-B15 alleles.

    PubMed

    Cereb, N; Kim, C; Hughes, A L; Yang, S Y

    1997-04-01

    The HLA-B35 serotype is one of the largest allelic groups of HLA class I molecules and includes four isotypes. Of the four, the B35 variant isoform is relatively rare and is the most acidic form. DNA sequencing of the rare isoforms revealed three alleles, B*1522, B*3511, and B*3517. A phylogenetic tree of HLA-B15- and HLA-B35-related alleles for the exon 2 and 3 nucleotide sequences showed that exon 2 of B*1522 clusters with B35 alleles whereas exon 3 clusters with B15 alleles. Branches of the tree suggest that the serodeterminants of B35, B62, B63, and B70 may reside in the alpha 1 domain, encoded by exon 2. The B*1520 and B*1522 genes, which type as B62 and B35, respectively, are hybrid molecules alternatively using exon 2 and exon 3 sequences of B*3501 and B*1501. A comparison of intron 2 sequences for B*3501, B*1501 and B*1522 suggests that the recombination site may have been in the region at the 3' end of intron 2. Despite being flanked by two highly polymorphic exons (exons 2 and 3), intron 2 is relatively well conserved in the B-locus, and it is characterized by seven to eight tandem repeats of the CGGGG pentanucleotide. A high degree of sequence homology and repetitive sequences are essential for a significant frequency of recombination. In this report, we reveal more about the complex evolutionary history of the HLA-B alleles.

  3. 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

  4. 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

  5. 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.

  6. Compression Ratio Adjuster

    NASA Technical Reports Server (NTRS)

    Akkerman, J. W.

    1982-01-01

    New mechanism alters compression ratio of internal-combustion engine according to load so that engine operates at top fuel efficiency. Ordinary gasoline, diesel and gas engines with their fixed compression ratios are inefficient at partial load and at low-speed full load. Mechanism ensures engines operate as efficiently under these conditions as they do at highload and high speed.

  7. 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…

  8. Detecting isotopic ratio outliers

    SciTech Connect

    Bayne, C.K.; Smith, D.H.

    1985-01-01

    An alternative method is proposed for improving isotopic ratio estimates. This method mathematically models pulse-count data and uses iterative reweighted Poisson regression to estimate model parameters to calculate the isotopic ratios. This computer-oriented approach provides theoretically better methods than conventional techniques to establish error limits and to identify outliers. 6 refs., 3 figs., 3 tabs.

  9. Specialized ratio analysis.

    PubMed

    Wyer, J C; Salzinger, F H

    1983-01-01

    Many common management techniques have little use in managing a medical group practice. Ratio analysis, however, can easily be adapted to the group practice setting. Acting as broad-gauge indicators, financial ratios provide an early warning of potential problems and can be very useful in planning for future operations. The author has gathered a collection of financial ratios which were developed by participants at an education seminar presented for the Virginia Medical Group Management Association. Classified according to the human element, system component, and financial factor, the ratios provide a good sampling of measurements relevant to medical group practices and can serve as an example for custom-tailoring a ratio analysis system for your medical group.

  10. 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...

  11. 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.

  12. 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.

  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. 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...

  16. Extensive allele-specific translational regulation in hybrid mice.

    PubMed

    Hou, Jingyi; Wang, Xi; McShane, Erik; Zauber, Henrik; Sun, Wei; Selbach, Matthias; Chen, Wei

    2015-08-07

    Translational regulation is mediated through the interaction between diffusible trans-factors and cis-elements residing within mRNA transcripts. In contrast to extensively studied transcriptional regulation, cis-regulation on translation remains underexplored. Using deep sequencing-based transcriptome and polysome profiling, we globally profiled allele-specific translational efficiency for the first time in an F1 hybrid mouse. Out of 7,156 genes with reliable quantification of both alleles, we found 1,008 (14.1%) exhibiting significant allelic divergence in translational efficiency. Systematic analysis of sequence features of the genes with biased allelic translation revealed that local RNA secondary structure surrounding the start codon and proximal out-of-frame upstream AUGs could affect translational efficiency. Finally, we observed that the cis-effect was quantitatively comparable between transcriptional and translational regulation. Such effects in the two regulatory processes were more frequently compensatory, suggesting that the regulation at the two levels could be coordinated in maintaining robustness of protein expression.

  17. 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.

  18. Even-odd effects in prompt emission of spontaneously fissioning even-even Pu isotopes

    NASA Astrophysics Data System (ADS)

    Tudora, A.; Hambsch, F.-J.; Giubega, G.; Visan, I.

    2015-01-01

    The available experimental Y (A , TKE) data for 236,238,240,242,244Pu(SF) together with the Zp model prescription with appropriate parameters allows the investigation of even-odd effects in fragment distributions. The size of the global even-odd effect in Y (Z) is decreasing from 244Pu(SF) to 236Pu(SF) confirming the general observation of a decrease of the even-odd effect with the fissility parameter. Charge polarizations (ΔZ) and root-mean squares (rms) as a function of A of 236-244Pu(SF) were obtained for the first time. In the asymmetric fission region both ΔZ (A) and rms (A) exhibit oscillations with a periodicity of about 5 mass units due to the even-odd effects. The total average charge deviations < ΔZ > (obtained by averaging ΔZ (A) over the experimental Y (A) distribution) are of about |0.5| for all studied Pu(SF) systems. The comparison of the calculated ΔZ (A) and rms (A) of 240Pu(SF) with those of 239Pu (nth , f) reported by Wahl shows an in-phase oscillation with a higher amplitude in the case of 240Pu(SF), confirming the higher even-odd effect in the case of SF. As in the previously studied cases (233,235U (nth , f), 239Pu (nth , f), 252Cf(SF)) the even-odd effects in the prompt emission of 236-244Pu(SF) are mainly due to the Z even-odd effects in fragment distributions and charge polarizations and the N even-odd effects in the average neutron separation energies from fragments < Sn >. The size of the global N even-odd effect in < Sn > is decreasing with the fissility parameter, being higher for the Pu(SF) systems compared to the previously studied systems. The prompt neutron multiplicities as a function of Z, ν (Z), exhibit sawtooth shapes with a visible staggering for asymmetric fragmentations. The size of the global Z even-odd effect in ν (Z) exhibits a decreasing trend with increasing fissility. The average prompt neutron multiplicities as a function of TKE show an increase of the even-odd effect with increasing TKE, with global effect

  19. Local even-odd effect based on the number of configurations of pre-formed and formed fragmentations in a fissioning nucleus

    NASA Astrophysics Data System (ADS)

    Tudora, A.; Hambsch, F.-J.; Giubega, G.

    2016-09-01

    The present paper proposes a modeling of the local even-odd effect based on the number of configurations in a nucleus undergoing fission at two stages along its fission path. One is the fissioning nucleus stage just after passing through the outer saddle point when the fragments are considered as pre-formed and the intrinsic energy is not yet shared. The other stage is at the end of the fission path when the scission is imminent. Then the intrinsic energy is already partitioned and the fragments are completely formed. The probability that a pre-formed fragmentation arrives at the end of the fission path (i.e. at scission) when the fragmentation is completely formed is expressed by the ratio of the number of configurations of the formed fragmentation to the one of pre-formed fragmentation. The local even-odd effect is defined as half of the difference between these normalized ratios corresponding to even-Z and odd-Z fragmentations. Both numbers of configurations in the fissioning nucleus, in which the fragments are pre-formed and completely formed, are calculated using level densities described by the constant temperature function (justified by the small values of the intrinsic energy before scission). The obtained local even-odd effect results describe well the experimental data, including the increase at asymmetry values corresponding to fragmentations in which one of the fragments is magic or double magic (i.e. fragmentations in which ZH = 50 and/or NH = 82 and very asymmetric fragmentations in which ZL = 28).

  20. Testing allele homogeneity: the problem of nested hypotheses

    PubMed Central

    2012-01-01

    Background The evaluation of associations between genotypes and diseases in a case-control framework plays an important role in genetic epidemiology. This paper focuses on the evaluation of the homogeneity of both genotypic and allelic frequencies. The traditional test that is used to check allelic homogeneity is known to be valid only under Hardy-Weinberg equilibrium, a property that may not hold in practice. Results We first describe the flaws of the traditional (chi-squared) tests for both allelic and genotypic homogeneity. Besides the known problem of the allelic procedure, we show that whenever these tests are used, an incoherence may arise: sometimes the genotypic homogeneity hypothesis is not rejected, but the allelic hypothesis is. As we argue, this is logically impossible. Some methods that were recently proposed implicitly rely on the idea that this does not happen. In an attempt to correct this incoherence, we describe an alternative frequentist approach that is appropriate even when Hardy-Weinberg equilibrium does not hold. It is then shown that the problem remains and is intrinsic of frequentist procedures. Finally, we introduce the Full Bayesian Significance Test to test both hypotheses and prove that the incoherence cannot happen with these new tests. To illustrate this, all five tests are applied to real and simulated datasets. Using the celebrated power analysis, we show that the Bayesian method is comparable to the frequentist one and has the advantage of being coherent. Conclusions Contrary to more traditional approaches, the Full Bayesian Significance Test for association studies provides a simple, coherent and powerful tool for detecting associations. PMID:23176636

  1. Variant Alleles of the WNT Antagonist FRZB Are Determinants of Hip Shape and Modify the Relationship between Hip Shape and Osteoarthritis

    PubMed Central

    Baker-LePain, Julie C.; Lynch, John A.; Parimi, Neeta; McCulloch, Charles E.; Nevitt, Michael C.; Corr, Maripat; Lane, Nancy E.

    2011-01-01

    Objectives (1) To test whether single nucleotide polymorphisms (SNPs) of the FRZB gene are associated with hip shape. (2) To determine whether FRZB variant alleles affect the relationship between hip shape and radiographic hip osteoarthritis (RHOA). Methods A nested case-control study of Caucasian women aged ≥ 65 years in the Study of Osteoporotic Fractures (SOF) was performed. Cases (n = 451) demonstrated incident RHOA during follow-up (mean 8.0 ± 0.4 years). Controls (n = 601) had no RHOA at baseline or follow-up. Statistical shape modeling (SSM) of digitized hip radiographs was used to assess proximal femur shape, and center-edge angle and acetabular depth were used to assess acetabular shape. The association of the rs288326 and rs7775 FRZB variant alleles with hip shape was analyzed using linear regression. The effect of these alleles on the relationship between hip shape and RHOA was analyzed using logistic regression with and without interaction terms. Results The rs288326 and rs7775 alleles were associated with shape of the proximal femur (SSM Mode 2). There was a significant interaction between the rs288326 SNP and proximal femur shape (Mode 2) in predicting RHOA (p for interaction = 0.022). Among subjects with the rs288326 variant allele, there were increasing odds of RHOA with increasing quartiles of proximal femur shape Mode 2 (OR for 4th quartile of Mode 2 = 2.5, 95% confidence interval 1.2–5.3; p for linear trend = 0.02). Conclusions The rs288326 and rs7775 FRZB SNPs are associated with the shape of the proximal femur. The presence of the rs288326 SNP alters the relationship between proximal femur shape and incident RHOA. Together, these findings suggest that FRZB may serve an important role in determining hip shape and may modify the relationship between hip shape and OA. PMID:22544526

  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. Suspension Array for Multiplex Detection of Eight Fungicide-Resistance Related Alleles in Botrytis cinerea

    PubMed Central

    Zhang, Xin; Xie, Fei; Lv, Baobei; Zhao, Pengxiang; Ma, Xuemei

    2016-01-01

    A simple and high-throughput assay to detect fungicide resistance is required for large-scale monitoring of the emergence of resistant strains of Botrytis cinerea. Using suspension array technology performed on a Bio-Plex 200 System, we developed a single-tube allele-specific primer extension assay that can simultaneously detect eight alleles in one reaction. These eight alleles include E198 and 198A of the β-Tubulin gene (BenA), H272 and 272Y of the Succinate dehydrogenase iron–sulfur subunit gene (SdhB), I365 and 365S of the putative osmosensor histidine kinase gene (BcOS1), and F412 and 412S of the 3-ketoreductase gene (erg27). This assay was first established and optimized with eight plasmid templates containing the DNA sequence variants BenA-E198, BenA-198A, SdhB-H272, SdhB-272Y, BcOS1-I365, BcOS1-365S, erg27-F412, and erg27-412S. Results indicated that none of the probes showed cross-reactivity with one another. The minimum limit of detection for these genotypes was one copy per test. Four mutant plasmids were mixed with 10 ng/μL wild-type genomic DNA in different ratios. Detection sensitivity of mutant loci was 0.45% for BenA-E198A, BcOS1-I365S, and erg27-F412S, and was 4.5% for SdhB-H272Y. A minimum quantity of 0.1 ng of genomic DNA was necessary to obtain reliable results. This is the first reported assay that can simultaneously detect mutations in BenA, SdhB, BcOS1, and erg27. PMID:27708631

  4. 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. PMID:26748964

  5. 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.

  6. Birthweight ratio revisited.

    PubMed Central

    Brownlee, K G; Ng, P C; Roussounis, S H; Dear, P R

    1991-01-01

    In order to test the hypothesis suggested in a recent report that the birthweight ratio might be a useful predictor of several important clinical outcome measures in babies of less than 31 weeks' gestation, we examined the association between the birthweight ratio and aspects of both short and long term outcome in 436 Leeds babies of less than 31 weeks' gestation. Unlike the report, and contrary to what we had expected, we were unable to find any significant association between birthweight ratio and length of time on the ventilator, mortality, neurological outcome, or intellectual outcome. PMID:2025035

  7. Allelic imbalance analysis by high-density single-nucleotide polymorphic allele (SNP) array with whole genome amplified DNA

    PubMed Central

    Wong, Kwong-Kwok; Tsang, Yvonne T. M.; Shen, Jianhe; Cheng, Rita S.; Chang, Yi-Mieng; Man, Tsz-Kwong; Lau, Ching C.

    2004-01-01

    Besides their use in mRNA expression profiling, oligonucleotide microarrays have also been applied to single-nucleotide polymorphism (SNP) and loss of heterozygosity (LOH) or allelic imbalance studies. In this report, we evaluate the reliability of using whole genome amplified DNA for analysis with an oligonucleotide microarray containing 11 560 SNPs to detect allelic imbalance and chromosomal copy number abnormalities. Whole genome SNP analyses were performed with DNA extracted from osteosarcoma tissues and patient-matched blood. SNP calls were then generated by Affymetrix® GeneChip® DNA Analysis Software. In two osteosarcoma cases, using unamplified DNA, we identified 793 and 1070 SNP loci with allelic imbalance, respectively. In a parallel experiment with amplified DNA, 78% and 83% of these SNP loci with allelic imbalance was detected. The average false-positive rate is 13.8%. Furthermore, using the Affymetrix® GeneChip® Chromosome Copy Number Tool to analyze the SNP array data, we were able to detect identical chromosomal regions with gain or loss in both amplified and unamplified DNA at cytoband resolution. PMID:15148342

  8. 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.

  9. KIR2DL2/2DL3-E35 alleles are functionally stronger than -Q35 alleles

    PubMed Central

    Bari, Rafijul; Thapa, Rajoo; Bao, Ju; Li, Ying; Zheng, Jie; Leung, Wing

    2016-01-01

    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. PMID:27030405

  10. Alternative 3' splice acceptor sites modulate enzymic activity in derivative alleles of the maize bronze1-mutable 13 allele.

    PubMed Central

    Okagaki, R J; Sullivan, T D; Schiefelbein, J W; Nelson, O E

    1992-01-01

    The defective Suppressor-mutator (dSpm)-induced allele bronze1-mutable 13 (bz1-m13) and many of its derivative alleles are leaky mutants with measurable levels of flavonol O3-glucosyltransferase activity. This activity results from splicing at acceptor site-1, one of two cryptic 3' splice sites within the dSpm insertion in bz1-m13. In this study, splicing in bz1-m13 change-in-state (CS) alleles CS-3 and CS-64 was shown to be altered from bz1-m13; previous work found altered splicing in CS-9. CS-64 is a null allele and lacks the acceptor site-1-spliced transcript because this site is deleted. CS-3 and CS-9 had increased levels of the acceptor site-1 transcript relative to bz1-m13 and increased enzymic activities. A deletion in CS-9 altered splicing by eliminating acceptor site-2. Both acceptor sites were intact in CS-3, but a deletion removed most of a 275-bp GC-rich sequence in dSpm. This suggests that GC-rich sequences affect splicing and is consistent with models postulating a role for AU content in the splicing of plant introns. Splicing does not necessarily occur, however, at the junction of AU-rich intron sequences and GC-rich exon sequences. PMID:1477558

  11. 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...

  12. 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.

  13. 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.

  14. Odd-frequency Cooper pairs in two-band superconductors and their magnetic response

    NASA Astrophysics Data System (ADS)

    Asano, Yasuhiro; Sasaki, Akihiro

    2015-12-01

    We discuss the appearance of odd-frequency Cooper pairs in two-band superconductors by solving the Gor'kov equation analytically. We introduce the equal-time s -wave pair potentials as realized in MgB2 and iron pnictides. Although the order parameter symmetry is conventional, the band degree of freedom enriches the symmetry variety of pairing correlations. The hybridization and the asymmetry between the two conduction bands induce odd-frequency pairs as a subdominant pairing correlation in the uniform ground state. To study the magnetic response of odd-frequency Cooper pairs, we analyze the Meissner kernel represented by the Gor'kov Green function. In contrast to the even-frequency pairs linked to the pair potential, the induced odd-frequency Cooper pairs indicate a paramagnetic property. We also discuss the relation between the amplitude of the odd-frequency pairing correlation and the stability of superconducting states in terms of the self-consistent equation for the pair potential.

  15. [Odd- and branched-chain fatty acids in milk fat--characteristic and health properties].

    PubMed

    Adamska, Agata; Rutkowska, Jarosława

    2014-01-01

    This review analyzes the current state of knowledge on odd- and branched-chain fatty acids present in milk fat. Special attention is devoted to the characteristic, synthesis in ruminants, factors affecting their content in milk fat and pro-health properties of these compounds. The group of odd- and branched-chain fatty acids includes mainly saturated fatty acids with one or more methyl branches in the iso or anteiso position. These fatty acids are largely derived from ruminal bacteria and they have been transferred to ruminant tissue (milk and meat). For that reason they have been used as biomarkers of rumen fermentation. Odd- and branched-chain fatty acids are exogenous products for humans, and therefore have specific properties. The results of research from recent decades show that odd- and branched-chain fatty acids have anti-cancer activity. Branched-chain fatty acids may reduce the incidence of necrotizing enterocolitis. Additionally, these compounds have a beneficial effect on proper tissue function and on functioning and development of the infant gut, whereas odd-chain fatty acids are considered as biomarkers of milk fat intake by humans. So far, not all the mechanisms of activity of these compounds are known thoroughly. They should be more carefully studied for application of their biological effects in prevention and treatment. PMID:25228507

  16. Oppositional defiant disorder (ODD), the forerunner of alcohol dependence: a controlled study.

    PubMed

    Ghosh, Abhishek; Malhotra, Savita; Basu, Debasish

    2014-10-01

    There are common genetic, neurobiological and psycho-social substrates for oppositional defiant disorder (ODD) and substance dependence. ODD can be regarded as the mildest and earliest form of disruptive behavioral disorder and also represents the threshold of vulnerability for substance dependence. But it is a less researched area. The aim of this research was to study any possible association between childhood ODD and adult alcohol dependence. Data are presented from a non probability sample of 100 adult alcohol dependent subjects and equal number of biologically unrelated control subjects. Assessment was conducted by the instrument Semi-Structured Assessment for the Genetics of Alcoholism for both the assessment of ODD and alcohol dependence. The results of this study demonstrated significant association between childhood ODD and adult alcohol dependence. The association remained significant even after the exclusion of the possible confounding effects of the presence of conduct disorder and attention deficit hyperactivity disorder. Our study should encourage further research in this area and is expected to open up an opportunity for preventive research.

  17. Maximizing allele detection: Effects of analytical threshold and DNA levels on rates of allele and locus drop-out.

    PubMed

    Rakay, Christine A; Bregu, Joli; Grgicak, Catherine M

    2012-12-01

    Interpretation of DNA evidence depends upon the ability of the analyst to accurately compare the DNA profile obtained from an item of evidence and the DNA profile of a standard. This interpretation becomes progressively more difficult as the number of 'drop-out' and 'drop-in' events increase. Analytical thresholds (AT) are typically selected to ensure the false detection of noise is minimized. However, there exists a tradeoff between the erroneous labeling of noise as alleles and the false non-detection of alleles (i.e. drop-out). In this study, the effect ATs had on both types of error was characterized. Various ATs were tested, where three relied upon the analysis of baseline signals obtained from 31 negative samples. The fourth AT was determined by utilizing the relationship between RFU signal and DNA input. The other ATs were the commonly employed 50, 150 and 200 RFU thresholds. Receiver Operating Characteristic (ROC) plots showed that although high ATs completely negated the false labeling of noise, DNA analyzed with ATs derived using analysis of the baseline signal exhibited the lowest rates of drop-out and the lowest total error rates. In another experiment, the effect small changes in ATs had on drop-out was examined. This study showed that as the AT increased from ∼10 to 60 RFU, the number of heterozygous loci exhibiting the loss of one allele increased. Between ATs of 60 and 150 RFU, the frequency of allelic drop-out remained constant at 0.27 (±0.02) and began to decrease when ATs of 150 RFU or greater were utilized. In contrast, the frequency of heterozygous loci exhibiting the loss of both alleles consistently increased with AT. In summary, for samples amplified with less than 0.5ng of DNA, ATs derived from baseline analysis of negatives were shown to decrease the frequency of drop-out by a factor of 100 without significantly increasing rates of erroneous noise detection.

  18. CE determination of secaloindoline allelic forms in hexaploid triticale (x Triticosecale Wittmack).

    PubMed

    Salmanowicz, Bolesław P

    2010-03-01

    Differences in kernel texture are mainly caused by specific secaloindoline (SIN) proteins occurring in friabilin fraction of hexaploid triticale (x Triticosecale Wittmack) grain. SINs were isolated using Triton X-114 partitioning from either kernels/flour or starch of five triticale cultivars with wide range of different hardness. Crude SIN fraction was obtained by size-exclusion HPLC. SINs were separated on an uncoated fused-silica capillary using the iminodiacetic (IDA) buffer in conjunction with lower-concentrated poly(ethylene oxide) and ACN. A low-concentrate mixture of hydrophilic polymers, PVP and hydroxypropylmethylcellulose in IDA buffer was employed for dynamic coating of capillary inner wall. In total, on the basis of CZE profiles, two SIN-a proteins and two SIN-b proteins were identified. Allelic forms SIN-a1 and SIN-b1 have both two soft and one medium hard genotypes, however other allelic forms, designed as SIN-a2 and SIN-b2, were identified in hard and other medium hard cultivars. The CZE profiles showed that the ratio of the peak areas of SIN-b proteins isolated from triticale starch can be preliminarily used to distinguish cultivars with soft and hard grain.

  19. Modification of an HLA-B PCR-SSOP typing system leading to improved allele determination.

    PubMed

    Middleton, D; Williams, F; Cullen, C; Mallon, E

    1995-04-01

    Modifications have been introduced to a previously reported HLA-B PCR-SSOP typing system. This has enabled further definition of alleles, determination of the probe pattern of some alleles not previously examined and identification of patterns of possible new alleles. However there are still some alleles that cannot be differentiated and there are several alleles which when present as a homozygote have the same pattern as in combination with another allele. When the method was applied to the typing of 66 consecutive cadaveric donors there were three donors whose type differed from the serological type.

  20. Beyond-mean-field boson-fermion model for odd-mass nuclei

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

    A novel method for calculating spectroscopic properties of medium-mass and heavy atomic nuclei with an odd number of nucleons is introduced, based on the framework of nuclear energy density functional theory and the particle-core coupling scheme. The deformation energy surface of the even-even core, as well as the spherical single-particle energies and occupation probabilities of the odd particle(s), are obtained in a self-consistent mean-field calculation determined by the choice of the energy density functional and pairing interaction. This method uniquely determines the parameters of the Hamiltonian of the boson core, and only the strength of the particle-core coupling is specifically adjusted to selected data for a particular nucleus. The approach is illustrated in a systematic study of low-energy excitation spectra and transition rates of axially deformed odd-mass Eu isotopes.

  1. 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

  2. Odd Viscosity in the Quantum Critical Region of a Holographic Weyl Semimetal.

    PubMed

    Landsteiner, Karl; Liu, Yan; Sun, Ya-Wen

    2016-08-19

    We study odd viscosity in a holographic model of a Weyl semimetal. The model is characterized by a quantum phase transition from a topological semimetal to a trivial semimetal state. Since the model is axisymmetric in three spatial dimensions there are two independent odd viscosities. Both odd viscosity coefficients are nonvanishing in the quantum critical region and nonzero only due to the mixed axial gravitational anomaly. It is therefore a novel example in which the mixed axial gravitational anomaly gives rise to a transport coefficient at first order in derivatives at finite temperature. In the quantum critical region, the physics of viscosities as well as conductivities is governed by the quantum critical point. PMID:27588846

  3. Innovative Bimolecular-Based Advanced Logic Operations: A Prime Discriminator and An Odd Parity Checker.

    PubMed

    Zhou, Chunyang; Liu, Dali; Dong, Shaojun

    2016-08-17

    Herein, a novel logic operation of prime discriminator is first performed for the function of identifying the prime numbers from natural numbers less than 10. The prime discriminator logic operation is developed by DNA hybridizations and the conjugation of graphene oxide and single-stranded DNA as a reacting platform. On the basis of the similar reaction principle, an odd parity checker is also developed. The odd parity checker logic operation can identify the even numbers and odd numbers from natural numbers less than 10. Such advanced logic operations with digital recognition ability can provide a new field of vision toward prototypical DNA-based logic operations and promote the development of advanced logic circuits. PMID:27459592

  4. Odd-Even Pattern Observed in Polyaniline/(Au0 – Au8) Composites

    SciTech Connect

    Jonke, Alex P.; Josowicz, Mira A.; Janata, Jiri

    2012-01-12

    Theoretically predicted effect of odd-even pattern of electron pairing on behavior of gold clusters in polyaniline/AuN (N = 0 to 8) has been confirmed experimentally. In these composites the atomic Au clusters with even number of atoms exhibit higher catalytic activity for electrochemical oxidation of n-propanol in 1 M NaOH than the odd-number atoms clusters. Also, infrared spectroscopy shows that even numbered PANI/AuN composites affect the N-H stretching vibration more strongly than the corresponding odd numbered ones. This behavior matches the theoretically predicted variations of HOMO-LUMO gap energy and the stability of the atomic Au clusters. It also agrees with the earlier experimental work in which the UPS spectra of isolated, mass-selected Au clusters have been reported.

  5. SU(6) quadrupole phonon model for even and odd nuclei and the SU(3) limit

    NASA Astrophysics Data System (ADS)

    Paar, V.; Brant, S.; Canto, L. F.; Leander, G.; Vouk, M.

    1982-04-01

    Analogous to the equivalence between the SU(6) quadrupole-phonon model (TQM) and the interacting boson model (IBM), the equivalence is pointed out for odd systems between the SU(6) particle quadrupole-phonon coupling model (PTQM) and the interacting boson-fermion model (IBFM). PTQM is formulated starting from the Dyson representation for the odd system. Different aspects of the SU(3) limit of TQM and PTQM are studied; the quadrupole-phonon block structure of rotational bands in even and odd nuclei and analytic expressions based on the coherent state; signature effects generated in PTQM; electromagnetic properties and correction factors for PTQM; overlaps of the PTQM analogs of Nilsson states with Coriolis-coupled Nilsson states and the relation to the rotational model representation.

  6. Electric dipole moments as probes of new CP-odd physics

    SciTech Connect

    Ritz, Adam

    2009-12-17

    We review the importance of precision probes for flavor-diagonal CP-violation, specifically searches for electric dipole moments of nucleons, atoms and molecules, in accessing new CP-odd physics at high scales. We summarize the effective field theory analysis of observable EDMs in terms of a general set of CP-odd operators at 1 GeV, and the ensuing model-independent new physics constraints, incorporating the recently improved limit on the Hg EDM. We also discuss the current status of these limits in the context of 1- and 2-loop contributions in supersymmetric models.

  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. 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.

  9. 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.

  10. Stimulus-parity synaesthesia versus stimulus-dichotomy synaesthesia: Odd, even or something else?

    PubMed Central

    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. PMID:26034572

  11. Odd-numbered oxacalix[n]arenes (n = 5, 7): synthesis and solid-state structures.

    PubMed

    Van Rossom, Wim; Robeyns, Koen; Ovaere, Magriet; Van Meervelt, Luc; Dehaen, Wim; Maes, Wouter

    2011-01-01

    The critical synthetic access to odd-numbered calix[n]arenes has evidently resulted in less attention for these macrocycles, although specific molecular recognition phenomena have been observed for some of them. A straightforward fragment coupling approach has been designed, applying kinetically controlled nucleophilic aromatic substitution reaction conditions, affording odd-numbered oxacalix[n]arenes (n = 5, 7) selectively in high yields. The solid-state conformational behavior and the oxacalix[n]arene cavity size were explored by single-crystal X-ray diffraction studies.

  12. Parallel Mapping of Antibiotic Resistance Alleles in Escherichia coli

    PubMed Central

    Mortazavi, Pooneh; Knight, Rob; Gill, Ryan T.

    2016-01-01

    Chemical genomics expands our understanding of microbial tolerance to inhibitory chemicals, but its scope is often limited by the throughput of genome-scale library construction and genotype-phenotype mapping. Here we report a method for rapid, parallel, and deep characterization of the response to antibiotics in Escherichia coli using a barcoded genome-scale library, next-generation sequencing, and streamlined bioinformatics software. The method provides quantitative growth data (over 200,000 measurements) and identifies contributing antimicrobial resistance and susceptibility alleles. Using multivariate analysis, we also find that subtle differences in the population responses resonate across multiple levels of functional hierarchy. Finally, we use machine learning to identify a unique allelic and proteomic fingerprint for each antibiotic. The method can be broadly applied to tolerance for any chemical from toxic metabolites to next-generation biofuels and antibiotics. PMID:26771672

  13. Dense deposit disease and the factor H H402 allele.

    PubMed

    Lau, Keith K; Smith, Richard J; Kolbeck, Peter C; Butani, Lavjay

    2008-06-01

    Herein, we describe the case of an 8-year-old boy who presented with a nephritic nephrotic syndrome. His laboratory investigation was significant for a persistently low serum complement 3 level. A renal biopsy was performed, based on which, he was diagnosed with dense deposit disease/membranoproliferative glomerulonephritis type II (DDD/MPGN II). He was treated with alternate-day oral corticosteroids, angiotensin-converting enzyme (ACE) inhibitors and tacrolimus. Factor H mutational analysis showed the Y402H and I62V allele polymorphisms. The purpose of our report is to discuss the association of the H402 allele variant of factor H with the DDD/MPGN II phenotype and its possible therapeutic implications.

  14. Clostridium difficile Genome Editing Using pyrE Alleles.

    PubMed

    Ehsaan, Muhammad; Kuehne, Sarah A; Minton, Nigel P

    2016-01-01

    Precise manipulation (in-frame deletions and substitutions) of the Clostridium difficile genome is possible through a two-stage process of single-crossover integration and subsequent isolation of double-crossover excision events using replication-defective plasmids that carry a counterselection marker. Use of a codA (cytosine deaminase) or pyrE (orotate phosphoribosyltransferase) as counter selection markers appears equally effective, but there is considerable merit in using a pyrE mutant as the host as, through the use of allele-coupled exchange (ACE) vectors, mutants created (by whatever means) can be rapidly complemented concomitant with restoration of the pyrE allele. This avoids the phenotypic effects frequently observed with high-copy-number plasmids and dispenses with the need to add antibiotic to ensure plasmid retention. PMID:27507332

  15. 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

  16. 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

  17. 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.

  18. 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. PMID:27375658

  19. Inferring Selection Intensity and Allele Age from Multilocus Haplotype Structure

    PubMed Central

    Chen, Hua; Slatkin, Montgomery

    2013-01-01

    It is a challenging task to infer selection intensity and allele age from population genetic data. Here we present a method that can efficiently estimate selection intensity and allele age from the multilocus haplotype structure in the vicinity of a segregating mutant under positive selection. We use a structured-coalescent approach to model the effect of directional selection on the gene genealogies of neutral markers linked to the selected mutant. The frequency trajectory of the selected allele follows the Wright-Fisher model. Given the position of the selected mutant, we propose a simplified multilocus haplotype model that can efficiently model the dynamics of the ancestral haplotypes under the joint influence of selection and recombination. This model approximates the ancestral genealogies of the sample, which reduces the number of states from an exponential function of the number of single-nucleotide polymorphism loci to a quadratic function. That allows parameter inference from data covering DNA regions as large as several hundred kilo-bases. Importance sampling algorithms are adopted to evaluate the probability of a sample by exploring the space of both allele frequency trajectories of the selected mutation and gene genealogies of the linked sites. We demonstrate by simulation that the method can accurately estimate selection intensity for moderate and strong positive selection. We apply the method to a data set of the G6PD gene in an African population and obtain an estimate of 0.0456 (95% confidence interval 0.0144−0.0769) for the selection intensity. The proposed method is novel in jointly modeling the multilocus haplotype pattern caused by recombination and mutation, allowing the analysis of haplotype data in recombining regions. Moreover, the method is applicable to data from populations under exponential growth and a variety of other demographic histories. PMID:23797107

  20. CYP2D6*4 Allele Polymorphism Increases the Risk of Parkinson’s Disease: Evidence from Meta-Analysis

    PubMed Central

    Chen, Siyuan; Xie, Yantong; Peng, Qiliu; He, Yu; Deng, Yan; Wang, Jian; Xie, Li; Zeng, Jie; Li, Shan; Qin, Xue

    2013-01-01

    Background Many epidemiological studies have been conducted to explore the association between a single CYP2D6 gene polymorphism and Parkinson’s disease (PD) susceptibility. However, the results remain controversial. Objectives To clarify the effects of a single CYP2D6 gene polymorphism on the risk of PD, a meta-analysis of all available studies relating to CYP2D6*4 polymorphism and the risk of PD was conducted. Methods A comprehensive literature search of PubMed, EMBASE, and the China National Knowledge Infrastructure (CNKI) up to September 1, 2013 was conducted. Data were extracted by two independent authors and pooled odds ratio (OR) with 95% confidence interval (CI) were calculated. Meta-regression, Galbraith plots, subgroup analysis, sensitivity analysis, and publication bias analysis were also performed. Results Twenty-two separate comparisons consisting of 2,629 patients and 3,601 controls were included in our meta-analysis. The pooled analyses showed a significant association between CYP2D6*4G/A polymorphism and PD risk in all of the comparisons (A vs. G allele: OR = 1.28, 95% CI = 1.14–1.43, P = 0.001; AA vs. GG: OR = 1.43, 95% CI = 1.06–1.93, P = 0.018; AG vs. GG: OR = 1.22, 95% CI = 1.06–1.40, P = 0.006; AG+AA vs. GG: OR = 1.26, 95% CI = 1.10–1.44, P = 0.001; AA vs. AG+GG: OR = 1.37, 95% CI = 1.02–1.83, P = 0.036). In subgroup analysis stratified by ethnicity, significant associations were also demonstrated in Caucasians but not in Asians. No significant association was found in subgroup analysis stratified by age of onset or disease form. Conclusions We concluded that the CYP2D6*4G/A polymorphism denotes an increased genetic susceptibility to PD in the overall population, especially in Caucasians. Further large and well-designed studies are needed to confirm this association. PMID:24376807

  1. 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

  2. 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. PMID:24704073

  3. The Joint Allele-Frequency Spectrum in Closely Related Species

    PubMed Central

    Chen, Hua; Green, Richard E.; Pääbo, Svante; Slatkin, Montgomery

    2007-01-01

    We develop the theory for computing the joint frequency spectra of alleles in two closely related species. We allow for arbitrary population growth in both species after they had a common ancestor. We focus on the case in which a single chromosome is sequenced from one of the species. We use classical diffusion theory to show that, if the ancestral species was at equilibrium under mutation and drift and a chromosome from one of the descendant species carries the derived allele, the frequency spectrum in the other species is uniform, independently of the demographic history of both species. We also predict the expected densities of segregating and fixed sites when the chromosome from the other species carries the ancestral allele. We compare the predictions of our model with the site-frequency spectra of SNPs in the four HapMap populations of humans when the nucleotide present in the Neanderthal DNA sequence is ancestral or derived, using the chimp genome as the outgroup. PMID:17603120

  4. FKBP5 risk alleles and the development of intrusive memories.

    PubMed

    Cheung, Jessica; Bryant, Richard A

    2015-11-01

    Intrusive memories are unwanted recollections that maintain distress and are central to numerous psychological disorders, including posttraumatic stress disorder (PTSD). Convergent evidence suggests that glucocorticoid increases enhance the strength of emotional memories. The FKBP5 polymorphism modulates glucocorticoid receptor sensitivity, and has been shown to increase risk for PTSD. Healthy high and low risk FKBP5 allele carriers (N=46) underwent a cold pressor task, and then viewed negative and neutral images. Two days later participants were given a surprise recall test and measure of intrusive memories of the images. Following the cold pressor task, high-risk allele participants had a higher cortisol response than low-risk participants. High-risk carriers also reported more intrusive memories of the negative and neutral images than low-risk carriers. These findings point to the minor alleles of the FKBP5 polymorphism being a risk factor for development of intrusive memories, possibly as a result of impaired glucocorticoid receptor sensitivity. This may explain one mechanism for FKBP5 being a risk factor for PTSD following traumatic events.

  5. 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.

  6. 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.

  7. 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.

  8. A Recipe for Ratio

    ERIC Educational Resources Information Center

    Moffett, Pamela

    2012-01-01

    Many learners still struggled to appreciate, and understand the difference between, the concepts of fractions and ratio. This is not just a UK phenomenon, which is demonstrated here by the use of a resource developed by the Wisconsin Centre for Education, in association with the Freudenthal Institute of the University of Utrecht, with a group of…

  9. Area Ratios of Quadrilaterals.

    ERIC Educational Resources Information Center

    Anderson, David R.; Arcidiacono, Michael J.

    1989-01-01

    Shows that the ratio of the area of the quadrilateral formed by joining the kth points to the area of the original quadrilateral is constant whether it is convex or concave quadrilateral. Presents many geoboard or dot paper diagrams and geometrical expresssions. (YP)

  10. 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.

  11. Power of IRT in GWAS: successful QTL mapping of sum score phenotypes depends on interplay between risk allele frequency, variance explained by the risk allele, and test characteristics.

    PubMed

    van den Berg, Stéphanie M; Service, Susan K

    2012-12-01

    As data from sequencing studies in humans accumulate, rare genetic variants influencing liability to disease and disorders are expected to be identified. Three simulation studies show that characteristics and properties of diagnostic instruments interact with risk allele frequency to affect the power to detect a quantitative trait locus (QTL) based on a test score derived from symptom counts or questionnaire items. Clinical tests, that is, tests that show a positively skewed phenotypic sum score distribution in the general population, are optimal to find rare risk alleles of large effect. Tests that show a negatively skewed sum score distribution are optimal to find rare protective alleles of large effect. For alleles of small effect, tests with normally distributed item parameters give best power for a wide range of allele frequencies. The item-response theory framework can help understand why an existing measurement instrument has more power to detect risk alleles with either low or high frequency, or both kinds.

  12. 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.

  13. 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…

  14. C P -odd invariants for multi-Higgs models: Applications with discrete symmetry

    NASA Astrophysics Data System (ADS)

    de Medeiros Varzielas, Ivo; King, Stephen F.; Luhn, Christoph; Neder, Thomas

    2016-09-01

    C P -odd invariants provide a basis independent way of studying the C P properties of Lagrangians. We propose powerful methods for constructing basis invariants and determining whether they are C P odd or C P even, then systematically construct all of the simplest C P -odd invariants up to a given order, finding many new ones. The C P -odd invariants are valid for general potentials when expressed in a standard form. We then apply our results to scalar potentials involving three (or six) Higgs fields which form irreducible triplets under a discrete symmetry, including invariants for both explicit as well as spontaneous C P violation. The considered cases include one triplet of Standard Model (SM) gauge singlet scalars, one triplet of SM Higgs doublets, two triplets of SM singlets, and two triplets of SM Higgs doublets. For each case, we study the potential symmetric under one of the simplest discrete symmetries with irreducible triplet representations, namely A4, S4, Δ (27 ) or Δ (54 ), as well as the infinite classes of discrete symmetries Δ (3 n2) or Δ (6 n2).

  15. Symptom Prevalence of ADHD and ODD in a Pediatric Population in Argentina

    ERIC Educational Resources Information Center

    Michanie, Claudio; Kunst, Gabriel; Margulies, Daniel S.; Yakhkind, Aleksandra

    2007-01-01

    Objective: To assess the prevalence of DSM III-R symptoms of attention deficit hyperactivity disorder (ADHD) and oppositional defiant disorder (ODD) in an outpatient pediatric population; to compare oppositional behavior and grade retention rates; and to establish local means and standard deviations (SD) for the ADHD rating scale. Method: 300…

  16. 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

  17. Odd-even staggering of binding energy for nuclei in the s d shell

    NASA Astrophysics Data System (ADS)

    Fu, G. J.; Cheng, Y. Y.; Jiang, H.; Zhao, Y. M.; Arima, A.

    2016-08-01

    In this paper we study odd-even staggering phenomena of binding energy in the framework of the nuclear shell model for nuclei in the s d shell. We decompose the USDB effective interaction into the monopole interaction and multipole (residual) interactions. We extract the empirical proton-neutron interaction, the Wigner energy, and the one-neutron separation energy using calculated binding energies. The monopole interaction, which represents the spherical mean field, provides contributions to the empirical proton-neutron interaction, the symmetry energy, and the Wigner energy. It does not induce odd-even staggering of the empirical proton-neutron interaction or the one-neutron separation energy. Isovector monopole and quadrupole pairing interactions and isoscalar spin-1 pairing interactions play a key role in reproducing an additional binding energy in both even-even and odd-odd nuclei. The Wigner energy coefficients are sensitive to residual two-body interactions. The nuclear shell structure has a strong influence on the evolution of the one-neutron separation energy, but not on empirical proton-neutron interactions. The so-called three-point formula is a good probe of the shell structure.

  18. 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.)

  19. Beating the Odds Summer School: A Dropout Prevention Program for At-Risk Students (1990).

    ERIC Educational Resources Information Center

    Opuni, Kwame A.; And Others

    The 1990 Beating the Odds (BTO) Summer School was an intensive instructional, counseling, and guidance program sponsored by the Houston (Texas) Independent School District for a group of at-risk students in grades 5-9. The program was designed to provide a supportive and nurturing learning environment in which the academic and sociopsychological…

  20. 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.