Science.gov

Sample records for allelic discrimination method

  1. Exquisite allele discrimination by toehold hairpin primers

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2017-01-01

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

  3. 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.

  4. HLA alleles may serve as a tool to discriminate atypical type 2 diabetic patients

    PubMed Central

    Fernández, Mariana; Fabregat, Matías; Javiel, Gerardo; Mimbacas, Adriana

    2014-01-01

    AIM: To investigate whether the presence of human leukocyte antigen (HLA) marker could add new information to discriminated atypical diabetic type 2 patients. METHODS: We analyzed 199 patients initially diagnosed as type 2 diabetes who are treated in special care diabetes clinics (3rd level). This population was classified in “atypical” (sample A) and “classic” (sample B) according to HLA typing. We consider “classic patient” when has absence of type 1 diabetes associated HLA alleles and no difficulties in their diagnosis and treatments. By the other hand, we considered “atypical patient” when show type 1 diabetes associated HLA alleles and difficulties in their diagnosis and treatments. The standard protocol Asociacion Latinoamericana de Diabetes 2006 was used for patients follow up. To analyze differences between both populations in paraclinical parameters we used unpaired t tests and contingence tables. Bivariate and multivariate analyses were carried out using the SPSS software program. In all studies we assume differences statistically significant, with a P-value < 0.05 corrected and 95%CI. RESULTS: The typing HLA in the “atypical” populations show that 92.47% patients presented at list one type 1 diabetes associated HLA alleles (DQB1*0201-0302 and DR 3-4) and 7.53% had two of its. The results showed for categorical variables (family history, presence or absence of hypertension and/or dyslipidemia, reason for initial consultation) the only difference found was at dyslipidemia (OR = 0.45, 0.243 < OD < 0.822 (P < 0.001). In relation to continuous variables we found significant differences between atypical vs classic only in cholesterol (5.07 ± 1.1 vs 5.56 ± 1.5, P < 0.05), high density lipoproteins (1.23 ± 0.3 vs 1.33 ± 0.3, P < 0.05) and low density lipoproteins (2.86 ± 0.9 vs 3.38 ± 1.7, P < 0.01). None of the variables had discriminating power when logistic regression was done. CONCLUSION: We propose an algorithm including HLA

  5. Hyperspectral data discrimination methods

    NASA Astrophysics Data System (ADS)

    Casasent, David P.; Chen, Xuewen

    2000-12-01

    Hyperspectral data provides spectral response information that provides detailed chemical, moisture, and other description of constituent parts of an item. These new sensor data are useful in USDA product inspection. However, such data introduce problems such as the curse of dimensionality, the need to reduce the number of features used to accommodate realistic small training set sizes, and the need to employ discriminatory features and still achieve good generalization (comparable training and test set performance). Several two-step methods are compared to a new and preferable single-step spectral decomposition algorithm. Initial results on hyperspectral data for good/bad almonds and for good/bad (aflatoxin infested) corn kernels are presented. The hyperspectral application addressed differs greatly from prior USDA work (PLS) in which the level of a specific channel constituent in food was estimated. A validation set (separate from the test set) is used in selecting algorithm parameters. Threshold parameters are varied to select the best Pc operating point. Initial results show that nonlinear features yield improved performance.

  6. Statistical classification methods applied to seismic discrimination

    SciTech Connect

    Ryan, F.M.; Anderson, D.N.; Anderson, K.K.; Hagedorn, D.N.; Higbee, K.T.; Miller, N.E.; Redgate, T.; Rohay, A.C.

    1996-06-11

    To verify compliance with a Comprehensive Test Ban Treaty (CTBT), low energy seismic activity must be detected and discriminated. Monitoring small-scale activity will require regional (within {approx}2000 km) monitoring capabilities. This report provides background information on various statistical classification methods and discusses the relevance of each method in the CTBT seismic discrimination setting. Criteria for classification method selection are explained and examples are given to illustrate several key issues. This report describes in more detail the issues and analyses that were initially outlined in a poster presentation at a recent American Geophysical Union (AGU) meeting. Section 2 of this report describes both the CTBT seismic discrimination setting and the general statistical classification approach to this setting. Seismic data examples illustrate the importance of synergistically using multivariate data as well as the difficulties due to missing observations. Classification method selection criteria are presented and discussed in Section 3. These criteria are grouped into the broad classes of simplicity, robustness, applicability, and performance. Section 4 follows with a description of several statistical classification methods: linear discriminant analysis, quadratic discriminant analysis, variably regularized discriminant analysis, flexible discriminant analysis, logistic discriminant analysis, K-th Nearest Neighbor discrimination, kernel discrimination, and classification and regression tree discrimination. The advantages and disadvantages of these methods are summarized in Section 5.

  7. A novel TaqMAMA assay for allelic discrimination of TLR9 rs352140 polymorphism.

    PubMed

    Bergallo, Massimiliano; Montanari, Paola; Mareschi, Katia; Rassu, Marco; Galliano, Ilaria; Ravanini, Paolo

    2017-05-01

    TaqMAMA is an allele-specific PCR-based (ASPCR) method that may be suitable for broad and cost-effective genotyping applications in all types of laboratories. There is evidence that interactions between some toll like receptors (TLRs) with viruses influence both the immune response and outcome of HCMV infection. We developed a TaqMAMA genotyping assay for the detection of rs352140 TLR9 polymorphism in transplant recipients with and without HCMV infections. Performance parameters to ensure a solid pre-validation protocol have been here argued. We analysed a population of 74 kidney transplants recipients subdivided in 58 HCMV PCR positive and 16 HCMV PCR negative in the post-transplant routine control. All 74 samples were tested with 31/74 (41.9%) homozygotes (11 CC and 20 TT) and 43/74 (58.1%) heterozygotes (CT). Our preliminary data suggest that there is no correlation between TLR9 rs352140 polymorphism and frequency of HCMV infection.

  8. Method for discriminative particle selection

    DOEpatents

    Post, Richard F.

    1992-01-01

    The invention is a method and means for separating ions or providing an ion beam. The invention generates ions of the isotopes to be separated, and then provides a traveling electric potential hill created by a sequential series of quasi static electric potential hills. By regulating the velocity and potential amplitude of the traveling electric potential hill ionized isotopes are selectively positively or negatively accelerated. Since the ionized isotopes have differing final velocities, the isotopes may be collected separately or used to produce an ion beam of a selected isotope.

  9. Non-Equilibrium Allele Frequency Spectra Via Spectral Methods

    PubMed Central

    Hey, Jody; Chen, Kevin

    2011-01-01

    A major challenge in the analysis of population genomics data consists of isolating signatures of natural selection from background noise caused by random drift and gene flow. Analyses of massive amounts of data from many related populations require high-performance algorithms to determine the likelihood of different demographic scenarios that could have shaped the observed neutral single nucleotide polymorphism (SNP) allele frequency spectrum. In many areas of applied mathematics, Fourier Transforms and Spectral Methods are firmly established tools to analyze spectra of signals and model their dynamics as solutions of certain Partial Differential Equations (PDEs). When spectral methods are applicable, they have excellent error properties and are the fastest possible in high dimension; see [15]. In this paper we present an explicit numerical solution, using spectral methods, to the forward Kolmogorov equations for a Wright-Fisher process with migration of K populations, influx of mutations, and multiple population splitting events. PMID:21376069

  10. Discriminant forest classification method and system

    SciTech Connect

    Chen, Barry Y.; Hanley, William G.; Lemmond, Tracy D.; Hiller, Lawrence J.; Knapp, David A.; Mugge, Marshall J.

    2012-11-06

    A hybrid machine learning methodology and system for classification that combines classical random forest (RF) methodology with discriminant analysis (DA) techniques to provide enhanced classification capability. A DA technique which uses feature measurements of an object to predict its class membership, such as linear discriminant analysis (LDA) or Andersen-Bahadur linear discriminant technique (AB), is used to split the data at each node in each of its classification trees to train and grow the trees and the forest. When training is finished, a set of n DA-based decision trees of a discriminant forest is produced for use in predicting the classification of new samples of unknown class.

  11. Novel method for analysis of allele specific expression in triploid Oryzias latipes reveals consistent pattern of allele exclusion.

    PubMed

    Garcia, Tzintzuni I; Matos, Isa; Shen, Yingjia; Pabuwal, Vagmita; Coelho, Maria Manuela; Wakamatsu, Yuko; Schartl, Manfred; Walter, Ronald B

    2014-01-01

    Assessing allele-specific gene expression (ASE) on a large scale continues to be a technically challenging problem. Certain biological phenomena, such as X chromosome inactivation and parental imprinting, affect ASE most drastically by completely shutting down the expression of a whole set of alleles. Other more subtle effects on ASE are likely to be much more complex and dependent on the genetic environment and are perhaps more important to understand since they may be responsible for a significant amount of biological diversity. Tools to assess ASE in a diploid biological system are becoming more reliable. Non-diploid systems are, however, not uncommon. In humans full or partial polyploid states are regularly found in both healthy (meiotic cells, polynucleated cell types) and diseased tissues (trisomies, non-disjunction events, cancerous tissues). In this work we have studied ASE in the medaka fish model system. We have developed a method for determining ASE in polyploid organisms from RNAseq data and we have implemented this method in a software tool set. As a biological model system we have used nuclear transplantation to experimentally produce artificial triploid medaka composed of three different haplomes. We measured ASE in RNA isolated from the livers of two adult, triploid medaka fish that showed a high degree of similarity. The majority of genes examined (82%) shared expression more or less evenly among the three alleles in both triploids. The rest of the genes (18%) displayed a wide range of ASE levels. Interestingly the majority of genes (78%) displayed generally consistent ASE levels in both triploid individuals. A large contingent of these genes had the same allele entirely suppressed in both triploids. When viewed in a chromosomal context, it is revealed that these genes are from large sections of 4 chromosomes and may be indicative of some broad scale suppression of gene expression.

  12. An allele-specific PCR system for rapid detection and discrimination of the CYP2C19∗4A, ∗4B, and ∗17 alleles: implications for clopidogrel response testing.

    PubMed

    Scott, Stuart A; Tan, Qian; Baber, Usman; Yang, Yao; Martis, Suparna; Bander, Jeffrey; Kornreich, Ruth; Hulot, Jean-Sébastien; Desnick, Robert J

    2013-11-01

    CYP2C19 is involved in the metabolism of clinically relevant drugs, including the antiplatelet prodrug clopidogrel, which has prompted interest in clinical CYP2C19 genotyping. The CYP2C19∗4B allele is defined by both gain-of-function [c.-806C>T (∗17)] and loss-of-function [c.1A>G (∗4)] variants on the same haplotype; however, current genotyping and sequencing assays are unable to determine the phase of these variants. Thus, the aim of this study was to develop an assay that could rapidly detect and discriminate the related ∗4A, ∗4B, and ∗17 alleles. An allele-specific PCR assay, composed of four unique primer mixes that specifically interrogate the defining ∗17 and ∗4 variants, was developed by using samples (n = 20) with known genotypes, including the ∗4A, ∗4B, and/or ∗17 alleles. The assay was validated by testing 135 blinded samples, and the results were correlated with CYP2C19 genotyping and allele-specific cloning/sequencing. Importantly, among the six ∗4 carriers in the validation cohort, after allele-specific PCR testing both samples with a ∗1/∗4 genotype were reclassified to ∗1/∗4A, all three samples with a ∗4/∗17 genotype were reclassified to ∗1/∗4B, and a sample with a ∗4/∗17/∗17 genotype was reclassified to ∗4B/∗17. In conclusion, this rapid and robust allele-specific PCR assay can refine CYP2C19 genotyping and metabolizer phenotype classification by determining the phase of the defining ∗17 and ∗4 variants, which may have utility when testing CYP2C19 for clopidogrel response.

  13. Determination of allele frequency in pooled DNA: comparison of three PCR-based methods.

    PubMed

    Wilkening, Stefan; Hemminki, Kari; Thirumaran, Ranjit Kumar; Bermejo, Justo Lorenzo; Bonn, Stefan; Försti, Asta; Kumar, Rajiv

    2005-12-01

    Determination of allele frequency in pooled DNA samples is a powerful and efficient tool for large-scale association studies. In this study, we tested and compared three PCR-based methods for accuracy, reproducibility, cost, and convenience. The methods compared were: (i) real-time PCR with allele-specific primers, (ii) real-time PCR with allele-specific TaqMan probes, and (iii) quantitative sequencing. Allele frequencies of three single nucleotide polymorphisms in three different genes were estimated from pooled DNA. The pools were made of genomic DNA samples from 96 cases with basal cell carcinoma of the skin and 96 healthy controls with known genotypes. In this study, the allele frequency estimation made by real-time PCR with allele-specific primers had the smallest median deviation (MD) from the real allele frequency with 1.12% (absolute percentage points) and was also the cheapest method. However; this method required the most time for optimization and showed the highest variation between replicates (SD = 6.47%). Quantitative sequencing, the simplest method, was found to have intermediate accuracies (MD = 1.44%, SD = 4.2%). Real-time PCR with TaqMan probes, a convenient but very expensive method, had an MD of 1.47% and the lowest variation between replicates (SD = 3.18%).

  14. Comparing two methods of univariate discriminant analysis for sex discrimination in an Iberian population.

    PubMed

    Jiménez-Arenas, Juan Manuel; Esquivel, José Antonio

    2013-05-10

    This study assesses the performance of two analytical approaches to sex discrimination based on single linear variables: discriminant analysis and the Lubischew's test. Ninety individuals from an archaeological population (La Torrecilla-Arenas del Rey, Granada, southern Spain) and 17 craniometrical variables were included in the analyses. Most craniometrical variables were higher for men. The bizygomatic breadth enabled the highest level of discrimination: 87.5% and 88.5%, using discriminant analysis and Lubischew's test, respectively. Bizygomatic breadth proved highly dimorphic in comparison to other populations reported in the literature. Lubischew's test raised the discrimination percentage in specific craniometrical variables, while others showed a superior performance by means of the discriminant analysis. The inconsistent results across statistical methods resulted from the specific formulation of each procedure. Discriminant analysis accounts both for within-group and between-group variance, while Lubischew's test emphasizes between-group variation only. Therefore, both techniques are recommended, as they provide different means of achieving optimal discrimination percentages.

  15. Reliability assessment of null allele detection: inconsistencies between and within different methods.

    PubMed

    Dąbrowski, M J; Pilot, M; Kruczyk, M; Żmihorski, M; Umer, H M; Gliwicz, J

    2014-03-01

    Microsatellite loci are widely used in population genetic studies, but the presence of null alleles may lead to biased results. Here, we assessed five methods that indirectly detect null alleles and found large inconsistencies among them. Our analysis was based on 20 microsatellite loci genotyped in a natural population of Microtus oeconomus sampled during 8 years, together with 1200 simulated populations without null alleles, but experiencing bottlenecks of varying duration and intensity, and 120 simulated populations with known null alleles. In the natural population, 29% of positive results were consistent between the methods in pairwise comparisons, and in the simulated data set, this proportion was 14%. The positive results were also inconsistent between different years in the natural population. In the null-allele-free simulated data set, the number of false positives increased with increased bottleneck intensity and duration. We also found a low concordance in null allele detection between the original simulated populations and their 20% random subsets. In the populations simulated to include null alleles, between 22% and 42% of true null alleles remained undetected, which highlighted that detection errors are not restricted to false positives. None of the evaluated methods clearly outperformed the others when both false-positive and false-negative rates were considered. Accepting only the positive results consistent between at least two methods should considerably reduce the false-positive rate, but this approach may increase the false-negative rate. Our study demonstrates the need for novel null allele detection methods that could be reliably applied to natural populations.

  16. Rapid discrimination of MHC class I and killer cell lectin-like receptor allele variants by high-resolution melt analysis.

    PubMed

    Lundgren, Alyssa; Kim, Sharon; Stadnisky, Michael D; Brown, Michael G

    2012-08-01

    Ly49G and H-2 class I D(k) molecules are critical to natural killer cell-mediated viral control. To examine their contributions in greater depth, we established NK gene complex (NKC)/Ly49 congenic strains and a novel genetic model defined by MHC class I D(k) disparity in congenic and transgenic mouse strains. Generation and maintenance of Ly49 and H-2 class I select strains require efficient and reproducible genotyping assays for highly polygenic and polymorphic sequences. Thus, we coupled gene- and allele-specific PCR with high-resolution melt (HRM) analysis to discriminate Ly49g and H-2 class I D and K alleles in select strains and in the F(2) and backcross hybrid offspring of different genetic crosses. We show that HRM typing for these critical immune response genes is fast, accurate, and dependable. We further demonstrate that H-2 class I D HRM typing is competent to detect and quantify transgene copy numbers in different mice with distinct genetic backgrounds. Our findings substantiate the utility and practicality of HRM genotyping for highly related genes and alleles, even those belonging to clustered multigene families. Based on these findings, we envision that HRM is capable to interrogate and quantify gene- and allele-specific variations due to differential regulation of gene expression.

  17. 'True' null allele detection in microsatellite loci: a comparison of methods, assessment of difficulties and survey of possible improvements.

    PubMed

    Dąbrowski, M J; Bornelöv, S; Kruczyk, M; Baltzer, N; Komorowski, J

    2015-05-01

    Null alleles are alleles that for various reasons fail to amplify in a PCR assay. The presence of null alleles in microsatellite data is known to bias the genetic parameter estimates. Thus, efficient detection of null alleles is crucial, but the methods available for indirect null allele detection return inconsistent results. Here, our aim was to compare different methods for null allele detection, to explain their respective performance and to provide improvements. We applied several approaches to identify the 'true' null alleles based on the predictions made by five different methods, used either individually or in combination. First, we introduced simulated 'true' null alleles into 240 population data sets and applied the methods to measure their success in detecting the simulated null alleles. The single best-performing method was ML-NullFreq_frequency. Furthermore, we applied different noise reduction approaches to improve the results. For instance, by combining the results of several methods, we obtained more reliable results than using a single one. Rule-based classification was applied to identify population properties linked to the false discovery rate. Rules obtained from the classifier described which population genetic estimates and loci characteristics were linked to the success of each method. We have shown that by simulating 'true' null alleles into a population data set, we may define a null allele frequency threshold, related to a desired true or false discovery rate. Moreover, using such simulated data sets, the expected null allele homozygote frequency may be estimated independently of the equilibrium state of the population.

  18. Comparison of high-resolution melting analysis, TaqMan Allelic discrimination assay, and sanger sequencing for Clopidogrel efficacy genotyping in routine molecular diagnostics.

    PubMed

    Zhang, Lina; Cui, Guanglin; Li, Zongzhe; Wang, Haoran; Ding, Hu; Wang, Dao Wen

    2013-09-01

    Clopidogrel, as a routine antiplatelet drug, is widely used in patients to reduce cardiovascular events following percutaneous coronary intervention. Because of genetic variation, patients undergoing percutaneous coronary intervention show differing responses to clopidogrel therapy. Recently, five single nucleotide polymorphisms (SNPs) within CYP2C19 (rs4244285, rs4986893, rs12248560), ABCB1 (rs1045642), and ITGB3 (rs5918) were identified that contribute prominently to variability in response to clopidogrel. Given that Sanger sequencing is labor intensive and time consuming, rapid genotyping methods for SNP detection are urgently required before clopidogrel therapy. Accordingly, we developed a high-resolution melting analysis (HRMA) and TaqMan allelic discrimination assay (TaqMan) to genotype those five SNPs, and compared these two assays with Sanger sequencing on accuracy of genotyping as well as operational characteristics. These two assays showed high accuracy (0.995, 95% CI 0.991 to 0.998 for HRMA; 0.997, 95% CI 0.994 to 0.999 for TaqMan, respectively), sensitivity (0.996, 95% CI 0.989 to 1.002 for HRMA; 0.998, 95% CI 0.993 to 1.002 for TaqMan, respectively), and specificity (0.995, 95% CI 0.991 to 0.999 for HRMA; 0.996, 95% CI 0.993 to 1.000 for TaqMan, respectively). Our study indicates that HRMA and TaqMan are easier to operate and obviously faster than Sanger sequencing. In conclusion, HRMA and TaqMan are rapid, convenient, and reliable assays for clopidogrel efficacy genotyping.

  19. Comparison of allelic discrimination by dHPLC, HRM, and TaqMan in the detection of BRAF mutation V600E.

    PubMed

    Carbonell, Pablo; Turpin, María C; Torres-Moreno, Daniel; Molina-Martínez, Irene; García-Solano, José; Perez-Guillermo, Miguel; Conesa-Zamora, Pablo

    2011-09-01

    The V600E mutation in the BRAF oncogene is associated with colorectal carcinomas, with mismatch-repair deficiency and, recently, with nonresponse to epidermal growth factor receptor inhibitor therapy. The use of reliable techniques for its detection is important. The aim of our study was to compare the performance characteristics in V600E detection of denaturing high-performance liquid chromatography (dHPLC) and high-resolution melting (HRM) with TaqMan allelic discrimination as well as direct-sequencing methods in a series of 195 colorectal paraffin-embedded specimens up to the age of 15 years. The effectiveness for obtaining results on mutation status was best using TaqMan (96.9%), followed by dHPLC (93.3%), HRM (88.7%), and sequencing (88.2%). In general, TaqMan was best for analyzing older tissues, whereas sequencing was the least efficient. Heterozygotic V600E was detected in 11.6%, 9.9%, 11.6%, and 9.9% of tissues using TaqMan, dHPLC, HRM, and sequencing, respectively. Result concordances between dHPLC and TaqMan or sequencing were excellent (κ = 0.9411 and κ = 0.8988, respectively); for HRM, the concordances were good (κ = 0.7973 and κ = 0.7488, respectively). By using DNA dilutions from tumor tissue, a minimum of 10% of V600E harboring cancer content was required for the analysis by dHPLC and HRM. dHPLC could detect four non-V600E mutations, whereas HRM detected one. Our results indicate that dHPLC and HRM are techniques that can be reliably used for the detection of the BRAFV600E mutation in archival paraffin-embedded tissues.

  20. Graphical methods for the sensitivity analysis in discriminant analysis

    DOE PAGES

    Kim, Youngil; Anderson-Cook, Christine M.; Dae-Heung, Jang

    2015-09-30

    Similar to regression, many measures to detect influential data points in discriminant analysis have been developed. Many follow similar principles as the diagnostic measures used in linear regression in the context of discriminant analysis. Here we focus on the impact on the predicted classification posterior probability when a data point is omitted. The new method is intuitive and easily interpretative compared to existing methods. We also propose a graphical display to show the individual movement of the posterior probability of other data points when a specific data point is omitted. This enables the summaries to capture the overall pattern ofmore » the change.« less

  1. Graphical methods for the sensitivity analysis in discriminant analysis

    SciTech Connect

    Kim, Youngil; Anderson-Cook, Christine M.; Dae-Heung, Jang

    2015-09-30

    Similar to regression, many measures to detect influential data points in discriminant analysis have been developed. Many follow similar principles as the diagnostic measures used in linear regression in the context of discriminant analysis. Here we focus on the impact on the predicted classification posterior probability when a data point is omitted. The new method is intuitive and easily interpretative compared to existing methods. We also propose a graphical display to show the individual movement of the posterior probability of other data points when a specific data point is omitted. This enables the summaries to capture the overall pattern of the change.

  2. Efficient Simulation and Likelihood Methods for Non-Neutral Multi-Allele Models

    PubMed Central

    Joyce, Paul; Genz, Alan

    2012-01-01

    Abstract Throughout the 1980s, Simon Tavaré made numerous significant contributions to population genetics theory. As genetic data, in particular DNA sequence, became more readily available, a need to connect population-genetic models to data became the central issue. The seminal work of Griffiths and Tavaré (1994a, 1994b, 1994c) was among the first to develop a likelihood method to estimate the population-genetic parameters using full DNA sequences. Now, we are in the genomics era where methods need to scale-up to handle massive data sets, and Tavaré has led the way to new approaches. However, performing statistical inference under non-neutral models has proved elusive. In tribute to Simon Tavaré, we present an article in spirit of his work that provides a computationally tractable method for simulating and analyzing data under a class of non-neutral population-genetic models. Computational methods for approximating likelihood functions and generating samples under a class of allele-frequency based non-neutral parent-independent mutation models were proposed by Donnelly, Nordborg, and Joyce (DNJ) (Donnelly et al., 2001). DNJ (2001) simulated samples of allele frequencies from non-neutral models using neutral models as auxiliary distribution in a rejection algorithm. However, patterns of allele frequencies produced by neutral models are dissimilar to patterns of allele frequencies produced by non-neutral models, making the rejection method inefficient. For example, in some cases the methods in DNJ (2001) require 109 rejections before a sample from the non-neutral model is accepted. Our method simulates samples directly from the distribution of non-neutral models, making simulation methods a practical tool to study the behavior of the likelihood and to perform inference on the strength of selection. PMID:22697240

  3. Regularized discriminative spectral regression method for heterogeneous face matching.

    PubMed

    Huang, Xiangsheng; Lei, Zhen; Fan, Mingyu; Wang, Xiao; Li, Stan Z

    2013-01-01

    Face recognition is confronted with situations in which face images are captured in various modalities, such as the visual modality, the near infrared modality, and the sketch modality. This is known as heterogeneous face recognition. To solve this problem, we propose a new method called discriminative spectral regression (DSR). The DSR maps heterogeneous face images into a common discriminative subspace in which robust classification can be achieved. In the proposed method, the subspace learning problem is transformed into a least squares problem. Different mappings should map heterogeneous images from the same class close to each other, while images from different classes should be separated as far as possible. To realize this, we introduce two novel regularization terms, which reflect the category relationships among data, into the least squares approach. Experiments conducted on two heterogeneous face databases validate the superiority of the proposed method over the previous methods.

  4. Discriminant power analyses of non-linear dimension expansion methods

    NASA Astrophysics Data System (ADS)

    Woo, Seongyoun; Lee, Chulhee

    2016-05-01

    Most non-linear classification methods can be viewed as non-linear dimension expansion methods followed by a linear classifier. For example, the support vector machine (SVM) expands the dimensions of the original data using various kernels and classifies the data in the expanded data space using a linear SVM. In case of extreme learning machines or neural networks, the dimensions are expanded by hidden neurons and the final layer represents the linear classification. In this paper, we analyze the discriminant powers of various non-linear classifiers. Some analyses of the discriminating powers of non-linear dimension expansion methods are presented along with a suggestion of how to improve separability in non-linear classifiers.

  5. A Data Transfer Fusion Method for Discriminating Similar Spectral Classes

    PubMed Central

    Wang, Qingyan; Zhang, Junping

    2016-01-01

    Hyperspectral data provide new capabilities for discriminating spectrally similar classes, but such class signatures sometimes will be difficult to analyze. To incorporate reliable useful information could help, but at the same time, may also lead increased dimensionality of the feature vector making the hyperspectral data larger than expected. It is challenging to apply discriminative information from these training data to testing data that are not in the same feature space and with different data distributions. A data fusion method based on transfer learning is proposed, in which transfer learning is introduced into boosting algorithm, and other out-date data are used to instruct hyperspectral image classification. In order to validate the method, experiments are conducted on EO-1 Hyperion hyperspectral data and ROSIS hyperspectral data. Significant improvements have been achieved in terms of accuracy compared to the results generated by conventional classification approaches. PMID:27854238

  6. A U-235 confirmation method with a discriminating view

    SciTech Connect

    McLaughlin, G.D.; Hartwell, J.K.; Reed, B.M.

    1998-09-01

    Reprocessed spent nuclear fuel that has gone through various stages of chemical processing is currently stored at the INEEL. The material consists of three categories: clean U-235 with radiation readings in the mR/h range, U-235 and fission products up to 900 mR/h, and U-235 with U-232 from 100--200 mR/h. The material is contained in plastic bottles and stored in steel structures consisting of seven vertically arranged individual compartments. A total of forty stacks reside in individual concrete wells. This material is considered hard to measure due to excessive radiation exposure to personnel involved with handling the material during mass and NaI U-235 confirmation measurements for Safeguards inventory purposes. A U-235 confirmation method was developed to assay the individual items in place with the ability to discriminate one item from the other items in the stack. Equipment used with this method includes a portable high-resolution gamma-ray detection system, an appropriate tungsten shield and collimator, and a laser-positioning device. A discrimination control test was incorporated to compare the gamma-ray signal of an item in place to the background signal when the item is removed. Total discrimination of the 186-keV gamma ray signal was achieved.

  7. Discrimination of inflammatory bowel disease using Raman spectroscopy and linear discriminant analysis methods

    NASA Astrophysics Data System (ADS)

    Ding, Hao; Cao, Ming; DuPont, Andrew W.; Scott, Larry D.; Guha, Sushovan; Singhal, Shashideep; Younes, Mamoun; Pence, Isaac; Herline, Alan; Schwartz, David; Xu, Hua; Mahadevan-Jansen, Anita; Bi, Xiaohong

    2016-03-01

    Inflammatory bowel disease (IBD) is an idiopathic disease that is typically characterized by chronic inflammation of the gastrointestinal tract. Recently much effort has been devoted to the development of novel diagnostic tools that can assist physicians for fast, accurate, and automated diagnosis of the disease. Previous research based on Raman spectroscopy has shown promising results in differentiating IBD patients from normal screening cases. In the current study, we examined IBD patients in vivo through a colonoscope-coupled Raman system. Optical diagnosis for IBD discrimination was conducted based on full-range spectra using multivariate statistical methods. Further, we incorporated several feature selection methods in machine learning into the classification model. The diagnostic performance for disease differentiation was significantly improved after feature selection. Our results showed that improved IBD diagnosis can be achieved using Raman spectroscopy in combination with multivariate analysis and feature selection.

  8. Simple and sensitive method for identification of human DNA by allele-specific polymerase chain reaction of FOXP2.

    PubMed

    Hiroshige, Kenichi; Soejima, Mikiko; Nishioka, Tomoki; Kamimura, Shigeo; Koda, Yoshiro

    2009-07-01

    The forkhead box P2 (FOXP2) gene is specifically involved in speech and language development in humans. The sequence is well conserved among many vertebrate species but has accumulated amino acid changes in the human lineage. The aim of this study was to develop a simple method to discriminate between human and nonhuman vertebrate DNA in forensic specimens by amplification of a human-specific genomic region. In the present study, we designed an allele-specific polymerase chain reaction (PCR) using primers to amplify smaller than 70-bp regions of FOXP2 to identify DNA as being of human or nonhuman, including ape, origin. PCR amplification was also successfully performed using fluorescence-labeled primers, and this method allows a single PCR reaction with a genomic DNA sample as small as 0.01 ng. This system also identified the presence of human DNA in two blood stains stored for 20 and 38 years. The results suggested the potential usefulness of FOXP2 as an identifier of human DNA in forensic samples.

  9. A comparison of stimulus presentation methods in temporal discrimination testing.

    PubMed

    Mc Govern, Eavan M; Butler, John S; Beiser, Ines; Williams, Laura; Quinlivan, Brendan; Narasiham, Shruti; Beck, Rebecca; O'Riordan, Sean; Reilly, Richard B; Hutchinson, Michael

    2017-02-01

    The temporal discrimination threshold (TDT) is the shortest time interval at which an individual detects two stimuli to be asynchronous (normal  =  30-50 ms). It has been shown to be abnormal in patients with disorders affecting the basal ganglia including adult onset idiopathic focal dystonia (AOIFD). Up to 97% of patients have an abnormal TDT with age- and sex-related penetrance in unaffected relatives, demonstrating an autosomal dominant inheritance pattern. These findings support the use of the TDT as a pre-clinical biomarker for AOIFD. The usual stimulus presentation method involves the presentation of progressively asynchronous stimuli; when three sequential stimuli are reported asynchronous is taken as a participant's TDT. To investigate the robustness of the 'staircase' method of presentation, we introduced a method of randomised presentation order to explore any potential 'learning effect' that may be associated with this existing method. The aim of this study was to investigate differences in temporal discrimination using two methods of stimulus presentation. Thirty healthy volunteers were recruited to the study (mean age 33.73  ±  3.4 years). Visual and tactile TDT testing using a staircase and randomised method of presentation order was carried out in a single session. There was a strong relationship between the staircase and random method for TDT values. This observed consistency between testing methods suggests that the existing experimental approach is a robust method of recording an individual's TDT. In addition, our newly devised randomised paradigm is a reproducible and more efficient method for data acquisition in the clinic setting. However, the two presentation methods yield different absolute TDT results and either of the two methods should be used uniformly in all participants in any one particular study.

  10. Absolute quantification of the alleles in somatic point mutations by bioluminometric methods based on competitive polymerase chain reaction in the presence of a locked nucleic acid blocker or an allele-specific primer.

    PubMed

    Iliadi, Alexandra; Petropoulou, Margarita; Ioannou, Penelope C; Christopoulos, Theodore K; Anagnostopoulos, Nikolaos I; Kanavakis, Emmanuel; Traeger-Synodinos, Jan

    2011-09-01

    In somatic (acquired) point mutations, the challenge is to quantify minute amounts of the mutant allele in the presence of a large excess of the normal allele that differs only in a single base pair. We report two bioluminometric methods that enable absolute quantification of the alleles. The first method exploits the ability of a locked nucleic acid (LNA) oligonucleotide to bind to and inhibit effectively the polymerase chain reaction (PCR) amplification of the normal allele while the amplification of the mutant allele remains unaffected. The second method employs allele-specific PCR primers, thereby allowing the amplification of the corresponding allele only. DNA internal standards (competitors) are added to the PCR mixture to compensate for any sample-to-sample variation in the amplification efficiency. The amplification products from the two alleles and the internal standards are quantified by a microtiter well-based bioluminometric hybridization assay using the photoprotein aequorin as a reporter. The methods allow absolute quantification of less than 300 copies of the mutant allele even in samples containing less than 1% of the mutant allele.

  11. 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

  12. Discriminative detection of low-abundance point mutations using a PCR/ligase detection reaction/capillary gel electrophoresis method and fluorescence dual-channel monitoring.

    PubMed

    Hamada, Mariko; Shimase, Koji; Tsukagoshi, Kazuhiko; Hashimoto, Masahiko

    2014-04-01

    We applied a facile LIF dual-channel monitoring system recently developed and reported by our group to the polymerase chain reaction/ligase detection reaction/CGE method for detecting low-abundance point mutations present in a wild-type sequence-dominated population. Mutation discrimination limits and signaling fidelity of the analytical system were evaluated using three mutant variations in codon 12 of the K-ras oncogene that have high diagnostic value for colorectal cancer. We demonstrated the high sensitivity of the present method by detecting rare mutations present among an excess of wild-type alleles (one mutation among ~100 normal sequences). This method also simultaneously interrogated the allelic compositions of the test samples with high specificity through spectral discrimination of the dye-tagged ligase detection reaction products using the dual-channel monitoring system.

  13. Spatial discrimination and visual discrimination: two methods evaluating learning and memory in juvenile Göttingen minipigs.

    PubMed

    Haagensen, Annika M J; Grand, Nanna; Klastrup, Signe; Skytte, Christina; Sørensen, Dorte B

    2013-06-01

    Two methods investigating learning and memory in juvenile Göttingen minipigs were evaluated for potential use in preclinical toxicity testing. Twelve minipigs were tested using a spatial hole-board discrimination test including a learning phase and two memory phases. Five minipigs were tested in a visual discrimination test. The juvenile minipigs were able to learn the spatial hole-board discrimination test and showed improved working and reference memory during the learning phase. Performance in the memory phases was affected by the retention intervals, but the minipigs were able to remember the concept of the test in both memory phases. Working memory and reference memory were significantly improved in the last trials of the memory phases. In the visual discrimination test, the minipigs learned to discriminate between the three figures presented to them within 9-14 sessions. For the memory test, all minipigs performed 9/12 correct choices or better. Juvenile Göttingen minipigs are able to learn to perform in a spatial hole-board discrimination test as well as in a visual discrimination test, showing an increase in performance over time. Both tests have considerable scope to assess learning and memory of pigs, and we seem to have succeeded in establishing two test systems suitable for performing preclinical toxicity testing in juvenile minipigs.

  14. Discrimination of particulate matter emission sources using stochastic methods

    NASA Astrophysics Data System (ADS)

    Szczurek, Andrzej; Maciejewska, Monika; Wyłomańska, Agnieszka; Sikora, Grzegorz; Balcerek, Michał; Teuerle, Marek

    2016-12-01

    Particulate matter (PM) is one of the criteria pollutants which has been determined as harmful to public health and the environment. For this reason the ability to recognize its emission sources is very important. There are a number of measurement methods which allow to characterize PM in terms of concentration, particles size distribution, and chemical composition. All these information are useful to establish a link between the dust found in the air, its emission sources and influence on human as well as the environment. However, the methods are typically quite sophisticated and not applicable outside laboratories. In this work, we considered PM emission source discrimination method which is based on continuous measurements of PM concentration with a relatively cheap instrument and stochastic analysis of the obtained data. The stochastic analysis is focused on the temporal variation of PM concentration and it involves two steps: (1) recognition of the category of distribution for the data i.e. stable or the domain of attraction of stable distribution and (2) finding best matching distribution out of Gaussian, stable and normal-inverse Gaussian (NIG). We examined six PM emission sources. They were associated with material processing in industrial environment, namely machining and welding aluminum, forged carbon steel and plastic with various tools. As shown by the obtained results, PM emission sources may be distinguished based on statistical distribution of PM concentration variations. Major factor responsible for the differences detectable with our method was the type of material processing and the tool applied. In case different materials were processed by the same tool the distinction of emission sources was difficult. For successful discrimination it was crucial to consider size-segregated mass fraction concentrations. In our opinion the presented approach is very promising. It deserves further study and development.

  15. A maximum-likelihood method to correct for allelic dropout in microsatellite data with no replicate genotypes.

    PubMed

    Wang, Chaolong; Schroeder, Kari B; Rosenberg, Noah A

    2012-10-01

    Allelic dropout is a commonly observed source of missing data in microsatellite genotypes, in which one or both allelic copies at a locus fail to be amplified by the polymerase chain reaction. Especially for samples with poor DNA quality, this problem causes a downward bias in estimates of observed heterozygosity and an upward bias in estimates of inbreeding, owing to mistaken classifications of heterozygotes as homozygotes when one of the two copies drops out. One general approach for avoiding allelic dropout involves repeated genotyping of homozygous loci to minimize the effects of experimental error. Existing computational alternatives often require replicate genotyping as well. These approaches, however, are costly and are suitable only when enough DNA is available for repeated genotyping. In this study, we propose a maximum-likelihood approach together with an expectation-maximization algorithm to jointly estimate allelic dropout rates and allele frequencies when only one set of nonreplicated genotypes is available. Our method considers estimates of allelic dropout caused by both sample-specific factors and locus-specific factors, and it allows for deviation from Hardy-Weinberg equilibrium owing to inbreeding. Using the estimated parameters, we correct the bias in the estimation of observed heterozygosity through the use of multiple imputations of alleles in cases where dropout might have occurred. With simulated data, we show that our method can (1) effectively reproduce patterns of missing data and heterozygosity observed in real data; (2) correctly estimate model parameters, including sample-specific dropout rates, locus-specific dropout rates, and the inbreeding coefficient; and (3) successfully correct the downward bias in estimating the observed heterozygosity. We find that our method is fairly robust to violations of model assumptions caused by population structure and by genotyping errors from sources other than allelic dropout. Because the data sets

  16. Identification and characterization of novel HLA alleles: Utility of next-generation sequencing methods.

    PubMed

    Brown, Nicholas K; Kheradmand, Taba; Wang, Jinguo; Marino, Susana R

    2016-04-01

    The HLA genes are the most polymorphic of the human genome, and novel HLA alleles are continuously identified, often by clinical Sanger sequencing-based typing (SBT) assays. Introduction of next-generation sequencing (NGS) technologies for clinical HLA typing may significantly improve this process. Here we compare four cases of novel HLA alleles identified and characterized by both SBT and NGS. The tested NGS system sequenced broader regions of the HLA loci, and identified novel polymorphisms undetected by SBT. Subsequent characterization of the novel alleles in isolation of coencoded alleles by SBT required custom-designed primers, while the NGS system was able to sequence both alleles in phase. However, the tested assay was unable to amplify buccal cell DNA for subsequent NGS sequencing, presumably due to the lower quality of these samples. While NGS assays will undoubtedly increase novel allele identification, more stringent DNA sample requirements may be necessary for this new technology.

  17. The free energy method and the Wright-Fisher model with 2 alleles.

    PubMed

    Tran, Tat Dat; Hofrichter, Julian; Jost, Jürgen

    2015-12-01

    We systematically investigate the Wright-Fisher model of population genetics with the free energy functional formalism of statistical mechanics and in the light of recent mathematical work on the connection between Fokker-Planck equations and free energy functionals. In statistical physics, entropy increases, or equivalently, free energy decreases, and the asymptotic state is given by a Gibbs-type distribution. This also works for the Wright-Fisher model when rewritten in divergence to identify the correct free energy functional. We not only recover the known results about the stationary distribution, that is, the asymptotic equilibrium state of the model, in the presence of positive mutation rates and possibly also selection, but can also provide detailed formulae for the rate of convergence towards that stationary distribution. In the present paper, the method is illustrated for the simplest case only, that of two alleles.

  18. Method of Discriminant Gravity Tolerance using Heart Rate Variability

    NASA Astrophysics Data System (ADS)

    Yoshida, Yutaka; Yokoyama, Kiyoko; Takada, Hiroki; Iwase, Satoshi

    When returning on the earth by the space flight, the space deconditioning may be developed. As this countermeasure, the artificial gravity load device using the centrifuge is proposed in the space station. But the gravity load might cause the faint, and safe gravity load is uncertainty. We proposed that discriminate strength of gravity tolerance using heart rate variability time series. Step function was inputted to AR model estimated from heart rate variability time series during rest or under light gravity load, and strength of the gravity tolerance was discriminated by the step response function. On the result, discriminant accuracy was 87.5% by using heart rate variability time series when gravity load of 1.0 G was added to the human lying on the supine. Therefore, possibility of discriminant of gravity tolerance was obtained by using heart rate variability time series when sympathetic hyperactivity. Discriminant of the gravity tolerance is expected before countermeasure of space deconditioning is executed.

  19. 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.

  20. Method and apparatus for sub-hysteresis discrimination

    DOEpatents

    De Geronimo, Gianluigi

    2015-12-29

    Embodiments of comparator circuits are disclosed. A comparator circuit may include a differential input circuit, an output circuit, a positive feedback circuit operably coupled between the differential input circuit and the output circuit, and a hysteresis control circuit operably coupled with the positive feedback circuit. The hysteresis control circuit includes a switching device and a transistor. The comparator circuit provides sub-hysteresis discrimination and high speed discrimination.

  1. Development of a ligase detection reaction/CGE method using a LIF dual-channel detection system for direct identification of allelic composition of mutated DNA in a mixed population of excess wild-type DNA.

    PubMed

    Hamada, Mariko; Shimase, Koji; Noda, Keiichi; Tsukagoshi, Kazuhiko; Hashimoto, Masahiko

    2013-05-01

    We developed an inexpensive LIF dual-channel detection system and applied it to a ligase detection reaction (LDR)/CGE method to identify the allelic composition of low-abundance point mutations in a large excess of wild-type DNA in a single reaction with a high degree of certainty. Ligation was performed in a tube with a nonlabeled common primer and multiplex discriminating primers, each labeled with a different standard fluorophore. The discriminating primers were directed against three mutant variations in codon 12 of the K-ras oncogene that have a high diagnostic value for colorectal cancer. LDR products generated from a particular K-ras mutation through successful ligation events were separated from remaining discriminating primers by CGE, followed by LIF detection using the new system, which consists of two photomultiplier tubes, each with a unique optical filter. Each fluorophore label conjugated to the corresponding LDR product produced a distinct fluorescence signal intensity ratio from the two detection channels, allowing spectral discrimination of the three labels. The ability of this system to detect point mutations in a wild-type sequence-dominated population, and to disclose their allelic composition, was thus demonstrated successfully.

  2. Applications of discriminant analysis methods in medical diagnostics

    NASA Astrophysics Data System (ADS)

    Martyniuk, T. B.; Kupershtein, L. M.; Medvid, A. V.; Kozhemiako, A. V.; Wojcik, W.; Yuchshenko, O.

    2013-01-01

    In this work the process of forming and processing the discriminant functions (DF) on a base of neural network classifier is researched. The research goal is the analysis of simulation educt of the process of the output vector forming appurtenances to certain class for the proposed neural network classifier.

  3. Methods for the Scientific Study of Discrimination and Health: An Ecosocial Approach

    PubMed Central

    2012-01-01

    The scientific study of how discrimination harms health requires theoretically grounded methods. At issue is how discrimination, as one form of societal injustice, becomes embodied inequality and is manifested as health inequities. As clarified by ecosocial theory, methods must address the lived realities of discrimination as an exploitative and oppressive societal phenomenon operating at multiple levels and involving myriad pathways across both the life course and historical generations. An integrated embodied research approach hence must consider (1) the structural level—past and present de jure and de facto discrimination; (2) the individual level—issues of domains, nativity, and use of both explicit and implicit discrimination measures; and (3) how current research methods likely underestimate the impact of racism on health. PMID:22420803

  4. Allele-specific conventional reverse-transcription polymerase chain reaction as a screening assay for discriminating influenza a H1N1 (H275Y) oseltamivir-resistant and wild-type viruses.

    PubMed

    Ngai, Karry L K; Lam, Wai-Yip; Lee, Nelson; Leung, Ting Fan; Hui, David S C; Chan, Paul K S

    2010-08-01

    In early 2008, a sudden increase in oseltamivir (Tamiflu)-resistant influenza A H1N1 viruses was reported from several European countries. This resistant virus has spread globally and accounted for more than 95% of H1N1 viruses isolated in the following influenza season. A continuous close monitoring on the prevalence of this resistant virus is necessary to rationalize the choice of antiviral agents. The resistance of this novel strain to oseltamivir is conferred by an amino acid substitution from histidine to tyrosine at position 275 (H275Y) of the neuraminidase protein. This study developed and evaluated allele-specific conventional reverse-transcription polymerase chain reaction (cRT-PCR) assays to provide a simple, rapid, and low-cost option for discriminating oseltamivir-resistant influenza A H1N1 (H275Y) mutant from wild-type viruses. The evaluation was based on 90 nasopharyngeal aspirate specimens collected before, during the initial phase and at the peak of emergence of resistance. Thirty-six (40%) of these specimens were H275Y mutant, whereas the other 54 (60%) were wild-type viruses as confirmed by sequencing of the neuraminidase gene. When applied directly on the 90 nasopharyngeal aspirate specimens, the allele-specific cRT-PCR assays achieved an unequivocal discrimination for 82 (91%) specimens. Further improvement in performance is expected when applied to cell culture isolates with a higher viral titer. These allele-specific cRT-PCR assays can be a simple, low-cost option for large-scale screening of influenza isolates.

  5. Fast discrimination of hydroxypropyl methyl cellulose using portable Raman spectrometer and multivariate methods

    NASA Astrophysics Data System (ADS)

    Song, Biao; Lu, Dan; Peng, Ming; Li, Xia; Zou, Ye; Huang, Meizhen; Lu, Feng

    2017-02-01

    Raman spectroscopy is developed as a fast and non-destructive method for the discrimination and classification of hydroxypropyl methyl cellulose (HPMC) samples. 44 E series and 41 K series of HPMC samples are measured by a self-developed portable Raman spectrometer (Hx-Raman) which is excited by a 785 nm diode laser and the spectrum range is 200-2700 cm-1 with a resolution (FWHM) of 6 cm-1. Multivariate analysis is applied for discrimination of E series from K series. By methods of principal components analysis (PCA) and Fisher discriminant analysis (FDA), a discrimination result with sensitivity of 90.91% and specificity of 95.12% is achieved. The corresponding receiver operating characteristic (ROC) is 0.99, indicting the accuracy of the predictive model. This result demonstrates the prospect of portable Raman spectrometer for rapid, non-destructive classification and discrimination of E series and K series samples of HPMC.

  6. Automated fine structure image analysis method for discrimination of diabetic retinopathy stage using conjunctival microvasculature images

    PubMed Central

    Khansari, Maziyar M; O’Neill, William; Penn, Richard; Chau, Felix; Blair, Norman P; Shahidi, Mahnaz

    2016-01-01

    The conjunctiva is a densely vascularized mucus membrane covering the sclera of the eye with a unique advantage of accessibility for direct visualization and non-invasive imaging. The purpose of this study is to apply an automated quantitative method for discrimination of different stages of diabetic retinopathy (DR) using conjunctival microvasculature images. Fine structural analysis of conjunctival microvasculature images was performed by ordinary least square regression and Fisher linear discriminant analysis. Conjunctival images between groups of non-diabetic and diabetic subjects at different stages of DR were discriminated. The automated method’s discriminate rates were higher than those determined by human observers. The method allowed sensitive and rapid discrimination by assessment of conjunctival microvasculature images and can be potentially useful for DR screening and monitoring. PMID:27446692

  7. Plethysmographic arterial waveform strain discrimination by Fisher's method.

    PubMed

    Kucewicz, John C; Huang, Lingyun; Beach, Kirk W

    2004-06-01

    Plethysmography has been used for over 50 years to measure gross change in tissue blood volume. Over the cardiac cycle, perfused tissue initially expands as the blood flow into the arterioles exceeds the flow through the capillary bed. Later in the cardiac cycle, the accumulated blood drains into the venous vasculature, allowing the tissue to return to its presystolic blood volume. Specific features in the plethysmographic waveform can be used to identify normal and abnormal perfusion. We are developing a Doppler strain-imaging technique to measure the local pulsatile expansion and relaxation of tissue analogous to the gross measurement of tissue volume change with conventional plethysmography. A phantom has been built to generate plethysmographic-style strains with amplitudes of less than 0.1% in a tissue-mimicking material. With Fisher's discriminant analysis, it is shown that normal and abnormal plethysmographic-style strains can be differentiated with high sensitivities using the Fourier components of the strain waveforms normalized to compensate for the variance in the strain amplitude estimate.

  8. Analytical Methods for Discriminating Stardust in Aerogel Capture Media

    SciTech Connect

    Brennan, S; Ishii, H A; Bradley, J P; Luening, K; Ignatyev, K; Pianetta, P

    2007-09-04

    Comet 81P/Wild 2's serendipitous orbit change to the inner solar system in 1974 offered researchers a rare opportunity to sample cometary material from the Kuiper belt, a repository of material left over from solar system formation {approx}4.6 Gyr ago. NASA's Stardust mission intercepted the comet in January 2004 and returned with material collected from its tail in January 2006. The cometary material, consisting of particles ranging from 10 microns down to <2 nm, was collected in aerogel, a very low density ({approx}3 mg/cm cm3) silica foam, to minimize the effects of deceleration from 6.1 km/s. The entire deceleration track is extracted from the aerogel block as a pyramidal shape known as a keystone which can be mapped using x-ray fluorescence prior to extraction of terminal or intermediate particles for other analyses. One goal of the track mapping is to determine the bulk composition of the cometary material returned. Unfortunately, although the aerogel is predominantly SiO{sub 2}, there are sufficient quantities of trace elements similar to those expected in the cometary material to require sophisticated discrimination techniques in order to decide whether a fluorescence map pixel contains only aerogel or both aerogel and cometary material. We have developed a dual threshold analysis approach for better distinguishing cometary material from aerogel contaminants and have applied it to five Stardust impact tracks and terminal particles. Here, we present aspects of the dual threshold approach and demonstrate its impact on track composition for one track.

  9. Comparison of discriminant analysis methods: Application to occupational exposure to particulate matter

    NASA Astrophysics Data System (ADS)

    Ramos, M. Rosário; Carolino, E.; Viegas, Carla; Viegas, Sandra

    2016-06-01

    Health effects associated with occupational exposure to particulate matter have been studied by several authors. In this study were selected six industries of five different areas: Cork company 1, Cork company 2, poultry, slaughterhouse for cattle, riding arena and production of animal feed. The measurements tool was a portable device for direct reading. This tool provides information on the particle number concentration for six different diameters, namely 0.3 µm, 0.5 µm, 1 µm, 2.5 µm, 5 µm and 10 µm. The focus on these features is because they might be more closely related with adverse health effects. The aim is to identify the particles that better discriminate the industries, with the ultimate goal of classifying industries regarding potential negative effects on workers' health. Several methods of discriminant analysis were applied to data of occupational exposure to particulate matter and compared with respect to classification accuracy. The selected methods were linear discriminant analyses (LDA); linear quadratic discriminant analysis (QDA), robust linear discriminant analysis with selected estimators (MLE (Maximum Likelihood Estimators), MVE (Minimum Volume Elipsoid), "t", MCD (Minimum Covariance Determinant), MCD-A, MCD-B), multinomial logistic regression and artificial neural networks (ANN). The predictive accuracy of the methods was accessed through a simulation study. ANN yielded the highest rate of classification accuracy in the data set under study. Results indicate that the particle number concentration of diameter size 0.5 µm is the parameter that better discriminates industries.

  10. An acoustic startle-based method of assessing frequency discrimination in mice.

    PubMed

    Clause, Amanda; Nguyen, Tuan; Kandler, Karl

    2011-08-30

    The acoustic startle response (ASR) is a reflexive contraction of skeletal muscles in response to a loud, abrupt acoustic stimulus. ASR magnitude is reduced if the startle stimulus is preceded by a weaker acoustic or non-acoustic stimulus, a phenomenon known as prepulse inhibition (PPI). PPI has been used to test various aspects of sensory discrimination in both animals and humans. Here we show that PPI of the ASR is an advantageous method of assessing frequency discrimination. We describe the apparatus and its performance testing frequency discrimination in young CD1 mice. Compared to classical conditioning paradigms, PPI of the ASR is less time consuming, produces robust results, and can be used without training even in young animals. This approach can be used to investigate the neuronal mechanisms underlying frequency discrimination, its maturation during development, and its relationship to tonotopic organization.

  11. Discriminative power of Campylobacter phenotypic and genotypic typing methods.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The aim of this study was to compare typing methods, individually and combined, to use in the routine surveillance of Campylobacter in broiler carcasses. C. jejuni (n=94) and C. coli (n=52) isolated from different broiler carcasses were characterized using different typing methods: multilocus sequen...

  12. Automated Discrimination Method of Muscular and Subcutaneous Fat Layers Based on Tissue Elasticity

    NASA Astrophysics Data System (ADS)

    Inoue, Masahiro; Fukuda, Osamu; Tsubai, Masayoshi; Muraki, Satoshi; Okumura, Hiroshi; Arai, Kohei

    Balance between human body composition, e.g. bones, muscles, and fat, is a major and basic indicator of personal health. Body composition analysis using ultrasound has been developed rapidly. However, interpretation of echo signal is conducted manually, and accuracy and confidence in interpretation requires experience. This paper proposes an automated discrimination method of tissue boundaries for measuring the thickness of subcutaneous fat and muscular layers. A portable one-dimensional ultrasound device was used in this study. The proposed method discriminated tissue boundaries based on tissue elasticity. Validity of the proposed method was evaluated in twenty-one subjects (twelve women, nine men; aged 20-70 yr) at three anatomical sites. Experimental results show that the proposed method can achieve considerably high discrimination performance.

  13. Discrimination of Rice with Different Pretreatment Methods by Using a Voltammetric Electronic Tongue

    PubMed Central

    Wang, Li; Niu, Qunfeng; Hui, Yanbo; Jin, Huali

    2015-01-01

    In this study, an application of a voltammetric electronic tongue for discrimination and prediction of different varieties of rice was investigated. Different pretreatment methods were selected, which were subsequently used for the discrimination of different varieties of rice and prediction of unknown rice samples. To this aim, a voltammetric array of sensors based on metallic electrodes was used as the sensing part. The different samples were analyzed by cyclic voltammetry with two sample-pretreatment methods. Discriminant Factorial Analysis was used to visualize the different categories of rice samples; however, radial basis function (RBF) artificial neural network with leave-one-out cross-validation method was employed for prediction modeling. The collected signal data were first compressed employing fast Fourier transform (FFT) and then significant features were extracted from the voltammetric signals. The experimental results indicated that the sample solutions obtained by the non-crushed pretreatment method could efficiently meet the effect of discrimination and recognition. The satisfactory prediction results of voltammetric electronic tongue based on RBF artificial neural network were obtained with less than five-fold dilution of the sample solution. The main objective of this study was to develop primary research on the application of an electronic tongue system for the discrimination and prediction of solid foods and provide an objective assessment tool for the food industry. PMID:26205274

  14. Discriminative Dissolution Method for Benzoyl Metronidazole Oral Suspension.

    PubMed

    da Silva, Aline Santos; da Rosa Silva, Carlos Eduardo; Paula, Fávero Reisdorfer; da Silva, Fabiana Ernestina Barcellos

    2016-06-01

    A dissolution method for benzoyl metronidazole (BMZ) oral suspensions was developed and validated using a high-performance liquid chromatography (HPLC) method. After determination of sink conditions, dissolution profiles were evaluated using different dissolution media and agitation speeds. The sample insertion mode in dissolution media was also evaluated. The best conditions were obtained using a paddle, 50 rpm stirring speed, simulated gastric fluid (without pepsin) as the dissolution medium, and sample insertion by a syringe. These conditions were suitable for providing sink conditions and discriminatory power between different formulations. Through the tested conditions, the results can be considered specific, linear, precise, accurate, and robust. The dissolution profiles of five samples were compared using the similarity factor (f 2) and dissolution efficiency. The dissolution kinetics were evaluated and described by the Weibull model. Whereas there is no monograph for this pharmaceutical formulation, the dissolution method proposed can be considered suitable for quality control and dissolution profile comparison of different commercial formulations.

  15. Identification of discriminant proteins through antibody profiling, methods and apparatus for identifying an individual

    DOEpatents

    Thompson, Vicki S; Lacey, Jeffrey A; Gentillon, Cynthia A; Apel, William A

    2015-03-03

    A method for determining a plurality of proteins for discriminating and positively identifying an individual based from a biological sample. The method may include profiling a biological sample from a plurality of individuals against a protein array including a plurality of proteins. The protein array may include proteins attached to a support in a preselected pattern such that locations of the proteins are known. The biological sample may be contacted with the protein array such that a portion of antibodies in the biological sample reacts with and binds to the proteins forming immune complexes. A statistical analysis method, such as discriminant analysis, may be performed to determine discriminating proteins for distinguishing individuals. Proteins of interest may be used to form a protein array. Such a protein array may be used, for example, to compare a forensic sample from an unknown source with a sample from a known source.

  16. Identification of discriminant proteins through antibody profiling, methods and apparatus for identifying an individual

    DOEpatents

    Apel, William A.; Thompson, Vicki S; Lacey, Jeffrey A.; Gentillon, Cynthia A.

    2016-08-09

    A method for determining a plurality of proteins for discriminating and positively identifying an individual based from a biological sample. The method may include profiling a biological sample from a plurality of individuals against a protein array including a plurality of proteins. The protein array may include proteins attached to a support in a preselected pattern such that locations of the proteins are known. The biological sample may be contacted with the protein array such that a portion of antibodies in the biological sample reacts with and binds to the proteins forming immune complexes. A statistical analysis method, such as discriminant analysis, may be performed to determine discriminating proteins for distinguishing individuals. Proteins of interest may be used to form a protein array. Such a protein array may be used, for example, to compare a forensic sample from an unknown source with a sample from a known source.

  17. [Study on the method of feature extraction for brain-computer interface using discriminative common vector].

    PubMed

    Wang, Jinjia; Hu, Bei

    2013-02-01

    Discriminative common vector (DCV) is an effective method that was proposed for the small sample size problems of face recognition. There is the same problem in brain-computer interface (BCI). Using directly the linear discriminative analysis (LDA) could result in errors because of the singularity of the within-class matrix of data. In our studies, we used the DCV method from the common vector theory in the within-class scatter matrix of data of all classes, and then applied eigenvalue decomposition to the common vectors to obtain the final projected vectors. Then we used kernel discriminative common vector (KDCV) with different kernel. Three data sets that include BCI Competition I data set, Competition II data set IV, and a data set collected by ourselves were used in the experiments. The experiment results of 93%, 77% and 97% showed that this feature extraction method could be used well in the classification of imagine data in BCI.

  18. Evaluation of Three Methods for Discrimination of Bacillus anthracis From Other Bacillus Species

    DTIC Science & Technology

    2003-07-01

    EVALUATION OF THREE METHODS FOR DISCRIMINATION OF BACILLUS ANTHRACIS FROM OTHER BACILLUS SPECIES. Diane L. Dutt Geo-Centers Aberdeen...ABSTRACT Bacillus anthracis shares the same ecological niche with other members of the B. cereus group: especially B. cereus and B. thuringiensis...Techniques that differentiate among Bacillus species using metabolic characteristics can be used to compliment PCR-based methods. These

  19. A method for allelic replacement that uses the conjugative transposon Tn916: deletion of the emm6.1 allele in Streptococcus pyogenes JRS4.

    PubMed

    Norgren, M; Caparon, M G; Scott, J R

    1989-12-01

    The emm6.1 allele of Streptococcus pyogenes JRS4 was deleted by using the conjugative transposon Tn916. The aphA-3 gene, conferring resistance to kanamycin, was cloned between the sequences flanking the structural gene for the type 6 M protein (emm6.1) and inserted into the BstXI site of Tn916 to generate the chimeric transposon Tn916-5K3. Because the BstXI site lies in a nonessential region of Tn916, the chimeric transposon could transfer by conjugation from Bacillus subtilis into JRS4. In some of the transconjugants, Tn916-5K3 replaced the emm6.1 locus of JRS4 by homologous recombination between the cloned emm6.1-flanking regions and the resident chromosome. One recombinant studied in detail, JRS75, was kanamycin resistant and tetracycline sensitive and lacked immunologically detectable M6 protein. Furthermore, by Southern blot analysis, the DNA region encompassing the emm6.1 structural gene was found to have been replaced by aphA-3.

  20. SNPs and real-time quantitative PCR method for constitutional allelic copy number determination, the VPREB1 marker case

    PubMed Central

    2011-01-01

    Background 22q11.2 microdeletion is responsible for the DiGeorge Syndrome, characterized by heart defects, psychiatric disorders, endocrine and immune alterations and a 1 in 4000 live birth prevalence. Real-time quantitative PCR (qPCR) approaches for allelic copy number determination have recently been investigated in 22q11.2 microdeletions detection. The qPCR method was performed for 22q11.2 microdeletions detection as a first-level screening approach in a genetically unknown series of patients with congenital heart defects. A technical issue related to the VPREB1 qPCR marker was pointed out. Methods A set of 100 unrelated Italian patients with congenital heart defects were tested for 22q11.2 microdeletions by a qPCR method using six different markers. Fluorescence In Situ Hybridization technique (FISH) was used for confirmation. Results qPCR identified six patients harbouring the 22q11.2 microdeletion, confirmed by FISH. The VPREB1 gene marker presented with a pattern consistent with hemideletion in one 3 Mb deleted patient, suggestive for a long distal deletion, and in additional five non-deleted patients. The long distal 22q11.2 deletion was not confirmed by Comparative Genomic Hybridization. Indeed, the VPREB1 gene marker generated false positive results in association with the rs1320 G/A SNP, a polymorphism localized within the VPREB1 marker reverse primer sequence. Patients heterozygous for rs1320 SNP, showed a qPCR profile consistent with the presence of a hemideletion. Conclusions Though the qPCR technique showed advantages as a screening approach in terms of cost and time, the VPREB1 marker case revealed that single nucleotide polymorphisms can interfere with qPCR data generating erroneous allelic copy number interpretations. PMID:21545739

  1. A new discrimination method for the Concealed Information Test using pretest data and within-individual comparisons.

    PubMed

    Matsuda, Izumi; Hirota, Akihisa; Ogawa, Tokihiro; Takasawa, Noriyoshi; Shigemasu, Kazuo

    2006-08-01

    A latent class discrimination method is proposed for analyzing autonomic responses on the concealed information test. Because there are significant individual differences in autonomic responses, individual response patterns are estimated on the pretest. Then an appropriate discriminant formula for the response pattern of each individual is applied to the CIT test results. The probability that the individual concealed information is calculated by comparing the discriminant formula value of the crime-related item to that of non-crime-related items. The discrimination performance of the latent class discrimination method was higher than those of the logistic regression method and the discriminant analysis method in an experimental demonstration applying the three methods to the same data set.

  2. Kinematic background discrimination methods using a fully digital data acquisition system for TOFOR

    NASA Astrophysics Data System (ADS)

    Skiba, Mateusz; Ericsson, Göran; Hjalmarsson, Anders; Hellesen, Carl; Conroy, Sean; Andersson-Sundén, Erik; Eriksson, Jacob; JET Contributors

    2016-12-01

    A fully digital, prototype data acquisition system upgrade for the TOFOR neutron time-of-flight neutron spectrometer at the JET experimental fusion reactor in Culham, England, has been constructed. This upgrade, TOFu (Time-of-Flight upgrade), enables digitization of associated time and energy deposition information from the TOFOR scintillator detectors, facilitating discrimination of spectral background due to unrelated neutron events based on kinematic considerations. In this publication, a kinematic background discrimination method is presented using synthetic data and validated with experimental results. It is found that an improvement in signal-to-background ratio of 500% in certain spectral regions is possible with the new DAQ system.

  3. A new method for fingerprinting sediments source contributions using distances from discriminant function analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mixing models have been used to predict sediment source contributions. The inherent problem of the mixing models limited the number of sediment sources. The objective of this study is to develop and evaluate a new method using Discriminant Function Analysis (DFA) to fingerprint sediment source contr...

  4. Discrimination of planting area of white peach based near-infrared spectra and chemometrics methods

    NASA Astrophysics Data System (ADS)

    Fu, Xiaping; Ying, Yibin; Zhou, Ying; Xu, Huirong; Xie, Lijuan; Jiang, Xuesong

    2007-09-01

    White peach is a famous peach variety for its super-quality and high economic benefit. It is originally planted in Yuandong Villiage, Jinhua County, Zhejiang province. By now, it has been planted in many other places in southeast of China. However, peaches from different planting areas have dissimilar quality and taste, which result in different selling price. The objective of this research was to discriminate peaches from different planting areas by using near-infrared (NIR) spectra and chemometrics methods. Diffuse reflectance spectra were collected by a fiber spectrometer in the range of 800-2500 nm. Discriminant analysis (DA), soft independent modeling of class analogy (SIMCA), and discriminant partial least square regression (DPLS) methods were employed to classify the peaches from three planting areas 'Jinhua', 'Wuyi', and 'Yongkang' of Zhejiang province. 360 samples were used in this study, 120 samples per planting area. The classifying correctness were above 92% for both DA and SIMCA mdoels. And the result of DPLS model was slightly better. By using DPLS method, two 'Jinhua' peaches, three 'Wuyi' peaches, and three 'Yongkang' peaches were misclassified, the accruacy was above 95%. The results of this study indicate that the three chemometrics methods DA, SIMCA, and DPLS are effective for discriminating peaches from different planting areas based on NIR spectroscopy.

  5. Machine vision methods for use in grain variety discrimination and quality analysis

    NASA Astrophysics Data System (ADS)

    Winter, Philip W.; Sokhansanj, Shahab; Wood, Hugh C.

    1996-12-01

    Decreasing cost of computer technology has made it feasible to incorporate machine vision technology into the agriculture industry. The biggest attraction to using a machine vision system is the computer's ability to be completely consistent and objective. One use is in the variety discrimination and quality inspection of grains. Algorithms have been developed using Fourier descriptors and neural networks for use in variety discrimination of barley seeds. RGB and morphology features have been used in the quality analysis of lentils, and probability distribution functions and L,a,b color values for borage dockage testing. These methods have been shown to be very accurate and have a high potential for agriculture. This paper presents the techniques used and results obtained from projects including: a lentil quality discriminator, a barley variety classifier, a borage dockage tester, a popcorn quality analyzer, and a pistachio nut grading system.

  6. [Research on discrimination method of tomato via space mutation breeding based on spectroscopy technology].

    PubMed

    Shi, Jia-Hui; Shao, Yong-Ni; He, Yong; Li, Duo; Feng, Pan; Zhu, Jia-Jin

    2009-11-01

    In order to quickly analyze varieties of tomato via space mutation breeding with near infrared spectra, firstly, principal component analysis was used to analyze the clustering of tomato leaf samples, and then abundant spectral data were compressed by wavelet transform and the model was built with radial basis function neural network, which offered a quantitative analysis of tomato varieties discrimination. The model regarded the compressed data as the input of neural network input vectors and the training process speeded up. One hundred and five leaf samples of CK, M1 and M2 were selected randomly to build the training model, and forty five samples formed the prediction set. The discrimination rate of 97.8% was achieved by this method. It offered a new approach to the fast discrimination of varieties of tomato via space mutation breeding.

  7. The allele-specific probe and primer amplification assay, a new real-time PCR method for fine quantification of single-nucleotide polymorphisms in pooled DNA.

    PubMed

    Billard, A; Laval, V; Fillinger, S; Leroux, P; Lachaise, H; Beffa, R; Debieu, D

    2012-02-01

    The evolution of fungicide resistance within populations of plant pathogens must be monitored to develop management strategies. Such monitoring often is based on microbiological tests, such as microtiter plate assays. Molecular monitoring methods can be considered if the mutations responsible for resistance have been identified. Allele-specific real-time PCR approaches, such as amplification refractory mutation system (ARMS) PCR and mismatch amplification mutation assay (MAMA) PCR, are, despite their moderate efficacy, among the most precise methods for refining SNP quantification. We describe here a new real-time PCR method, the allele-specific probe and primer amplification assay (ASPPAA PCR). This method makes use of mixtures of allele-specific minor groove binder (MGB) TaqMan probes and allele-specific primers for the fine quantification of SNPs from a pool of DNA extracted from a mixture of conidia. It was developed for a single-nucleotide polymorphism (SNP) that is responsible for resistance to the sterol biosynthesis inhibitor fungicide fenhexamid, resulting in the replacement of the phenylalanine residue (encoded by the TTC codon) in position 412 of the enzymatic target (3-ketoreductase) by a serine (TCC), valine (GTC), or isoleucine (ATC) residue. The levels of nonspecific amplification with the ASPPAA PCR were reduced at least four times below the level of currently available allele-specific real-time PCR approaches due to strong allele specificity in amplification cycles, including two allele selectors. This new method can be used to quantify a complex quadriallelic SNP in a DNA pool with a false discovery rate of less than 1%.

  8. A simplified PCR-based method for detection of gray coat color allele in horse.

    PubMed

    Kavar, Tatjana; Čeh, Eva; Dovč, Peter

    2012-12-01

    Coat color of gray horses is associated with a 4.6-kb duplication, which can be determined using PCR amplification of about 5-kb DNA fragment. In practice, this means that amplification might fail frequently. Therefore, a novel genetic screening method based on amplification of the 246 bp DNA fragment has been developed.

  9. [Near infrared spectroscopy analysis method of maize hybrid seed purity discrimination].

    PubMed

    Huang, Hua-Jun; Yan, Yan-Lu; Shen, Bing-Hui; Liu, Zhe; Gu, Jian-Cheng; Li, Shao-Ming; Zhu, De-Hai; Zhang, Xiao-Dong; Ma, Qin; Li, Lin; An, Dong

    2014-05-01

    Near infrared spectroscopy analysis method of discrimination of maize hybrid seed purity was studied with the sample of Nong Hua 101 (NH101) from different origins and years. Spectral acquisition time lasted for 10 months. Using Fourier transform (FT) near infrared spectroscopy instruments, including 23 days in different seasons (divided into five time periods), a total of 920 near infrared diffuse reflectance spectra of single corn grain of those samples were collected. Moving window average, first derivative and vector normalization were used to pretreat all original spectra, principal component analysis (PCA) and linear discriminant analysis (LDA) were applied to reduce data dimensionality, and the discrimination model was established based on biomimetic pattern recognition (BPR) method. Spectral distortion was calibrated by spectra pretreatment, which makes characteristics spatial distribution range of sample spectra set contract. The relative distance between hybrid and female parent increased by nearly 70-fold, and the discrimination model achieved the identification of hybrid and female parent seeds. Through the choice of representative samples, the model's response capacity to the changes in spectral acquisition time, place and environment, etc. was improved. Besides, the model's response capacity to the changes in time and site of seed production was also improved, and the robustness of the model was enhanced. The average correct acceptance rate (CAR) of the test set reached more than 95% while the average correct rejection rate (CRR) of the test set also reached 85%.

  10. A Method Of Evaluating A Subsurface Region Using Gather Sensitive Data Discrimination

    DOEpatents

    Lazaratos, Spyridon K.

    2000-01-11

    A method of evaluating a subsurface region by separating/enhancing a certain type of seismic event data of interest from an overall set of seismic event data which includes other, different types of seismic event data is disclosed herein. In accordance with one feature, a particular type of gather is generated from the seismic event data such that the gather includes at least a portion of the data which is of interest and at least a portion of the other data. A series of data discrimination lines are incorporated into the gather at positions and directions which are established in the gather in a predetermined way. Using the data discrimination lines, the data of interest which is present in the gather is separated/enhanced with respect to the other data within the gather. The separated data may be used for example in producing a map of the particular subterranean region. In accordance with another feature, the gather is selected such that the incorporated discrimination lines approach a near parallel relationship with one another. Thereby, the data is transformed in a way which causes the discrimination lines to be parallel with one another, resulting in reduced frequency distortion accompanied by improved accuracy in the separation/enhancement of data. In accordance with still another feature, the disclosed data separation/enhancement method is compatible with an iterative approach.

  11. Allele-specific enzymatic amplification of. beta. -globin genomic DNA for diagnosis of sickle cell anemia

    SciTech Connect

    Wu, D.Y.; Ugozzoli, L.; Pal, B.K.; Wallace, B. )

    1989-04-01

    A rapid nonradioactive approach to the diagnosis of sickle cell anemia is described based on an allele-specific polymerase chain reaction (ASPCR). This method allows direct detection of the normal or the sickle cell {beta}-globin allele in genomic DNA without additional steps of probe hybridization, ligation, or restriction enzyme cleavage. Two allele-specific oligonucleotide primers, one specific for the sickle cell allele and one specific for the normal allele, together with another primer complementary to both alleles were used in the polymerase chain reaction with genomic DNA templates. The allele-specific primers differed from each other in their terminal 3{prime} nucleotide. Under the proper annealing temperature and polymerase chain reaction conditions, these primers only directed amplification on their complementary allele. In a single blind study of DNA samples from 12 individuals, this method correctly and unambiguously allowed for the determination of the genotypes with no false negatives or positives. If ASPCR is able to discriminate all allelic variation (both transition and transversion mutations), this method has the potential to be a powerful approach for genetic disease diagnosis, carrier screening, HLA typing, human gene mapping, forensics, and paternity testing.

  12. Development and testing of a rapid method for measuring shoal size discrimination.

    PubMed

    Lucon-Xiccato, Tyrone; Dadda, Marco; Gatto, Elia; Bisazza, Angelo

    2017-03-01

    The shoal-choice test is a popular method to investigate quantity discrimination in social fish based on their spontaneous preference for the larger of two shoals. The shoal-choice test usually requires a long observation time (20-30 min), mainly because fish switch between the two shoals with low frequency, thus reducing the possibilities of comparison. This duration limits the use of the shoal-choice test for large-scale screenings. Here, we developed a new version of the shoal-choice test in which the subject was confined in a large transparent cylinder in the middle of the tank throughout the experiment to bound the minimum distance from the stimulus shoals and favour switching. We tested the new method by observing guppies (Poecilia reticulata) in a 4 versus 6 fish discrimination (experiment 1). The new method allowed for a faster assessment of the preference for the larger shoal (<5 min), resulting in potential application for large population screenings. Guppies switched five times more frequently between the two shoals and remained close to the first chosen shoal ten times less compared to experiments with the old method. In experiment 2, we found that with the new method guppies were able to discriminate up to 5 versus 6 fish, a discrimination that was not achieved with the classical method. This last result indicates that minor methodological modifications can lead to very different findings in the same species and suggests that caution should be exercised when interpreting inter-specific differences in quantitative abilities.

  13. SNP-Based Quantification of Allele-Specific DNA Methylation Patterns by Pyrosequencing®.

    PubMed

    Busato, Florence; Tost, Jörg

    2015-01-01

    The analysis of allele-specific DNA methylation patterns has recently attracted much interest as loci of allele-specific DNA methylation overlap with known risk loci for complex diseases and the analysis might contribute to the fine-mapping and interpretation of non-coding genetic variants associated with complex diseases and improve the understanding between genotype and phenotype. In the presented protocol, we present a method for the analysis of DNA methylation patterns on both alleles separately using heterozygous Single Nucleotide Polymorphisms (SNPs) as anchor for allele-specific PCR amplification followed by analysis of the allele-specific DNA methylation patterns by Pyrosequencing(®). Pyrosequencing is an easy-to-handle, quantitative real-time sequencing method that is frequently used for genotyping as well as for the analysis of DNA methylation patterns. The protocol consists of three major steps: (1) identification of individuals heterozygous for a SNP in a region of interest using Pyrosequencing; (2) analysis of the DNA methylation patterns surrounding the SNP on bisulfite-treated DNA to identify regions of potential allele-specific DNA methylation; and (3) the analysis of the DNA methylation patterns associated with each of the two alleles, which are individually amplified using allele-specific PCR. The enrichment of the targeted allele is re-enforced by modification of the allele-specific primers at the allele-discriminating base with Locked Nucleic Acids (LNA). For the proof-of-principle of the developed approach, we provide assay details for three imprinted genes (IGF2, IGF2R, and PEG3) within this chapter. The mean of the DNA methylation patterns derived from the individual alleles corresponds well to the overall DNA methylation patterns and the developed approach proved more reliable compared to other protocols for allele-specific DNA methylation analysis.

  14. Geophysical technique for mineral exploration and discrimination based on electromagnetic methods and associated systems

    DOEpatents

    Zhdanov; Michael S.

    2008-01-29

    Mineral exploration needs a reliable method to distinguish between uneconomic mineral deposits and economic mineralization. A method and system includes a geophysical technique for subsurface material characterization, mineral exploration and mineral discrimination. The technique introduced in this invention detects induced polarization effects in electromagnetic data and uses remote geophysical observations to determine the parameters of an effective conductivity relaxation model using a composite analytical multi-phase model of the rock formations. The conductivity relaxation model and analytical model can be used to determine parameters related by analytical expressions to the physical characteristics of the microstructure of the rocks and minerals. These parameters are ultimately used for the discrimination of different components in underground formations, and in this way provide an ability to distinguish between uneconomic mineral deposits and zones of economic mineralization using geophysical remote sensing technology.

  15. UV-vis absorption spectroscopy and multivariate analysis as a method to discriminate tequila.

    PubMed

    Barbosa-García, O; Ramos-Ortíz, G; Maldonado, J L; Pichardo-Molina, J L; Meneses-Nava, M A; Landgrave, J E A; Cervantes-Martínez, J

    2007-01-01

    Based on the UV-vis absorption spectra of commercially bottled tequilas, and with the aid of multivariate analysis, it is proved that different brands of white tequila can be identified from such spectra, and that 100% agave and mixed tequilas can be discriminated as well. Our study was done with 60 tequilas, 58 of them purchased at liquor stores in various Mexican cities, and two directly acquired from a distillery. All the tequilas were of the "white" type, that is, no aged spirits were considered. For the purposes of discrimination and quality control of tequilas, the spectroscopic method that we present here offers an attractive alternative to the traditional methods, like gas chromatography, which is expensive and time-consuming.

  16. UV-vis absorption spectroscopy and multivariate analysis as a method to discriminate tequila

    NASA Astrophysics Data System (ADS)

    Barbosa-García, O.; Ramos-Ortíz, G.; Maldonado, J. L.; Pichardo-Molina, J. L.; Meneses-Nava, M. A.; Landgrave, J. E. A.; Cervantes-Martínez, J.

    2007-01-01

    Based on the UV-vis absorption spectra of commercially bottled tequilas, and with the aid of multivariate analysis, it is proved that different brands of white tequila can be identified from such spectra, and that 100% agave and mixed tequilas can be discriminated as well. Our study was done with 60 tequilas, 58 of them purchased at liquor stores in various Mexican cities, and two directly acquired from a distillery. All the tequilas were of the "white" type, that is, no aged spirits were considered. For the purposes of discrimination and quality control of tequilas, the spectroscopic method that we present here offers an attractive alternative to the traditional methods, like gas chromatography, which is expensive and time-consuming.

  17. Early discriminant method of infected kernel based on the erosion effects of laser ultrasonics

    NASA Astrophysics Data System (ADS)

    Fan, Chao

    2015-07-01

    To discriminate the infected kernel of the wheat as early as possible, a new kind of detection method of hidden insects, especially in their egg and larvae stage, was put forward based on the erosion effect of the laser ultrasonic in this paper. The surface of the grain is exposured by the pulsed laser, the energy of which is absorbed and the ultrasonic is excited, and the infected kernel can be recognized by appropriate signal analyzing. Firstly, the detection principle was given based on the classical wave equation and the platform was established. Then, the detected ultrasonic signal was processed both in the time domain and the frequency domain by using FFT and DCT , and six significant features were selected as the characteristic parameters of the signal by the method of stepwise discriminant analysis. Finally, a BP neural network was designed by using these six parameters as the input to classify the infected kernels from the normal ones. Numerous experiments were performed by using twenty wheat varieties, the results shown that the the infected kernels can be recognized effectively, and the false negative error and the false positive error was 12% and 9% respectively, the discriminant method of the infected kernels based on the erosion effect of laser ultrasonics is feasible.

  18. Robust and discriminating method for face recognition based on correlation technique and independent component analysis model.

    PubMed

    Alfalou, A; Brosseau, C

    2011-03-01

    We demonstrate a novel technique for face recognition. Our approach relies on the performances of a strongly discriminating optical correlation method along with the robustness of the independent component analysis (ICA) model. Simulations were performed to illustrate how this algorithm can identify a face with images from the Pointing Head Pose Image Database. While maintaining algorithmic simplicity, this approach based on ICA representation significantly increases the true recognition rate compared to that obtained using our previously developed all-numerical ICA identity recognition method and another method based on optical correlation and a standard composite filter.

  19. A convenient method for discriminating between natural and depleted uranium by gamma-ray spectrometry.

    PubMed

    Shoji, M; Hamajima, Y; Takatsuka, K; Honoki, H; Nakajima, T; Kondo, T; Nakanishi, T

    2001-08-01

    A convenient method for discriminating between natural and depleted uranium reagent was developed by measuring and analyzing the gamma-ray spectra of some reagents with no standard source. The counting rates (R) of photoelectric peaks of gamma-rays from nuclides with the same radioactivity divided by their emission probability (B) are expressed as a function of gamma-ray energy. The radioactivities of 234Th and 234mPa and 21.72 times that of 235U are equal to the radioactivity of 235U in natural uranium. Therefore, the plot of 21.72-fold R/B for 235U should be on a curve fitted to the points for 234Th and 234mPa in natural uranium. Depleted uranium with a 235U isotopic composition of less than 0.68% could be discriminated from natural uranium in the case of a reagent containing 4.0 g of uranium.

  20. Molecular method for discrimination between Francisella tularensis and Francisella-like endosymbionts.

    PubMed

    Escudero, Raquel; Toledo, A; Gil, Horacio; Kovácsová, Katarina; Rodríguez-Vargas, Manuela; Jado, Isabel; García-Amil, Cristina; Lobo, Bruno; Bhide, Mangesh; Anda, Pedro

    2008-09-01

    Environmental studies on the distribution of Francisella spp. are hampered by the frequency of Francisella-like endosymbionts that can produce a misleading positive result. A new, efficient molecular method for detection of Francisella tularensis and its discrimination from Francisella-like endosymbionts, as well as two variants associated with human disease (unusual F. tularensis strain FnSp1 and F. tularensis subsp. novicida-like strain 3523), is described. The method is highly specific and sensitive, detecting up to one plasmid copy or 10 genome equivalents.

  1. Enantioseparation of cetirizine by chromatographic methods and discrimination by 1H-NMR.

    PubMed

    Taha, Elham A; Salama, Nahla N; Wang, Shudong

    2009-03-01

    Cetirizine is an antihistaminic drug used to prevent and treat allergic conditions. It is currently marketed as a racemate. The H1-antagonist activity of cetirizine is primarily due to (R)-levocetirizine. This has led to the introduction of (R)-levocetirizine into clinical practice, and the chiral switching is expected to be more selective and safer. The present work represents three methods for the analysis and chiral discrimination of cetirizine. The first method was based on the enantioseparation of cetirizine on silica gel TLC plates using different chiral selectors as mobile phase additives. The mobile phase enabling successful resolution was acetonitrile-water 17: 3, (v/v) containing 1 mM of chiral selector, namely hydroxypropyl-beta-cyclodextrin, chondroitin sulphate or vancomycin hydrochloride. The second method was a validated high performance liquid chromatography (HPLC), based on stereoselective separation of cetirizine and quantitative determination of its eutomer (R)-levocetirizine on a monolithic C18 column using hydroxypropyl-beta-cyclodextrin as a chiral mobile phase additive. The resolved peaks of (R)-levocetirizine and (S)-dextrocetirizine were confirmed by further mass spectrometry. The third method used a (1)H-NMR technique to characterize cetirizine and (R)-levocetirizine. These methods are selective and accurate, and can be easily applied for chiral discrimination and determination of cetirizine in drug substance and drug product in quality control laboratory. Moreover, chiral purity testing of (R)-levocetirizine can also be monitored by the chromatographic methods.

  2. Canine DLA-79 gene: an improved typing method, identification of new alleles and its role in graft rejection and graft-versus-host disease.

    PubMed

    Venkataraman, G M; Geraghty, D; Fox, J; Graves, S S; Zellmer, E; Storer, B E; Torok-Storb, B J; Storb, R

    2013-04-01

    Developing a preclinical canine model that predicts outcomes for hematopoietic cell transplantation in humans requires a model that mimics the degree of matching between human donor and recipient major histocompatibility complex (MHC) genes. The polymorphic class I and class II genes in mammals are typically located in a single chromosome as part of the MHC complex. However, a divergent class I gene in dogs, designated dog leukocyte antigen-79 (DLA-79), is located on chromosome 18 while other MHC genes are on chromosome 12. This gene is not taken into account while DLA matching for transplantation. Though divergent, this gene shares significant similarity in sequence and exon-intron architecture with other class I genes, and is transcribed. Little is known about the polymorphisms of DLA-79 and their potential role in transplantation. This study was aimed at exploring the reason for high rate of rejection seen in DLA-matched dogs given reduced intensity conditioning, in particular, the possibility that DLA-79 allele mismatches may be the cause. We found that about 82% of 407 dogs typed were homozygous for a single, reference allele. Owing to the high prevalence of a single allele, 87 of the 108 dogs (∼80%) transplanted were matched for DLA-79 with their donor. In conclusion, we have developed an efficient method to type alleles of a divergent MHC gene in dogs and identified two new alleles. We did not find any statistical correlation between DLA-79 allele disparity and graft rejection or graft-versus-host disease, among our transplant dogs.

  3. Association of BoLA-DRB3 alleles identified by a sequence-based typing method with mastitis pathogens in Japanese Holstein cows.

    PubMed

    Yoshida, Tatsuyuki; Mukoyama, Harutaka; Furuta, Hiroki; Kondo, Yasuko; Takeshima, Shin-nosuke; Aida, Yoko; Kosugiyama, Motoaki; Tomogane, Hiroshi

    2009-10-01

    The association of the polymorphism of bovine leukocyte antigen (BoLA-DRB3) genes identified by the polymerase chain reaction sequence-based typing (PCR-SBT) method with resistance and susceptibility to mastitis caused by pathogenic bacteria was investigated. Blood samples for DNA extraction were collected from 194 Holstein cows (41 healthy cows and 153 mastitis cows including 24 mixed-infection cows infected with 2 or 3 species of pathogens) from 5 districts of Chiba prefecture, Japan. Sixteen BoLA-DRB3 alleles were detected. The 4 main alleles of DRB3*0101, *1501, *1201, and *1101 constituted 56.8% of the total number of alleles detected. Mastitis cows were divided into 2 groups: group 1 with single-infection cows and group 2 with all mastitis cows including 24 mixed-infection cows. The differences in the frequencies of BoLA-DRB3 alleles and the number of cows homozygous or heterozygous for each BoLA-DRB3 allele between healthy cows and the 2 groups of mastitis cows were evaluated. Furthermore, similar comparisons were performed between healthy cows and the 2 groups of mastitis cows for each mastitis pathogen. It was considered that the 4 alleles, namely, DRB3*0101, *1501, *1201, and *1101 had specific resistance and susceptibility to 4 different mastitis pathogens. Thus, DRB3*0101 might be associated with susceptibility to coagulase-negative Staphylococci and Escherichia coli, and DRB3*1501 might be associated with susceptibility to Escherichia coli. However, DRB3*1101 might be associated with resistance to Streptococci and coagulase-negative Staphylococci, and DRB3*1201, with resistance to Streptococci, Escherichia coli, and Staphylococcus aureus.

  4. Effectiveness of dereverberation, feature transformation, discriminative training methods, and system combination approach for various reverberant environments

    NASA Astrophysics Data System (ADS)

    Tachioka, Yuuki; Narita, Tomohiro; Watanabe, Shinji

    2015-12-01

    The recently released REverberant Voice Enhancement and Recognition Benchmark (REVERB) challenge includes a reverberant automatic speech recognition (ASR) task. This paper describes our proposed system based on multi-channel speech enhancement preprocessing and state-of-the-art ASR techniques. For preprocessing, we propose a single-channel dereverberation method with reverberation time estimation, which is combined with multichannel beamforming that enhances direct sound compared with the reflected sound. In addition, this paper also focuses on state-of-the-art ASR techniques such as discriminative training of acoustic models including the Gaussian mixture model, subspace Gaussian mixture model, and deep neural networks, as well as various feature transformation techniques. Although, for the REVERB challenge, it is necessary to handle various acoustic environments, a single ASR system tends to be overly tuned for a specific environment, which degrades the performance in the mismatch environments. To overcome this mismatch problem with a single ASR system, we use a system combination approach using multiple ASR systems with different features and different model types because a combination of various systems that have different error patterns is beneficial. In particular, we use our discriminative training technique for system combination that achieves better generalization by making systems complementary with the modified discriminative criteria. Experiments show the effectiveness of these approaches, reaching 6.76 and 18.60 % word error rates on the REVERB simulated and real test sets. These are 68.8 and 61.5 % relative improvements over the baseline.

  5. A robust non-linear tissue-component discrimination method for computational pathology

    PubMed Central

    Sarnecki, Jacob S.; Burns, Kathleen H.; Wood, Laura D.; Waters, Kevin M.; Hruban, Ralph H.; Wirtz, Denis; Wu, Pei-Hsun

    2015-01-01

    Advances in digital pathology, specifically imaging instrumentation and data management, have allowed for the development of computational pathology tools with the potential for better, faster, and cheaper diagnosis, prognosis, and prediction of disease. Images of tissue sections frequently vary in color appearance across research laboratories and medical facilities due to differences in tissue fixation, staining protocols, and imaging instrumentation, leading to difficulty in the development of robust computational tools. To address this challenge, we propose a novel non-linear tissue-component discrimination (NLTD) method to automatically register the color space of histopathology images and visualize individual tissue components, independent of color differences between images. Our results show that the NLTD method could effectively discriminate different tissue components from different types of tissues prepared at different institutions. Further, we demonstrate that NLTD can improve the accuracy of nuclear detection and segmentation algorithms, compared to using conventional color deconvolution methods, and can quantitatively analyze immunohistochemistry images. Together, the NLTD method is objective, robust, and effective, and can be easily implemented in the emerging field of computational pathology. PMID:26779829

  6. A Feature Selection Method Based on Fisher's Discriminant Ratio for Text Sentiment Classification

    NASA Astrophysics Data System (ADS)

    Wang, Suge; Li, Deyu; Wei, Yingjie; Li, Hongxia

    With the rapid growth of e-commerce, product reviews on the Web have become an important information source for customers' decision making when they intend to buy some product. As the reviews are often too many for customers to go through, how to automatically classify them into different sentiment orientation categories (i.e. positive/negative) has become a research problem. In this paper, based on Fisher's discriminant ratio, an effective feature selection method is proposed for product review text sentiment classification. In order to validate the validity of the proposed method, we compared it with other methods respectively based on information gain and mutual information while support vector machine is adopted as the classifier. In this paper, 6 subexperiments are conducted by combining different feature selection methods with 2 kinds of candidate feature sets. Under 1006 review documents of cars, the experimental results indicate that the Fisher's discriminant ratio based on word frequency estimation has the best performance with F value 83.3% while the candidate features are the words which appear in both positive and negative texts.

  7. Pulse-shape discrimination in neutron depth profiling radioanalytical methods. Part II

    NASA Astrophysics Data System (ADS)

    Vacík, J.; Červená, J.; Hnatowicz, V.; Havránek, V.; Hoffmann, J.; Pošta, S.; Fink, D.

    1999-01-01

    Pulse shape discrimination (PSD) is used for the reduction of radiation background in the depth sensitive neutron depth profiling method (NDP) based on the detection of charged particles from the (n, α) and (n, p) nuclear reactions induced by thermal neutrons on some light elements. The experimental NDP-PSD arrangement is described and its performance is demonstrated on the measurement of real samples. Background reduction by several orders of magnitude in the region below 1 MeV leads to a corresponding sensitivity improvement and to an extension of the measurable depth region for some light elements.

  8. Multiplex PCR method to discriminate Artemisia iwayomogi from other Artemisia plants.

    PubMed

    Doh, Eui Jeong; Oh, Seung-Eun

    2012-01-01

    Some plants in the genus Artemisia have been used for medicinal purposes. Among them, Artemisia iwayomogi, commonly referred to as "Haninjin," is one of the major medicinal materials used in traditional Korean medicine. By contrast, Artemisia capillaris and both Artemisia argyi and Artemisia princeps, referred to as "Injinho" and "Aeyup," respectively, are used to treat diseases different from those for which "Haninjin" is prescribed. Therefore, the development of a reliable method to differentiate each Artemisia herb is necessary. We found that a random amplified polymorphic DNA (RAPD) method can be used to efficiently discriminate a few Artemisia plants from one another. To improve the reliability of RAPD amplification, we designed primer sets based on the nucleotide sequences of RAPD products to amplify a sequence-characterized amplified region (SCAR) marker of A. iwayomogi. In addition, we designed two other primer sets to amplify SCAR markers of "Aeyup" (A. argyi and A. princeps) along with "Injinho" (A. capillaris) and Artemisia japonica, which are also traded in Korean herbal markets. Using these three primer sets, we developed a multiplex PCR method concurrently not only to discriminate A. iwayomogi from other Artemisia plants, but also to identify Artemisia plants using a single PCR process.

  9. CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation

    PubMed Central

    Ortiz-Estevez, Maria; Aramburu, Ander; Bengtsson, Henrik; Neuvial, Pierre; Rubio, Angel

    2012-01-01

    Summary: CalMaTe calibrates preprocessed allele-specific copy number estimates (ASCNs) from DNA microarrays by controlling for single-nucleotide polymorphism-specific allelic crosstalk. The resulting ASCNs are on average more accurate, which increases the power of segmentation methods for detecting changes between copy number states in tumor studies including copy neutral loss of heterozygosity. CalMaTe applies to any ASCNs regardless of preprocessing method and microarray technology, e.g. Affymetrix and Illumina. Availability: The method is available on CRAN (http://cran.r-project.org/) in the open-source R package calmate, which also includes an add-on to the Aroma Project framework (http://www.aroma-project.org/). Contact: arubio@ceit.es Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22576175

  10. Pulse shape discrimination and classification methods for continuous depth of interaction encoding PET detectors

    NASA Astrophysics Data System (ADS)

    Roncali, Emilie; Phipps, Jennifer E.; Marcu, Laura; Cherry, Simon R.

    2012-10-01

    In previous work we demonstrated the potential of positron emission tomography (PET) detectors with depth-of-interaction (DOI) encoding capability based on phosphor-coated crystals. A DOI resolution of 8 mm full-width at half-maximum was obtained for 20 mm long scintillator crystals using a delayed charge integration linear regression method (DCI-LR). Phosphor-coated crystals modify the pulse shape to allow continuous DOI information determination, but the relationship between pulse shape and DOI is complex. We are therefore interested in developing a sensitive and robust method to estimate the DOI. Here, linear discriminant analysis (LDA) was implemented to classify the events based on information extracted from the pulse shape. Pulses were acquired with 2×2×20 mm3 phosphor-coated crystals at five irradiation depths and characterized by their DCI values or Laguerre coefficients. These coefficients were obtained by expanding the pulses on a Laguerre basis set and constituted a unique signature for each pulse. The DOI of individual events was predicted using LDA based on Laguerre coefficients (Laguerre-LDA) or DCI values (DCI-LDA) as discriminant features. Predicted DOIs were compared to true irradiation depths. Laguerre-LDA showed higher sensitivity and accuracy than DCI-LDA and DCI-LR and was also more robust to predict the DOI of pulses with higher statistical noise due to low light levels (interaction depths further from the photodetector face). This indicates that Laguerre-LDA may be more suitable to DOI estimation in smaller crystals where lower collected light levels are expected. This novel approach is promising for calculating DOI using pulse shape discrimination in single-ended readout depth-encoding PET detectors.

  11. Color model and method for video fire flame and smoke detection using Fisher linear discriminant

    NASA Astrophysics Data System (ADS)

    Wei, Yuan; Jie, Li; Jun, Fang; Yongming, Zhang

    2013-02-01

    Video fire detection is playing an increasingly important role in our life. But recent research is often based on a traditional RGB color model used to analyze the flame, which may be not the optimal color space for fire recognition. It is worse when we research smoke simply using gray images instead of color ones. We clarify the importance of color information for fire detection. We present a fire discriminant color (FDC) model for flame or smoke recognition based on color images. The FDC models aim to unify fire color image representation and fire recognition task into one framework. With the definition of between-class scatter matrices and within-class scatter matrices of Fisher linear discriminant, the proposed models seek to obtain one color-space-transform matrix and a discriminate projection basis vector by maximizing the ratio of these two scatter matrices. First, an iterative basic algorithm is designed to get one-component color space transformed from RGB. Then, a general algorithm is extended to generate three-component color space for further improvement. Moreover, we propose a method for video fire detection based on the models using the kNN classifier. To evaluate the recognition performance, we create a database including flame, smoke, and nonfire images for training and testing. The test experiments show that the proposed model achieves a flame verification rate receiver operating characteristic (ROC I) of 97.5% at a false alarm rate (FAR) of 1.06% and a smoke verification rate (ROC II) of 91.5% at a FAR of 1.2%, and lots of fire video experiments demonstrate that our method reaches a high accuracy for fire recognition.

  12. Improved neutron-gamma discrimination for a 3He neutron detector using subspace learning methods

    DOE PAGES

    Wang, C. L.; Funk, L. L.; Riedel, R. A.; ...

    2017-02-10

    3He gas based neutron linear-position-sensitive detectors (LPSDs) have been applied for many neutron scattering instruments. Traditional Pulse-Height Analysis (PHA) for Neutron-Gamma Discrimination (NGD) resulted in the neutron-gamma efficiency ratio on the orders of 105-106. The NGD ratios of 3He detectors need to be improved for even better scientific results from neutron scattering. Digital Signal Processing (DSP) analyses of waveforms were proposed for obtaining better NGD ratios, based on features extracted from rise-time, pulse amplitude, charge integration, a simplified Wiener filter, and the cross-correlation between individual and template waveforms of neutron and gamma events. Fisher linear discriminant analysis (FLDA) and threemore » multivariate analyses (MVAs) of the features were performed. The NGD ratios are improved by about 102-103 times compared with the traditional PHA method. Finally, our results indicate the NGD capabilities of 3He tube detectors can be significantly improved with subspace-learning based methods, which may result in a reduced data-collection time and better data quality for further data reduction.« less

  13. New Geophysical Technique for Mineral Exploration and Mineral Discrimination Based on Electromagnetic Methods

    SciTech Connect

    Michael S. Zhdanov

    2005-03-09

    The research during the first year of the project was focused on developing the foundations of a new geophysical technique for mineral exploration and mineral discrimination, based on electromagnetic (EM) methods. The proposed new technique is based on examining the spectral induced polarization effects in electromagnetic data using modern distributed acquisition systems and advanced methods of 3-D inversion. The analysis of IP phenomena is usually based on models with frequency dependent complex conductivity distribution. One of the most popular is the Cole-Cole relaxation model. In this progress report we have constructed and analyzed a different physical and mathematical model of the IP effect based on the effective-medium theory. We have developed a rigorous mathematical model of multi-phase conductive media, which can provide a quantitative tool for evaluation of the type of mineralization, using the conductivity relaxation model parameters. The parameters of the new conductivity relaxation model can be used for discrimination of the different types of rock formations, which is an important goal in mineral exploration. The solution of this problem requires development of an effective numerical method for EM forward modeling in 3-D inhomogeneous media. During the first year of the project we have developed a prototype 3-D IP modeling algorithm using the integral equation (IP) method. Our IE forward modeling code INTEM3DIP is based on the contraction IE method, which improves the convergence rate of the iterative solvers. This code can handle various types of sources and receivers to compute the effect of a complex resistivity model. We have tested the working version of the INTEM3DIP code for computer simulation of the IP data for several models including a southwest US porphyry model and a Kambalda-style nickel sulfide deposit. The numerical modeling study clearly demonstrates how the various complex resistivity models manifest differently in the observed EM

  14. Joints and their relations as critical features in action discrimination: evidence from a classification image method.

    PubMed

    van Boxtel, Jeroen J A; Lu, Hongjing

    2015-01-20

    Classifying an action as a runner or a walker is a seemingly effortless process. However, it is difficult to determine which features are used with hypothesis-driven research, because biological motion stimuli generally consist of about a dozen joints, yielding an enormous number of potential relationships among them. Here, we develop a hypothesis-free approach based on a classification image method, using experimental data from relatively few trials (∼1,000 trials per subject). Employing ambiguous actions morphed between a walker and a runner, we identified three types of features that play important roles in discriminating bipedal locomotion presented in a side view: (a) critical joint feature, supported by the finding that the similarity of the movements of feet and wrists to prototypical movements of these joints were most reliably used across all participants; (b) structural features, indicated by contributions from almost all other joints, potentially through a form-based analysis; and (c) relational features, revealed by statistical correlations between joint contributions, specifically relations between the two feet, and relations between the wrists/elbow and the hips. When the actions were inverted, only critical joint features remained to significantly influence discrimination responses. When actions were presented with continuous depth rotation, critical joint features and relational features associated strongly with responses. Using a double-pass paradigm, we estimated that the internal noise is about twice as large as the external noise, consistent with previous findings. Overall, our novel design revealed a rich set of critical features that are used in action discrimination. The visual system flexibly selects a subset of features depending on viewing conditions.

  15. Isolation of S-locus F-box alleles in Prunus avium and their application in a novel method to determine self-incompatibility genotype.

    PubMed

    Vaughan, S P; Russell, K; Sargent, D J; Tobutt, K R

    2006-03-01

    This study characterises a series of 12 S-locus haplotype-specific F-box protein genes (SFB) in cherry (Prunus avium) that are likely candidates for the pollen component of gametophytic self-incompatibility in this species. Primers were designed to amplify 12 SFB alleles,including the introns present in the 50 untranslated region;sequences representing the S-alleles S1, S2, S3, S4, S40, S5,S6, S7, S10, S12, S13 and S16 were cloned and characterized. [The nucleotide sequences reported in this paper have been submitted to the EMBL/GenBank database under the following accession numbers: PaSFB1(AY805048), PaSFB2 (AY805049), PaSFB3 (AY805057),PaSFB4 (AY649872), PaSFB40 (AY649873), PaSFB5(AY805050), PaSFB6 (AY805051), PaSFB7 (AY805052),PaSFB10 (AY805053), PaSFB12 (AY805054), PaSFB13(AY805055), PaSFB16 (AY805056).] Though the coding regions of six of these alleles have been reported previously,the intron sequence has previously been reported only for S6. Analysis of the introns revealed sequence and length polymorphisms. A novel, PCR-based method to genotype cultivars and wild accessions was developed which combines fluorescently labelled primers amplifying the intron of SFB with similar primers for the first intron of S-RNase alleles. Intron length polymorphisms were then ascertained using a semi-automated sequencer. The convenience and reliability of this method for the determination of the self-incompatibility (SI) genotype was demonstrated both in sweet cherry cultivars representing alleles S1 to S16 and in individuals from a wild population encompassing S-alleles S17 to S22. This method will greatly expedite SI characterisation in sweet cherry and also facilitate large-scale studies of self-incompatibility in wild cherry and other Prunus populations.

  16. Contrast discrimination by the methods of adjustment and two-alternative forced choice.

    PubMed

    Laming, Donald

    2013-11-01

    Fifty years after the advent of signal-detection theory, some visual scientists still adhere to the notion of a high, fixed threshold. Indeed, experienced observers are able to deliver consistent settings of thresholds using the method of adjustment, but those settings are different from the thresholds obtained with two-alternative forced choice (2AFC) procedures. This article illustrates the difference by reference to four existing studies of contrast discrimination. All four sets of data show clear subthreshold facilitation, but the method of adjustment produces a rectilinear characteristic that corresponds to the use of different criteria over different ranges of contrast, whereas 2AFC procedures produce a curvilinear characteristic with generally lower thresholds. This article proposes a theoretical explanation for the difference.

  17. A new measurement method for color discrimination thresholds of human eyes based on PWM light-mixing technology

    NASA Astrophysics Data System (ADS)

    Zhang, Jiyan; Dong, Jinxin

    2016-09-01

    The color discrimination is a powerful tool for detection of eye diseases, and it is is necessary to produce different kinds of color rapidly and precisely for testing color discrimination thresholds of human eyes. Three channels' pulse-width modulation (PWM) and light-mixing technology is a new way to mixing color, and a new measurement method for color discrimination thresholds of human eyes based on PWM light-mix technology can generate kinds of color stimuli. In this study, 5 youth volunteers were measured via this equipment after the test for the stability of the device's illumination and chrominance. Though the theory of Macadam ellipses and the interleaved staircase method, a psychophysical experiment was made to study the color discrimination threshold of the human eyes around a basic color center. By analyzing the data of the chromatic ellipse and the color discrimination threshold, the result shows that each color is not uniform in a single color region and the color difference threshold of normal human is around the third Macadam ellipses. The experimental results show that the repeatability and accuracy of the observer can meet the accuracy requirements of the relevant experiments, and the data is reliable and effective, which means the measurement method is an effective way to measure the color discrimination thresholds of human visual system.

  18. Frequency of the arylsulphatase A pseudodeficiency allele in the Spanish population.

    PubMed

    Chabás, A; Castellvi, S; Bayés, M; Balcells, S; Grinberg, D; Vilageliu, L; Marfany, G; Lissens, W; Gonzàlez-Duarte, R

    1993-12-01

    Pseudodeficiency in arylsulphatase A (ASA) is a relatively frequent condition in healthy individuals. It produces a reduction in enzyme activity similar to that found in metachromatic leukodystrophy (MLD). Unambiguous discrimination between the two conditions cannot be achieved through conventional enzyme activity assays. A PCR method has been developed which detects the pseudodeficiency (pd) allele using a single pair of primers encompassing the mutation site and hair follicles as the source of DNA. The frequency of this allele in the Spanish population has been evaluated and correlations between different genotypes and ASA activity levels have been established. Ten out of 55 individuals were heterozygous for the ASA pd allele, while two were homozygous. The allele frequency was thus 12.7%.

  19. [Geographical origin discrimination of Auricularia auricula using variable selection method of modeling power].

    PubMed

    Liu, Fei; Sun, Guang-ming; He, Yong

    2010-01-01

    Near infrared (NIR) spectroscopy combined with variable selection method of modeling power was investigated for the fast and accurate geographical origin discrimination of auricularia auricula. A total of 240 samples of auriculari auricula were collected in the market, and the spectra of all samples were scanned within the spectral region of 1100-2500 nm. The calibration set was composed of 180 (45 samples for each origin) samples, and the remaining 60 samples were employed as the validation set. The optimal partial least squares (PLS) discriminant model was achieved after performance comparison of different preprocessing (Savitzky-Golay smoothing, standard normal variate, 1-derivative, and 2-derivative). The effective wavelengths, which were selected by modeling power (MP) and used as input data matrix of least squares-support vector machine (LS-SVM), were employed for the development of modeling power-least squares-support vector machine (MP-LS-SVM) model. Radial basis function (RBF) kernel was applied as kernel function. Three threshold methods for variable selection by modeling power were applied in MP-LSSVM models, and there were the values of modeling power higher than 0.95, higher than 0.90, and higher than 0.90 combined with peak location (0.90+Peak). The correct recognition ratio in the validation set was used as evaluation standards. The absolute error of prediction was set as 0.1, 0.2 and 0.5, which showed the wrong recognition threshold value. The results indicated that the MP-LS-SVM (0.90+Peak) model could achieve the optimal performance in all three absolute error standards (0.1, 0.2 and 0.5), and the correct recognition ratio was 98.3%, 100% and 100%, respectively. The variable selection threshold (0.90+Peak) was the most suitable one in the application of modeling power. It was concluded that modeling power was an effective variable selection method, and near infrared spectroscopy combined with MP-LS-SVM model was successfully applied for the origin

  20. Improving Cognitive Diagnostic Computerized Adaptive Testing by Balancing Attribute Coverage: The Modified Maximum Global Discrimination Index Method

    ERIC Educational Resources Information Center

    Cheng, Ying

    2010-01-01

    This article proposes a new item selection method, namely, the modified maximum global discrimination index (MMGDI) method, for cognitive diagnostic computerized adaptive testing (CD-CAT). The new method captures two aspects of the appeal of an item: (a) the amount of contribution it can make toward adequate coverage of every attribute and (b) the…

  1. Disagreement in genotyping results of drug resistance alleles of the Plasmodium falciparum dihydrofolate reductase (Pfdhfr) gene by allele-specific PCR (ASPCR) assays and Sanger sequencing.

    PubMed

    Sharma, Divya; Lather, Manila; Dykes, Cherry L; Dang, Amita S; Adak, Tridibes; Singh, Om P

    2016-01-01

    The rapid spread of antimalarial drug resistance in Plasmodium falciparum over the past few decades has necessitated intensive monitoring of such resistance for an effective malaria control strategy. P. falciparum dihydropteroate synthase (Pfdhps) and P. falciparum dihydrofolate reductase (Pfdhfr) genes act as molecular markers for resistance against the antimalarial drugs sulphadoxine and pyrimethamine, respectively. Resistance to pyrimethamine which is used as a partner drug in artemisinin combination therapy (ACT) is associated with several mutations in the Pfdhfr gene, namely A16V, N51I, C59R, S108N/T and I164L. Therefore, routine monitoring of Pfdhfr-drug-resistant alleles in a population may help in effective drug resistance management. Allele-specific PCR (ASPCR) is one of the commonly used methods for molecular genotyping of these alleles. In this study, we genotyped 55 samples of P. falciparum for allele discrimination at four codons of Pfdhfr (N51, C59, S108 and I164) by ASPCR using published methods and by Sanger's DNA sequencing method. We found that the ASPCR identified a significantly higher number of mutant alleles as compared to the DNA sequencing method. Such discrepancies arise due to the non-specificity of some of the allele-specific primer sets and due to the lack of sensitivity of Sanger's DNA sequencing method to detect minor alleles present in multiple clone infections. This study reveals the need of a highly specific and sensitive method for genotyping and detecting minor drug-resistant alleles present in multiple clonal infections.

  2. A new two-alternative forced choice method for the unbiased characterization of perceptual bias and discriminability.

    PubMed

    Jogan, Matjaž; Stocker, Alan A

    2014-03-13

    Perception is often biased by secondary stimulus attributes (e.g., stimulus noise, attention, or spatial context). A correct quantitative characterization of perceptual bias is essential for testing hypotheses about the underlying perceptual mechanisms and computations. We demonstrate that the standard two-alternative forced choice (2AFC) method can lead to incorrect estimates of perceptual bias. We present a new 2AFC method that solves this problem by asking subjects to judge the relative perceptual distances between the test and each of two reference stimuli. Naïve subjects can easily perform this task. We successfully validated the new method with a visual motion-discrimination experiment. We demonstrate that the method permits an efficient and accurate characterization of perceptual bias and simultaneously provides measures of discriminability for both the reference and test stimulus, all from a single stimulus condition. This makes it an attractive choice for the characterization of perceptual bias and discriminability in a wide variety of psychophysical experiments.

  3. Monitoring of facial stress during space flight: Optical computer recognition combining discriminative and generative methods

    NASA Astrophysics Data System (ADS)

    Dinges, David F.; Venkataraman, Sundara; McGlinchey, Eleanor L.; Metaxas, Dimitris N.

    2007-02-01

    Astronauts are required to perform mission-critical tasks at a high level of functional capability throughout spaceflight. Stressors can compromise their ability to do so, making early objective detection of neurobehavioral problems in spaceflight a priority. Computer optical approaches offer a completely unobtrusive way to detect distress during critical operations in space flight. A methodology was developed and a study completed to determine whether optical computer recognition algorithms could be used to discriminate facial expressions during stress induced by performance demands. Stress recognition from a facial image sequence is a subject that has not received much attention although it is an important problem for many applications beyond space flight (security, human-computer interaction, etc.). This paper proposes a comprehensive method to detect stress from facial image sequences by using a model-based tracker. The image sequences were captured as subjects underwent a battery of psychological tests under high- and low-stress conditions. A cue integration-based tracking system accurately captured the rigid and non-rigid parameters of different parts of the face (eyebrows, lips). The labeled sequences were used to train the recognition system, which consisted of generative (hidden Markov model) and discriminative (support vector machine) parts that yield results superior to using either approach individually. The current optical algorithm methods performed at a 68% accuracy rate in an experimental study of 60 healthy adults undergoing periods of high-stress versus low-stress performance demands. Accuracy and practical feasibility of the technique is being improved further with automatic multi-resolution selection for the discretization of the mask, and automated face detection and mask initialization algorithms.

  4. Discriminating between HuR and TTP binding sites using the k-spectrum kernel method

    PubMed Central

    Goldberg, Debra S.; Dowell, Robin

    2017-01-01

    Background The RNA binding proteins (RBPs) human antigen R (HuR) and Tristetraprolin (TTP) are known to exhibit competitive binding but have opposing effects on the bound messenger RNA (mRNA). How cells discriminate between the two proteins is an interesting problem. Machine learning approaches, such as support vector machines (SVMs), may be useful in the identification of discriminative features. However, this method has yet to be applied to studies of RNA binding protein motifs. Results Applying the k-spectrum kernel to a support vector machine (SVM), we first verified the published binding sites of both HuR and TTP. Additional feature engineering highlighted the U-rich binding preference of HuR and AU-rich binding preference for TTP. Domain adaptation along with multi-task learning was used to predict the common binding sites. Conclusion The distinction between HuR and TTP binding appears to be subtle content features. HuR prefers strongly U-rich sequences whereas TTP prefers AU-rich as with increasing A content, the sequences are more likely to be bound only by TTP. Our model is consistent with competitive binding of the two proteins, particularly at intermediate AU-balanced sequences. This suggests that fine changes in the A/U balance within a untranslated region (UTR) can alter the binding and subsequent stability of the message. Both feature engineering and domain adaptation emphasized the extent to which these proteins recognize similar general sequence features. This work suggests that the k-spectrum kernel method could be useful when studying RNA binding proteins and domain adaptation techniques such as feature augmentation could be employed particularly when examining RBPs with similar binding preferences. PMID:28333956

  5. New Geophysical Technique for Mineral Exploration and Mineral Discrimination Based on Electromagnetic Methods

    SciTech Connect

    Michael S. Zhdanov

    2009-03-09

    The research during the first two years of the project was focused on developing the foundations of a new geophysical technique for mineral exploration and mineral discrimination, based on electromagnetic (EM) methods. The developed new technique is based on examining the spectral induced polarization effects in electromagnetic data using effective-medium theory and advanced methods of 3-D modeling and inversion. The analysis of IP phenomena is usually based on models with frequency dependent complex conductivity distribution. In this project, we have developed a rigorous physical/mathematical model of heterogeneous conductive media based on the effective-medium approach. The new generalized effective-medium theory of IP effect (GEMTIP) provides a unified mathematical method to study heterogeneity, multi-phase structure, and polarizability of rocks. The geoelectrical parameters of a new composite conductivity model are determined by the intrinsic petrophysical and geometrical characteristics of composite media: mineralization and/or fluid content of rocks, matrix composition, porosity, anisotropy, and polarizability of formations. The new GEMTIP model of multi-phase conductive media provides a quantitative tool for evaluation of the type of mineralization, and the volume content of different minerals using electromagnetic data. We have developed a 3-D EM-IP modeling algorithm using the integral equation (IE) method. Our IE forward modeling software is based on the contraction IE method, which improves the convergence rate of the iterative solvers. This code can handle various types of sources and receivers to compute the effect of a complex resistivity model. We have demonstrated that the generalized effective-medium theory of induced polarization (GEMTIP) in combination with the IE forward modeling method can be used for rock-scale forward modeling from grain-scale parameters. The numerical modeling study clearly demonstrates how the various complex resistivity

  6. Short communication: The combined use of linkage disequilibrium-based haploblocks and allele frequency-based haplotype selection methods enhances genomic evaluation accuracy in dairy cattle.

    PubMed

    Jónás, Dávid; Ducrocq, Vincent; Croiseau, Pascal

    2017-04-01

    The construction and use of haploblocks [adjacent single nucleotide polymorphisms (SNP) in strong linkage disequilibrium] for genomic evaluation is advantageous, because the number of effects to be estimated can be reduced without discarding relevant genomic information. Furthermore, haplotypes (the combination of 2 or more SNP) can increase the probability of capturing the quantitative trait loci effect compared with individual SNP markers. With regards to haplotypes, the allele frequency parameter is also of interest, because as a selection criterion, it allows the number of rare alleles to be reduced, and the effects of those alleles are usually difficult to estimate. We have proposed a simple pipeline that simultaneously incorporates linkage disequilibrium and allele frequency information in genomic evaluation, and here we present the first results obtained with this procedure. We used a population of 2,235 progeny-tested bulls from the Montbéliarde breed for the tests. Phenotype data were available in the form of daughter yield deviations on 5 production traits, and genotype data were available from the 50K SNP chip. We conducted a classical validation study by splitting the population into training (80% oldest animals) and validation (20% youngest animals) sets to emulate a real-life scenario in which the selection candidates had no available phenotype data. We measured all reported parameters for the validation set. Our results proved that the proposed method was indeed advantageous, and that the accuracy of genomic evaluation could be improved. Compared with results from a genomic BLUP analysis, correlations between daughter yield deviations (a proxy for true) and genomic estimated breeding values increased by an average of 2.7 percentage points for the 5 traits. Inflation of the genomic evaluation of the selection candidates was also significantly reduced. The proposed method outperformed the other SNP and haplotype-based tests we had evaluated in a

  7. Competitive allele-specific TaqMan PCR (Cast-PCR) is a sensitive, specific and fast method for BRAF V600 mutation detection in Melanoma patients

    PubMed Central

    Barbano, Raffaela; Pasculli, Barbara; Coco, Michelina; Fontana, Andrea; Copetti, Massimiliano; Rendina, Michelina; Valori, Vanna Maria; Graziano, Paolo; Maiello, Evaristo; Fazio, Vito Michele; Parrella, Paola

    2015-01-01

    BRAF codon 600 mutation testing of melanoma patients is mandatory for the choice of the most appropriate therapy in the clinical setting. Competitive allele specific TaqMan PCR (Cast-PCR) technology allows not only the selective amplification of minor alleles, but it also blocks the amplification of non-mutant allele. We genotyped codon 600 of the BRAF gene in 54 patients’ samples by Cast-PCR and bidirectional direct sequence analysis. All the mutations detected by sequencing were also identified by Cast-PCR. In addition, Cast-PCR assay detected four samples carrying mutations and was able to clearly identify two mutations of uncertain interpretation by Sanger sequencing. The limit of detection of Cast-PCR was evaluated by constructing dilution curves of BRAFV600E and BRAFV600K mutated clinical samples mixed with a not-mutated specimens. Both mutations could be detected until a 1:100 mutated/not mutated ratio. Cloning and sequencing of the clones was used to confirm mutations on representative discrepant cases. Cast PCR performances were not affected by intratumour heterogeneity, and less affected by melanin content. Our results indicate that Cast-PCR is a reliable diagnostic tool for the identification of melanoma patients as eligible to be treated with TKIs and might be implemented in the clinical setting as elective screening method. PMID:26690267

  8. THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites

    PubMed Central

    Chang, Hsiao-Han; Worby, Colin J.; Yeka, Adoke; Nankabirwa, Joaniter; Kamya, Moses R.; Staedke, Sarah G.; Hubbart, Christina; Amato, Roberto; Kwiatkowski, Dominic P.

    2017-01-01

    As many malaria-endemic countries move towards elimination of Plasmodium falciparum, the most virulent human malaria parasite, effective tools for monitoring malaria epidemiology are urgent priorities. P. falciparum population genetic approaches offer promising tools for understanding transmission and spread of the disease, but a high prevalence of multi-clone or polygenomic infections can render estimation of even the most basic parameters, such as allele frequencies, challenging. A previous method, COIL, was developed to estimate complexity of infection (COI) from single nucleotide polymorphism (SNP) data, but relies on monogenomic infections to estimate allele frequencies or requires external allele frequency data which may not available. Estimates limited to monogenomic infections may not be representative, however, and when the average COI is high, they can be difficult or impossible to obtain. Therefore, we developed THE REAL McCOIL, Turning HEterozygous SNP data into Robust Estimates of ALelle frequency, via Markov chain Monte Carlo, and Complexity Of Infection using Likelihood, to incorporate polygenomic samples and simultaneously estimate allele frequency and COI. This approach was tested via simulations then applied to SNP data from cross-sectional surveys performed in three Ugandan sites with varying malaria transmission. We show that THE REAL McCOIL consistently outperforms COIL on simulated data, particularly when most infections are polygenomic. Using field data we show that, unlike with COIL, we can distinguish epidemiologically relevant differences in COI between and within these sites. Surprisingly, for example, we estimated high average COI in a peri-urban subregion with lower transmission intensity, suggesting that many of these cases were imported from surrounding regions with higher transmission intensity. THE REAL McCOIL therefore provides a robust tool for understanding the molecular epidemiology of malaria across transmission settings. PMID

  9. Comparing the Classification Accuracy among Nonparametric, Parametric Discriminant Analysis and Logistic Regression Methods.

    ERIC Educational Resources Information Center

    Ferrer, Alvaro J. Arce; Wang, Lin

    This study compared the classification performance among parametric discriminant analysis, nonparametric discriminant analysis, and logistic regression in a two-group classification application. Field data from an organizational survey were analyzed and bootstrapped for additional exploration. The data were observed to depart from multivariate…

  10. A rapid and robust sequence-based genotyping method for BoLA-DRB3 alleles in large numbers of heterozygous cattle.

    PubMed

    Baxter, R; Hastings, N; Law, A; Glass, E J

    2008-10-01

    The BoLA-DRB3 gene is a highly polymorphic major histocompatibility complex class II gene of cattle with over one hundred alleles reported. Most of the polymorphisms are located in exon 2, which encodes the peptide-binding cleft, and these sequence differences play a role in variability of immune responsiveness and disease resistance. However, the high degree of polymorphism in exon 2 leads to difficulty in accurately genotyping cattle, especially heterozygous animals. In this study, we have improved and simplified an earlier sequence-based typing method to easily and reliably genotype cattle for BoLA-DRB3. In contrast to the earlier method, which used a nested primer set to amplify exon 2 followed by sequencing with internal primers, the new method uses only internal primers for both amplification and sequencing, which results in high-quality sequence across the entire exon. The haplofinder software, which assigns alleles from the heterozygous sequence, now has a pre-processing step that uses a consensus of all known alleles and checks for errors in base calling, thus improving the ability to process large numbers of samples. In addition, advances in sequencing technology have reduced the requirement for manual editing and improved the clarity of heterozygous base calls, resulting in longer and clearer sequence reads. Taken together, this has resulted in a rapid and robust method for genotyping large numbers of heterozygous samples for BoLA-DRB3 polymorphisms. Over 400 Holstein-Charolais cattle have now been genotyped for BoLA-DRB3 using this approach.

  11. Discrimination of coherent features in turbulent boundary layers by the entropy method

    NASA Technical Reports Server (NTRS)

    Corke, T. C.; Guezennec, Y. G.

    1984-01-01

    Entropy in information theory is defined as the expected or mean value of the measure of the amount of self-information contained in the ith point of a distribution series x sub i, based on its probability of occurrence p(x sub i). If p(x sub i) is the probability of the ith state of the system in probability space, then the entropy, E(X) = - sigma p(x sub i) logp (x sub i), is a measure of the disorder in the system. Based on this concept, a method was devised which sought to minimize the entropy in a time series in order to construct the signature of the most coherent motions. The constrained minimization was performed using a Lagrange multiplier approach which resulted in the solution of a simultaneous set of non-linear coupled equations to obtain the coherent time series. The application of the method to space-time data taken by a rake of sensors in the near-wall region of a turbulent boundary layer was presented. The results yielded coherent velocity motions made up of locally decelerated or accelerated fluid having a streamwise scale of approximately 100 nu/u(tau), which is in qualitative agreement with the results from other less objective discrimination methods.

  12. A method for discriminating systemic and cortical hemodynamic changes by time domain fNIRS

    NASA Astrophysics Data System (ADS)

    Zucchelli, Lucia; Spinelli, Lorenzo; Contini, Davide; Re, Rebecca; Torricelli, Alessandro

    2013-06-01

    Functional near-infrared spectroscopy (fNIRS) is a non-invasive optical technique able to measure hemodynamic response in the brain cortex. Among the different approaches the fNIRS can be based on, the time resolved one allows a straightforward relationship between the photon detection time and its path within the medium, improving the discrimination of the information content relative to the different layers the tissues are composed of. Thus absorption and scattering properties of the probed tissue can be estimated, and from them the oxy- and deoxy-hemoglobin concentration. However, an open issue in the optical imaging studies is still the accuracy in separating the superficial hemodynamic changes from those happening in deeper regions of the head and more likely involving the cerebral cortex. In fact a crucial point is the precise estimate of the time dependent pathlength spent by photons within the perturbed medium. A novel method for the calculus of the absorption properties in time domain fNIRS, based on a refined computation of photon pathlength in multilayered media, is proposed. The method takes into account the non-ideality of the measurement system (its instrument response function) and the heterogeneous structure of the head. The better accuracy in computing the optical pathlength can improve the NIRS data analysis, especially for the deeper layer. Simulations and preliminary analysis on in vivo data have been performed to validate the method and are here presented.

  13. An Improved Method for High-throughput Discrimination and Enumeration of Sedimentary Cells Using Flow Cytometry

    NASA Astrophysics Data System (ADS)

    Morono, Y.; Kallmeyer, J.; Terada, T.; Inagaki, F.; IODP Expedition 329 Shipboard Science Party

    2011-12-01

    Detection and enumeration of microbial life in marine subsurface environments provides primary information on the extent and habitability of the Earth's biosphere. Flow cytometry (FCM) is a powerful tool for identifying and enumerating fluorescence-stained cells with high throughput, using fluorescent intensity, range of wavelength, and cell size. FCM is widely used in medical sciences and aquatic microbial ecology. However, mineral grains and difficulties in distinguishing between life cells and non-specific background fluorescence prevented FCM to be applied for counting microbial cells in sediment or rock samples. SYBR Green I-stained cells can be distinguished from non-biological background signals based on differences in their fluorescence spectra. Here we extended this technique to FCM analysis by modifying the cell detachment protocol using a density gradient method, and then standardized an FCM cell counting method for various types of marine subsurface sediments. Microbial cells in sediment samples could effectively be detached and analyzed discriminatively with FCM. The high capacity of FCM to count particles (up to 10,000 cells/sec) and its high sensitivity will provide information about microbial cell abundance at high spatial resolution and with unprecedented accuracy. This improved cell count method will be useful to evaluate samples with high depth resolution, including narrow geochemical and geological interfaces as potential specific microbial niches, and may even help to asses very low population densities at the fringe of the biosphere.

  14. Using a Euclid distance discriminant method to find protein coding genes in the yeast genome.

    PubMed

    Zhang, Chun-Ting; Wang, Ju; Zhang, Ren

    2002-02-01

    The Euclid distance discriminant method is used to find protein coding genes in the yeast genome, based on the single nucleotide frequencies at three codon positions in the ORFs. The method is extremely simple and may be extended to find genes in prokaryotic genomes or eukaryotic genomes with less introns. Six-fold cross-validation tests have demonstrated that the accuracy of the algorithm is better than 93%. Based on this, it is found that the total number of protein coding genes in the yeast genome is less than or equal to 5579 only, about 3.8-7.0% less than 5800-6000, which is currently widely accepted. The base compositions at three codon positions are analyzed in details using a graphic method. The result shows that the preference codons adopted by yeast genes are of the RGW type, where R, G and W indicate the bases of purine, non-G and A/T, whereas the 'codons' in the intergenic sequences are of the form NNN, where N denotes any base. This fact constitutes the basis of the algorithm to distinguish between coding and non-coding ORFs in the yeast genome. The names of putative non-coding ORFs are listed here in detail.

  15. Photoacoustic discrimination of vascular and pigmented lesions using classical and Bayesian methods

    NASA Astrophysics Data System (ADS)

    Swearingen, Jennifer A.; Holan, Scott H.; Feldman, Mary M.; Viator, John A.

    2010-01-01

    Discrimination of pigmented and vascular lesions in skin can be difficult due to factors such as size, subungual location, and the nature of lesions containing both melanin and vascularity. Misdiagnosis may lead to precancerous or cancerous lesions not receiving proper medical care. To aid in the rapid and accurate diagnosis of such pathologies, we develop a photoacoustic system to determine the nature of skin lesions in vivo. By irradiating skin with two laser wavelengths, 422 and 530 nm, we induce photoacoustic responses, and the relative response at these two wavelengths indicates whether the lesion is pigmented or vascular. This response is due to the distinct absorption spectrum of melanin and hemoglobin. In particular, pigmented lesions have ratios of photoacoustic amplitudes of approximately 1.4 to 1 at the two wavelengths, while vascular lesions have ratios of about 4.0 to 1. Furthermore, we consider two statistical methods for conducting classification of lesions: standard multivariate analysis classification techniques and a Bayesian-model-based approach. We study 15 human subjects with eight vascular and seven pigmented lesions. Using the classical method, we achieve a perfect classification rate, while the Bayesian approach has an error rate of 20%.

  16. Passive fetal heart rate monitoring apparatus and method with enhanced fetal heart beat discrimination

    NASA Technical Reports Server (NTRS)

    Zahorian, Stephen A. (Inventor); Livingston, David L. (Inventor); Pretlow, III, Robert A. (Inventor)

    1996-01-01

    An apparatus for acquiring signals emitted by a fetus, identifying fetal heart beats and determining a fetal heart rate. Multiple sensor signals are outputted by a passive fetal heart rate monitoring sensor. Multiple parallel nonlinear filters filter these multiple sensor signals to identify fetal heart beats in the signal data. A processor determines a fetal heart rate based on these identified fetal heart beats. The processor includes the use of a figure of merit weighting of heart rate estimates based on the identified heart beats from each filter for each signal. The fetal heart rate thus determined is outputted to a display, storage, or communications channel. A method for enhanced fetal heart beat discrimination includes acquiring signals from a fetus, identifying fetal heart beats from the signals by multiple parallel nonlinear filtering, and determining a fetal heart rate based on the identified fetal heart beats. A figure of merit operation in this method provides for weighting a plurality of fetal heart rate estimates based on the identified fetal heart beats and selecting the highest ranking fetal heart rate estimate.

  17. Reduction of truncation artifacts in CT images via a discriminative dictionary representation method

    NASA Astrophysics Data System (ADS)

    Chen, Yang; Li, Ke; Li, Yinsheng; Hsieh, Jiang; Chen, Guang-Hong

    2016-04-01

    When the scan field of view (SFOV) of a CT system is not large enough to enclose the entire cross-section of a patient, or the patient needs to be intentionally positioned partially outside the SFOV for certain clinical CT scans, truncation artifacts are often observed in the reconstructed CT images. Conventional wisdom to reduce truncation artifacts is to complete the truncated projection data via data extrapolation with different a priori assumptions. This paper presents a novel truncation artifact reduction method that directly works in the CT image domain. Specifically, a discriminative dictionary that includes a sub-dictionary of truncation artifacts and a sub-dictionary of non-artifact image information was used to separate a truncation artifact-contaminated image into two sub-images, one with reduced truncation artifacts, and the other one containing only the truncation artifacts. Both experimental phantom and retrospective human subject studies have been performed to characterize the performance of the proposed truncation artifact reduction method.

  18. Haptic exploratory behavior during object discrimination: a novel automatic annotation method.

    PubMed

    Jansen, Sander E M; Bergmann Tiest, Wouter M; Kappers, Astrid M L

    2015-01-01

    In order to acquire information concerning the geometry and material of handheld objects, people tend to execute stereotypical hand movement patterns called haptic Exploratory Procedures (EPs). Manual annotation of haptic exploration trials with these EPs is a laborious task that is affected by subjectivity, attentional lapses, and viewing angle limitations. In this paper we propose an automatic EP annotation method based on position and orientation data from motion tracking sensors placed on both hands and inside a stimulus. A set of kinematic variables is computed from these data and compared to sets of predefined criteria for each of four EPs. Whenever all criteria for a specific EP are met, it is assumed that that particular hand movement pattern was performed. This method is applied to data from an experiment where blindfolded participants haptically discriminated between objects differing in hardness, roughness, volume, and weight. In order to validate the method, its output is compared to manual annotation based on video recordings of the same trials. Although mean pairwise agreement is less between human-automatic pairs than between human-human pairs (55.7% vs 74.5%), the proposed method performs much better than random annotation (2.4%). Furthermore, each EP is linked to a specific object property for which it is optimal (e.g., Lateral Motion for roughness). We found that the percentage of trials where the expected EP was found does not differ between manual and automatic annotation. For now, this method cannot yet completely replace a manual annotation procedure. However, it could be used as a starting point that can be supplemented by manual annotation.

  19. DISCOVER: a feature-based discriminative method for motif search in complex genomes

    PubMed Central

    Fu, Wenjie; Ray, Pradipta; Xing, Eric P.

    2009-01-01

    Motivation: Identifying transcription factor binding sites (TFBSs) encoding complex regulatory signals in metazoan genomes remains a challenging problem in computational genomics. Due to degeneracy of nucleotide content among binding site instances or motifs, and intricate ‘grammatical organization’ of motifs within cis-regulatory modules (CRMs), extant pattern matching-based in silico motif search methods often suffer from impractically high false positive rates, especially in the context of analyzing large genomic datasets, and noisy position weight matrices which characterize binding sites. Here, we try to address this problem by using a framework to maximally utilize the information content of the genomic DNA in the region of query, taking cues from values of various biologically meaningful genetic and epigenetic factors in the query region such as clade-specific evolutionary parameters, presence/absence of nearby coding regions, etc. We present a new method for TFBS prediction in metazoan genomes that utilizes both the CRM architecture of sequences and a variety of features of individual motifs. Our proposed approach is based on a discriminative probabilistic model known as conditional random fields that explicitly optimizes the predictive probability of motif presence in large sequences, based on the joint effect of all such features. Results: This model overcomes weaknesses in earlier methods based on less effective statistical formalisms that are sensitive to spurious signals in the data. We evaluate our method on both simulated CRMs and real Drosophila sequences in comparison with a wide spectrum of existing models, and outperform the state of the art by 22% in F1 score. Availability and Implementation: The code is publicly available at http://www.sailing.cs.cmu.edu/discover.html. Contact: epxing@cs.cmu.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19478006

  20. An Improved Method for Discriminating ECG Signals using Typical Nonlinear Dynamic Parameters and Recurrence Quantification Analysis in Cardiac Disease Therapy.

    PubMed

    Tang, M; Chang, C Q; Fung, P C W; Chau, K T; Chan, F H Y

    2005-01-01

    The discrimination of ECG signals using nonlinear dynamic parameters is of crucial importance in the cardiac disease therapy and chaos control for arrhythmia defibrillation in the cardiac system. However, the discrimination results of previous studies using features such as maximal Lyapunov exponent (λmax) and correlation dimension (D2) alone are somewhat limited in recognition rate. In this paper, improved methods for computing λmaxand D2are purposed. Another parameter from recurrence quantification analysis is incorporated to the new multi-feature Bayesian classifier with λmaxand D2so as to improve the discrimination power. Experimental results have verified the prediction using Fisher discriminant that the maximal vertical line length (Vmax) from recurrence quantification analysis is the best to distinguish different ECG classes. Experimental results using the MIT-BIH Arrhythmia Database show improved and excellent overall accuracy (96.3%), average sensitivity (96.3%) and average specificity (98.15%) for discriminating sinus, premature ventricular contraction and ventricular flutter signals.

  1. A review of simultaneous visual discrimination as a method of training octopuses.

    PubMed

    Boal, J G

    1996-05-01

    I have presented a review and critique of the procedures employed in simultaneous discrimination training experiments using octopuses as subjects. Procedural variables were analyzed statistically for their influence on experimental outcome. The variables most significantly associated with successful discriminations included use of a specific start location for subjects, shock as negative reinforcement, fewer trials per session, more sessions per day, and discriminations based on stimulus brightness. No experiment controlled all potential sources of inadvertent cues, and subjects' performances appeared to be sensitive to exact procedural details. The most common practice diminishing evidence for learning involved reward that coincided with the subject's pre-existing preferences. I found no evidence that sub-optimal experimental designs biased experimental outcomes in any significant and systematic way. Although there is sufficient reason for rejecting results of published simultaneous discrimination training experiments, careful conclusive experiments remain to be performed.

  2. [Outlier sample discriminating methods for building calibration model in melons quality detecting using NIR spectra].

    PubMed

    Tian, Hai-Qing; Wang, Chun-Guang; Zhang, Hai-Jun; Yu, Zhi-Hong; Li, Jian-Kang

    2012-11-01

    Outlier samples strongly influence the precision of the calibration model in soluble solids content measurement of melons using NIR Spectra. According to the possible sources of outlier samples, three methods (predicted concentration residual test; Chauvenet test; leverage and studentized residual test) were used to discriminate these outliers respectively. Nine suspicious outliers were detected from calibration set which including 85 fruit samples. Considering the 9 suspicious outlier samples maybe contain some no-outlier samples, they were reclaimed to the model one by one to see whether they influence the model and prediction precision or not. In this way, 5 samples which were helpful to the model joined in calibration set again, and a new model was developed with the correlation coefficient (r) 0. 889 and root mean square errors for calibration (RMSEC) 0.6010 Brix. For 35 unknown samples, the root mean square errors prediction (RMSEP) was 0.854 degrees Brix. The performance of this model was more better than that developed with non outlier was eliminated from calibration set (r = 0.797, RMSEC= 0.849 degrees Brix, RMSEP = 1.19 degrees Brix), and more representative and stable with all 9 samples were eliminated from calibration set (r = 0.892, RMSEC = 0.605 degrees Brix, RMSEP = 0.862 degrees).

  3. A simple method for discriminating between cell membrane and cytosolic proteins.

    PubMed

    Serna, Laura

    2005-03-01

    * Transgenic plants expressing either green fluorescent protein (GFP)-genomic DNA or GFP-cDNA fusions have been used as powerful tools to define the subcellular localization of many proteins. Because most plant cells are highly vacuolated, the cytosol is confined to a thin layer at the periphery of the cells, making it very difficult to distinguish among cell wall, cell membrane and cytosolic GFP-fusion proteins. * Plasmolysis tests inform about cell-wall localization of GFP-tagged proteins, but they do not discriminate between its cell membrane and/or cytoplasmic localization. By observing the GFP signal in transgenic protoplasts placed at a hypotonic solution, it was possible to distinguish between cell membrane and cytosolic GFP-tagged proteins. * The osmotic disruption of the protoplast vacuole in the hypotonic solution allows the diffusion of the GFP signal from the cell periphery to the central part of the cell volume when the GFP is fused to a soluble protein. By contrast, such diffusion does not occur when the protein under study is attached to the cell membrane. * The present method is easier, faster and cheaper than subcellular fractionating studies and/or immunoelectron microscopy, which have been traditionally used to discern between cell membrane and cytosolic proteins.

  4. Saturation-recovery electron paramagnetic resonance discrimination by oxygen transport (DOT) method for characterizing membrane domains.

    PubMed

    Subczynski, Witold K; Widomska, Justyna; Wisniewska, Anna; Kusumi, Akihiro

    2007-01-01

    The discrimination by oxygen transport (DOT) method is a dual-probe saturation-recovery electron paramagnetic resonance approach in which the observable parameter is the spin-lattice relaxation time (T1) of lipid spin labels, and the measured value is the bimolecular collision rate between molecular oxygen and the nitroxide moiety of spin labels. This method has proven to be extremely sensitive to changes in the local oxygen diffusion-concentration product (around the nitroxide moiety) because of the long T1 of lipid spin labels (1-10 micros) and also because molecular oxygen is a unique probe molecule. Molecular oxygen is paramagnetic, small, and has the appropriate level of hydrophobicity that allows it to partition into various supramolecular structures such as different membrane domains. When located in two different membrane domains, the spin label alone most often cannot differentiate between these domains, giving very similar (indistinguishable) conventional electron paramagnetic resonance spectra and similar T1 values. However, even small differences in lipid packing in these domains will affect oxygen partitioning and oxygen diffusion, which can be easily detected by observing the different T1s from spin labels in these two locations in the presence of molecular oxygen. The DOT method allows one not only to distinguish between the different domains, but also to obtain the value of the oxygen diffusion-concentration product in these domains, which is a useful physical characteristic of the organization of lipids in domains. Profiles of the oxygen diffusion-concentration product (the oxygen transport parameter) in coexisting domains can be obtained in situ without the need for the physical separation of the two domains. Furthermore, under optimal conditions, the exchange rate of spin-labeled molecules between the two domains could be measured.

  5. Allelic diversity at MHC class II DQ loci in buffalo (Bubalus bubalis): evidence for duplication.

    PubMed

    Niranjan, Saket K; Deb, Sitangsu M; Kumar, Subodh; Mitra, Abhijit; Sharma, Arjava; Sakaram, Durgam; Naskar, Soumen; Sharma, Deepak; Sharma, Sita R

    2010-12-01

    The genetic diversity of MHC class II DQ genes was investigated in riverine buffalo (Bubalus bubalis) by PCR-RFLP and sequencing. Highly variable regions (exons 2-3) of DQ genes were amplified from 152 buffaloes and genotyped by PCR-RFLP. Alleles identified by differential restriction patterns were sequenced for the characterization. PCR-RFLP was a rapid method to discriminate between DQA1 and duplicated DQA2 genes in buffalo, however, the method appeared to be inadequate for determining the more complicated DQB genotypes. A total of 7 and 10 alleles were identified for DQA and DQB loci, respectively. Nucleotide as well as amino acid variations among DQ alleles particularly at peptide binding regions were high. Such variations were as expected higher in DQB than DQA alleles. The phylogenetic analysis for both genes revealed the grouping of alleles into two major sub-groups with higher genetic divergence. High divergence among DQ allelic families and the isolation of two diverse DQA and DQB sequences from individual samples indicated duplication of DQ loci was similar in buffalo to other ruminants.

  6. Novel methods for the molecular discrimination of Fasciola spp. on the basis of nuclear protein-coding genes.

    PubMed

    Shoriki, Takuya; Ichikawa-Seki, Madoka; Suganuma, Keisuke; Naito, Ikunori; Hayashi, Kei; Nakao, Minoru; Aita, Junya; Mohanta, Uday Kumar; Inoue, Noboru; Murakami, Kenji; Itagaki, Tadashi

    2016-06-01

    Fasciolosis is an economically important disease of livestock caused by Fasciola hepatica, Fasciola gigantica, and aspermic Fasciola flukes. The aspermic Fasciola flukes have been discriminated morphologically from the two other species by the absence of sperm in their seminal vesicles. To date, the molecular discrimination of F. hepatica and F. gigantica has relied on the nucleotide sequences of the internal transcribed spacer 1 (ITS1) region. However, ITS1 genotypes of aspermic Fasciola flukes cannot be clearly differentiated from those of F. hepatica and F. gigantica. Therefore, more precise and robust methods are required to discriminate Fasciola spp. In this study, we developed PCR restriction fragment length polymorphism and multiplex PCR methods to discriminate F. hepatica, F. gigantica, and aspermic Fasciola flukes on the basis of the nuclear protein-coding genes, phosphoenolpyruvate carboxykinase and DNA polymerase delta, which are single locus genes in most eukaryotes. All aspermic Fasciola flukes used in this study had mixed fragment pattern of F. hepatica and F. gigantica for both of these genes, suggesting that the flukes are descended through hybridization between the two species. These molecular methods will facilitate the identification of F. hepatica, F. gigantica, and aspermic Fasciola flukes, and will also prove useful in etiological studies of fasciolosis.

  7. THE BOLOCAM GALACTIC PLANE SURVEY. VIII. A MID-INFRARED KINEMATIC DISTANCE DISCRIMINATION METHOD

    SciTech Connect

    Ellsworth-Bowers, Timothy P.; Glenn, Jason; Battersby, Cara; Ginsburg, Adam; Bally, John; Rosolowsky, Erik; Mairs, Steven; Evans, Neal J. II; Shirley, Yancy L.

    2013-06-10

    We present a new distance estimation method for dust-continuum-identified molecular cloud clumps. Recent (sub-)millimeter Galactic plane surveys have cataloged tens of thousands of these objects, plausible precursors to stellar clusters, but detailed study of their physical properties requires robust distance determinations. We derive Bayesian distance probability density functions (DPDFs) for 770 objects from the Bolocam Galactic Plane Survey in the Galactic longitude range 7. Degree-Sign 5 {<=} l {<=} 65 Degree-Sign . The DPDF formalism is based on kinematic distances, and uses any number of external data sets to place prior distance probabilities to resolve the kinematic distance ambiguity (KDA) for objects in the inner Galaxy. We present here priors related to the mid-infrared absorption of dust in dense molecular regions and the distribution of molecular gas in the Galactic disk. By assuming a numerical model of Galactic mid-infrared emission and simple radiative transfer, we match the morphology of (sub-)millimeter thermal dust emission with mid-infrared absorption to compute a prior DPDF for distance discrimination. Selecting objects first from (sub-)millimeter source catalogs avoids a bias towards the darkest infrared dark clouds (IRDCs) and extends the range of heliocentric distance probed by mid-infrared extinction and includes lower-contrast sources. We derive well-constrained KDA resolutions for 618 molecular cloud clumps, with approximately 15% placed at or beyond the tangent distance. Objects with mid-infrared contrast sufficient to be cataloged as IRDCs are generally placed at the near kinematic distance. Distance comparisons with Galactic Ring Survey KDA resolutions yield a 92% agreement. A face-on view of the Milky Way using resolved distances reveals sections of the Sagittarius and Scutum-Centaurus Arms. This KDA-resolution method for large catalogs of sources through the combination of (sub-)millimeter and mid-infrared observations of molecular

  8. Non-parametric bootstrapping method for measuring the temporal discrimination threshold for movement disorders

    NASA Astrophysics Data System (ADS)

    Butler, John S.; Molloy, Anna; Williams, Laura; Kimmich, Okka; Quinlivan, Brendan; O'Riordan, Sean; Hutchinson, Michael; Reilly, Richard B.

    2015-08-01

    Objective. Recent studies have proposed that the temporal discrimination threshold (TDT), the shortest detectable time period between two stimuli, is a possible endophenotype for adult onset idiopathic isolated focal dystonia (AOIFD). Patients with AOIFD, the third most common movement disorder, and their first-degree relatives have been shown to have abnormal visual and tactile TDTs. For this reason it is important to fully characterize each participant’s data. To date the TDT has only been reported as a single value. Approach. Here, we fit individual participant data with a cumulative Gaussian to extract the mean and standard deviation of the distribution. The mean represents the point of subjective equality (PSE), the inter-stimulus interval at which participants are equally likely to respond that two stimuli are one stimulus (synchronous) or two different stimuli (asynchronous). The standard deviation represents the just noticeable difference (JND) which is how sensitive participants are to changes in temporal asynchrony around the PSE. We extended this method by submitting the data to a non-parametric bootstrapped analysis to get 95% confidence intervals on individual participant data. Main results. Both the JND and PSE correlate with the TDT value but are independent of each other. Hence this suggests that they represent different facets of the TDT. Furthermore, we divided groups by age and compared the TDT, PSE, and JND values. The analysis revealed a statistical difference for the PSE which was only trending for the TDT. Significance. The analysis method will enable deeper analysis of the TDT to leverage subtle differences within and between control and patient groups, not apparent in the standard TDT measure.

  9. Discrimination of Maize Haploid Seeds from Hybrid Seeds Using Vis Spectroscopy and Support Vector Machine Method.

    PubMed

    Liu, Jin; Guo, Ting-ting; Li, Hao-chuan; Jia, Shi-qiang; Yan, Yan-lu; An, Dong; Zhang, Yao; Chen, Shao-jiang

    2015-11-01

    Doubled haploid (DH) lines are routinely applied in the hybrid maize breeding programs of many institutes and companies for their advantages of complete homozygosity and short breeding cycle length. A key issue in this approach is an efficient screening system to identify haploid kernels from the hybrid kernels crossed with the inducer. At present, haploid kernel selection is carried out manually using the"red-crown" kernel trait (the haploid kernel has a non-pigmented embryo and pigmented endosperm) controlled by the R1-nj gene. Manual selection is time-consuming and unreliable. Furthermore, the color of the kernel embryo is concealed by the pericarp. Here, we establish a novel approach for identifying maize haploid kernels based on visible (Vis) spectroscopy and support vector machine (SVM) pattern recognition technology. The diffuse transmittance spectra of individual kernels (141 haploid kernels and 141 hybrid kernels from 9 genotypes) were collected using a portable UV-Vis spectrometer and integrating sphere. The raw spectral data were preprocessed using smoothing and vector normalization methods. The desired feature wavelengths were selected based on the results of the Kolmogorov-Smirnov test. The wavelengths with p values above 0. 05 were eliminated because the distributions of absorbance data in these wavelengths show no significant difference between haploid and hybrid kernels. Principal component analysis was then performed to reduce the number of variables. The SVM model was evaluated by 9-fold cross-validation. In each round, samples of one genotype were used as the testing set, while those of other genotypes were used as the training set. The mean rate of correct discrimination was 92.06%. This result demonstrates the feasibility of using Vis spectroscopy to identify haploid maize kernels. The method would help develop a rapid and accurate automated screening-system for haploid kernels.

  10. Two dimensional template matching method for buried object discrimination in GPR data

    NASA Astrophysics Data System (ADS)

    Sezgin, Mehmet

    2009-05-01

    In this study discrimination of two different metallic object classes were studied, utilizing Ground Penetrating Radar (GPR). Feature sets of both classes have almost the same information for both Metal Detector (MD) and GPR data. There were no evident features those are easily discriminate classes. Background removal has been applied to original B-Scan data and then a normalization process was performed. Image thresholding was applied to segment B-Scan GPR images. So, main hyperbolic shape of buried object reflection was extracted and then a morphological process was performed optionally. Templates of each class representatives have been obtained and they were searched whether they match with true class or not. Two data sets were examined experimentally. Actually they were obtained in different time and burial for the same objects. Considerably high discrimination performance was obtained which was not possible by using individual Metal Detector data.

  11. Optimization of short tandem repeats (STR) typing method and allele frequency of 8 STR markers in referring to forensic medicine of Semnan Province.

    PubMed

    Eskandarion, M; Najafi, M; Akbari Eidgahi, M; Alipour Tabrizi, A; Golmohamadi, T

    2015-01-01

    Background and Objective: Short Tandem Repeats (STR) show considerable differences among individuals in the population from which they used for identification. There are various methods for analysis of these STR loci, and capillary electrophoresis method already used as an international standard. Due to the high costs of this process, this study aimed to set up a Multiplex PCR method in some standard STR loci so that we can use its PCR product in STR analysis with different methods of HPLC, GC-Mass, and Capillary Electrophoresis. Materials and Methods: 8 typical STR loci in the identification selected according to their size in the two groups of four (CSF1PO, VWA, D18S51, PentaD and TPOX, Amelogenin, FGA, SE33) from NIST (National Institute of Standards and Technology). The above SSR primers prepared from Genbank and Monoplex PCR was designed based on their size. Then, with the changes in temperature conditions, magnesium ion, primers concentration, and setting-up, Hot Start Multiplex PCR of four markers was carried out. PCR product investigated on the agarose gel electrophoresis (3%) and the results of genotyping analyzed by Genetic Analyzer. Results: The Results showed that all STR loci under study are detectable as Monoplex PCR at a temperature of 62°-66° and 1.5 mM magnesium ion. Moreover, Multiplex PCR results showed that when the concentration of primer and temperature measured by the fixed concentration of magnesium, CSF1PO, and D18S51 loci bands are weaker than desired. Using a standard buffer and set Magnesium conditions against changes in the primer concentration and temperature, when Taq polymerase enzyme is added to test tubes at a temperature of 94°, Multiplex PCR bands are visible desirably. Capillary electrophoresis genotyping results obtained in all eight loci and the Locus FGA had the most allelic diversity and the loci TPOX and CSF1PO had the lowest allelic diversity. TPOX and CSF1PO loci had the lowest allelic frequencies, and FGA locus had

  12. Optimization of short tandem repeats (STR) typing method and allele frequency of 8 STR markers in referring to forensic medicine of Semnan Province

    PubMed Central

    Eskandarion, M; Najafi, M; Akbari Eidgahi, M; Alipour Tabrizi, A; Golmohamadi, T

    2015-01-01

    Background and Objective: Short Tandem Repeats (STR) show considerable differences among individuals in the population from which they used for identification. There are various methods for analysis of these STR loci, and capillary electrophoresis method already used as an international standard. Due to the high costs of this process, this study aimed to set up a Multiplex PCR method in some standard STR loci so that we can use its PCR product in STR analysis with different methods of HPLC, GC-Mass, and Capillary Electrophoresis. Materials and Methods: 8 typical STR loci in the identification selected according to their size in the two groups of four (CSF1PO, VWA, D18S51, PentaD and TPOX, Amelogenin, FGA, SE33) from NIST (National Institute of Standards and Technology). The above SSR primers prepared from Genbank and Monoplex PCR was designed based on their size. Then, with the changes in temperature conditions, magnesium ion, primers concentration, and setting-up, Hot Start Multiplex PCR of four markers was carried out. PCR product investigated on the agarose gel electrophoresis (3%) and the results of genotyping analyzed by Genetic Analyzer. Results: The Results showed that all STR loci under study are detectable as Monoplex PCR at a temperature of 62°-66° and 1.5 mM magnesium ion. Moreover, Multiplex PCR results showed that when the concentration of primer and temperature measured by the fixed concentration of magnesium, CSF1PO, and D18S51 loci bands are weaker than desired. Using a standard buffer and set Magnesium conditions against changes in the primer concentration and temperature, when Taq polymerase enzyme is added to test tubes at a temperature of 94°, Multiplex PCR bands are visible desirably. Capillary electrophoresis genotyping results obtained in all eight loci and the Locus FGA had the most allelic diversity and the loci TPOX and CSF1PO had the lowest allelic diversity. TPOX and CSF1PO loci had the lowest allelic frequencies, and FGA locus had

  13. Digital pulse shape discrimination methods for n-γ separation in an EJ-301 liquid scintillation detector

    NASA Astrophysics Data System (ADS)

    Wan, Bo; Zhang, Xue-Ying; Chen, Liang; Ge, Hong-Lin; Ma, Fei; Zhang, Hong-Bin; Ju, Yong-Qin; Zhang, Yan-Bin; Li, Yan-Yan; Xu, Xiao-Wei

    2015-11-01

    A digital pulse shape discrimination system based on a programmable module NI-5772 has been established and tested with an EJ-301 liquid scintillation detector. The module was operated by running programs developed in LabVIEW, with a sampling frequency up to 1.6 GS/s. Standard gamma sources 22Na, 137Cs and 60Co were used to calibrate the EJ-301 liquid scintillation detector, and the gamma response function was obtained. Digital algorithms for the charge comparison method and zero-crossing method have been developed. The experimental results show that both digital signal processing (DSP) algorithms can discriminate neutrons from γ-rays. Moreover, the zero-crossing method shows better n-γ discrimination at 80 keVee and lower, whereas the charge comparison method gives better results at higher thresholds. In addition, the figure-of-merit (FOM) for detectors of two different dimensions were extracted at 9 energy thresholds, and it was found that the smaller detector presented better n-γ separation for fission neutrons. Supported by National Natural Science Foundation of China (91226107, 11305229) and the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA03030300)

  14. A novel HLA-B allele, B*58:01:12, detected in a Taiwanese volunteer bone marrow stem cell donor using sequence-based typing method.

    PubMed

    Yang, K L; Lee, S K; Kao, R H; Lin, C L; Lin, P Y

    2013-08-01

    Human leukocyte antigen-B*58:01:12, a novel rare allele of HLA-B*58:01 variant, was found in a Taiwanese volunteer bone marrow donor by SBT (sequence-based typing) method. The DNA sequence of B*58:01:12 is identical to the sequence of B*58:01:01 in exons 2, 3 and 4 except at nucleotide position 483 where nucleotide C is substituted by T (at codon 137; GAC GAT). Due to the silent point mutation, the amino acid sequence of B*58:01:12 is identical to the sequence of B*58:01:01. The HLA haplotype in association with B*58:01:12 may be deduced as A*33:03-B*58:01:12-DRB1*03:01. The discovery of B*58:01:12 adds further polymorphism of B*58:01 in Taiwanese population.

  15. Testing Allele Transmission of an SNP Set Using a Family-Based Generalized Genetic Random Field Method.

    PubMed

    Li, Ming; Li, Jingyun; He, Zihuai; Lu, Qing; Witte, John S; Macleod, Stewart L; Hobbs, Charlotte A; Cleves, Mario A

    2016-05-01

    Family-based association studies are commonly used in genetic research because they can be robust to population stratification (PS). Recent advances in high-throughput genotyping technologies have produced a massive amount of genomic data in family-based studies. However, current family-based association tests are mainly focused on evaluating individual variants one at a time. In this article, we introduce a family-based generalized genetic random field (FB-GGRF) method to test the joint association between a set of autosomal SNPs (i.e., single-nucleotide polymorphisms) and disease phenotypes. The proposed method is a natural extension of a recently developed GGRF method for population-based case-control studies. It models offspring genotypes conditional on parental genotypes, and, thus, is robust to PS. Through simulations, we presented that under various disease scenarios the FB-GGRF has improved power over a commonly used family-based sequence kernel association test (FB-SKAT). Further, similar to GGRF, the proposed FB-GGRF method is asymptotically well-behaved, and does not require empirical adjustment of the type I error rates. We illustrate the proposed method using a study of congenital heart defects with family trios from the National Birth Defects Prevention Study (NBDPS).

  16. Least squares parameter estimation methods for material decomposition with energy discriminating detectors

    SciTech Connect

    Le, Huy Q.; Molloi, Sabee

    2011-01-15

    Purpose: Energy resolving detectors provide more than one spectral measurement in one image acquisition. The purpose of this study is to investigate, with simulation, the ability to decompose four materials using energy discriminating detectors and least squares minimization techniques. Methods: Three least squares parameter estimation decomposition techniques were investigated for four-material breast imaging tasks in the image domain. The first technique treats the voxel as if it consisted of fractions of all the materials. The second method assumes that a voxel primarily contains one material and divides the decomposition process into segmentation and quantification tasks. The third is similar to the second method but a calibration was used. The simulated computed tomography (CT) system consisted of an 80 kVp spectrum and a CdZnTe (CZT) detector that could resolve the x-ray spectrum into five energy bins. A postmortem breast specimen was imaged with flat panel CT to provide a model for the digital phantoms. Hydroxyapatite (HA) (50, 150, 250, 350, 450, and 550 mg/ml) and iodine (4, 12, 20, 28, 36, and 44 mg/ml) contrast elements were embedded into the glandular region of the phantoms. Calibration phantoms consisted of a 30/70 glandular-to-adipose tissue ratio with embedded HA (100, 200, 300, 400, and 500 mg/ml) and iodine (5, 15, 25, 35, and 45 mg/ml). The x-ray transport process was simulated where the Beer-Lambert law, Poisson process, and CZT absorption efficiency were applied. Qualitative and quantitative evaluations of the decomposition techniques were performed and compared. The effect of breast size was also investigated. Results: The first technique decomposed iodine adequately but failed for other materials. The second method separated the materials but was unable to quantify the materials. With the addition of a calibration, the third technique provided good separation and quantification of hydroxyapatite, iodine, glandular, and adipose tissues

  17. Development of a digital method for neutron/gamma-ray discrimination based on matched filtering

    NASA Astrophysics Data System (ADS)

    Korolczuk, S.; Linczuk, M.; Romaniuk, R.; Zychor, I.

    2016-09-01

    Neutron/gamma-ray discrimination is crucial for measurements with detectors sensitive to both neutron and gamma-ray radiation. Different techniques to discriminate between neutrons and gamma-rays based on pulse shape analysis are widely used in many applications, e.g., homeland security, radiation dosimetry, environmental monitoring, fusion experiments, nuclear spectroscopy. A common requirement is to improve a radiation detection level with a high detection reliability. Modern electronic components, such as high speed analog to digital converters and powerful programmable digital circuits for signal processing, allow us to develop a fully digital measurement system. With this solution it is possible to optimize digital signal processing algorithms without changing any electronic components in an acquisition signal path. We report on results obtained with a digital acquisition system DNG@NCBJ designed at the National Centre for Nuclear Research. A 2'' × 2'' EJ309 liquid scintillator was used to register mixed neutron and gamma-ray radiation from PuBe sources. A dedicated algorithm for pulse shape discrimination, based on real-time filtering, was developed and implemented in hardware.

  18. Discrimination Method of Pop-up Conditions according to PC Usage Situation for Dissemination of Business Information

    NASA Astrophysics Data System (ADS)

    Matsumoto, Toshiko; Onoyama, Takashi; Akiyoshi, Masanori

    Recently, digital documents in companies increase rapidly and are required to be ensured. Pop-up of business information according to PC usage situation can achieve this goal. Two functions are required to it: One is to correctly discriminate pop-up conditions from contents of business-use application, and the other is to select suppression keywords from incorrect pop-up documents. The suppression keywords should improve true negative rate without drop of recall. Based on observation of typical phrases and increase of frequencies for characteristic phrases in contents of business-use applications, we select suppression keywords according to their frequency in positive and negative cases and their occurrence in feedback document. Our evaluation using three kinds of business information shows that the proposed method can achieve both high true negative rate and high recall, and to correctly discriminate pop-up conditions.

  19. Cargo and Container X-Ray Inspection with Intra-Pulse Multi-Energy Method for Material Discrimination

    NASA Astrophysics Data System (ADS)

    Saverskiy, Aleksandr Y.; Dinca, Dan-Cristian; Rommel, J. Martin

    The Intra-Pulse Multi-Energy (IPME) method of material discrimination mitigates main disadvantages of the traditional "interlaced" approach: ambiguity caused by sampling different regions of cargo and reduction of effective scanning speed. A novel concept of creating multi-energy probing pulses using a standing-wave structure allows maintaining a constant energy spectrum while changing the time duration of each sub-pulse and thus enables adaptive cargo inspection. Depending on the cargo density, the dose delivered to the inspected object is optimized for best material discrimination, maximum material penetration, or lowest dose to cargo. A model based on Monte-Carlo simulation and experimental reference points were developed for the optimization of inspection conditions.

  20. Novel method based on chromogenic media for discrimination and selective enumeration of lactic acid bacteria in fermented milk products.

    PubMed

    Galat, Anna; Dufresne, Jérôme; Combrisson, Jérôme; Thépaut, Jérôme; Boumghar-Bourtchai, Leyla; Boyer, Mickaël; Fourmestraux, Candice

    2016-05-01

    Microbial analyses of fermented milk products require selective methods to discriminate between close species simultaneously present in high amounts. A culture-based method combining novel chromogenic agar media and appropriate incubation conditions was developed to enumerate lactic acid bacteria (LAB) strains in fermented milk. M1 agar, containing two chromogenic substrates, allowed selective enumeration of Lactobacillus rhamnosus, two strains of Lactobacillus paracasei subsp. paracasei and Streptococcus salivarius subsp. thermophilus based on differential β-galactosidase and β-glucosidase activities. Depending on the presence of some or all of the above strains, M1 agar was supplemented with L-rhamnose or vancomycin and incubations were carried out at 37 °C or 44 °C to increase selectivity. A second agar medium, M2, containing one chromogenic substrates was used to selectively enumerate β-galactosidase producing Lactobacillus delbrueckii subsp. bulgaricus at 47 °C. By contrast with the usual culture media, the chromogenic method allowed unambiguous enumeration of each species, including discrimination between the two L. paracasei, up to 10(9) CFU/g of fermented milk. In addition, the relevance of the method was approved by enumerating reference ATCC strains in pure cultures and fermented milk product. The method could also be used for enumerations on non-Danone commercial fermented milk products containing strains different from those used in this study, showing versatility of the method. To our knowledge, this is the first description of a chromogenic culture method applied to selective enumeration of LAB.

  1. [Study on identification of cistanche hebra and its adulterants by PCR amplification of specific alleles based on ITS sequences].

    PubMed

    Li, Zhen-Hua; Long, Ping; Zou, De-Zhi; Li, Yue; Cui, Zhan-Hu; Li, Min-Hui

    2014-10-01

    To explore the new method of discriminating Cistanche deserticola, Cynomorium songaricum and Orobanche pycnostachya by using PCR amplification of specific alleles. 30 samples of the different C. deserticola, 21 samples of C. songaricum and O. pycnostachya were collected. The total DNA of the samples were extracted, the ITS sequences from C. deserticola, C. songaricum and O. pycnostachya were amplified by PCR and sequenced unidirectionally. These sequences were aligned by using ClustulW. Specific primer was designed according to the ITS sequences of specific alleles, and PCR reaction system was optimized. Additionally, compare with the identification of specific PCR method and DNA sequence analysis method. The result showed that the 331 bp identification band for C. deserticola and the adulterants not amplified bands by a single PCR reaction, which showed good identification ability to the three species. PCR amplification of specific alleles can be used to identify C. deserticola, C. songaricum and O. pycnostachya successfully.

  2. A mixture detection method based on separate amplification using primer specific alleles of INDELs-a study based on two person's DNA mixture.

    PubMed

    Liu, Jinding; Wang, Jiaqi; Zhang, Xiaojia; Li, Zeqin; Yun, Keming; Liu, Zhizhen; Zhang, Gengqian

    2017-02-01

    Samples containing unbalanced DNA mixtures from individuals often occur in forensic DNA examination and clinical detection. Because of the PCR amplification bias, the minor contributor DNA is often masked by the major contributor DNA when using traditional STR or SNP typing techniques. Here we propose a method based in allele-specific Insertion/Deletion (INDEL) genotyping to detect DNA mixtures in forensic samples. Fourteen INDELs were surveyed in the Chinese Han population of Shanxi Province. The INDELs were amplified using two separate primer-specific reactions by real-time PCR. The difference Ct value of the 2 reactions (D-value) were used for determination of the single source DNA. INDELs types and further confirmed by electrophoresis separation. The minor allele frequency (MAF) was above 0.2 in 10 INDELs. The detection limit was 0.3125 ng-1.25 ng template DNA for real-time PCR in all 14 INDEL markers. For single source 10 ng DNA, the average D-value was 0.31 ± 0.14 for LS type, 6.96 ± 1.05 for LL type and 7.20 ± 1.09 for SS type. For the series of simulated DNA mixture, the Ct value varied between the ranges of single source DNA, depending on their INDEL typing and mixture ratios. This method can detect the specific allele of the minor DNA contributor as little as 1:50 in rs397782455 and rs397696936; 1:100 in rs397832665, rs397822382 and rs397897230; the detection limit of the minor DNA contributor was as little as 1:500-1:1000 in the rest INDEL markers, a much higher sensitivity compared with traditional STR typing. The D-value variation depended on the alternation of dilution ratio and INDEL types. When the dilution was 1:1000, the maximum and minimum D-values were 8.84 ± 0.11 in rs397897230 and 4.27 ± 0.19 in rs397897239 for LL and SS type mixture, the maximum and minimum D-values were 9.32 ± 0.54 in rs397897230 and 4.38 ± 0.26 in rs 397897239 for LL(SS) and LS type mixture, separately. Any D-value between 0.86 and 5.11 in the 14

  3. HLA-B*51 allele analysis by the PCR-SBT method and a strong association of HLA-B*5101 with Japanese patients with Behçet's disease.

    PubMed

    Mizuki, N; Ota, M; Katsuyama, Y; Yabuki, K; Ando, H; Shiina, T; Nomura, E; Onari, K; Ohno, S; Inoko, H

    2001-09-01

    Behçet's disease (BD) is known to be associated with human leukocyte antigen (HLA) B51 in many different ethnic groups. An increased incidence of HLA-B51 in the patient group has also been reported in a Japanese population. Recently, the B51 antigen has been identified to comprise 21 alleles, B*5101-B*5121. Further, not only HLA-B*5101 but also HLA-B*5108 were found to be relatively increased in the patient groups among Italian and Saudi Arabian populations. Therefore, we performed HLA-B*51 allele genotyping by the polymerase chain reaction-sequencing based typing (PCR-SBT) method in order to investigate whether there is any correlation of one particular B51-associated allele with Japanese BD. Ninety-six Japanese patients with BD and 132 healthy Japanese volunteers were enrolled in this study. As a result, the phenotype frequency of the B51 antigen was confirmed to be remarkably increased in the patient group as compared to the ethnically matched control group (59.4% in patients vs. 13.6% in controls; Pc=0.0000000000098, R.R.=9.3). In the B*51 allele genotyping, 56 out of 57 B51-positive patients were defined as B*5101 and the remaining one was B*5102. In contrast, all of 18 B51-positive normal controls were B*5101. None of the Japanese patients and healthy controls carried the HLA-B*5108 allele. This study revealed that B*51 allelic distribution in Japanese was different from those in Italian and Saudi Arabian populations, and that the significantly high incidence of the HLA-B51 antigen in the Japanese BD patient group was mostly caused by the significant increase of the HLA-B*5101 allele.

  4. A comparison of two methods of prompting in training discrimination of communication book pictures by autistic students.

    PubMed

    Berkowitz, S

    1990-06-01

    Two methods of prompting were compared for their relative effectiveness in teaching a group of autistic students to discriminate line drawings used in picture communication books. All four students required fewer trials to meet the task criterion using a delayed-prompting technique. Further, students made significantly more errors in the fading-of-prompts design than in the delayed-prompting design. The high rate of errors in faded-prompt sessions resulted in some students displaying aberrant behaviors. The results are discussed in terms of effectiveness of the two teaching methodologies, as well as the consequences of error patterns. Suggestions are made for further research.

  5. Discrimination of the ITS1 types of Fasciola spp. based on a PCR-RFLP method.

    PubMed

    Ichikawa, Madoka; Itagaki, Tadashi

    2010-02-01

    Molecular characterization is important for discriminating Fasciola specimens having the deoxyribonucleic acid (DNA) sequences of Fasciola hepatica, Fasciola gigantica, and both Fasciola species, since three Fasciola forms coexist in Asian countries. We have developed a restriction fragment length polymorphism of amplified DNA (PCR-RFLP) of the nuclear ribosomal internal transcribed spacer 1 (ITS1) region in Fasciola species. The band patterns of the fragments digested with a restriction enzyme, Rsa I, were accurately distinguished among the three forms of Fasciola. Amplicons with the sequences of F. hepatica and F. gigantica were divided into fragments of about 360, 100, and 60 bp, and 360, 170, and 60 bp, respectively, and amplicons with the sequences of both Fasciola species yielded fragments of 360, 170, 100, and 60 bp. The results of PCR-RFLP completely coincided with those of sequence analysis, and thus PCR-RFLP is a useful technique for determining the ITS1 type in Fasciola species.

  6. Determination and discrimination of intraspecific diversity of Astragalus gossypinus by eco-phytosociological method from west of Iran.

    PubMed

    Atri, Morteza; Nematian, Mahtab Asgari; Shahgolzari, Mehdi

    2007-06-15

    Astragalus gossypinus Fischer with wide distribution in Iran belongs to the genus Astragalus (Fabaceae). According to existing references and information, individuals of this species are present in many stations with different ecological conditions. This study carried out for determination and discrimination of intraspecific diversity of Astragalus gossypinus by Eco-phytosociological method from west of Iran. In this method, the principle of data collecting and analyzing based on floristical composition (as floristical markers) of each Endogenous milieu (as the unit of study in Eco-phytosociological method). In this order, application of Endogenous milieu (special station) for data collecting and then their analyzing permit us only determine existence of inter and intraspecific diversity. Then for determinating kind and level of intraspecific diversity (Ecophene, Chemotype, Cytotype, Ecotype ...), can use other studies such as: morphological, anatomical, phytochemical, cytological and etc. In this survey, 29 special stations were studied and 195 species distinguished as companions for Astragalus gossypinus. Then floristic-ecologic data collected from each 29 special stations and analyzed by Anaphyto software (F.C.A, A.H.C, B.O, Marquag methods). Comparison of obtained results on multiple coordinate axes from F.C.A method with results from B.O, Marquag and A.H.C methods led to determination of 7 main groups of Endogenous milieus (special station). Flavonoid analyses were used for determinating kind and level of intraspecific diversity in 7 discriminated groups. Leaves flavonoid components of all collected individuals of Astragalus gossypinus were investigated by TLC method. Obtained data from flavonoid survey analyzed by SPSS and MVSP package with WARD and UPGMA methods. Finally, the results of flavonoid studies confirmed the same 7 groups that identified by floristical composition study and showed intraspecific diversity in chemotype level. So according to these

  7. [RDBH-method and big DyeTM terminator technology in accurate diagnosis of β-thalassemia and the allelic polymorphism of β-globin cluster].

    PubMed

    Akperova, G A

    2014-11-01

    IThe purpose of this study was to evaluate of the efficiency of RDBH-method and Big DyeTM Terminator technology in an accurate diagnosis of β-thalassemia and the allelic polymorphism of β-globin cluster. It was done a complete hematology analysis (HB, MCH, MCV, MCHC, RBC, Hct, HbA2, HbF, Serum iron, Serum ferritin at four children (males, 6-10 years old) and their parents. Molecular analysis included Reverse Dot-Blot Hybridization StripAssay (RDBH) and DNA sequencing on ABI PRISM Big DyeTM Terminator. Hematologic and molecular parameters were contradictory. The homozygosity for β0-thalassemia (β0IVS2.1[G>A] and β0codon 8[-AA]) at three boys with the mild clinical manifestation and heterozygosity of their parents for mutations, and the absence of β-globin mutations at parents and a boy who holds monthly transfusion was established by RDBH-analysis. DNA sequencing by technology Big DyeTM Terminator showed polymorphism at positions -551 and -521 of Cap5'-region (-650-250) - (AT)7(T)7 and (AT)8(T)5. Application of the integrated clinical-molecular approach is an ideal method for an accurate diagnosis, identification of asymptomatic carriers and a reduce of the risk of complications from β-thalassemia, moreover screening of γG-gene and the level of fetal hemoglobin in early childhood will help manage of β-thalassemia clinic and prevent heavy consequences of the disease.

  8. Development of a simple-material discrimination method with three plastic scintillator strips for visualizing nuclear reactors

    NASA Astrophysics Data System (ADS)

    Takamatsu, k.; Tanaka, h.; Shoji, d.

    2012-04-01

    The Fukushima Daiichi nuclear disaster is a series of equipment failures and nuclear meltdowns, following the T¯o hoku earthquake and tsunami on 11 March 2011. We present a new method for visualizing nuclear reactors. Muon radiography based on the multiple Coulomb scattering of cosmic-ray muons has been performed. In this work, we discuss experimental results obtained with a cost-effective simple detection system assembled with three plastic scintillator strips. Actually, we counted the number of muons that were not largely deflected by restricting the zenith angle in one direction to 0.8o. The system could discriminate Fe, Pb and C. Materials lighter than Pb can be also discriminated with this system. This method only resolves the average material distribution along the muon path. Therefore the user must make assumptions or interpretations about the structure, or must use more than one detector to resolve the three dimensional material distribution. By applying this method to time-dependent muon radiography, we can detect changes with time, rendering the method suitable for real-time monitoring applications, possibly providing useful information about the reaction process in a nuclear reactor such as burnup of fuels. In nuclear power technology, burnup (also known as fuel utilization) is a measure of how much energy is extracted from a primary nuclear fuel source. Monitoring the burnup of fuels as a nondestructive inspection technique can contribute to safer operation. In nuclear reactor, the total mass is conserved so that the system cannot be monitored by conventional muon radiography. A plastic scintillator is relatively small and easy to setup compared to a gas or layered scintillation system. Thus, we think this simple radiographic method has the potential to visualize a core directly in cases of normal operations or meltdown accidents. Finally, we considered only three materials as a first step in this work. Further research is required to improve the

  9. Mono-allelic amplification of exons 2-4 using allele group-specific primers for sequence-based typing (SBT) of the HLA-A, -B and -C genes: preparation and validation of ready-to-use pre-SBT mini-kits.

    PubMed

    Dormoy, A; Froelich, N; Leisenbach, R; Weschler, B; Cazenave, J-P; Tongio, M-M

    2003-09-01

    Class I allelic typing based on sequencing is reliable, immutable and easy to analyse when only one allele is amplified using a specific mono-allelic technique. A strategy has been developed to selectively amplify exons 2, 3 and 4 of each allele of the three class I loci, previously identified by generic typing, in order to sequence these alleles from their intronic parts in only one direction. This procedure is based mainly on the polymorphism of exon 1 and intron 1 of the HLA-A, -B and -C genes with allele group-specific forward primers and locus-specific reverse primers so as to perform mono-allelic amplification in a 'One Step' pre-sequence-based typing (pre-SBT) PCR. The 5' polymorphism found at each locus is nevertheless not sufficient to discriminate all allelic combinations. Hence exon 2 and exon 3 polymorphism had to be used in a 'Two Step' pre-SBT PCR method to selectively amplify the two alleles in the 1.8%, 7.6% and 0.9% of unresolved combinations found in our laboratory for, respectively, the HLA-A, -B and -C loci. Preparation and validation of 'ready-to-use' aliquots of primer-mixes, pre-SBT buffer and sets of Dye terminator reaction mixtures containing locus-specific intronic primers makes the procedure easy and efficient. The SBT method is the only allelic typing technique used in our laboratory (to date, 742 HLA-A*, 802 HLA-B* and 615 HLA-Cw* alleles have been sequenced) and our successful participation in the national and international quality controls of 4 years ago testifies to the accuracy of the results.

  10. The Burden of JAK2V617F Mutated Allele in Turkish Patients With Myeloproliferative Neoplasms

    PubMed Central

    Yonal-Hindilerden, Ipek; Daglar-Aday, Aynur; Akadam-Teker, Basak; Yilmaz, Ceylan; Nalcaci, Meliha; Yavuz, Akif Selim; Sargin, Deniz

    2015-01-01

    Background Studies regarding the impact of JAK2V617F allele burden on phenotypic properties and clinical course in Philadelphia-negative myeloproliferative neoplasms (Ph-negative MPNs) have reported variable results. We aimed to analyze the association of mutated JAK2V617F allele burden with laboratory characteristics and clinical phenotype in Turkish patients (107 essential thrombocythemia (ET) and 77 primary myelofibrosis (PMF)). Methods Peripheral blood samples of 184 patients with Ph-negative MPNs were analyzed for JAK2V617F allele status and burden. JAK2 MutaScreen assay (Ipsogen, Luminy Biotech, Marseille, France) was used to detect the JAK2V617F status and quantitative JAK2V617F allele burdens in genomic DNA using TaqMan allelic discrimination. Results Frequency of JAK2V617F-positive patients with high mutation load (allele burden > 50%) was higher in PMF compared to ET (23.4% and 4.7%, respectively; P = 0.001). We found significant association between ET patients with high JAK2V617F allele burden and lower hemoglobin (Hgb) and hematocrit (Hct), higher LDH levels and more prevalent massive splenomegaly (P = 0.001, P = 0.001, P = 0.012 and P = 0.015, respectively). ET patients with high mutation load displayed higher prevalence of bleeding compared to low mutation load and wild-type mutational status (P = 0.003). Rate of DVT was significantly higher in ET patients with mutant allele burden in upper half compared to lower half and wild-type (P = 0.029). We observed significant association between PMF patients with high JAK2V617F allele burden and higher Hgb, Hct levels and leukocyte counts (P = 0.003, P = 0.021 and P = 0.001, respectively). Conclusions Our study demonstrated JAK2V617F allele burden correlates with clinical features in ET and PMF. We conclude quantification of JAK2V617F mutation contributes to the workup of Ph-negative MPNs. PMID:25584101

  11. Reliability and Discriminative Ability of a New Method for Soccer Kicking Evaluation

    PubMed Central

    Radman, Ivan; Wessner, Barbara; Bachl, Norbert; Ruzic, Lana; Hackl, Markus; Baca, Arnold; Markovic, Goran

    2016-01-01

    The study aimed to evaluate the test–retest reliability of a newly developed 356 Soccer Shooting Test (356-SST), and the discriminative ability of this test with respect to the soccer players' proficiency level and leg dominance. Sixty-six male soccer players, divided into three groups based on their proficiency level (amateur, n = 24; novice semi-professional, n = 18; and experienced semi-professional players, n = 24), performed 10 kicks following a two-step run up. Forty-eight of them repeated the test on a separate day. The following shooting variables were derived: ball velocity (BV; measured via radar gun), shooting accuracy (SA; average distance from the ball-entry point to the goal centre), and shooting quality (SQ; shooting accuracy divided by the time elapsed from hitting the ball to the point of entry). No systematic bias was evident in the selected shooting variables (SA: 1.98±0.65 vs. 2.00±0.63 m; BV: 24.6±2.3 vs. 24.5±1.9 m s-1; SQ: 2.92±1.0 vs. 2.93±1.0 m s-1; all p>0.05). The intra-class correlation coefficients were high (ICC = 0.70–0.88), and the coefficients of variation were low (CV = 5.3–5.4%). Finally, all three 356-SST variables identify, with adequate sensitivity, differences in soccer shooting ability with respect to the players' proficiency and leg dominance. The results suggest that the 356-SST is a reliable and sensitive test of specific shooting ability in men’s soccer. Future studies should test the validity of these findings in a fatigued state, as well as in other populations. PMID:26812247

  12. Reliability and Discriminative Ability of a New Method for Soccer Kicking Evaluation.

    PubMed

    Radman, Ivan; Wessner, Barbara; Bachl, Norbert; Ruzic, Lana; Hackl, Markus; Baca, Arnold; Markovic, Goran

    2016-01-01

    The study aimed to evaluate the test-retest reliability of a newly developed 356 Soccer Shooting Test (356-SST), and the discriminative ability of this test with respect to the soccer players' proficiency level and leg dominance. Sixty-six male soccer players, divided into three groups based on their proficiency level (amateur, n = 24; novice semi-professional, n = 18; and experienced semi-professional players, n = 24), performed 10 kicks following a two-step run up. Forty-eight of them repeated the test on a separate day. The following shooting variables were derived: ball velocity (BV; measured via radar gun), shooting accuracy (SA; average distance from the ball-entry point to the goal centre), and shooting quality (SQ; shooting accuracy divided by the time elapsed from hitting the ball to the point of entry). No systematic bias was evident in the selected shooting variables (SA: 1.98±0.65 vs. 2.00±0.63 m; BV: 24.6±2.3 vs. 24.5±1.9 m s-1; SQ: 2.92±1.0 vs. 2.93±1.0 m s-1; all p>0.05). The intra-class correlation coefficients were high (ICC = 0.70-0.88), and the coefficients of variation were low (CV = 5.3-5.4%). Finally, all three 356-SST variables identify, with adequate sensitivity, differences in soccer shooting ability with respect to the players' proficiency and leg dominance. The results suggest that the 356-SST is a reliable and sensitive test of specific shooting ability in men's soccer. Future studies should test the validity of these findings in a fatigued state, as well as in other populations.

  13. Multivariate analysis of dermatoglyphics of severe mental retardates: an application of the constellation graphical method for discriminant analysis.

    PubMed

    Wakita, Y; Narahara, K; Kimoto, H

    1988-06-01

    We studied the dermatoglyphics of 353 severe mental retardates (excluding those with chromosomal abnormalities and major limb malformations), using multivariate analysis, to determine how early intrauterine factors are related to the etiology of mental retardation. First, dermatoglyphics were compared between 140 individuals with undefined prenatal factors and 700 normal controls. After 6 and 9 dermatoglyphic traits were chosen as discriminative variables for males and females, respectively, the data were subjected separately for each sex to the constellation graphical method for discriminant analysis. The same formula as obtained in the idiopathic group was subsequently applied to data from cases in other etiological categories. When the misclassification rate was 0.03, the rates of correct classification of the male patients into the etiological categories of undefined prenatal, defined prenatal, perinatal, postnatal and unknown (no anamnestic data available) categories were 19.7% (13/66), 20.0% (3/15), 8.8% (5/57), 5.0% (1/20) and 7.7% (2/26), while the correct classification rates of females were 24.3% (18/74), 42.1% (8/19), 18.9% (7/37), 5.1% (1/16) and 13.0% (3/23), respectively. The results suggest that early intrauterine factors such as those producing dermatoglyphic deviations may contribute to the pathogenesis of severe mental retardation not only in patients with undefined prenatal etiological factors but also in those with perinatal factors, especially those of the female sex.

  14. Detection of Fusarium oxysporum f. sp. vasinfectum race 3 by single-base extension method and allele-specific polymerase chain reaction

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We developed allele specific (AS) SNP primers for rapid detection of Fusarium oxysporum f.sp vasinfectum (FOV) race 3. FOV_BT_SNP_R3 and FOV_BT_AS_R3 primers were designed based on single nucleotide polymorphisms of partial sequence alignment of the ß-tubulin (BT) gene from several FOV races. These ...

  15. Identification of the novel allele HLA-B*51:84 by sequence-based typing method in a Taiwanese individual.

    PubMed

    Chu, C-C; Lu, Y-T; Lai, S-K; Lee, H-L; Lin, M

    2010-10-01

    A new human leukocyte antigen-B allele, B*51:84 (B*5184), has been found in Taiwan. It differs from B*51:01:01(B*510101) by one nucleotide substitution at codon 145 (CGC →GGC), resulting to one amino acid change (Arginine to Glycine).

  16. dbQSNP: a database of SNPs in human promoter regions with allele frequency information determined by single-strand conformation polymorphism-based methods.

    PubMed

    Tahira, Tomoko; Baba, Shingo; Higasa, Koichiro; Kukita, Yoji; Suzuki, Yutaka; Sugano, Sumio; Hayashi, Kenshi

    2005-08-01

    We present a database, dbQSNP (http://qsnp.gen.kyushu-u.ac.jp/), that provides sequence and allele frequency information for single-nucleotide polymorphisms (SNPs) located in the promoter regions of human genes, which were defined by the 5' ends of full-length cDNA clones. We searched for the SNPs in these regions by sequencing or single-strand conformation polymorphism (SSCP) analysis. The allele frequencies of the identified SNPs in two ethnic groups were quantified by SSCP analyses of pooled DNA samples. The accuracy of our estimation is supported by strong correlations between the frequencies in our data and those in other databases for the same ethnic groups. The frequencies vary considerably between the two ethnic groups studied, suggesting the need for population-based collections and allele frequency determination of SNPs, in, e.g., association studies of diseases. We show profiles of SNP densities that are characteristic of transcription start site regions. A fraction of the SNPs revealed a significantly different allele frequency between the groups, suggesting differential selection of the genes involved.

  17. Human Y-chromosome haplotyping by allele-specific polymerase chain reaction.

    PubMed

    Gayden, Tenzin; Regueiro, Maria; Martinez, Laisel; Cadenas, Alicia M; Herrera, Rene J

    2008-06-01

    We describe the application of allele-specific PCR (AS-PCR) for screening biallelic markers, including SNPs, within the nonrecombining region of the human Y-chromosome (NRY). The AS-PCR method is based on the concept that the perfectly annealed primer-template complex is more stable, and therefore, more efficiently amplified under the appropriate annealing temperature than the complex with a mismatched 3'-residue. Furthermore, a mismatched nucleotide at the primer's 3'-OH end provides for a poor extension substrate for Taq DNA polymerase, allowing for discrimination between the two alleles. This method has the dual advantage of amplification and detection of alleles in a single expeditious and inexpensive procedure. The amplification conditions of over 50 binary markers, mostly SNPs, that define the major Y-haplogroups as well as their derived lineages were optimized and are provided for the first time. In addition, artificial restriction sites were designed for those markers that are not selectively amplified by AS-PCR. Our results are consistent with allele designations derived from other techniques such as RFLP and direct sequencing of PCR products.

  18. Discrimination Between Clouds and Snow in Landsat 8 Imagery: an Assessment of Current Methods and a New Approach

    NASA Astrophysics Data System (ADS)

    Stillinger, T.; Dozier, J.; Phares, N.; Rittger, K.

    2015-12-01

    Discrimination between snow and clouds poses a serious but tractable challenge to the consistent delivery of high-quality information on mountain snow from remote sensing. Clouds obstruct the surface from the sensor's view, and the similar optical properties of clouds and snow make accurate discrimination difficult. We assess the performance of the current Landsat 8 operational snow and cloud mask products (LDCM CCA and CFmask), along with a new method, using over one million manually identified snow and clouds pixels in Landsat 8 scenes. The new method uses physically based scattering models to generate spectra in each Landsat 8 band, at that scene's solar illumination, for snow and cloud particle sizes that cover the plausible range for each. The modeled spectra are compared to pixels' spectra via several independent ways to identify snow and clouds. The results are synthesized to create a final snow/cloud mask, and the method can be applied to any multispectral imager with bands covering the visible, near-infrared, and shortwave-infrared regions. Each algorithm we tested misidentifies snow and clouds in both directions to varying degrees. We assess performance with measures of Precision, Recall, and the F statistic, which are based on counts of true and false positives and negatives. Tests for significance in differences between spectra in the measured and modeled values among incorrectly identified pixels help ascertain reasons for misidentification. A cloud mask specifically designed to separate snow from clouds is a valuable tool for those interested in remotely sensing snow cover. Given freely available remote sensing datasets and computational tools to feasibly process entire mission histories for an area of interest, enabling researchers to reliably identify and separate snow and clouds increases the usability of the data for hydrological and climatological studies.

  19. Artifactual responses of mesophyll conductance to CO2 and irradiance estimated with the variable J and online isotope discrimination methods

    SciTech Connect

    Gu, Lianhong; Sun, Ying

    2013-01-01

    Studies with the variable J method have reported that mesophyll conductance (gm) rapidly decreases with increasing intercellular CO2 partial pressures (Ci) or decreasing irradiance. Similar responses have been suggested with the online isotope discrimination method, although with less consistency. Here we show that even when the true gm is constant, the variable J method can produce an artifactual dependence of gm on Ci or irradiance similar to those reported in previous studies for any of the following factors: day respiration and chloroplastic CO2 photocompensation point are estimated with Laisk method; Ci or electron transport rate is positively biased; net photosynthetic rate is negatively biased; insufficient NADPH is assumed while insufficient ATP limits RuBP regeneration. The isotopic method produces similar artifacts if fractionation of carboxylation or Ci are positively biased or 13 negatively biased. A nonzero chloroplastic resistance to CO2 movement results in a qualitatively different dependence of gm on Ci or irradiance and this dependence is only sensitive at low Ci. We thus cannot rule out the possibility that previously reported dependence of gm on Ci or irradiance is a methodological artifact. Recommendations are made to take advantage of sensitivities of the variable J and isotopic methods for estimating gm.

  20. Development and validation of a discriminative dissolution method for atorvastatin calcium tablets using in vivo data by LC and UV methods.

    PubMed

    Machado, J C; Lange, A D; Todeschini, V; Volpato, N M

    2014-02-01

    A dissolution method to analyze atorvastatin tablets using in vivo data for RP and test pilot (PB) was developed and validated. The appropriate conditions were determined after solubility tests using different media, and sink conditions were established. The conditions used were equipment paddle at 50 rpm and 900 mL of potassium phosphate buffer pH 6.0 as dissolution medium. In vivo release profiles were obtained from the bioequivalence study of RP and the generic candidate PB. The fraction of dose absorbed was calculated using the Loo-Riegelman method. It was necessary to use a scale factor of time similar to 6.0, to associate the values of absorbed fraction and dissolved fraction, obtaining an in vivo-in vitro correlation level A. The dissolution method to quantify the amount of drug dissolved was validated using high-performance liquid chromatography and ultraviolet spectrophotometry, and validated according to the USP protocol. The discriminative power of dissolution conditions was assessed using two different pilot batches of atorvastatin tablets (PA and PB) and RP. The dissolution test was validated and may be used as a discriminating method in quality control and in the development of the new formulations.

  1. SURE, why not? The SUbstitution-REciprocity method for measurement of odor quality discrimination thresholds: replication and extension to nonhuman primates.

    PubMed

    Laska, Matthias; Grimm, Nina

    2003-02-01

    Recently, Olsson and Cain (2000, Chem. Senses, 25: 493) introduced a psychometric method which, for the first time, allows the standardized determination of odor quality discrimination (OQD) thresholds. The method defines a threshold value that is an average fraction by which one odorant has to be substituted with another to reach a criterion level of discrimination. This measure of discrimination is reciprocal in the sense that it is a result of two separate psychometric functions involving two different standards but the same comparison stimuli. Using the same odor stimuli as Olsson and Cain, with six human subjects but adopting a slightly different experimental design, we were able to replicate their finding that the proportion of correct discriminations changes monotonically with the proportion of adulterant in mixtures of eugenol and citral. As the SURE (SUbstitution-REciprocity) method is based on discriminative responses, it should also be applicable with nonhuman species which can be trained to give unequivocal discriminative responses at the behavioral level. Using an olfactory conditioning paradigm, we therefore trained four squirrel monkeys to discriminate between exactly the same pairs of odor stimuli as our human subjects. We found the psychometric functions of the monkeys to be similar to those of the human subjects. Our results show that the SURE method can successfully be employed with nonhuman primates and thus offers a new approach to study the odor spaces of nonhuman species. Future studies should elucidate whether the SURE method allows for direct comparisons of OQD thresholds and of similarities and differences between odor quality perception of different species.

  2. Weighing in on a method to discriminate maize haploid from hybrid seed

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The doubled haploid breeding method can produce maize inbred lines faster than traditional methods, but there are challenges associated with it. Sorting haploid from hybrid seed based on visual color markers is time consuming, and can be difficult due to color inhibitors that obscure pigmentation n...

  3. A Method for Selecting between Linear and Quadratic Classification Models in Discriminant Analysis.

    ERIC Educational Resources Information Center

    Meshbane, Alice; Morris, John D.

    A method for comparing the cross validated classification accuracies of linear and quadratic classification rules is presented under varying data conditions for the k-group classification problem. With this method, separate-group as well as total-group proportions of correct classifications can be compared for the two rules. McNemar's test for…

  4. Determination and discrimination of biodiesel fuels by gas chromatographic and chemometric methods

    NASA Astrophysics Data System (ADS)

    Milina, R.; Mustafa, Z.; Bojilov, D.; Dagnon, S.; Moskovkina, M.

    2016-03-01

    Pattern recognition method (PRM) was applied to gas chromatographic (GC) data for a fatty acid methyl esters (FAME) composition of commercial and laboratory synthesized biodiesel fuels from vegetable oils including sunflower, rapeseed, corn and palm oils. Two GC quantitative methods to calculate individual fames were compared: Area % and internal standard. The both methods were applied for analysis of two certified reference materials. The statistical processing of the obtained results demonstrates the accuracy and precision of the two methods and allows them to be compared. For further chemometric investigations of biodiesel fuels by their FAME-profiles any of those methods can be used. PRM results of FAME profiles of samples from different vegetable oils show a successful recognition of biodiesels according to the feedstock. The information obtained can be used for selection of feedstock to produce biodiesels with certain properties, for assessing their interchangeability, for fuel spillage and remedial actions in the environment.

  5. VHICA, a New Method to Discriminate between Vertical and Horizontal Transposon Transfer: Application to the Mariner Family within Drosophila.

    PubMed

    Wallau, Gabriel Luz; Capy, Pierre; Loreto, Elgion; Le Rouzic, Arnaud; Hua-Van, Aurélie

    2016-04-01

    Transposable elements (TEs) are genomic repeated sequences that display complex evolutionary patterns. They are usually inherited vertically, but can occasionally be transmitted between sexually independent species, through so-called horizontal transposon transfers (HTTs). Recurrent HTTs are supposed to be essential in life cycle of TEs, which are otherwise destined for eventual decay. HTTs also impact the host genome evolution. However, the extent of HTTs in eukaryotes is largely unknown, due to the lack of efficient, statistically supported methods that can be applied to multiple species sequence data sets. Here, we developed a new automated method available as a R package "vhica" that discriminates whether a given TE family was vertically or horizontally transferred, and potentially infers donor and receptor species. The method is well suited for TE sequences extracted from complete genomes, and applicable to multiple TEs and species at the same time. We first validated our method using Drosophila TE families with well-known evolutionary histories, displaying both HTTs and vertical transmission. We then tested 26 different lineages of mariner elements recently characterized in 20 Drosophila genomes, and found HTTs in 24 of them. Furthermore, several independent HTT events could often be detected within the same mariner lineage. The VHICA (Vertical and Horizontal Inheritance Consistence Analysis) method thus appears as a valuable tool to analyze the evolutionary history of TEs across a large range of species.

  6. VHICA, a New Method to Discriminate between Vertical and Horizontal Transposon Transfer: Application to the Mariner Family within Drosophila

    PubMed Central

    Wallau, Gabriel Luz; Capy, Pierre; Loreto, Elgion; Le Rouzic, Arnaud; Hua-Van, Aurélie

    2016-01-01

    Transposable elements (TEs) are genomic repeated sequences that display complex evolutionary patterns. They are usually inherited vertically, but can occasionally be transmitted between sexually independent species, through so-called horizontal transposon transfers (HTTs). Recurrent HTTs are supposed to be essential in life cycle of TEs, which are otherwise destined for eventual decay. HTTs also impact the host genome evolution. However, the extent of HTTs in eukaryotes is largely unknown, due to the lack of efficient, statistically supported methods that can be applied to multiple species sequence data sets. Here, we developed a new automated method available as a R package “vhica” that discriminates whether a given TE family was vertically or horizontally transferred, and potentially infers donor and receptor species. The method is well suited for TE sequences extracted from complete genomes, and applicable to multiple TEs and species at the same time. We first validated our method using Drosophila TE families with well-known evolutionary histories, displaying both HTTs and vertical transmission. We then tested 26 different lineages of mariner elements recently characterized in 20 Drosophila genomes, and found HTTs in 24 of them. Furthermore, several independent HTT events could often be detected within the same mariner lineage. The VHICA (Vertical and Horizontal Inheritance Consistence Analysis) method thus appears as a valuable tool to analyze the evolutionary history of TEs across a large range of species. PMID:26685176

  7. 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.

  8. Hybrid random walk-linear discriminant analysis method for unwrapping quantitative phase microscopy images of biological samples

    PubMed Central

    Kim, Diane N. H.; Teitell, Michael A.; Reed, Jason; Zangle, Thomas A.

    2015-01-01

    Abstract. Standard algorithms for phase unwrapping often fail for interferometric quantitative phase imaging (QPI) of biological samples due to the variable morphology of these samples and the requirement to image at low light intensities to avoid phototoxicity. We describe a new algorithm combining random walk-based image segmentation with linear discriminant analysis (LDA)-based feature detection, using assumptions about the morphology of biological samples to account for phase ambiguities when standard methods have failed. We present three versions of our method: first, a method for LDA image segmentation based on a manually compiled training dataset; second, a method using a random walker (RW) algorithm informed by the assumed properties of a biological phase image; and third, an algorithm which combines LDA-based edge detection with an efficient RW algorithm. We show that the combination of LDA plus the RW algorithm gives the best overall performance with little speed penalty compared to LDA alone, and that this algorithm can be further optimized using a genetic algorithm to yield superior performance for phase unwrapping of QPI data from biological samples. PMID:26305212

  9. Automated Test Case Generator for Phishing Prevention Using Generative Grammars and Discriminative Methods

    ERIC Educational Resources Information Center

    Palka, Sean

    2015-01-01

    This research details a methodology designed for creating content in support of various phishing prevention tasks including live exercises and detection algorithm research. Our system uses probabilistic context-free grammars (PCFG) and variable interpolation as part of a multi-pass method to create diverse and consistent phishing email content on…

  10. The liquid-ordered phase in sphingomyelincholesterol membranes as detected by the discrimination by oxygen transport (DOT) method.

    PubMed

    Wisniewska, Anna; Subczynski, Witold K

    2008-01-01

    Membranes made from binary mixtures of egg sphingomyelin (ESM) and cholesterol were investigated using conventional and saturation-recovery EPR observations of the 5-doxylstearic acid spin label (5-SASL). The effects of cholesterol on membrane order and the oxygen transport parameter (bimolecular collision rate of molecular oxygen with the nitroxide spin label) were monitored at the depth of the fifth carbon in fluid- and gel-phase ESM membranes. The saturation-recovery EPR discrimination by oxygen transport (DOT) method allowed the discrimination of the liquid-ordered (l(o)), liquid-disordered (l(d)), and solid-ordered (s(o)) phases because the bimolecular collision rates of the molecular oxygen with the nitroxide spin label differ in these phases. Additionally, oxygen collision rates (the oxygen transport parameter) were obtained in coexisting phases without the need for their separation, which provides information about the internal dynamics of each phase. The addition of cholesterol causes a dramatic decrease in the oxygen transport parameter around the nitroxide moiety of 5-SASL in the l(o) phase, which at 50 mol% cholesterol becomes approximately 5 times smaller than in the pure ESM membrane in the l(d) phase, and approximately 2 times smaller than in the pure ESM membrane in the s(o) phase. The overall change in the oxygen transport parameter is as large as approximately 20-fold. Conventional EPR spectra show that 5-SASL is maximally immobilized at the phase boundary between regions with coexisting l(d) and l(o) phases or s(o) and l(o) phases and the region with a single l(o) phase. The obtained results allowed for the construction of a phase diagram for the ESM-cholesterol membrane.

  11. Evans Blue as a Simple Method to Discriminate Mosquitoes’ Feeding Choice on Small Laboratory Animals

    PubMed Central

    Maciel, Ceres; Fujita, André; Gueroni, Daniele I.; Ramos, Anderson D.; Capurro, Margareth L.; Sá-Nunes, Anderson

    2014-01-01

    Background Temperature, humidity, vision, and particularly odor, are external cues that play essential roles to mosquito blood feeding and oviposition. Entomological and behavioral studies employ well-established methods to evaluate mosquito attraction or repellency and to identify the source of the blood meal. Despite the efficacy of such methods, the costs involved in the production or acquisition of all parts, components and the chemical reagents involved are unaffordable for most researchers from poor countries. Thus, a simple and relatively low-cost method capable of evaluating mosquito preferences and the blood volume ingested is desirable. Principal Findings By using Evans blue (EB) vital dye and few standard laboratory supplies, we developed and validated a system capable of evaluating mosquito’s choice between two different host sources of blood. EB-injected and PBS-injected mice submitted to a number of situations were placed side by side on the top of a rounded recipient covered with tulle fabric and containing Aedes aegypti mosquitoes. Homogenates from engorged mosquitoes clearly revealed the blood source (EB- or PBS-injected host), either visually or spectrometrically. This method was able to estimate the number of engorded mosquitoes, the volume of blood ingested, the efficacy of a commercial repellent and the attractant effects of black color and human sweat. Significance Despite the obvious limitations due to its simplicity and to the dependence of a live source of blood, the present method can be used to assess a number of host variables (diet, aging, immunity, etc) and optimized for several aspects of mosquito blood feeding and vector-host interactions. Thus, it is proposed as an alternative to field studies, and it could be used for initial screenings of chemical compound candidates for repellents or attractants, since it replicates natural conditions of exposure to mosquitoes in a laboratory environment. PMID:25333369

  12. Identification of Genes Discriminating Multiple Sclerosis Patients from Controls by Adapting a Pathway Analysis Method

    PubMed Central

    Zhang, Lei; Wang, Linlin; Tian, Pu

    2016-01-01

    The focus of analyzing data from microarray experiments has shifted from the identification of associated individual genes to that of associated biological pathways or gene sets. In bioinformatics, a feature selection algorithm is usually used to cope with the high dimensionality of microarray data. In addition to those algorithms that use the biological information contained within a gene set as a priori to facilitate the process of feature selection, various gene set analysis methods can be applied directly or modified readily for the purpose of feature selection. Significance analysis of microarray to gene-set reduction analysis (SAM-GSR) algorithm, a novel direction of gene set analysis, is one of such methods. Here, we explore the feature selection property of SAM-GSR and provide a modification to better achieve the goal of feature selection. In a multiple sclerosis (MS) microarray data application, both SAM-GSR and our modification of SAM-GSR perform well. Our results show that SAM-GSR can carry out feature selection indeed, and modified SAM-GSR outperforms SAM-GSR. Given pathway information is far from completeness, a statistical method capable of constructing biologically meaningful gene networks is of interest. Consequently, both SAM-GSR algorithms will be continuously revaluated in our future work, and thus better characterized. PMID:27846233

  13. Comparison of HLA allelic imputation programs.

    PubMed

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

    2017-01-01

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

  14. Comparison of HLA allelic imputation programs

    PubMed Central

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

    2017-01-01

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

  15. Numerical Methods in Electromagnetics: Evanescent Nanometry for DNA Sequencing, and EM Induction for UXO Detection and Discrimination

    NASA Astrophysics Data System (ADS)

    Bijamov, Alex

    The main goals of this work are to extend forward and apply inverse EM numerical methods to enhance the fundamental understanding of ultra-wideband frequency range EM fields in complex geometries. The particular emphases are made on medical device development for whole human genome sequencing using force spectroscopy; and underwater target detection, and live sites UXO discrimination. Force spectroscopy is a powerful technique used to manipulate single biomolecules and study their interactions. In these experiments one end of a macromolecule is immobilized on a substrate, while its free end is attached to an externally-manipulated microscopic bead. Crucial to the application of force spectroscopy to DNA sequencing is the ability to apply pulling forces reaching hundreds of pico-Newtons and image molecular extensions with sub-nanometer resolution. To achieve both goals the behavior of EM fields in the vicinity of the beads and the associated far fields need to be investigated using numerical simulations. In recent years our group has developed a numerical technique---the Method of Auxiliary Sources---which was modified here for these problems. In this work the physics of bead scattering and fluorescent responses is studied for a variety of bead and substrate compositions and geometries, including layered structures, to understand their potential in increasing imaging sensitivity. This thesis also studies the inversion problems related to the underwater UXO detection and live-site UXO discrimination. Rigorous analysis of underlying physics of low-frequency EM field scattering from conducting objects in underwater environments is performed. The effects of seawater surface roughness on transmitted EM signals and the associated noise levels are analyzed. A new, magnetic field-based geolocation system is studied numerically for GPS-denied underwater environments. Finally, the performances of statistical and machine learning methods are analyzed for automatic

  16. Improved neutron-gamma discrimination for a 6Li-glass neutron detector using digital signal analysis methods

    NASA Astrophysics Data System (ADS)

    Wang, C. L.; Riedel, R. A.

    2016-01-01

    A 6Li-glass scintillator (GS20) based neutron Anger camera was developed for time-of-flight single-crystal diffraction instruments at Spallation Neutron Source. Traditional Pulse-Height Analysis (PHA) for Neutron-Gamma Discrimination (NGD) resulted in the neutron-gamma efficiency ratio (defined as NGD ratio) on the order of 104. The NGD ratios of Anger cameras need to be improved for broader applications including neutron reflectometers. For this purpose, six digital signal analysis methods of individual waveforms acquired from photomultiplier tubes were proposed using (i) charge integration, (ii) pulse-amplitude histograms, (iii) power spectrum analysis combined with the maximum pulse-amplitude, (iv) two event parameters (a1, b0) obtained from a Wiener filter, (v) an effective amplitude (m) obtained from an adaptive least-mean-square filter, and (vi) a cross-correlation coefficient between individual and reference waveforms. The NGD ratios are about 70 times those from the traditional PHA method. Our results indicate the NGD capabilities of neutron Anger cameras based on GS20 scintillators can be significantly improved with digital signal analysis methods.

  17. Improved neutron-gamma discrimination for a 6Li-glass neutron detector using digital signal analysis methods

    SciTech Connect

    Wang, Cai -Lin; Riedel, Richard A.

    2016-01-14

    A 6Li-glass scintillator (GS20) based neutron Anger camera was developed for time-of-flight single-crystal diffraction instruments at SNS. Traditional pulse-height analysis (PHA) for neutron-gamma discrimination (NGD) resulted in the neutron-gamma efficiency ratio (defined as NGD ratio) on the order of 104. The NGD ratios of Anger cameras need to be improved for broader applications including neutron reflectometers. For this purpose, five digital signal analysis methods of individual waveforms from PMTs were proposed using: i). pulse-amplitude histogram; ii). power spectrum analysis combined with the maximum pulse amplitude; iii). two event parameters (a1, b0) obtained from Wiener filter; iv). an effective amplitude (m) obtained from an adaptive least-mean-square (LMS) filter; and v). a cross-correlation (CC) coefficient between an individual waveform and a reference. The NGD ratios can be 1-102 times those from traditional PHA method. A brighter scintillator GS2 has better NGD ratio than GS20, but lower neutron detection efficiency. The ultimate NGD ratio is related to the ambient, high-energy background events. Moreover, our results indicate the NGD capability of neutron Anger cameras can be improved using digital signal analysis methods and brighter neutron scintillators.

  18. Improved neutron-gamma discrimination for a 6Li-glass neutron detector using digital signal analysis methods

    DOE PAGES

    Wang, Cai -Lin; Riedel, Richard A.

    2016-01-14

    A 6Li-glass scintillator (GS20) based neutron Anger camera was developed for time-of-flight single-crystal diffraction instruments at SNS. Traditional pulse-height analysis (PHA) for neutron-gamma discrimination (NGD) resulted in the neutron-gamma efficiency ratio (defined as NGD ratio) on the order of 104. The NGD ratios of Anger cameras need to be improved for broader applications including neutron reflectometers. For this purpose, five digital signal analysis methods of individual waveforms from PMTs were proposed using: i). pulse-amplitude histogram; ii). power spectrum analysis combined with the maximum pulse amplitude; iii). two event parameters (a1, b0) obtained from Wiener filter; iv). an effective amplitude (m)more » obtained from an adaptive least-mean-square (LMS) filter; and v). a cross-correlation (CC) coefficient between an individual waveform and a reference. The NGD ratios can be 1-102 times those from traditional PHA method. A brighter scintillator GS2 has better NGD ratio than GS20, but lower neutron detection efficiency. The ultimate NGD ratio is related to the ambient, high-energy background events. Moreover, our results indicate the NGD capability of neutron Anger cameras can be improved using digital signal analysis methods and brighter neutron scintillators.« less

  19. Improved neutron-gamma discrimination for a {sup 6}Li-glass neutron detector using digital signal analysis methods

    SciTech Connect

    Wang, C. L. Riedel, R. A.

    2016-01-15

    A {sup 6}Li-glass scintillator (GS20) based neutron Anger camera was developed for time-of-flight single-crystal diffraction instruments at Spallation Neutron Source. Traditional Pulse-Height Analysis (PHA) for Neutron-Gamma Discrimination (NGD) resulted in the neutron-gamma efficiency ratio (defined as NGD ratio) on the order of 10{sup 4}. The NGD ratios of Anger cameras need to be improved for broader applications including neutron reflectometers. For this purpose, six digital signal analysis methods of individual waveforms acquired from photomultiplier tubes were proposed using (i) charge integration, (ii) pulse-amplitude histograms, (iii) power spectrum analysis combined with the maximum pulse-amplitude, (iv) two event parameters (a{sub 1}, b{sub 0}) obtained from a Wiener filter, (v) an effective amplitude (m) obtained from an adaptive least-mean-square filter, and (vi) a cross-correlation coefficient between individual and reference waveforms. The NGD ratios are about 70 times those from the traditional PHA method. Our results indicate the NGD capabilities of neutron Anger cameras based on GS20 scintillators can be significantly improved with digital signal analysis methods.

  20. Quantitative and discriminative analysis of nucleic acid samples using luminometric nonspecific nanoparticle methods

    NASA Astrophysics Data System (ADS)

    Pihlasalo, S.; Mariani, L.; Härmä, H.

    2016-03-01

    Homogeneous simple assays utilizing luminescence quenching and time-resolved luminescence resonance energy transfer (TR-LRET) were developed for the quantification of nucleic acids without sequence information. Nucleic acids prevent the adsorption of a protein to europium nanoparticles which is detected as a luminescence quenching of europium nanoparticles with a soluble quencher or as a decrease of TR-LRET from europium nanoparticles to the acceptor dye. Contrary to the existing methods based on fluorescent dye binding to nucleic acids, equal sensitivities for both single- (ssDNA) and double-stranded DNA (dsDNA) were measured and a detection limit of 60 pg was calculated for the quenching assay. The average coefficient of variation was 5% for the quenching assay and 8% for the TR-LRET assay. The TR-LRET assay was also combined with a nucleic acid dye selective to dsDNA in a single tube assay to measure the total concentration of DNA and the ratio of ssDNA and dsDNA in the mixture. To our knowledge, such a multiplexed assay is not accomplished with commercially available assays.Homogeneous simple assays utilizing luminescence quenching and time-resolved luminescence resonance energy transfer (TR-LRET) were developed for the quantification of nucleic acids without sequence information. Nucleic acids prevent the adsorption of a protein to europium nanoparticles which is detected as a luminescence quenching of europium nanoparticles with a soluble quencher or as a decrease of TR-LRET from europium nanoparticles to the acceptor dye. Contrary to the existing methods based on fluorescent dye binding to nucleic acids, equal sensitivities for both single- (ssDNA) and double-stranded DNA (dsDNA) were measured and a detection limit of 60 pg was calculated for the quenching assay. The average coefficient of variation was 5% for the quenching assay and 8% for the TR-LRET assay. The TR-LRET assay was also combined with a nucleic acid dye selective to dsDNA in a single tube

  1. TRMM Microwave Radiometer Rain Rate Estimation Method with Convective and Stratiform Discrimination

    NASA Technical Reports Server (NTRS)

    Prabhakara, Cuddapah; Iacovazzi, R.; Weinman, J. A.; Dalu, G.; Einaudi, Franco (Technical Monitor)

    2000-01-01

    Tropical Rainfall Measuring Mission (TRMM) Microwave Imager (TMI) radiometer brightness temperature data in the 85 GHz channel (T85) reveal distinct local minima (T85min) in a regional map containing a Mesoscale Convective System (MCS). A map of surface rain rate for that region, deduced from simultaneous measurements made by the Precipitation Radar (PR) on board the TRMM satellite, reveals that these T85min, produced by scattering, correspond to local PR rain maxima. Utilizing the PR rain rate map as a guide, we have developed a TMI algorithm to retrieve convective and stratiform rain. In this algorithm, two parameters are used to classify three kinds of thunderstorms (Cbs) based on the T85 data: a) the magnitude of scattering depression deduced from local T85mi, and b) the mean horizontal gradient of T85 around such minima. Initially, the algorithm is optimized or tuned utilizing the PR and TMI data of a few MCS events. The areal distribution of light (1-10 mm/hr), moderate (10-20 mm/hr), and intense (greater than or equal to 20 mm/hr) rain rates are retrieved on the average with an accuracy of about 15%. Taking advantage of this ability of our retrieval method, one could derive the latent heat input into the atmosphere over the 760 km wide swath of the TMI radiometer in the tropics.

  2. Validation of a Rapid, Robust, Inexpensive Screening Method for Detecting the HLA-B*58:01 Allele in the Prevention of Allopurinol-Induced Severe Cutaneous Adverse Reactions.

    PubMed

    Nguyen, Dinh Van; Vida, Christopher; Chu, Hieu Chi; Fulton, Richard; Li, Jamma; Fernando, Suran L

    2017-01-01

    The HLA B*58:01 allele has been worldwide reported as a pharmacogenetic susceptibility to allopurinol-induced severe cutaneous adverse reactions (SCARs). To prevent these life-threatening conditions, the American College of Rheumatology hingly recommended that the HLA-B*58:01 be screened prior to the initiation of allopurinol therapy. Therefore, we developed a rapid, robust, inexpensive screening method using SYBR® Green real time PCR to detect the HLA-B*58:01 allele. A total of 119 samples were tested. The assay has a sensitivity of 100% (95% CI: 69.15%-100%), a specificity of 100% (95% CI: 96.67%-100%), a positive predictive value of 100% (95% CI: 69.15%-100%) and a negative predictive value of 100% (95% CI: 96.67%-100%). HLA-B*58:01 genotyping results showed 100% agreement with those obtained from Luminex SSO/SBT/SSP. The lowest limit of detection of this method is 0.8 ng/μL of DNA. The unit cost of the test is only $3.8 USD. This novel screening test using SYBR® real time PCR would be appropriate to identify individuals with the HLA-B*58:01 allele for the prevention of allopurinol-induced SCARs.

  3. A Non-Destructive Distinctive Method for Discrimination of Automobile Lubricant Variety by Visible and Short-Wave Infrared Spectroscopy

    PubMed Central

    Jiang, Lulu; Liu, Fei; He, Yong

    2012-01-01

    A novel method which is a combination of wavelet packet transform (WPT), uninformative variable elimination by partial least squares (UVE-PLS) and simulated annealing (SA) to extract best variance information among different varieties of lubricants is presented. A total of 180 samples (60 for each variety) were characterized on the basis of visible and short-wave infrared spectroscopy (VIS-SWNIR), and 90 samples (30 for each variety) were randomly selected for the calibration set, whereas, the remaining 90 samples (30 for each variety) were used for the validation set. The spectral data was split into different frequency bands by WPT, and different frequency bands were obtained. SA was employed to look for the best variance band (BVB) among different varieties of lubricants. In order to improve prediction precision further, BVB was processed by UVE-PLS and the optimal cutoff threshold of UVE was found by SA. Finally, five variables were mined, and were set as inputs for a least square-support vector machine (LS-SVM) to build the recognition model. An optimal model with a correlation coefficient (R) of 0.9850 and root mean square error of prediction (RMSEP) of 0.0827 was obtained. The overall results indicated that the method of combining WPT, UVE-PLS and SA was a powerful way to select diagnostic information for discrimination among different varieties of lubricating oil, furthermore, a more parsimonious and efficient LS-SVM model could be obtained. PMID:22737021

  4. Weak "A" blood subgroup discrimination by a rheo-optical method: a new application of laser backscattering

    NASA Astrophysics Data System (ADS)

    Rasia, Rodolfo J.; Rasia-Valverde, Juana R.; Stoltz, Jean F.

    1996-01-01

    Laser backscattering is an excellent tool to investigate size and concentration of suspended particles. It was successfully applied to the analysis of erythrocyte aggregation. A method is proposed that applies laser backscattering to the evaluation of the strength of the immunologic erythrocyte agglutination by approaching the energy required for the mechanical dissociation of agglutinates. Mills and Snabre have proposed a theory of laser backscattering for erythrocyte aggregation analysis. It is applied here to analyze the dissociation process of erythrocyte agglutinates performed by imposing a constant shear rate to the agglutinate suspension in a couette viscometer until a dispersion of isolated red cells is attained. Experimental verifications of the method were performed on the erythrocytes of the ABO group reacting against an anti-A test serum in twofold series dilutions. Spent energy is approached by a numerical process carried out on the backscattered intensity data registered during mechanical dissociation. Velocities of agglutination and dissociation lead to the calculation of dissociation parameters These values are used to evaluate the strength of the immunological reaction and to discriminate weak subgroups of ABO system.

  5. A comparison of methods for in situ discrimination of imaged phase boundaries using electrical capacitance tomography

    NASA Astrophysics Data System (ADS)

    Clark, P. J.; Tsoligkas, A. N.; Simmons, M. J. H.; Robbins, P. T.; Stitt, E. H.

    2016-02-01

    The detection of hard boundaries using tomographic techniques is challenging due to the measurement resolution inherent in the hardware and smoothing effects created during image reconstruction. This paper is concerned with the development of data processing approaches which enable the use of electrical capacitance tomography (ECT) in real-time applications to visualise interfaces in liquid/liquid and solid/liquid systems based upon phase permittivity differences in media with a high di-electric continuum. The methodologies developed were applied to a series of phantoms to investigate their validity as a tool for imaging phase boundaries in two and three phase systems. In an ECT based tomogram, the interface between phases is exhibited as a transition region; by applying a threshold technique based upon known areas of each respective phase within the system, the transient region can be resolved into a sharp interface. The image error of a tomogram, defined as the deviation of all pixels from their theoretical value, has been calculated using a pixel-by-pixel approach; however this requires exact a priori knowledge and is unsuitable for in-line application; the areal method used in this paper requires global phase distribution information thereby allowing for real-time application. A range of threshold values were applied to tomograms of phantoms of varying geometry and the corresponding image error for each threshold value calculated using both the areal and pixel-by-pixel approaches given above. The threshold value yielding lowest image error from this range is further used in the binary images giving improved tomograms with approximately 40% increase in image accuracy when compared with a default threshold value. Close to the sensor wall, the image becomes distorted due to reconstruction errors arising from decreased density in the electrical field lines, resulting in a circular phantom appearing elongated by approximately 10% when positioned near the wall.

  6. A TRMM Microwave Radiometer Rain Rate Estimation Method with Convective and Stratiform Discrimination

    NASA Technical Reports Server (NTRS)

    Prabhakara, C.; Iacovazzi, R., Jr.; Weinman, J. A.; Dalu, G.

    1999-01-01

    cases is on the average about 15 %. Taking advantage of this ability of our retrieval method, one could derive the latent heat input into the atmosphere over the 760 km wide swath of the TMI radiometer in the tropics.

  7. A two-step method for identification of the Chinese glutinous rice Suyunuo, based on ISSR-SCAR and allele-specific markers.

    PubMed

    Lin, Y B; Zhang, Y M; Hang, Y Y; Li, M M; Zhou, G C; Shen, X L; Sun, X Q

    2016-10-05

    Suyunuo is a valuable glutinous rice variety cultivated mainly in the Lake Taihu area of China. Historically, Suyunuo was presented to emperors as a tribute, and, still today, enjoys a great reputation in China. This study aimed to develop a unique, specific molecular marker for the identification of Suyunuo rice. Polymerase chain reaction (PCR) amplification of inter-simple sequence repeat (ISSR) molecular markers was performed on Suyunuo and 11 other glutinous rice varieties that are mainly cultivated in the Yangtze River Delta region. A Suyunuo-specific band was detected in the PCR products generated from primer ISSR-807. A sequence characterized amplified region (SCAR) primer pair targeting a Suyunuo-specific band was subsequently designed. The SCAR primers amplified a target band in all individuals of Suyunuo and in four glutinous indica varieties, whereas no bands were found in the seven glutinous japonica varieties. Subsequently, sequences amplified by the SCAR primer pair were analyzed to facilitate the design of Suyunuo allele-specific primers. The allele-specific primer pair produced target bands in all individuals of Suyunuo rice but no bands in individuals of any of the other 11 rice varieties. This study provides a theoretical guideline for rice germplasm identification and innovation of other valuable rice landraces.

  8. Efficiency of the Mantel, Generalized Mantel-Haenszel, and Logistic Discriminant Function Analysis Methods in Detecting Differential Item Functioning for Polytomous Items

    ERIC Educational Resources Information Center

    Su, Ya-Hui; Wang, Wen-Chung

    2005-01-01

    Simulations were conducted to investigate factors that influence the Mantel, generalized Mantel-Haenszel (GMH), and logistic discriminant function analysis (LDFA) methods in assessing differential item functioning (DIF) for polytomous items. The results show that the magnitude of DIF contamination in the matching score, as measured by the average…

  9. Multilocus sequence typing is a reliable alternative method to DNA fingerprinting for discriminating among strains of Candida albicans.

    PubMed

    Robles, Juan C; Koreen, Larry; Park, Steven; Perlin, David S

    2004-06-01

    Multilocus sequence typing (MLST) has emerged as a powerful new DNA-typing tool for the evaluation of intraspecies genetic relatedness. This method relies on DNA sequence analysis of nucleotide polymorphisms in housekeeping genes and has shown a high degree of intraspecies discriminatory power for bacterial and fungal pathogens. However, the results of the MLST scheme for Candida albicans have heretofore never been formally compared to those of other established typing techniques. To assess the value of MLST relative to those of other DNA fingerprinting tools for discriminating among strains of C. albicans, we applied it to a previously well-characterized set of 29 C. albicans isolates evaluated by the random amplified polymorphic DNA (RAPD), multilocus enzyme electrophoresis (MLEE), and Ca3 Southern hybridization probe techniques. MLST identified three clusters of genetically related isolates, with 82.3% direct concordance with MLEE, 82.7% with RAPD analysis, and 86.2% with the Ca3 Southern hybridization technique. When MLST was applied to a subset of 22 isolates of unrelated origins, it identified 21 independent diploid sequence types (DSTs), resulting in a discriminatory power of 99.6%. These DSTs were 96.9, 99.6, and 99.6% concordant with the genotypes identified by RAPD analysis, MLEE, and Ca3 Southern hybridization, respectively. These results demonstrate that MLST is a highly effective technique that performs at least comparably to other established DNA fingerprinting techniques.

  10. Fuzzy Discrimination Analysis Method for Earthquake Energy K-Class Estimation with respect to Local Magnitude Scale

    NASA Astrophysics Data System (ADS)

    Mumladze, T.; Gachechiladze, J.

    2014-12-01

    The purpose of the present study is to establish relation between earthquake energy K-class (the relative energy characteristic) defined as logarithm of seismic waves energy E in joules obtained from analog stations data and local (Richter) magnitude ML obtained from digital seismograms. As for these data contain uncertainties the effective tools of fuzzy discrimination analysis are suggested for subjective estimates. Application of fuzzy analysis methods is an innovative approach to solving a complicated problem of constracting a uniform energy scale through the whole earthquake catalogue, also it avoids many of the data collection problems associated with probabilistic approaches; and it can handle incomplete information, partial inconsistency and fuzzy descriptions of data in a natural way. Another important task is to obtain frequency-magnitude relation based on K parameter, calculation of the Gutenberg-Richter parameters (a, b) and examining seismic activity in Georgia. Earthquake data files are using for periods: from 1985 to 1990 and from 2004 to 2009 for area j=410 - 430.5, l=410 - 470.

  11. Inference about the number of contributors to a DNA mixture: Comparative analyses of a Bayesian network approach and the maximum allele count method.

    PubMed

    Biedermann, A; Bozza, S; Konis, K; Taroni, F

    2012-12-01

    In the forensic examination of DNA mixtures, the question of how to set the total number of contributors (N) presents a topic of ongoing interest. Part of the discussion gravitates around issues of bias, in particular when assessments of the number of contributors are not made prior to considering the genotypic configuration of potential donors. Further complication may stem from the observation that, in some cases, there may be numbers of contributors that are incompatible with the set of alleles seen in the profile of a mixed crime stain, given the genotype of a potential contributor. In such situations, procedures that take a single and fixed number contributors as their output can lead to inferential impasses. Assessing the number of contributors within a probabilistic framework can help avoiding such complication. Using elements of decision theory, this paper analyses two strategies for inference on the number of contributors. One procedure is deterministic and focuses on the minimum number of contributors required to 'explain' an observed set of alleles. The other procedure is probabilistic using Bayes' theorem and provides a probability distribution for a set of numbers of contributors, based on the set of observed alleles as well as their respective rates of occurrence. The discussion concentrates on mixed stains of varying quality (i.e., different numbers of loci for which genotyping information is available). A so-called qualitative interpretation is pursued since quantitative information such as peak area and height data are not taken into account. The competing procedures are compared using a standard scoring rule that penalizes the degree of divergence between a given agreed value for N, that is the number of contributors, and the actual value taken by N. Using only modest assumptions and a discussion with reference to a casework example, this paper reports on analyses using simulation techniques and graphical models (i.e., Bayesian networks) to

  12. Allele-specific DNA methylation: beyond imprinting.

    PubMed

    Tycko, Benjamin

    2010-10-15

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

  13. Physical profiling and IR spectroscopy: simple and effective methods to discriminate between genuine and counterfeit samples of Viagra® and Cialis®.

    PubMed

    Custers, Deborah; Vandemoortele, Suzanne; Bothy, Jean-Luc; De Beer, Jacques O; Courselle, Patricia; Apers, Sandra; Deconinck, Eric

    2016-01-01

    Counterfeit medicines are a global threat to public health. High amounts enter the European market, enforcing the need for simple techniques to help customs detect these pharmaceuticals. This study focused on physical profiling and IR spectroscopy to obtain a prime discrimination between genuine and illegal Viagra® and Cialis® medicines. Five post-tableting characteristics were explored: colour, mass, long length, short length, and thickness. Hypothesis testing showed that most illegal samples (between 60 and 100%) significantly differ from the genuine medicines, in particular for mass and long length. Classification and Regression Trees (CART) analysis resulted in a good discrimination between genuine and illegal medicines (98.93% correct classification rate for Viagra®, 99.42% for Cialis®). Moreover, CART confirmed the observation that mass and long length are the key physical characteristics which determine the observed discrimination. IR analysis was performed on tablets without blister and on tablets in intact blister. These data were analyzed using Soft Independent Modelling of Class Analogy (SIMCA) and Partial Least Squares - Discriminant Analysis (PLS-DA). Supervised techniques needed to be applied since Principal Component Analysis (PCA) was not able to generate the desired discrimination. Our study shows that a perfect discrimination between genuine and illegal medicines can be made by both SIMCA and PLS-DA without removing the tablets from the blister. This approach has the advantage of keeping the blister intact. Our study demonstrates that these user friendly techniques are reliable methods to aid customs to obtain a prime distinction between genuine and illegal samples on the spot. Copyright © 2015 John Wiley & Sons, Ltd.

  14. A novel and rapid diagnostic method for discriminating between feces of sika deer and Japanese serow by loop-mediated isothermal amplification.

    PubMed

    Aikawa, T; Horino, S; Ichihara, Y

    2015-08-01

    Severe damages to natural vegetation, agriculture, and forestry caused by overpopulation of sika deer (Cervus nippon) have markedly increased in Japan in recent years. To devise a population management plan of sika deer, information on the distribution and population size of the animal in each region is indispensable. An easy and effective method to obtain this information is to count the fecal pellets in the field. However, the habitat of sika deer in Japan overlaps that of Japanese serow (Capricornis crispus). Additionally, it is difficult to discriminate between the feces of both animals. Here, we present a rapid and precise diagnostic method for discriminating between the feces of sika deer and Japanese serow using loop-mediated isothermal amplification (LAMP) targeting cytochrome b gene in the mitochondrial DNA. Our results showed that the LAMP can discriminate between the feces of sika deer and Japanese serow, and the method is simpler and more sensitive than the conventional molecular diagnostic method. Since LAMP method does not require special skills for molecular biology techniques, even the field researchers who have never done a molecular experiment can easily carry out the protocol. In addition, the entire protocol, from DNA extraction from fecal pellet to identification of species, takes only about 75 min and does not require expensive equipment. Hence, this diagnostic method is simple, fast, and accessible to anyone. As such, the method can be a useful tool to estimate distribution and population size of sika deer.

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

    PubMed Central

    Burgess, Stephen; Thompson, Simon G

    2013-01-01

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

  16. Diffuse reflectance spectroscopy in Barrett's esophagus: developing a large field-of-view screening method discriminating dysplasia from metaplasia.

    PubMed

    Douplik, Alexandre; Zanati, Simon; Saiko, Guennadi; Streutker, Catherine; Loshchenov, Maxim; Adler, Desmond; Cho, Sarah; Chen, Dean; Cirocco, Maria; Marcon, Norman; Fengler, John; Wilson, Brian C

    2014-05-01

    We evaluated diffuse reflectance spectroscopy implemented as a small field-of-view technique for discrimination of dysplasia from metaplasia in Barrett's esophagus as an adjuvant to autofluorescence endoscopy. Using linear discriminant analysis on 2579 spectra measured in 54 patients identified an optimum a 4-wavelength classifier (at 485, 513, 598 and 629 nm). Sensitivity and specificity for a test data set were 0.67 and 0.85, respectively. Spectroscopic results show that this technique could be implemented in wide-field imaging mode to improve the accuracy of existing endoscopy techniques for finding early pre-malignant lesions in Barrett's esophagus. Results show that the discrimination occurs likely due to redistribution of blood content in the tissue sensed by the optical probing with the wavelength-dependent sampling depth.

  17. Characteristic Fingerprint Based on Low Polar Constituents for Discrimination of Wolfiporia extensa according to Geographical Origin Using UV Spectroscopy and Chemometrics Methods

    PubMed Central

    Li, Yan; Zhao, Yanli; Li, Zhimin; Li, Tao

    2014-01-01

    The fungus species Wolfiporia extensa has a long history of medicinal usage and has also been commercially used to formulate nutraceuticals and functional foods in certain Asian countries. In the present study, a practical and promising method has been developed to discriminate the dried sclerotium of W. extensa collected from different geographical sites based on UV spectroscopy together with chemometrics methods. Characteristic fingerprint of low polar constituents of sample extracts that originated from chloroform has been obtained in the interval 250–400 nm. Chemometric pattern recognition methods such as partial least squares discriminant analysis (PLS-DA) and hierarchical cluster analysis (HCA) were applied to enhance the authenticity of discrimination of the specimens. The results showed that W. extensa samples were well classified according to their geographical origins. The proposed method can fully utilize diversified fingerprint characteristics of sclerotium of W. extensa and requires low-cost equipment and short-time analysis in comparison with other techniques. Meanwhile, this simple and efficient method may serve as a basis for the authentication of other medicinal fungi. PMID:25544933

  18. Molecular strain typing of Brucella abortus isolates from Italy by two VNTR allele sizing technologies.

    PubMed

    De Santis, Riccardo; Ancora, Massimo; De Massis, Fabrizio; Ciammaruconi, Andrea; Zilli, Katiuscia; Di Giannatale, Elisabetta; Pittiglio, Valentina; Fillo, Silvia; Lista, Florigio

    2013-10-01

    Brucellosis, one of the most important re-emerging zoonoses in many countries, is caused by bacteria belonging to the genus Brucella. Furthermore these bacteria represent potential biological warfare agents and the identification of species and biovars of field strains may be crucial for tracing back source of infection, allowing to discriminate naturally occurring outbreaks instead of bioterrorist events. In the last years, multiple-locus variable-number tandem repeat analysis (MLVA) has been proposed as complement of the classical biotyping methods and it has been applied for genotyping large collections of Brucella spp. At present, the MLVA band profiles may be resolved by automated or manual procedures. The Lab on a chip technology represents a valid alternative to standard genotyping techniques (as agarose gel electrophoresis) and it has been previously used for Brucella genotyping. Recently, a new high-throughput genotyping analysis system based on capillary gel electrophoresis, the QIAxcel, has been described. The aim of the study was to evaluate the ability of two DNA sizing equipments, the QIAxcel System and the Lab chip GX, to correctly call alleles at the sixteen loci including one frequently used MLVA assay for Brucella genotyping. The results confirmed that these technologies represent a meaningful advancement in high-throughput Brucella genotyping. Considering the accuracy required to confidently resolve loci discrimination, QIAxcel shows a better ability to measure VNTR allele sizes compared to LabChip GX.

  19. Identification of Variables Associated with Group Separation in Descriptive Discriminant Analysis: Comparison of Methods for Interpreting Structure Coefficients

    ERIC Educational Resources Information Center

    Finch, Holmes

    2010-01-01

    Discriminant Analysis (DA) is a tool commonly used for differentiating among 2 or more groups based on 2 or more predictor variables. DA works by finding 1 or more linear combinations of the predictors that yield maximal difference among the groups. One common goal of researchers using DA is to characterize the nature of group difference by…

  20. Signal Detection Methods and Discriminant Analysis Applied to Categorization of Newspaper and Government Documents: A Preliminary Study.

    ERIC Educational Resources Information Center

    Ng, Kwong Bor; Rieh, Soo Young; Kantor, Paul

    2000-01-01

    Discussion of natural language processing focuses on experiments using linear discriminant analysis to distinguish "Wall Street Journal" texts from "Federal Register" tests using information about the frequency of occurrence of word boundaries, sentence boundaries, and punctuation marks. Displays and interprets results in terms…

  1. Microsatellite null alleles and estimation of population differentiation.

    PubMed

    Chapuis, Marie-Pierre; Estoup, Arnaud

    2007-03-01

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

  2. Accelerated test methods for life prediction of hermetic motor insulation systems exposed to alternative refrigerant/lubricant mixtures. Phase 3: Reproducibility and discrimination testing. Final report

    SciTech Connect

    Ellis, P.F. II; Ferguson, A.F.; Fuentes, K.T.

    1996-05-06

    In 1992, the Air-Conditioning and Refrigeration Technology Institute, Inc. (ARTI) contracted Radian Corporation to ascertain whether an improved accelerated test method or procedure could be developed that would allow prediction of the life of motor insulation materials used in hermetic motors for air-conditioning and refrigeration equipment operated with alternative refrigerant/lubricant mixtures. This report presents the results of phase three concerning the reproducibility and discrimination testing.

  3. A novel real-time PCR assay for quantitative analysis of methylated alleles (QAMA): analysis of the retinoblastoma locus.

    PubMed

    Zeschnigk, Michael; Böhringer, Stefan; Price, Elizabeth Ann; Onadim, Zerrin; Masshöfer, Lars; Lohmann, Dietmar R

    2004-09-07

    Altered methylation patterns have been found to play a role in developmental disorders, cancer and aging. Increasingly, changes in DNA methylation are used as molecular markers of disease. Therefore, there is a need for reliable and easy to use techniques to detect and measure DNA methylation in research and routine diagnostics. We have established a novel quantitative analysis of methylated alleles (QAMA) which is essentially a major improvement over a previous method based on real-time PCR (MethyLight). This method is based on real-time PCR on bisulfite-treated DNA. A significant advantage over conventional MethyLight is gained by the use of TaqMan probes based on minor groove binder (MGB) technology. Their improved sequence specificity facilitates relative quantification of methylated and unmethylated alleles that are simultaneously amplified in single tube. This improvement allows precise measurement of the ratio of methylated versus unmethylated alleles and cuts down potential sources of inter-assay variation. Therefore, fewer control assays are required. We have used this novel technical approach to identify hypermethylation of the CpG island located in the promoter region of the retinoblastoma (RB1) gene and found that QAMA facilitates reliable and fast measurement of the relative quantity of methylated alleles and improves handling of diagnostic methylation analysis. Moreover, the simplified reaction setup and robustness inherent to the single tube assay facilitates high-throughput methylation analysis. Because the high sequence specificity inherent to the MGB technology is widely used to discriminate single nucleotide polymorphisms, QAMA potentially can be used to discriminate the methylation status of single CpG dinucleotides.

  4. Identification of single-nucleotide polymorphisms by the oligonucleotide ligation reaction: a DNA biosensor for simultaneous visual detection of both alleles.

    PubMed

    Toubanaki, Dimitra K; Christopoulos, Theodore K; Ioannou, Penelope C; Flordellis, Christodoulos S

    2009-01-01

    Although single nucleotide polymorphisms (SNPs) can be identified by direct hybridization with allele-specific oligonucleotide probes, enzyme-based genotyping methods offer much higher specificity and robustness. Among enzymatic methods, the oligonucleotide ligation reaction (OLR) offers the highest specificity for allele discrimination because two hybridization events are required for ligation. We report the development of a DNA biosensor that offers significant advantages over currently available methods for detection of OLR products: It allows simultaneous visual discrimination of both alleles using a single ligation reaction. Detection is complete within minutes without the need for any specialized instruments. It does not involve multiple cycles of incubation and washing. The dry-reagent format minimizes the pipetting steps. The need for qualified personnel is much lower than current methods. The principle of the assay is as follows: Following PCR amplification, a single OLR is performed using a biotinylated common probe and two allele-specific probes labeled with the haptens digoxigenin and fluorescein. Ligation products corresponding to the normal and mutant allele are double-labeled with biotin and either digoxigenin or fluorescein, respectively. The products are captured by antidigoxigenin or antifluorescein antibodies, or both, that are immobilized at the two test zones of the biosensor and react with antibiotin-functionalized gold nanoparticle reporters. The excess nanoparticles bind to biotinylated albumin that is immobilized at the control zone of the biosensor. The genotype is assigned by the characteristic red lines that appear at the two test zones. The proposed DNA biosensor constitutes a significant step toward point-of-care SNP genotyping.

  5. 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)

  6. Method for manufacturing solid-state thermal neutron detectors with simultaneous high thermal neutron detection efficiency (>50%) and neutron to gamma discrimination (>1.0E4)

    DOEpatents

    Nikolic, Rebecca J.; Conway, Adam M.; Heineck, Daniel; Voss, Lars F.; Wang, Tzu Fang; Shao, Qinghui

    2013-10-15

    Methods for manufacturing solid-state thermal neutron detectors with simultaneous high thermal neutron detection efficiency (>50%) and neutron to gamma discrimination (>10.sup.4) are provided. A structure is provided that includes a p+ region on a first side of an intrinsic region and an n+ region on a second side of the intrinsic region. The thickness of the intrinsic region is minimized to achieve a desired gamma discrimination factor of at least 1.0E+04. Material is removed from one of the p+ region or the n+ region and into the intrinsic layer to produce pillars with open space between each pillar. The open space is filed with a neutron sensitive material. An electrode is placed in contact with the pillars and another electrode is placed in contact with the side that is opposite of the intrinsic layer with respect to the first electrode.

  7. Choreography of Ig allelic exclusion.

    PubMed

    Cedar, Howard; Bergman, Yehudit

    2008-06-01

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

  8. Frequency of FCGR3B Alleles in Thai Blood Donors

    PubMed Central

    Kaset, Chollanot; Leetrakool, Nipapan; Intharanut, Kamphon

    2013-01-01

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

  9. Airborne particulate discriminator

    DOEpatents

    Creek, Kathryn Louise; Castro, Alonso; Gray, Perry Clayton

    2009-08-11

    A method and apparatus for rapid and accurate detection and discrimination of biological, radiological, and chemical particles in air. A suspect aerosol of the target particulates is treated with a taggant aerosol of ultrafine particulates. Coagulation of the taggant and target particles causes a change in fluorescent properties of the cloud, providing an indication of the presence of the target.

  10. Discriminant learning analysis.

    PubMed

    Peng, Jing; Zhang, Peng; Riedel, Norbert

    2008-12-01

    Linear discriminant analysis (LDA) as a dimension reduction method is widely used in classification such as face recognition. However, it suffers from the small sample size (SSS) problem when data dimensionality is greater than the sample size, as in images where features are high dimensional and correlated. In this paper, we propose to address the SSS problem in the framework of statistical learning theory. We compute linear discriminants by regularized least squares regression, where the singularity problem is resolved. The resulting discriminants are complete in that they include both regular and irregular information. We show that our proposal and its nonlinear extension belong to the same framework where powerful classifiers such as support vector machines are formulated. In addition, our approach allows us to establish an error bound for LDA. Finally, our experiments validate our theoretical analysis results.

  11. [The osteometric method for the determination of sequential localization and sex characteristics of the ribs using discriminate analysis].

    PubMed

    Zviagin, V N; Permiakova, E Iu; Galitskaia, O I

    2009-01-01

    The study material was ribs of the Caucasoid carcasses from the collections of the Department of Anthropology, M.V. Lomonosov Moscow State University, and the Department of Personality Identification, Russian Centre of Forensic Medical Examination. Each rib was measured as stipulated by the 13 point program of A.I. Turovtsev (1972). The results were analysed with the use of the SPSS statistical packet. Diagnostic models were calculated for the purpose of forensic medicine practice based on step-by-step discriminative analysis. It is recommended to perform expert evaluation in two stages. The aim of the first stage, is to establish the group affiliation of a concrete rib. Group 1 comprises III-V ribs, group 2--ribs VI--VIII, and group 3--ribs IX-XI. Determination of the sequential localization of I, II, and XII ribs encounters practically no difficulty due to their unique anatomical structure. The accuracy of classication of group localization of the ribs amounts to 99.6%. At the second stage, individual number of a concrete rib within a group is determined. The accuracy of classification of ribs belonging to groups 1 and 3 is 80.2% and 85.7% respectively and that of ribs in group 2 is lightly lower (41.7-69%). Sexual identity of the ribs was determined by means of multidimensional discriminative analysis. The accuracy of diagnosis is directly related to the integrity of the study material; in other words, it depends on the amount of ribs available for the analysis. It is shown that sexual identity is best established for rib VI followed by ribs VIII, II, IV, and I respectively. The main discriminative features include the total arch length, costal plane curvature, and height-width dimension. Diagnostic equations are derived for the determination of sexual identity of individual ribs for the practical purposes of forensic medical examination.

  12. A discrimination task used as a novel method of testing decision-making behavior following traumatic brain injury.

    PubMed

    Martens, Kris M; Vonder Haar, Cole; Hutsell, Blake A; Hoane, Michael R

    2012-10-10

    Traumatic brain injury (TBI) results in a multitude of deficits following injury. Some of the most pervasive in humans are the changes that affect frontally-mediated cognitive functioning, such as decision making. The assessment of decision-making behavior in rodents has been extensively tested in the field of the experimental analysis of behavior. However, due to the narrow therapeutic window following TBI, time-intensive operant paradigms are rarely incorporated into the battery of tests traditionally used, the majority of which assess motor and sensory functioning. The cognitive measures that are used are frequently limited to memory and do not account for changes in decision-making behavior. The purpose of the present study was to develop a simplified discrimination task that can assess deficits in decision-making behavior in rodents. For the task, rats were required to dig in cocoa-scented sand (versus unscented sand) for a reinforcer. Rats were given 12 sessions per day until a criterion level of 80% accuracy for 3 days straight was reached. Once the criterion was achieved, cortical contusion injuries were induced (frontal, parietal, or sham). Following a recovery period, the rats were re-tested on cocoa versus unscented sand. Upon reaching criterion, a reversal discrimination was evaluated in which the reinforcer was placed in unscented sand. Finally, a novel scent discrimination (basil versus coffee with basil reinforced), and a reversal (coffee) were evaluated. The results indicated that the Dig task is a simple experimental preparation that can be used to assess deficits in decision-making behavior following TBI.

  13. Variable Selection in Discriminant Analysis.

    ERIC Educational Resources Information Center

    Huberty, Carl J.; Mourad, Salah A.

    Methods for ordering and selecting variables for discriminant analysis in multiple group comparison or group prediction studies include: univariate Fs, stepwise analysis, learning discriminant function (LDF) variable correlations, communalities, LDF standardized coefficients, and weighted standardized coefficients. Five indices based on distance,…

  14. 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

  15. Evolving window zone selection method followed by independent component analysis as useful chemometric tools to discriminate between grapefruit juice, orange juice and blends.

    PubMed

    Cuny, M; Le Gall, G; Colquhoun, I J; Lees, M; Rutledge, D N

    2007-08-06

    This study investigates the use of high resolution 1H NMR as a suitable alternative to the standard chromatographic method for the determination of adulteration of orange juice (Citrus sinensis) with grapefruit juice (Citrus paradisi) based on flavonoid glycoside content. Fifty-nine orange juices (OJ), 23 grapefruit juices (GJ) and 10 blends (OG), obtained from local retail outlets were used to assess the performance of the 1H NMR method. The work presented here introduces the Evolving Window Zone Selection (EWZS) function that holds promise for the automatic detection of spectral regions tailored to discriminate predefined groups. This technique was applied on the pre-processed 1H NMR spectra of the 92 juices. Independent Component Analysis (ICA) is a good alternative to Principal Component Analysis (PCA) for recovering linearly-mixed unobserved multidimensional independent signals and has been used in this study to build supervised models that classify the samples into three categories, OJ, GJ, OG. The regions containing the known flavonoid glycoside markers were selected as well as another zone containing the signals of sucrose, alpha-glucose and other components that were tentatively attributed. ICA was applied on three different groups of selected variables and showed good results for both discrimination and interpretation of the signals. Up to 97.8% of the juices were correctly attributed. This method gave better results than the commonly used PCA method. In addition, the time required to carry out the 1H NMR analysis was less than half the time of the standard chromatographic method.

  16. Color measurement and discrimination

    NASA Technical Reports Server (NTRS)

    Wandell, B. A.

    1985-01-01

    Theories of color measurement attempt to provide a quantative means for predicting whether two lights will be discriminable to an average observer. All color measurement theories can be characterized as follows: suppose lights a and b evoke responses from three color channels characterized as vectors, v(a) and v(b); the vector difference v(a) - v(b) corresponds to a set of channel responses that would be generated by some real light, call it *. According to theory a and b will be discriminable when * is detectable. A detailed development and test of the classic color measurement approach are reported. In the absence of a luminance component in the test stimuli, a and b, the theory holds well. In the presence of a luminance component, the theory is clearly false. When a luminance component is present discrimination judgements depend largely on whether the lights being discriminated fall in separate, categorical regions of color space. The results suggest that sensory estimation of surface color uses different methods, and the choice of method depends upon properties of the image. When there is significant luminance variation a categorical method is used, while in the absence of significant luminance variation judgments are continuous and consistant with the measurement approach.

  17. A new method for typing bovine major histocompatibility complex class II DRB3 alleles by combining two established PCR sequence-based techniques.

    PubMed

    Takeshima, S-N; Matsumoto, Y; Miyasaka, T; Arainga-Ramirez, M; Saito, H; Onuma, M; Aida, Y

    2011-09-01

    Recently, two polymerase chain reaction sequence-based typing (PCR-SBT) methods were reported for the genotyping of the bovine leukocyte antigen (BoLA)-DRB3. One technique is a single PCR-SBT (sPCR-SBT) method that generates heterozygous sequences that are subsequently analyzed by the haplofinder program, while the other technique is a nested PCR-SBT (nPCR-SBT) method that allows the analysis of heterozygous sequences using the assign 400ATF software. In this study, these techniques were compared and then integrated to produce an improved genotyping method. The primer set used for sPCR-SBT was more accurate than those used for nPCR-SBT. Combining sPCR-SBT with the assign 400ATF software previously reported for nPCR-SBT enables rapid and accurate genotyping of a large number of DNA samples.

  18. In silico and experimental evaluation of DNA-based detection methods for the ability to discriminate almond from other Prunus spp.

    PubMed

    Brežná, Barbara; Šmíd, Jiří; Costa, Joana; Radvanszky, Jan; Mafra, Isabel; Kuchta, Tomáš

    2015-04-01

    Ten published DNA-based analytical methods aiming at detecting material of almond (Prunus dulcis) were in silico evaluated for potential cross-reactivity with other stone fruits (Prunus spp.), including peach, apricot, plum, cherry, sour cherry and Sargent cherry. For most assays, the analysis of nucleotide databases suggested none or insufficient discrimination of at least some stone fruits. On the other hand, the assay targeting non-specific lipid transfer protein (Röder et al., 2011, Anal Chim Acta 685:74-83) was sufficiently discriminative, judging from nucleotide alignments. Empirical evaluation was performed for three of the published methods, one modification of a commercial kit (SureFood allergen almond) and one attempted novel method targeting thaumatin-like protein gene. Samples of leaves and kernels were used in the experiments. The empirical results were favourable for the method from Röder et al. (2011) and a modification of SureFood allergen almond kit, both showing cross-reactivity <10(-3) compared to the model almond.

  19. Estimating relatedness and relationships using microsatellite loci with null alleles.

    PubMed

    Wagner, A P; Creel, S; Kalinowski, S T

    2006-11-01

    Relatedness is often estimated from microsatellite genotypes that include null alleles. When null alleles are present, observed genotypes represent one of several possible true genotypes. If null alleles are detected, but analyses do not adjust for their presence (ie, observed genotypes are treated as true genotypes), then estimates of relatedness and relationship can be incorrect. The number of loci available in many wildlife studies is limited, and loci with null alleles are commonly a large proportion of data that cannot be discarded without substantial loss of power. To resolve this problem, we present a new approach for estimating relatedness and relationships from data sets that include null alleles. Once it is recognized that the probability of the observed genotypes is dependent on the probabilities of a limited number of possible true genotypes, the required adjustments are straightforward. The concept can be applied to any existing estimators of relatedness and relationships. We review established maximum likelihood estimators and apply the correction in that setting. In an application of the corrected method to data from striped hyenas, we demonstrate that correcting for the presence of null alleles affect results substantially. Finally, we use simulated data to confirm that this method works better than two common approaches, namely ignoring the presence of null alleles or discarding affected loci.

  20. Rapid discrimination between buffalo and cow milk and detection of adulteration of buffalo milk with cow milk using synchronous fluorescence spectroscopy in combination with multivariate methods.

    PubMed

    Durakli Velioglu, Serap; Ercioglu, Elif; Boyaci, Ismail Hakki

    2017-03-22

    This research paper describes the potential of synchronous fluorescence (SF) spectroscopy for authentication of buffalo milk, a favourable raw material in the production of some premium dairy products. Buffalo milk is subjected to fraudulent activities like many other high priced foodstuffs. The current methods widely used for the detection of adulteration of buffalo milk have various disadvantages making them unattractive for routine analysis. Thus, the aim of the present study was to assess the potential of SF spectroscopy in combination with multivariate methods for rapid discrimination between buffalo and cow milk and detection of the adulteration of buffalo milk with cow milk. SF spectra of cow and buffalo milk samples were recorded between 400-550 nm excitation range with Δλ of 10-100 nm, in steps of 10 nm. The data obtained for ∆λ = 10 nm were utilised to classify the samples using principal component analysis (PCA), and detect the adulteration level of buffalo milk with cow milk using partial least square (PLS) methods. Successful discrimination of samples and detection of adulteration of buffalo milk with limit of detection value (LOD) of 6% are achieved with the models having root mean square error of calibration (RMSEC) and the root mean square error of cross-validation (RMSECV) and root mean square error of prediction (RMSEP) values of 2, 7, and 4%, respectively. The results reveal the potential of SF spectroscopy for rapid authentication of buffalo milk.

  1. 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.

  2. Novel classical MHC class I alleles identified in horses by sequencing clones of reverse transcription-PCR products.

    PubMed

    Chung, C; Leib, S R; Fraser, D G; Ellis, S A; McGuire, T C

    2003-12-01

    Improved typing of horse classical MHC class I is required to more accurately define these molecules and to extend the number identified further than current serological assays. Defining classical MHC class I alleleic polymorphism is important in evaluating cytotoxic T lymphocyte (CTL) responses in horses. In this study, horse classical MHC class I genes were analyzed based on reverse transcription (RT)-PCR amplification of sequences encoding the polymorphic peptide binding region and the more conserved alpha 3, transmembrane and cytoplasmic regions followed by cloning and sequencing. Primer sets included a horse classical MHC class I-specific reverse primer and a forward primer conserved in all known horse MHC class I genes. Sequencing at least 25 clones containing MHC class I sequences from each of 13 horses identified 25 novel sequences and three others which had been described. Of these, nine alleles were identified from different horses or different RT-PCR and 19 putative alleles were identified in multiple clones from the same RT-PCR. The primer pairs did not amplify putative non-classical MHC class I genes as only classical MHC class I and related pseudogenes were found in 462 clones. This method also identified classical MHC class I alleles shared between horses by descent, and defined differences in alleles between horses varying in equine leukocyte antigen (ELA)-A haplotype as determined by serology. However, horses sharing ELA-A haplotypes defined by serotyping did not always share cDNA sequences, suggesting subhaplotypic variations within serologically defined ELA-A haplotypes. The 13 horses in this study had two to five classical MHC class I sequences, indicating that multiple loci code for these genes. Sequencing clones from RT-PCR with classical MHC class I-specific primers should be useful for selection of haplotype matched and mismatched horses for CTL studies, and provides sequence information needed to develop easier and more discriminating

  3. Racial/Ethnic Workplace Discrimination

    PubMed Central

    Chavez, Laura J.; Ornelas, India J.; Lyles, Courtney R.; Williams, Emily C.

    2014-01-01

    Background Experiences of discrimination are associated with tobacco and alcohol use, and work is a common setting where individuals experience racial/ethnic discrimination. Few studies have evaluated the association between workplace discrimination and these behaviors, and none have described associations across race/ethnicity. Purpose To examine the association between workplace discrimination and tobacco and alcohol use in a large, multistate sample of U.S. adult respondents to the Behavioral Risk Factor Surveillance System survey Reactions to Race Module (2004–2010). Methods Multivariable logistic regression analyses evaluated cross-sectional associations between self-reported workplace discrimination and tobacco (current and daily smoking) and alcohol use (any and heavy use, and binge drinking) among all participants and stratified by race/ethnicity, adjusting for relevant covariates. Data were analyzed in 2013. Results Among respondents, 70,080 completed the workplace discrimination measure. Discrimination was more common among black non-Hispanic (21%), Hispanic (12%), and other race respondents (11%) than white non-Hispanics (4%) (p<0.001). In the total sample, discrimination was associated with current smoking (risk ratio [RR]=1.32, 95% CI=1.19, 1.47), daily smoking (RR=1.41, 95% CI=1.24, 1.61), and heavy drinking (RR=1.11, 95% CI=1.01, 1.22), but not binge or any drinking. Among Hispanics, workplace discrimination was associated with increased heavy and binge drinking, but not any alcohol use or smoking. Workplace discrimination among black non-Hispanics and white Non-Hispanics was associated with increased current and daily smoking, but not alcohol outcomes. Conclusions Workplace discrimination is common, associated with smoking and alcohol use, and merits further policy attention given the impact of these behaviors on morbidity and mortality. PMID:25441232

  4. Discriminating harmonicity

    NASA Astrophysics Data System (ADS)

    Kidd, Gerald; Mason, Christine R.; Brughera, Andrew; Chiu, Chung-Yiu Peter

    2003-08-01

    Simultaneous tones that are harmonically related tend to be grouped perceptually to form a unitary auditory image. A partial that is mistuned stands out from the other tones, and harmonic complexes with different fundamental frequencies can readily be perceived as separate auditory objects. These phenomena are evidence for the strong role of harmonicity in perceptual grouping and segregation of sounds. This study measured the discriminability of harmonicity directly. In a two interval, two alternative forced-choice (2I2AFC) paradigm, the listener chose which of two sounds, signal or foil, was composed of tones that more closely matched an exact harmonic relationship. In one experiment, the signal was varied from perfectly harmonic to highly inharmonic by adding frequency perturbation to each component. The foil always had 100% perturbation. Group mean performance decreased from greater than 90% correct for 0% signal perturbation to near chance for 80% signal perturbation. In the second experiment, adding a masker presented simultaneously with the signals and foils disrupted harmonicity. Both monaural and dichotic conditions were tested. Signal level was varied relative to masker level to obtain psychometric functions from which slopes and midpoints were estimated. Dichotic presentation of these audible stimuli improved performance by 3-10 dB, due primarily to a release from ``informational masking'' by the perceptual segregation of the signal from the masker.

  5. 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.

  6. A dielectrophoretic method of discrimination between normal oral epithelium, and oral and oropharyngeal cancer in a clinical setting.

    PubMed

    Graham, K A; Mulhall, H J; Labeed, F H; Lewis, M P; Hoettges, K F; Kalavrezos, N; McCaul, J; Liew, C; Porter, S; Fedele, S; Hughes, M P

    2015-08-07

    Despite the accessibility of the oral cavity to clinical examination, delays in diagnosis of oral and oropharyngeal carcinoma (OOPC) are observed in a large majority of patients, with negative impact on prognosis. Diagnostic aids might help detection and improve early diagnosis, but there remains little robust evidence supporting the use of any particular diagnostic technology at the moment. The aim of the present feasibility first-in-human study was to evaluate the preliminary diagnostic validity of a novel technology platform based on dielectrophoresis (DEP). DEP does not require labeling with antibodies or stains and it is an ideal tool for rapid analysis of cell properties. Cells from OOPC/dysplasia tissue and healthy oral mucosa were collected from 57 study participants via minimally-invasive brush biopsies and tested with a prototype DEP platform using median membrane midpoint frequency as main analysis parameter. Results indicate that the current DEP platform can discriminate between brush biopsy samples from cancerous and healthy oral tissue with a diagnostic sensitivity of 81.6% and a specificity of 81.0%. The present ex vivo results support the potential application of DEP testing for identification of OOPC. This result indicates that DEP has the potential to be developed into a low-cost, rapid platform as an assistive tool for the early identification of oral cancer in primary care; given the rapid, minimally-invasive and non-expensive nature of the test, dielectric characterization represents a promising platform for cost-effective early cancer detection.

  7. The application of discriminant analysis and Machine Learning methods as tools to identify and classify compounds with potential as transdermal enhancers.

    PubMed

    Moss, G P; Shah, A J; Adams, R G; Davey, N; Wilkinson, S C; Pugh, W J; Sun, Y

    2012-01-23

    Discriminant analysis (DA) has previously been shown to allow the proposal of simple guidelines for the classification of 73 chemical enhancers of percutaneous absorption. Pugh et al. employed DA to classify such enhancers into simple categories, based on the physicochemical properties of the enhancer molecules (Pugh et al., 2005). While this approach provided a reasonable accuracy of classification it was unable to provide a consistently reliable estimate of enhancement ratio (ER, defined as the amount of hydrocortisone transferred after 24h, relative to control). Machine Learning methods, including Gaussian process (GP) regression, have recently been employed in the prediction of percutaneous absorption of exogenous chemicals (Moss et al., 2009; Lam et al., 2010; Sun et al., 2011). They have shown that they provide more accurate predictions of these phenomena. In this study several Machine Learning methods, including the K-nearest-neighbour (KNN) regression, single layer networks, radial basis function networks and the SVM classifier were applied to an enhancer dataset reported previously. The SMOTE sampling method was used to oversample chemical compounds with ER>10 in each training set in order to improve estimation of GP and KNN. Results show that models using five physicochemical descriptors exhibit better performance than those with three features. The best classification result was obtained by using the SVM method without dealing with imbalanced data. Following over-sampling, GP gives the best result. It correctly assigned 8 of the 12 "good" (ER>10) enhancers and 56 of the 59 "poor" enhancers (ER<10). Overall success rates were similar. However, the pharmaceutical advantages of the Machine Learning methods are that they can provide more accurate classification of enhancer type with fewer false-positive results and that, unlike discriminant analysis, they are able to make predictions of enhancer ability.

  8. Overdominant alleles in a population of variable size.

    PubMed Central

    Slatkin, M; Muirhead, C A

    1999-01-01

    An approximate method is developed to predict the number of strongly overdominant alleles in a population of which the size varies with time. The approximation relies on the strong-selection weak-mutation (SSWM) method introduced by J. H. Gillespie and leads to a Markov chain model that describes the number of common alleles in the population. The parameters of the transition matrix of the Markov chain depend in a simple way on the population size. For a population of constant size, the Markov chain leads to results that are nearly the same as those of N. Takahata. The Markov chain allows the prediction of the numbers of common alleles during and after a population bottleneck and the numbers of alleles surviving from before a bottleneck. This method is also adapted to modeling the case in which there are two classes of alleles, with one class causing a reduction in fitness relative to the other class. Very slight selection against one class can strongly affect the relative frequencies of the two classes and the relative ages of alleles in each class. PMID:10353917

  9. Discriminating between camouflaged targets by their time of detection by a human-based observer assessment method

    NASA Astrophysics Data System (ADS)

    Selj, G. K.; Søderblom, M.

    2015-10-01

    Detection of a camouflaged object in natural sceneries requires the target to be distinguishable from its local background. The development of any new camouflage pattern therefore has to rely on a well-founded test methodology - which has to be correlated with the final purpose of the pattern - as well as an evaluation procedure, containing the optimal criteria for i) discriminating between the targets and then eventually ii) for a final rank of the targets. In this study we present results from a recent camouflage assessment trial where human observers were used in a search by photo methodology to assess generic test camouflage patterns. We conducted a study to investigate possible improvements in camouflage patterns for battle dress uniforms. The aim was to do a comparative study of potential, and generic patterns intended for use in arid areas (sparsely vegetated, semi desert). We developed a test methodology that was intended to be simple, reliable and realistic with respect to the operational benefit of camouflage. Therefore we chose to conduct a human based observer trial founded on imagery of realistic targets in natural backgrounds. Inspired by a recent and similar trial in the UK, we developed new and purpose-based software to be able to conduct the observer trial. Our preferred assessment methodology - the observer trial - was based on target recordings in 12 different, but operational relevant scenes, collected in a dry and sparsely vegetated area (Rhodes). The scenes were chosen with the intention to span as broadly as possible. The targets were human-shaped mannequins and were situated identically in each of the scenes to allow for a relative comparison of camouflage effectiveness in each scene. Test of significance, among the targets' performance, was carried out by non-parametric tests as the corresponding time of detection distributions in overall were found to be difficult to parameterize. From the trial, containing 12 different scenes from

  10. 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.

  11. A simple method to discriminate diapause from non-diapause pupae in large and small white butterflies, Pieris brassicae and P. rapae crucivora.

    PubMed

    Kaneko, Junichi; Katagiri, Chihiro

    2006-08-01

    Differences in colour and shape have been used to discriminate diapause pupae from non-diapause pupae in butterflies. In the present study, we describe a simple discrimination method based on differences in the specific gravity of diapause and non-diapause pupae of large and small white butterflies, Pieris brassicae and Pieris rapae crucivora. When put into water, diapause pupae sink to the bottom (specific gravity is above 1.0), whereas non-diapause pupae float on the surface (specific gravity is below 1.0). Nuclear magnetic resonance microimaging revealed that this difference in specific gravity is due to a difference in the volume of an internal cavity located between the thorax and the abdomen in the pupae. The cavity appears quite early in development. We also examined the cavity in pupae of the unrelated swallowtail butterfly, Papilio xuthus, and found a similar cavity. However, in this species, the cavity is very small and, as a consequence, non-diapause as well as diapause pupae sink in water.

  12. [Microchip electrophoresis coupled with multiplex allele-specific am-plification for typing multiple single nucleotide polymorphisms (SNPs) simultaneously].

    PubMed

    Wang, Wei-Peng; Zhou, Guo-Hua

    2009-02-01

    A new method of DNA adapter ligation-mediated allele-specific amplification (ALM-ASA) was developed for typing multiple single nucleotide polymorphisms (SNPs) on the platform of microchip electrophoresis. Using seven SNPs of 794C>T, 1274C>T, 2143T>C, 2766T>del, 3298G>A, 5200G>A, and 5277C>T in the interleukin 1B (IL1B) gene as a target object, a long DNA fragment containing the seven SNPs of interest was pre-amplified to enhance the specificity. The pre-amplified DNA fragment was digested by a restriction endonuclease to form sticky ends; and then the adapter was ligated to either end of the digested fragment. Using the adapter-ligated fragments as templates, a 7-plex allele-specific amplification was performed by 7 allele-specific primers and a universal primer in one tube. The allele-specific products amplified were separated by chip electrophoresis and the types of SNPs were easily discriminated by the product sizes. The seven SNPs in IL1B gene in 48 healthy Chinese were successfully typed by microchip electrophoresis and the results coincided with those by PCR-restriction fragment length polymorphism and sequencing method. The method established was accurate and can be used to type multiple SNPs simultaneously. In combination with microchip electrophoresis for readout, ALM-ASA assay can be used for fast SNP detection with a small amount of sample. Using self-prepared gel matrix and reused chips for analysis, the SNP can be typed at an ultra low cost.

  13. Allele Mining Strategies: Principles and Utilisation for Blast Resistance Genes in Rice (Oryza sativa L.).

    PubMed

    Ashkani, Sadegh; Yusop, Mohd Rafii; Shabanimofrad, Mahmoodreza; Azady, Amin; Ghasemzadeh, Ali; Azizi, Parisa; Latif, Mohammad Abdul

    2015-01-01

    Allele mining is a promising way to dissect naturally occurring allelic variants of candidate genes with essential agronomic qualities. With the identification, isolation and characterisation of blast resistance genes in rice, it is now possible to dissect the actual allelic variants of these genes within an array of rice cultivars via allele mining. Multiple alleles from the complex locus serve as a reservoir of variation to generate functional genes. The routine sequence exchange is one of the main mechanisms of R gene evolution and development. Allele mining for resistance genes can be an important method to identify additional resistance alleles and new haplotypes along with the development of allele-specific markers for use in marker-assisted selection. Allele mining can be visualised as a vital link between effective utilisation of genetic and genomic resources in genomics-driven modern plant breeding. This review studies the actual concepts and potential of mining approaches for the discovery of alleles and their utilisation for blast resistance genes in rice. The details provided here will be important to provide the rice breeder with a worthwhile introduction to allele mining and its methodology for breakthrough discovery of fresh alleles hidden in hereditary diversity, which is vital for crop improvement.

  14. Automated analysis of sequence polymorphism in STR alleles by PCR and direct electrospray ionization mass spectrometry.

    PubMed

    Planz, John V; Sannes-Lowery, Kristen A; Duncan, David D; Manalili, Sheri; Budowle, Bruce; Chakraborty, Ranajit; Hofstadler, Steven A; Hall, Thomas A

    2012-09-01

    Short tandem repeats (STRs) are the primary genetic markers used for the analysis of biological samples in forensic and human identity testing. The discrimination power of a combination of STRs is sufficient in many human identity testing comparisons unless the evidence is substantially compromised and/or there are insufficient relatives or a potential mutation may have arisen in kinship analyses. An automated STR assay system that is based on electrospray ionization mass spectrometry (ESI-MS) has been developed that can increase the discrimination power of some of the CODIS core STR loci and thus provide more information in typical and challenged samples and cases. Data from the ESI-MS STR system is fully backwards compatible with existing STR typing results generated by capillary electrophoresis. In contrast, however, the ESI-MS analytical system also reveals nucleotide polymorphisms residing within the STR alleles. The presence of these polymorphisms expands the number of alleles at a locus. Population studies were performed on the 13 core CODIS STR loci from African Americans, Caucasians and Hispanics capturing both the length of the allele, as well as nucleotide variations contained within repeat motifs or flanking regions. Such additional polymorphisms were identified in 11 of the 13 loci examined whereby several nominal length alleles were subdivided. A substantial increase in heterozygosity was observed, with close to or greater than 5% of samples analyzed being heterozygous with equal-length alleles in at least one of five of the core CODIS loci. This additional polymorphism increases discrimination power significantly, whereby the seven most polymorphic STR loci have a discrimination power equivalent to the 10 most discriminating of the CODIS core loci. An analysis of substructure among the three population groups revealed a higher θ than would be observed compared with using alleles designated by nominal length, i.e., repeats solely. Two loci, D3S1358

  15. A Method for Selecting between Fisher's Linear Classification Functions and Least Absolute Deviation in Predictive Discriminant Analysis.

    ERIC Educational Resources Information Center

    Meshbane, Alice; Morris, John D.

    A method for comparing the cross-validated classification accuracy of Fisher's linear classification functions (FLCFs) and the least absolute deviation is presented under varying data conditions for the two-group classification problem. With this method, separate-group as well as total-sample proportions of current classifications can be compared…

  16. Fast method for multielemental analysis of plants and discrimination according to the anatomical part by total reflection X-ray fluorescence spectrometry.

    PubMed

    De la Calle, Inmaculada; Costas, Marta; Cabaleiro, Noelia; Lavilla, Isela; Bendicho, Carlos

    2013-05-01

    Fast and reliable analytical methodologies are required for quality control of plants in order to assure human health. Ultrasound-assisted extraction in combination with total reflection X-ray fluorescence is proposed as a fast and simple method for multielemental analysis of plants on a routine basis. For this purpose, five certified reference materials have been analysed for the determination of P, K, Ca, Cr, Mn, Fe, Ni, Cu, Zn and Pb. Different extractant media (acids and oxidants) were tried. A mixture of diluted HNO(3)+HCl+HF, was selected as the best option for the achievement of complete extractions. Accurate and precise results can be reached in most cases along with a high sample throughput. Different plants (i.e., herbs, spices and medicinal plants) were analysed. Linear discriminant analysis together with the elemental concentrations allowed the differentiation of commercial preparations corresponding to flower, fruit and leaf.

  17. A comparison of digital zero-crossing and charge-comparison methods for neutron/γ-ray discrimination with liquid scintillation detectors

    NASA Astrophysics Data System (ADS)

    Nakhostin, M.

    2015-10-01

    In this paper, we have compared the performances of the digital zero-crossing and charge-comparison methods for n/γ discrimination with liquid scintillation detectors at low light outputs. The measurements were performed with a 2″×2″ cylindrical liquid scintillation detector of type BC501A whose outputs were sampled by means of a fast waveform digitizer with 10-bit resolution, 4 GS/s sampling rate and one volt input range. Different light output ranges were measured by operating the photomultiplier tube at different voltages and a new recursive algorithm was developed to implement the digital zero-crossing method. The results of our study demonstrate the superior performance of the digital zero-crossing method at low light outputs when a large dynamic range is measured. However, when the input range of the digitizer is used to measure a narrow range of light outputs, the charge-comparison method slightly outperforms the zero-crossing method. The results are discussed in regard to the effects of the quantization noise and the noise filtration performance of the zero-crossing filter.

  18. 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.

  19. Comparison of geometric morphometric outline methods in the discrimination of age-related differences in feather shape

    PubMed Central

    Sheets, H David; Covino, Kristen M; Panasiewicz, Joanna M; Morris, Sara R

    2006-01-01

    Background Geometric morphometric methods of capturing information about curves or outlines of organismal structures may be used in conjunction with canonical variates analysis (CVA) to assign specimens to groups or populations based on their shapes. This methodological paper examines approaches to optimizing the classification of specimens based on their outlines. This study examines the performance of four approaches to the mathematical representation of outlines and two different approaches to curve measurement as applied to a collection of feather outlines. A new approach to the dimension reduction necessary to carry out a CVA on this type of outline data with modest sample sizes is also presented, and its performance is compared to two other approaches to dimension reduction. Results Two semi-landmark-based methods, bending energy alignment and perpendicular projection, are shown to produce roughly equal rates of classification, as do elliptical Fourier methods and the extended eigenshape method of outline measurement. Rates of classification were not highly dependent on the number of points used to represent a curve or the manner in which those points were acquired. The new approach to dimensionality reduction, which utilizes a variable number of principal component (PC) axes, produced higher cross-validation assignment rates than either the standard approach of using a fixed number of PC axes or a partial least squares method. Conclusion Classification of specimens based on feather shape was not highly dependent of the details of the method used to capture shape information. The choice of dimensionality reduction approach was more of a factor, and the cross validation rate of assignment may be optimized using the variable number of PC axes method presented herein. PMID:16978414

  20. An Empirical Approach to Salary Discrimination: With Case Study of Sex Discrimination in Education

    ERIC Educational Resources Information Center

    Anderson, Julie A.; Murphy, Norman C.

    1977-01-01

    A statistical method to determine sex discrimination in salaries considered known differential variables which can legitimately be used to determine salary level apart from discrimination based on improper criteria, such as race, sex, religion, etc. This case study of a group of educators exemplifies salary discrimination based on sex. (Author/MV)

  1. Distribution of BoLA-DRB3 allelic frequencies and identification of two new alleles in Iranian buffalo breed.

    PubMed

    Mosafer, J; Heydarpour, M; Manshad, E; Russell, G; Sulimova, G E

    2012-01-01

    The role of the major histocompatibility complex (MHC) in the immune response makes it an attractive candidate gene for associations with disease resistance and susceptibility. This study describes genetic variability in the BoLA-DRB3 in Iranian buffaloes. Heminested PCR-RFLP method was used to identify the frequency of BoLA-DRB3 alleles. The BoLA-DRB3 locus is highly polymorphic in the study herd (12 alleles). Almost 63.50% of the alleles were accounted for by four alleles (BoLA-DRB3.2 ∗48, ∗20, ∗21, and obe) in Iranian buffalo. The DRB3.2 ∗48 allele frequency (24.20%) was higher than the others. The frequencies of the DRB3.2 ∗20 and DRB3.2 ∗21 are 14.52 and 14.00, respectively, and obe and gbb have a new pattern. Significant distinctions have been found between Iranian buffalo and other cattle breed studied. In the Iranian buffaloes studied alleles associated with resistance to various diseases are found.

  2. Distribution of BoLA-DRB3 Allelic Frequencies and Identification of Two New Alleles in Iranian Buffalo Breed

    PubMed Central

    Mosafer, J.; Heydarpour, M.; Manshad, E.; Russell, G.; Sulimova, G. E.

    2012-01-01

    The role of the major histocompatibility complex (MHC) in the immune response makes it an attractive candidate gene for associations with disease resistance and susceptibility. This study describes genetic variability in the BoLA-DRB3 in Iranian buffaloes. Heminested PCR-RFLP method was used to identify the frequency of BoLA-DRB3 alleles. The BoLA-DRB3 locus is highly polymorphic in the study herd (12 alleles). Almost 63.50% of the alleles were accounted for by four alleles (BoLA-DRB3.2 ∗48, ∗20, ∗21, and obe) in Iranian buffalo. The DRB3.2 ∗48 allele frequency (24.20%) was higher than the others. The frequencies of the DRB3.2 ∗20 and DRB3.2 ∗21 are 14.52 and 14.00, respectively, and obe and gbb have a new pattern. Significant distinctions have been found between Iranian buffalo and other cattle breed studied. In the Iranian buffaloes studied alleles associated with resistance to various diseases are found. PMID:22454612

  3. Accurate size comparison of short tandem repeat alleles amplified by PCR.

    PubMed

    Smith, R N

    1995-01-01

    A strategy is presented for classifying complex short tandem repeat (STR) alleles by size. Such alleles can differ in length by only 1 bp. The HUMACTBP2 locus was used as a model. Dye-labeled, PCR-amplified alleles were analyzed on an automated DNA sequencer with laser-induced fluorescence detection and fragment-sizing software. Between-gel allele sizes calculated against an in-lane allelic ladder or viral DNA size standard were too imprecise to distinguish a 1-bp difference. However, the size difference between a sample allele and its matching ladder allele provided a reliable criterion for size classification. The mean size difference +/- 3 SDs was 0.5 bp, and so an individual result within this interval signified a match. Statistically, 99.7% of the results should lie within +/- 3 SDs with virtually no chance of encountering the 9-SD difference from the mean necessary to misclassify an allele by 1 bp. The method was valid for sample alleles sized against the allelic ladder and for both sample and ladder alleles sized against the viral DNA standard. A correction for the effect of different dye labels on mobility was included in the calculations.

  4. Workplace discrimination: experiences of practicing physicians.

    PubMed Central

    Coombs, Alice A. Tolbert; King, Roderick K.

    2005-01-01

    BACKGROUND: In response to a growing concern regarding physician discrimination in the workplace, this study was developed to: (1) describe the types of discrimination that exist for the practicing physician and (2) determine which groups of physicians are more likely to experience the various forms of discrimination. METHODS: Surveys were mailed to 1930 practicing physicians in Massachusetts. Participants were asked if they had encountered discrimination, how significant the discrimination was against a specific group, the frequency of personal discrimination, and the type of discrimination. Factor analysis identified four types of discrimination: career advancement, punitive behaviors, practice barriers and hiring barriers. RESULTS: A total of 445 responses were received (a 24% response rate). Sixty-three percent of responding physicians had experienced some form of discrimination. Respondents were women (46%), racial/ethnic minorities (42%) and international medical graduates (IMGs) (40%). In addition, 26% of those classified as white were also IMGs. Over 60% of respondents believed discrimination against IMGs was very or somewhat significant. Almost 27% of males acknowledged that gender bias against females was very or somewhat significant. IMGs were more likely to indicate that discrimination against IMGs was significant in their current organization. Of U.S. medical graduates (USMGs) 44% reported that discrimination against IMGs in their current organization was significant. Nonwhites were more likely to report that discrimination based on race/ethnicity was significant. Nearly 29% of white respondents also believed that such discrimination was very or somewhat significant. CONCLUSIONS: Physicians practicing in academic, research, and private practice sectors experience discrimination based on gender, ethnic/racial, and IMG status. Images Figure 3 Figure 4 Figure 5 PMID:15868767

  5. A method of discriminating transuranic radionuclides from radon progeny using low-resolution alpha spectroscopy and curve-fitting techniques.

    PubMed

    Konzen, Kevin; Brey, Richard

    2012-05-01

    ²²²Rn (radon) and ²²⁰Rn (thoron) progeny are known to interfere with determining the presence of long-lived transuranic radionuclides, such as plutonium and americium, and require from several hours up to several days for conclusive results. Methods are proposed that should expedite the analysis of air samples for determining the amount of transuranic radionuclides present using low-resolution alpha spectroscopy systems available from typical alpha continuous air monitors (CAMs) with multi-channel analyzer (MCA) capabilities. An alpha spectra simulation program was developed in Microsoft Excel visual basic that employed the use of Monte Carlo numerical methods and serial-decay differential equations that resembled actual spectra. Transuranic radionuclides were able to be quantified with statistical certainty by applying peak fitting equations using the method of least squares. Initial favorable results were achieved when samples containing radon progeny were decayed 15 to 30 min, and samples containing both radon and thoron progeny were decayed at least 60 min. The effort indicates that timely decisions can be made when determining transuranic activity using available alpha CAMs with alpha spectroscopy capabilities for counting retrospective air samples if accompanied by analyses that consider the characteristics of serial decay.

  6. 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

  7. Discrimination of edible oils and fats by combination of multivariate pattern recognition and FT-IR spectroscopy: A comparative study between different modeling methods

    NASA Astrophysics Data System (ADS)

    Javidnia, Katayoun; Parish, Maryam; Karimi, Sadegh; Hemmateenejad, Bahram

    2013-03-01

    By using FT-IR spectroscopy, many researchers from different disciplines enrich the experimental complexity of their research for obtaining more precise information. Moreover chemometrics techniques have boosted the use of IR instruments. In the present study we aimed to emphasize on the power of FT-IR spectroscopy for discrimination between different oil samples (especially fat from vegetable oils). Also our data were used to compare the performance of different classification methods. FT-IR transmittance spectra of oil samples (Corn, Colona, Sunflower, Soya, Olive, and Butter) were measured in the wave-number interval of 450-4000 cm-1. Classification analysis was performed utilizing PLS-DA, interval PLS-DA, extended canonical variate analysis (ECVA) and interval ECVA methods. The effect of data preprocessing by extended multiplicative signal correction was investigated. Whilst all employed method could distinguish butter from vegetable oils, iECVA resulted in the best performances for calibration and external test set with 100% sensitivity and specificity.

  8. Advancing allele group-specific amplification of the complete HLA-C gene--isolation of novel alleles from three allele groups (C*04, C*07 and C*08).

    PubMed

    Cisneros, E; Martínez-Pomar, N; Vilches, M; Martín, P; de Pablo, R; Nuñez Del Prado, N; Nieto, A; Matamoros, N; Moraru, M; Vilches, C

    2013-10-01

    A variety of strategies have been designed for sequence-based HLA typing (SBT) and for the isolation of new human leucocyte antigen (HLA) alleles, but unambiguous characterization of complete genomic sequences remains a challenge. We recently reported a simple method for the group-specific amplification (GSA) and sequencing of a full-length C*04 genomic sequence in isolation from the accompanying allele. Here we build on this strategy and present homologous methods that enable the isolation of HLA-C alleles belonging to another two allele groups. Using this approach, which can be applied to sequence-based typing in some clinical settings, we have successfully characterized three novel HLA-C alleles (C*04:128, C*07:01:01:02, and C*08:62).

  9. Error-rate estimation in discriminant analysis of non-linear longitudinal data: A comparison of resampling methods.

    PubMed

    de la Cruz, Rolando; Fuentes, Claudio; Meza, Cristian; Núñez-Antón, Vicente

    2016-07-08

    Consider longitudinal observations across different subjects such that the underlying distribution is determined by a non-linear mixed-effects model. In this context, we look at the misclassification error rate for allocating future subjects using cross-validation, bootstrap algorithms (parametric bootstrap, leave-one-out, .632 and [Formula: see text]), and bootstrap cross-validation (which combines the first two approaches), and conduct a numerical study to compare the performance of the different methods. The simulation and comparisons in this study are motivated by real observations from a pregnancy study in which one of the main objectives is to predict normal versus abnormal pregnancy outcomes based on information gathered at early stages. Since in this type of studies it is not uncommon to have insufficient data to simultaneously solve the classification problem and estimate the misclassification error rate, we put special attention to situations when only a small sample size is available. We discuss how the misclassification error rate estimates may be affected by the sample size in terms of variability and bias, and examine conditions under which the misclassification error rate estimates perform reasonably well.

  10. Evaluation of the resolving power of three different DNA fingerprinting methods to discriminate among isolates of a natural Rhizobium meliloti population.

    PubMed

    Niemann, S; Pühler, A; Tichy, H V; Simon, R; Selbitschka, W

    1997-04-01

    In a comparative study, the PCR-based RAPD and ERIC fingerprint methods were evaluated for their resolving power to discriminate among 21 isolates of a natural Rhizobium meliloti population. PCR fingerprint patterns were analysed by using an automated laser fluorescent (ALF) DNA sequencer, thus allowing the automated on-line storage of data. Results obtained were compared to a classification system using insertion sequence (IS) fingerprinting. Both PCR fingerprint methods were comparable in their ability to resolve differences amongst Rh. meliloti isolates. Grouping of strains on the basis of their RAPD as well as their ERIC fingerprints correlated with grouping of strains according to their IS fingerprints. Moreover, strains displaying identical PCR patterns could be further differentiated according to their IS fingerprints, thus allowing a detailed insight into phylogenetic relationship among strains. The automated evaluation of strain-specific fingerprint patterns has the potential to become a valuable tool for studies of bacterial population genetics. Moreover, the rapid identification of single strains, e.g. pathogens in epidemiological studies seems feasible.

  11. Development and validation of an HPTLC method for apigenin 7-O-glucoside in chamomile flowers and its application for fingerprint discrimination of chamomile-like materials.

    PubMed

    Guzelmeric, Etil; Vovk, Irena; Yesilada, Erdem

    2015-03-25

    Brewed tea of chamomile flowers (Matricaria recutita L.) (Asteraceae) has been extensively consumed for centuries due to either its pleasant taste or medicinal purposes. On the other hand, the major problem is difficulty in distinguishing the genuine specimen when supplying chamomile through nature-picking. Consequently flowers of other Asteraceae members resembling to chamomile in appearance may frequently be practiced by lay people or marketed in spice shops or bazaars. Evidently detection of such adulterations plays a vital role in terms of public health to avoid risk of toxicity (i.e. pyrazolidin alkaloids) and ineffective treatments (lack or insufficient concentration of the active constituents). This work presents either development and validation of a high performance thin-layer chromatographic (HPTLC) method for apigenin 7-O-glucoside which is one of the active markers in chamomile flowers or its application for the fingerprint discrimination of chamomile-like materials i.e. Anthemis spp., Bellis spp., Chrysanthemum sp. and Tanacetum sp. gathered by local people assuming as chamomile. Separation was performed on the silica gel 60 NH2 F254s HPTLC plates using the developing solvent system of ethyl acetate-formic acid-acetic acid-water (30:1.5:1.5:3, v/v/v/v). The proposed HPTLC method may also be a leading guide for the quality assessment of chamomile tea products on the market.

  12. Visualization of Term Discrimination Analysis.

    ERIC Educational Resources Information Center

    Zhang, Jin; Wolfram, Dietmar

    2001-01-01

    Discusses information visualization techniques and introduces a visual term discrimination value analysis method using a document density space within a distance-angle-based visual information retrieval environment. Explains that applications of these methods facilitate more effective assignment of term weights to index terms within documents and…

  13. 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.

  14. Association between ACE D allele and elite short distance swimming.

    PubMed

    Costa, Aldo Matos; Silva, António José; Garrido, Nuno Domingos; Louro, Hugo; de Oliveira, Ricardo Jacó; Breitenfeld, Luiza

    2009-08-01

    The influence of ACE gene on athletic performance has been widely explored, and most of the published data refers to an I/D polymorphism leading to the presence (I allele) or absence (D allele) of a 287-bp sequence in intron 16, determining ACE activity in serum and tissues. A higher I allele frequency has been reported among elite endurance athletes, while the D allele was more frequent among those engaged in more power-orientated sports. However, on competitive swimming, the reproducibility of such associations is controversial. We thus compared the ACE genotype of elite swimmers with that of non-elite swimming cohort and of healthy control subjects. We thus sought an association of the ACE genotype of elite swimmers with their competitive distance. 39 Portuguese Olympic swimming candidates were classified as: short (<200 m) and middle (400-1,500 m) distance swimmers, respectively. A group of 32 non-elite swimmers were studied and classified as well, and a control group (n = 100) was selected from the Portuguese population. Chelex 100 was used for DNA extraction and genotype was determined by PCR-RFLP methods. We found that ACE genotype distribution and allelic frequency differs significantly by event distance only among elite swimmers (P < or = 0.05). Moreover, the allelic frequency of the elite short distance swimmers differed significantly from that of the controls (P = 0.021). No associations were found between middle distance swimmers and controls. Our results seem to support an association between the D allele and elite short distance swimming.

  15. Construction of a library of cloned short tandem repeat (STR) alleles as universal templates for allelic ladder preparation.

    PubMed

    Wang, Le; Zhao, Xing-Chun; Ye, Jian; Liu, Jin-Jie; Chen, Ting; Bai, Xue; Zhang, Jian; Ou, Yuan; Hu, Lan; Jiang, Bo-Wei; Wang, Feng

    2014-09-01

    Short tandem repeat (STR) genotyping methods are widely used for human identity testing applications, including forensic DNA analysis. Samples of DNA containing the length-variant STR alleles are typically separated and genotyped by comparison to an allelic ladder. Here, we describe a newly devised library of cloned STR alleles. The library covers alleles X and Y for the sex-determining locus Amelogenin and 259 other alleles for 22 autosomal STR loci (TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, vWA, D13S317, D16S539, D18S51, D21S11, D2S1338, D6S1043, D12S391, Penta E, D19S433, D11S4463, D17S974, D3S4529 and D12ATA63). New primers were designed for all these loci to construct recombinant plasmids so that the library retains core repeat elements of STR as well as 5'- and 3'-flanking sequences of ∼500 base pairs. Since amplicons of commercial STR genotyping kits and systems developed in laboratories are usually distributed from 50 to <500 base pairs, this library could provide universal templates for allelic ladder preparation. We prepared three different sets of allelic ladders for this locus TH01 and an updated version of an allelic ladder for the DNATyper(®)19 multiplex system using these plasmids to confirm the suitability of the library as a good source for allelic ladder preparation. Importantly, the authenticity of each construct was confirmed by bidirectional nucleotide sequencing and we report the repeat structures of the 259 STR alleles. The sequencing results showed all repeat structures we obtained for TPOX, CSF1PO, D7S820, TH01, D16S539, D18S51 and Penta E were the same as reported. However, we identified 102 unreported repeat structures from the other 15 STR loci, supplementing our current knowledge of repeat structures and leading to further understanding of these widely used loci.

  16. Discriminative clustering via extreme learning machine.

    PubMed

    Huang, Gao; Liu, Tianchi; Yang, Yan; Lin, Zhiping; Song, Shiji; Wu, Cheng

    2015-10-01

    Discriminative clustering is an unsupervised learning framework which introduces the discriminative learning rule of supervised classification into clustering. The underlying assumption is that a good partition (clustering) of the data should yield high discrimination, namely, the partitioned data can be easily classified by some classification algorithms. In this paper, we propose three discriminative clustering approaches based on Extreme Learning Machine (ELM). The first algorithm iteratively trains weighted ELM (W-ELM) classifier to gradually maximize the data discrimination. The second and third methods are both built on Fisher's Linear Discriminant Analysis (LDA); but one approach adopts alternative optimization, while the other leverages kernel k-means. We show that the proposed algorithms can be easily implemented, and yield competitive clustering accuracy on real world data sets compared to state-of-the-art clustering methods.

  17. Investigating the limitations of tree species classification using the Combined Cluster and Discriminant Analysis method for low density ALS data from a dense forest region in Aggtelek (Hungary)

    NASA Astrophysics Data System (ADS)

    Koma, Zsófia; Deák, Márton; Kovács, József; Székely, Balázs; Kelemen, Kristóf; Standovár, Tibor

    2016-04-01

    Airborne Laser Scanning (ALS) is a widely used technology for forestry classification applications. However, single tree detection and species classification from low density ALS point cloud is limited in a dense forest region. In this study we investigate the division of a forest into homogenous groups at stand level. The study area is located in the Aggtelek karst region (Northeast Hungary) with a complex relief topography. The ALS dataset contained only 4 discrete echoes (at 2-4 pt/m2 density) from the study area during leaf-on season. Ground-truth measurements about canopy closure and proportion of tree species cover are available for every 70 meter in 500 square meter circular plots. In the first step, ALS data were processed and geometrical and intensity based features were calculated into a 5×5 meter raster based grid. The derived features contained: basic statistics of relative height, canopy RMS, echo ratio, openness, pulse penetration ratio, basic statistics of radiometric feature. In the second step the data were investigated using Combined Cluster and Discriminant Analysis (CCDA, Kovács et al., 2014). The CCDA method first determines a basic grouping for the multiple circle shaped sampling locations using hierarchical clustering and then for the arising grouping possibilities a core cycle is executed comparing the goodness of the investigated groupings with random ones. Out of these comparisons difference values arise, yielding information about the optimal grouping out of the investigated ones. If sub-groups are then further investigated, one might even find homogeneous groups. We found that low density ALS data classification into homogeneous groups are highly dependent on canopy closure, and the proportion of the dominant tree species. The presented results show high potential using CCDA for determination of homogenous separable groups in LiDAR based tree species classification. Aggtelek Karst/Slovakian Karst Caves" (HUSK/1101/221/0180, Aggtelek NP

  18. Perceived age discrimination in older adults

    PubMed Central

    Rippon, Isla; Kneale, Dylan; de Oliveira, Cesar; Demakakos, Panayotes; Steptoe, Andrew

    2014-01-01

    Objectives: to examine perceived age discrimination in a large representative sample of older adults in England. Methods: this cross-sectional study of over 7,500 individuals used data from the fifth wave of the English Longitudinal Study of Ageing (ELSA), a longitudinal cohort study of men and women aged 52 years and older in England. Wave 5 asked respondents about the frequency of five everyday discriminatory situations. Participants who attributed any experiences of discrimination to their age were treated as cases of perceived age discrimination. Multivariable logistic regression analysis was used to estimate the odds ratios of experiencing perceived age discrimination in relation to selected sociodemographic factors. Results: approximately a third (33.3%) of all respondents experienced age discrimination, rising to 36.8% in those aged 65 and over. Perceived age discrimination was associated with older age, higher education, lower levels of household wealth and being retired or not in employment. The correlates of age discrimination across the five discriminatory situations were similar. Conclusion: understanding age discrimination is vital if we are to develop appropriate policies and to target future interventions effectively. These findings highlight the scale of the challenge of age discrimination for older adults in England and illustrate that those groups are particularly vulnerable to this form of discrimination. PMID:24077751

  19. Color measurement and discrimination

    NASA Technical Reports Server (NTRS)

    Wandell, B. A.

    1985-01-01

    The present investigation is concerned with new results which show that for test lights with slow temporal modulations, and thus little effect on the luminance system, the vector-difference hypothesis represents an adequate characterization of discrimination data. It is pointed out that for certain experimental conditions color measurements can be successfully extended to include a difference measure which predicts the discriminability of pairs of lights. When discrimination depends principally on opponent-channel responses, discrimination thresholds can be predicted from the detection contour alone. Attention is given to discriminations with a 6-Hz Gabor function, the categorization of stimulus regions, and the nature of the visual mechanisms.

  20. A genotype probability index for multiple alleles and haplotypes.

    PubMed

    Percy, A; Kinghorn, B P

    2005-12-01

    We use linear algebra to calculate an index of information content in genotype probabilities which has previously been calculated using trigonometry. The new method can be generalized allowing the index to be calculated for loci with more than two alleles. Applications of this index include its use in genotyping strategies, strategies to manage genetic disorders and in estimation of genotype effects.

  1. Allele-specific disparity in breast cancer

    PubMed Central

    2011-01-01

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

  2. Model discrimination using data collaboration.

    PubMed

    Feeley, Ryan; Frenklach, Michael; Onsum, Matt; Russi, Trent; Arkin, Adam; Packard, Andrew

    2006-06-01

    This paper introduces a practical data-driven method to discriminate among large-scale kinetic reaction models. The approach centers around a computable measure of model/data mismatch. We introduce two provably convergent algorithms that were developed to accommodate large ranges of uncertainty in the model parameters. The algorithms are demonstrated on a simple toy example and a methane combustion model with more than 100 uncertain parameters. They are subsequently used to discriminate between two models for a contemporarily studied biological signaling network.

  3. Host species exploitation and discrimination by animal parasites.

    PubMed

    Forbes, Mark R; Morrill, André; Schellinck, Jennifer

    2017-05-05

    Parasite species often show differential fitness on different host species. We developed an equation-based model to explore conditions favouring host species exploitation and discrimination. In our model, diploid infective stages randomly encountered hosts of two species; the parasite's relative fitness in exploiting each host species, and its ability to discriminate between them, was determined by the parasite's genotype at two independent diallelic loci. Relative host species frequency determined allele frequencies at the exploitation locus, whereas differential fitness and combined host density determined frequency of discrimination alleles. The model predicts instances where populations contain mixes of discriminatory and non-discriminatory infective stages. Also, non-discriminatory parasites should evolve when differential fitness is low to moderate and when combined host densities are low, but not so low as to cause parasite extinction. A corollary is that parasite discrimination (and host-specificity) increases with higher combined host densities. Instances in nature where parasites fail to discriminate when differential fitness is extreme could be explained by one host species evolving resistance, following from earlier selection for parasite non-discrimination. Similar results overall were obtained for haploid extensions of the model. Our model emulates multi-host associations and has implications for understanding broadening of host species ranges by parasites.This article is part of the themed issue 'Opening the black box: re-examining the ecology and evolution of parasite transmission'.

  4. Host species exploitation and discrimination by animal parasites

    PubMed Central

    Forbes, Mark R.; Morrill, André; Schellinck, Jennifer

    2017-01-01

    Parasite species often show differential fitness on different host species. We developed an equation-based model to explore conditions favouring host species exploitation and discrimination. In our model, diploid infective stages randomly encountered hosts of two species; the parasite's relative fitness in exploiting each host species, and its ability to discriminate between them, was determined by the parasite's genotype at two independent diallelic loci. Relative host species frequency determined allele frequencies at the exploitation locus, whereas differential fitness and combined host density determined frequency of discrimination alleles. The model predicts instances where populations contain mixes of discriminatory and non-discriminatory infective stages. Also, non-discriminatory parasites should evolve when differential fitness is low to moderate and when combined host densities are low, but not so low as to cause parasite extinction. A corollary is that parasite discrimination (and host-specificity) increases with higher combined host densities. Instances in nature where parasites fail to discriminate when differential fitness is extreme could be explained by one host species evolving resistance, following from earlier selection for parasite non-discrimination. Similar results overall were obtained for haploid extensions of the model. Our model emulates multi-host associations and has implications for understanding broadening of host species ranges by parasites. This article is part of the themed issue ‘Opening the black box: re-examining the ecology and evolution of parasite transmission’. PMID:28289258

  5. 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.

  6. Allelic selection of human IL-2 gene.

    PubMed

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

    2000-12-01

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

  7. Distribution-free discriminant analysis

    SciTech Connect

    Burr, T.; Doak, J.

    1997-05-01

    This report describes our experience in implementing a non-parametric (distribution-free) discriminant analysis module for use in a wide range of pattern recognition problems. Issues discussed include performance results on both real and simulated data sets, comparisons to other methods, and the computational environment. In some cases, this module performs better than other existing methods. Nearly all cases can benefit from the application of multiple methods.

  8. Rotary pin-in-maze discriminator

    DOEpatents

    Benavides, Gilbert L.

    1997-01-01

    A discriminator apparatus and method that discriminates between a unique signal and any other (incorrect) signal. The unique signal is a sequence of events; each event can assume one of two possible event states. Given the unique signal, a maze wheel is allowed to rotate fully in one direction. Given an incorrect signal, both the maze wheel and a pin wheel lock in position.

  9. On the Measurement of Discrimination against Women.

    ERIC Educational Resources Information Center

    Davis, Joe C.; Hubbard, Carl M.

    1979-01-01

    Estimates of discrimination represent poor guides to decision making when discrimination is defined too broadly, when earnings differentials are not properly adjusted for changes in relative productivity, and when the present-value method used is not well-suited to the problem. Available from The American Journal of Economics and Sociology, 50…

  10. The use of partial thickness method and zero wet bulb temperature for discriminating precipitation type during winter months at the Ebro basin in Spain

    NASA Astrophysics Data System (ADS)

    Buisan, S.; Revuelto, J.

    2010-09-01

    environment favouring each precipitation type. This method is a simple technique for discriminating the different precipitation types. It also provides climatology of snowfall events for each airport, showing the differences due to their geographical location and how different synoptic conditions affect each place.. In the middle of Ebro basin, where Zaragoza airport is placed, the critical parameter to determine the precipitation type is the 1000 - 850 mb thickness. It is possible to find many episodes of snowfall with a very thin 1000-850 mb layer within a wide range of zero wet bulb temperature values. This shows the pool of cold air in the valley over which warm and moist air is advected from the Mediterranean Sea. Located close to the Cantabric sea, Pamplona is about 150 km north of Zaragoza. The snow episodes in this location are more related with cold air in all levels together with a narrow range of zero wet bulb temperature values. The results show that the Logroño area, 150 km northwest of Zaragoza, is influenced by both conditions. This method became operational during 2009-2010 winter season showing a high degree of accuracy in discriminating precipitation type.

  11. Genetic stability and evolution of sigB allele used for Listeria sensu stricto subtyping and phylogenetic inference.

    PubMed

    Liao, Jingqiu; Wiedmann, Martin; Kovac, Jasna

    2017-04-07

    Sequencing of single genes remains an important tool that allows for rapid classification of bacteria. Sequencing of a portion of sigB, which encodes a stress responsive alternative sigma factor, has emerged as a commonly used molecular tool for initial characterization of diverse Listeria isolates. In this study, evolutionary approaches were used to assess the validity of sigB allelic typing for Listeria For a dataset of 4,280 isolates, sigB allelic typing showed a Simson Index of Discrimination of 0.96. Analyses of 164 sigB allelic types (ATs) found among the 6 Listeria sensu stricto (s.s.) species, representing these 4,280 isolates, indicates that neither frequent homologous recombination nor positive selection significantly contributed to the evolution of sigB, confirming its genetic stability. The molecular clock test provided evidence for unequal evolution rates across clades; L. welshimeri displayed the lowest sigB diversity and was the only species in which sigB evolved in a clocklike manner, implying a unique natural history. Among the four L. monocytogenes lineages, sigB evolution followed a molecular clock only in lineage IV. Moreover, sigB displayed a significant negative Tajima's D value in lineage II, suggesting a recent population bottleneck followed by lineage expansion. Absence of positive selection along with violation of the molecular clock suggested a nearly neutral mechanism of Listeria s.s. sigB evolution. While comparison with a whole genome sequence-based phylogeny revealed that sigB phylogeny did not correctly reflect the ancestry of L. monocytogenes lineage IV, the availability of a large sigB AT database did allow for accurate species classification.IMPORTANCEsigB allelic typing has been widely used for species delineation and subtyping of Listeria However, an informative evaluation of this method from an evolutionary perspective was missing to date. Our data indicate genetic stability of sigB, which supports that sigB allelic typing

  12. Regional seismic discrimination research at LLNL

    SciTech Connect

    Walter, W.R.; Mayeda, K.M.; Goldstein, P.; Patton, H.J.; Jarpe, S.; Glenn, L.

    1995-10-01

    The ability to verify a Comprehensive Test Ban Treaty (CTBT) depends in part on the ability to seismically detect and discriminate between potential clandestine underground nuclear tests and other seismic sources, including earthquakes and mining activities. Regional techniques are necessary to push detection and discrimination levels down to small magnitudes, but existing methods of event discrimination are mainly empirical and show much variability from region to region. The goals of Lawrence Livermore National Laboratory`s (LLNL`s) regional discriminant research are to evaluate the most promising discriminants, improve the understanding of their physical basis and use this information to develop new and more effective discriminants that can be transported to new regions of high monitoring interest. In this report the authors discuss preliminary efforts to geophysically characterize the Middle East and North Africa. They show that the remarkable stability of coda allows one to develop physically based, stable single station magnitude scales in new regions. They then discuss progress to date on evaluating and improving physical understanding and ability to model regional discriminants, focusing on the comprehensive NTS dataset. The authors apply this modeling ability to develop improved discriminants including slopes of P to S ratios. They find combining disparate discriminant techniques is particularly effective in identifying consistent outliers such as shallow earthquakes and mine seismicity. Finally they discuss development and use of new coda and waveform modeling tools to investigate special events.

  13. LLNL`s regional seismic discrimination research

    SciTech Connect

    Walter, W.R.; Mayeda, K.M.; Goldstein, P.

    1995-07-01

    The ability to negotiate and verify a Comprehensive Test Ban Treaty (CTBT) depends in part on the ability to seismically detect and discriminate between potential clandestine underground nuclear tests and other seismic sources, including earthquakes and mining activities. Regional techniques are necessary to push detection and discrimination levels down to small magnitudes, but existing methods of event discrimination are mainly empirical and show much variability from region to region. The goals of Lawrence Livermore National Laboratory`s (LLNL`s) regional discriminant research are to evaluate the most promising discriminants, improve our understanding of their physical basis and use this information to develop new and more effective discriminants that can be transported to new regions of high monitoring interest. In this report we discuss our preliminary efforts to geophysically characterize two regions, the Korean Peninsula and the Middle East-North Africa. We show that the remarkable stability of coda allows us to develop physically based, stable single station magnitude scales in new regions. We then discuss our progress to date on evaluating and improving our physical understanding and ability to model regional discriminants, focusing on the comprehensive NTS dataset. We apply this modeling ability to develop improved discriminants including slopes of P to S ratios. We find combining disparate discriminant techniques is particularly effective in identifying consistent outliers such as shallow earthquakes and mine seismicity. Finally we discuss our development and use of new coda and waveform modeling tools to investigate special events.

  14. Introduction to multivariate discrimination

    NASA Astrophysics Data System (ADS)

    Kégl, Balázs

    2013-07-01

    Multivariate discrimination or classification is one of the best-studied problem in machine learning, with a plethora of well-tested and well-performing algorithms. There are also several good general textbooks [1-9] on the subject written to an average engineering, computer science, or statistics graduate student; most of them are also accessible for an average physics student with some background on computer science and statistics. Hence, instead of writing a generic introduction, we concentrate here on relating the subject to a practitioner experimental physicist. After a short introduction on the basic setup (Section 1) we delve into the practical issues of complexity regularization, model selection, and hyperparameter optimization (Section 2), since it is this step that makes high-complexity non-parametric fitting so different from low-dimensional parametric fitting. To emphasize that this issue is not restricted to classification, we illustrate the concept on a low-dimensional but non-parametric regression example (Section 2.1). Section 3 describes the common algorithmic-statistical formal framework that unifies the main families of multivariate classification algorithms. We explain here the large-margin principle that partly explains why these algorithms work. Section 4 is devoted to the description of the three main (families of) classification algorithms, neural networks, the support vector machine, and AdaBoost. We do not go into the algorithmic details; the goal is to give an overview on the form of the functions these methods learn and on the objective functions they optimize. Besides their technical description, we also make an attempt to put these algorithm into a socio-historical context. We then briefly describe some rather heterogeneous applications to illustrate the pattern recognition pipeline and to show how widespread the use of these methods is (Section 5). We conclude the chapter with three essentially open research problems that are either

  15. Earthquake-explosion discrimination using diffusion maps

    NASA Astrophysics Data System (ADS)

    Rabin, N.; Bregman, Y.; Lindenbaum, O.; Ben-Horin, Y.; Averbuch, A.

    2016-12-01

    Discrimination between earthquakes and explosions is an essential component of nuclear test monitoring and it is also important for maintaining the quality of earthquake catalogues. Currently used discrimination methods provide a partial solution to the problem. In this work, we apply advanced machine learning methods and in particular diffusion maps for modelling and discriminating between seismic signals. Diffusion maps enable us to construct a geometric representation that capture the intrinsic structure of the seismograms. The diffusion maps are applied after a pre-processing step, in which seismograms are converted to normalized sonograms. The constructed low-dimensional model is used for automatic earthquake-explosion discrimination of data that are collected in single seismic stations. We demonstrate our approach on a data set comprising seismic events from the Dead Sea area. The diffusion-based algorithm provides correct discrimination rate that is higher than 90 per cent.

  16. Specific Silencing of L392V PSEN1 Mutant Allele by RNA Interference

    PubMed Central

    Sierant, Malgorzata; Paduszynska, Alina; Kazmierczak-Baranska, Julia; Nacmias, Benedetta; Sorbi, Sandro; Bagnoli, Silvia; Sochacka, Elzbieta; Nawrot, Barbara

    2011-01-01

    RNA interference (RNAi) technology provides a powerful molecular tool to reduce an expression of selected genes in eukaryotic cells. Short interfering RNAs (siRNAs) are the effector molecules that trigger RNAi. Here, we describe siRNAs that discriminate between the wild type and mutant (1174 C→G) alleles of human Presenilin1 gene (PSEN1). This mutation, resulting in L392V PSEN1 variant, contributes to early onset familial Alzheimer's disease. Using the dual fluorescence assay, flow cytometry and fluorescent microscopy we identified positions 8th–11th, within the central part of the antisense strand, as the most sensitive to mismatches. 2-Thiouridine chemical modification introduced at the 3′-end of the antisense strand improved the allele discrimination, but wobble base pairing adjacent to the mutation site abolished the siRNA activity. Our data indicate that siRNAs can be designed to discriminate between the wild type and mutant alleles of genes that differ by just a single nucleotide. PMID:21559198

  17. OPLS-DA as a suitable method for selecting a set of gene transcripts discriminating RAS- and PTPN11-mutated cells in acute lymphoblastic leukaemia.

    PubMed

    Musumarra, Giuseppe; Condorelli, Daniele F; Fortuna, Cosimo G

    2011-01-01

    OPLS discriminant analysis (OPLS-DA) was successfully applied for the selection of a limited number of gene transcripts necessary to discriminate PTPN11 and RAS mutated cells in acute lymphoblastic leukaemia (ALL) patients. The original set of 273 variables with VIP (1) values higher than 2.0 in the OPLS-DA model could be further reduced to 200 by elimination of less informative variables in the PCA class models adopted for SIMCA classification. The above 200 transcripts not only achieve a satisfactory discrimination accuracy between PTPN11 and RAS mutated cells but also indicate clearly that wild type samples belong to none of the mutated class models. In this list it was possible to identify candidate genes that could be involved in the molecular mechanisms discriminating PTPN11 and RAS mutations in ALL. Among them CBFA2T2, a member of the "ETO" family, is known because of its homology and association with the product of RUNX1-CBFA2T1 gene fusion generated by t(8;21) translocation, one frequent cause of acute myeloid leukemia.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. TGDA: Nonparametric Discriminant Analysis

    ERIC Educational Resources Information Center

    Pohl, Norval F.; Bruno, Albert V.

    1976-01-01

    A computer program for two-group nonparametric discriminant analysis is presented. Based on Bayes' Theorem for probability revision, the statistical rationale for this program uses the calculation of maximum likelihood estimates of group membership. The program compares the Bayesian procedure to the standard Linear Discriminant Function.…

  3. Flash-Type Discrimination

    NASA Technical Reports Server (NTRS)

    Koshak, William J.

    2010-01-01

    This viewgraph presentation describes the significant progress made in the flash-type discrimination algorithm development. The contents include: 1) Highlights of Progress for GLM-R3 Flash-Type discrimination Algorithm Development; 2) Maximum Group Area (MGA) Data; 3) Retrieval Errors from Simulations; and 4) Preliminary Global-scale Retrieval.

  4. The "Taste" for Discrimination.

    ERIC Educational Resources Information Center

    Chiswick, Barry R.

    1985-01-01

    Discusses, in terms of consumers, employers, and employees, how a "taste for discrimination," that is, someone's preference for or against association with some group in the labor market, can influence behavior and hence who gets hired. Argues that people with the strongest tastes for discrimination pay the heaviest cost. (RDN)

  5. Discrimination against Black Students

    ERIC Educational Resources Information Center

    Aloud, Ashwaq; Alsulayyim, Maryam

    2016-01-01

    Discrimination is a structured way of abusing people based on racial differences, hence barring them from accessing wealth, political participation and engagement in many spheres of human life. Racism and discrimination are inherently rooted in institutions in the society, the problem has spread across many social segments of the society including…

  6. Microscale acceleration history discriminators

    DOEpatents

    Polosky, Marc A.; Plummer, David W.

    2002-01-01

    A new class of micromechanical acceleration history discriminators is claimed. These discriminators allow the precise differentiation of a wide range of acceleration-time histories, thereby allowing adaptive events to be triggered in response to the severity (or lack thereof) of an external environment. Such devices have applications in airbag activation, and other safety and surety applications.

  7. Perceived Discrimination and Substance Use among Latino Adolescents

    ERIC Educational Resources Information Center

    Okamoto, Janet; Ritt-Olson, Anamara; Soto, Daniel; Baezconde-Garbanati, Lourdes; Unger, Jennifer B.

    2009-01-01

    Objective: To examine perceived discrimination and substance use among Latino high school students. Methods: Latino 9th graders (N=1332) completed self-report measures of perceived discrimination and substance use behavior. Results: Perceived discrimination was associated with lifetime use measures of smoking (OR=1.73, P less than 0.01), alcohol…

  8. Multilocus Microsatellite Typing as a New Tool for Discrimination of Leishmania infantum MON-1 Strains

    PubMed Central

    Ochsenreither, Sebastian; Kuhls, Katrin; Schaar, Matthias; Presber, Wolfgang; Schönian, Gabriele

    2006-01-01

    The Leishmania donovani complex, which consists of L. donovani, L. infantum-L. chagasi, and L. archibaldi, is responsible for visceral manifestations of leishmaniasis. Multilocus enzyme electrophoresis is the standard method for the characterization and identification of strains of Leishmania. For L. infantum, the predominance of zymodeme MON-1 significantly reduces the discriminative power of this approach. In the present study, we developed 17 independent polymorphic microsatellite markers for the typing of strains of L. infantum, with the main emphasis on zymodeme MON-1. The discriminative powers of 11 markers selected from among these markers were tested by using a panel of 63 isolates of the L. donovani complex. Unique multilocus genotypes were observed for the strains analyzed, with only three exceptions. Model-based and distance-based analyses of the data set showed comparable results. It was possible to discriminate between L. donovani sensu stricto, a non-MON-1 group of L. infantum isolates, and a MON-1 group of L. infantum isolates. Within MON-1, three clusters with geographical correlations became apparent. The frequency of heterozygosity in the alleles analyzed varied extremely between the different groups of isolates. The main clusters described are not consistent with species definitions based on isoenzyme analysis but confirm the results of former PCR-based investigations. PMID:16455904

  9. 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

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

    PubMed

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

    2005-10-01

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

  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. A Molecular Method to Discriminate between Mass-Reared Sterile and Wild Tsetse Flies during Eradication Programmes That Have a Sterile Insect Technique Component

    PubMed Central

    Pagabeleguem, Soumaïla; Gimonneau, Geoffrey; Seck, Momar Talla; Vreysen, Marc J. B.; Sall, Baba; Rayaissé, Jean-Baptiste; Sidibé, Issa; Bouyer, Jérémy; Ravel, Sophie

    2016-01-01

    Background The Government of Senegal has embarked several years ago on a project that aims to eradicate Glossina palpalis gambiensis from the Niayes area. The removal of the animal trypanosomosis would allow the development more efficient livestock production systems. The project was implemented using an area-wide integrated pest management strategy including a sterile insect technique (SIT) component. The released sterile male flies originated from a colony from Burkina Faso. Methodology/Principal Findings Monitoring the efficacy of the sterile male releases requires the discrimination between wild and sterile male G. p. gambiensis that are sampled in monitoring traps. Before being released, sterile male flies were marked with a fluorescent dye powder. The marking was however not infallible with some sterile flies only slightly marked or some wild flies contaminated with a few dye particles in the monitoring traps. Trapped flies can also be damaged due to predation by ants, making it difficult to discriminate between wild and sterile males using a fluorescence camera and / or a fluorescence microscope. We developed a molecular technique based on the determination of cytochrome oxidase haplotypes of G. p. gambiensis to discriminate between wild and sterile males. DNA was isolated from the head of flies and a portion of the 5’ end of the mitochondrial gene cytochrome oxidase I was amplified to be finally sequenced. Our results indicated that all the sterile males from the Burkina Faso colony displayed the same haplotype and systematically differed from wild male flies trapped in Senegal and Burkina Faso. This allowed 100% discrimination between sterile and wild male G. p. gambiensis. Conclusions/Significance This tool might be useful for other tsetse control campaigns with a SIT component in the framework of the Pan-African Tsetse and Trypanosomosis Eradication Campaign (PATTEC) and, more generally, for other vector or insect pest control programs. PMID:26901049

  13. High frequency of SLC22A12 variants causing renal hypouricemia 1 in the Czech and Slovak Roma population; simple and rapid detection method by allele-specific polymerase chain reaction.

    PubMed

    Gabrikova, Dana; Bernasovska, Jarmila; Sokolova, Jitka; Stiburkova, Blanka

    2015-10-01

    Renal hypouricemia is a rare heterogeneous inherited disorder characterized by impaired tubular uric acid transport with severe complications, such as acute kidney injury. Type 1 and 2 are caused by loss-of-function mutations in the SLC22A12 and SLC2A9 gene, respectively. A cohort of 881 randomly chosen ethnic Roma from two regions in Eastern Slovakia and two regions in the Czech Republic participated. Genomic DNA was isolated from buccal swabs and/or from blood samples. The c.1245_1253del and c.1400C>T genotypes were determined using polymerase chain reaction with allele-specific primers in a multiplex arrangement and/or direct sequencing of exon 7 and 9. Allele frequencies and genotypes were tested for Hardy-Weinberg equilibrium using the Chi-square test. 25 subjects were heterozygous and three were homozygous for the c.1245_1253del, while 92 subjects were heterozygous and two were homozygous for the c.1400C>T. Moreover, two participants were compound heterozygotes. Frequencies of the c.1245_1253del and c.1400C>T variants were 1.87 and 5.56 %, respectively. Our finding confirms an uneven geographical and ethnic distribution of SLC22A12 mutant variants. We found that the c.1245_1253del and c.1400C>T variants were present in the Czech and Slovak Roma population at unexpectedly high frequencies. Renal hypouricemia should be kept in mind during differential diagnostic on Roma patients with low serum uric acid concentrations.

  14. Self-recognition in social amoebae is mediated by allelic pairs of tiger genes.

    PubMed

    Hirose, Shigenori; Benabentos, Rocio; Ho, Hsing-I; Kuspa, Adam; Shaulsky, Gad

    2011-07-22

    Free-living cells of the social amoebae Dictyostelium discoideum can aggregate and develop into multicellular fruiting bodies in which many die altruistically as they become stalk cells that support the surviving spores. Dictyostelium cells exhibit kin discrimination--a potential defense against cheaters, which sporulate without contributing to the stalk. Kin discrimination depends on strain relatedness, and the polymorphic genes tgrB1 and tgrC1 are potential components of that mechanism. Here, we demonstrate a direct role for these genes in kin discrimination. We show that a matching pair of tgrB1 and tgrC1 alleles is necessary and sufficient for attractive self-recognition, which is mediated by differential cell-cell adhesion. We propose that TgrB1 and TgrC1 proteins mediate this adhesion through direct binding. This system is a genetically tractable ancient model of eukaryotic self-recognition.

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

    DTIC Science & Technology

    2006-05-31

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

  16. Multi-primer target PCR for rapid identification of bovine DRB3 alleles.

    PubMed

    Ledwidge, S A; Mallard, B A; Gibson, J P; Jansen, G B; Jiang, Z H

    2001-08-01

    Multi-primer target polymerase chain reaction (MPT-PCR) is a rapid method for the identification of specific BoLA-DRB3 alleles. In a single PCR reaction, the presence of two alleles associated with increased risk, DRB3.2*23 (DRB3*2701-2703, 2705-2707) and decreased risk, DRB3.2*16 (DRB3*1501, 1502), of mastitis in Canadian Holstein can be detected. Two outer primers amplify exon 2 of DRB3. Simultaneously, two inner, allele-specific primers amplify individual alleles. Initially, 40 cows previously typed by PCR-restriction fragment length polymorphism (PCR-RFLP) were genotyped using the multi-primer approach. An additional 30 cows were first genotyped by multi-primer target PCR, then by PCR-RFLP. All animals were correctly identified and there were no false positives. This technique can readily be modified to identify other BoLA alleles of interest.

  17. BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes.

    PubMed

    de Santiago, Ines; Liu, Wei; Yuan, Ke; O'Reilly, Martin; Chilamakuri, Chandra Sekhar Reddy; Ponder, Bruce A J; Meyer, Kerstin B; Markowetz, Florian

    2017-02-24

    Allele-specific measurements of transcription factor binding from ChIP-seq data are key to dissecting the allelic effects of non-coding variants and their contribution to phenotypic diversity. However, most methods of detecting an allelic imbalance assume diploid genomes. This assumption severely limits their applicability to cancer samples with frequent DNA copy-number changes. Here we present a Bayesian statistical approach called BaalChIP to correct for the effect of background allele frequency on the observed ChIP-seq read counts. BaalChIP allows the joint analysis of multiple ChIP-seq samples across a single variant and outperforms competing approaches in simulations. Using 548 ENCODE ChIP-seq and six targeted FAIRE-seq samples, we show that BaalChIP effectively corrects allele-specific analysis for copy-number variation and increases the power to detect putative cis-acting regulatory variants in cancer genomes.

  18. An Updated Collection of Sequence Barcoded Temperature-Sensitive Alleles of Yeast Essential Genes.

    PubMed

    Kofoed, Megan; Milbury, Karissa L; Chiang, Jennifer H; Sinha, Sunita; Ben-Aroya, Shay; Giaever, Guri; Nislow, Corey; Hieter, Philip; Stirling, Peter C

    2015-07-14

    Systematic analyses of essential gene function using mutant collections in Saccharomyces cerevisiae have been conducted using collections of heterozygous diploids, promoter shut-off alleles, through alleles with destabilized mRNA, destabilized protein, or bearing mutations that lead to a temperature-sensitive (ts) phenotype. We previously described a method for construction of barcoded ts alleles in a systematic fashion. Here we report the completion of this collection of alleles covering 600 essential yeast genes. This resource covers a larger gene repertoire than previous collections and provides a complementary set of strains suitable for single gene and genomic analyses. We use deep sequencing to characterize the amino acid changes leading to the ts phenotype in half of the alleles. We also use high-throughput approaches to describe the relative ts behavior of the alleles. Finally, we demonstrate the experimental usefulness of the collection in a high-content, functional genomic screen for ts alleles that increase spontaneous P-body formation. By increasing the number of alleles and improving the annotation, this ts collection will serve as a community resource for probing new aspects of biology for essential yeast genes.

  19. An Updated Collection of Sequence Barcoded Temperature-Sensitive Alleles of Yeast Essential Genes

    PubMed Central

    Kofoed, Megan; Milbury, Karissa L.; Chiang, Jennifer H.; Sinha, Sunita; Ben-Aroya, Shay; Giaever, Guri; Nislow, Corey; Hieter, Philip; Stirling, Peter C.

    2015-01-01

    Systematic analyses of essential gene function using mutant collections in Saccharomyces cerevisiae have been conducted using collections of heterozygous diploids, promoter shut-off alleles, through alleles with destabilized mRNA, destabilized protein, or bearing mutations that lead to a temperature-sensitive (ts) phenotype. We previously described a method for construction of barcoded ts alleles in a systematic fashion. Here we report the completion of this collection of alleles covering 600 essential yeast genes. This resource covers a larger gene repertoire than previous collections and provides a complementary set of strains suitable for single gene and genomic analyses. We use deep sequencing to characterize the amino acid changes leading to the ts phenotype in half of the alleles. We also use high-throughput approaches to describe the relative ts behavior of the alleles. Finally, we demonstrate the experimental usefulness of the collection in a high-content, functional genomic screen for ts alleles that increase spontaneous P-body formation. By increasing the number of alleles and improving the annotation, this ts collection will serve as a community resource for probing new aspects of biology for essential yeast genes. PMID:26175450

  20. Dealing with allelic dropout when reporting the evidential value in DNA relatedness analysis.

    PubMed

    Buckleton, John; Triggs, Chris

    2006-07-13

    A method is suggested that allows the use of loci that have shown allelic dropout in kinship analysis as used for disaster victim identification (DVI) and missing person work (MP). This approach uses an extension of a previously published approach to modelling allelic dropout. This method may salvage some information in cases where allelic dropout is hindering DVI or MP work particularly in reconciliations involving a large number of bodies and pedigrees. It should not replace the pursuit of more complete DNA profiles by the normal rework process for such samples.

  1. Multicolor-based discrimination of 21 short tandem repeats and amelogenin using four fluorescent universal primers.

    PubMed

    Asari, Masaru; Okuda, Katsuhiro; Hoshina, Chisato; Omura, Tomohiro; Tasaki, Yoshikazu; Shiono, Hiroshi; Matsubara, Kazuo; Shimizu, Keiko

    2016-02-01

    The aim of this study was to develop a cost-effective genotyping method using high-quality DNA for human identification. A total of 21 short tandem repeats (STRs) and amelogenin were selected, and fluorescent fragments at 22 loci were simultaneously amplified in a single-tube reaction using locus-specific primers with 24-base universal tails and four fluorescent universal primers. Several nucleotide substitutions in universal tails and fluorescent universal primers enabled the detection of specific fluorescent fragments from the 22 loci. Multiplex polymerase chain reaction (PCR) produced intense FAM-, VIC-, NED-, and PET-labeled fragments ranging from 90 to 400 bp, and these fragments were discriminated using standard capillary electrophoretic analysis. The selected 22 loci were also analyzed using two commercial kits (the AmpFLSTR Identifiler Kit and the PowerPlex ESX 17 System), and results for two loci (D19S433 and D16S539) were discordant between these kits due to mutations at the primer binding sites. All genotypes from the 100 samples were determined using 2.5 ng of DNA by our method, and the expected alleles were completely recovered. Multiplex 22-locus genotyping using four fluorescent universal primers effectively reduces the costs to less than 20% of genotyping using commercial kits, and our method would be useful to detect silent alleles from commercial kit analysis.

  2. Quantity discrimination in salamanders.

    PubMed

    Krusche, Paul; Uller, Claudia; Dicke, Ursula

    2010-06-01

    We investigated discrimination of large quantities in salamanders of the genus Plethodon. Animals were challenged with two different quantities (8 vs 12 or 8 vs 16) in a two-alternative choice task. Stimuli were live crickets, videos of live crickets or images animated by a computer program. Salamanders reliably chose the larger of two quantities when the ratio between the sets was 1:2 and stimuli were live crickets or videos thereof. Magnitude discrimination was not successful when the ratio was 2:3, or when the ratio was 1:2 when stimuli were computer animated. Analysis of the salamanders' success and failure as well as analysis of stimulus features points towards movement as a dominant feature for quantity discrimination. The results are generally consistent with large quantity discrimination investigated in many other animals (e.g. primates, fish), current models of quantity representation (analogue magnitudes) and data on sensory aspects of amphibian prey-catching behaviour (neuronal motion processing).

  3. Mass discrimination during weightlessness

    NASA Technical Reports Server (NTRS)

    Ross, H.

    1981-01-01

    An experiment concerned with the ability of astronauts to discriminate between the mass of objects when both the objects and the astronauts are in weightless states is described. The main object of the experiment is to compare the threshold for weight-discrimination on Earth with that for mass-discrimination in orbit. Tests will be conducted premission and postmission and early and late during the mission while the crew is experiencing weightlessness. A comparison of early and late tests inflight and postflight will reveal the rate of adaptation to zero-gravity and 1-g. The mass discrimination box holds 24 balls which the astronaut will compare to one another in a random routine.

  4. Angular velocity discrimination

    NASA Technical Reports Server (NTRS)

    Kaiser, Mary K.

    1990-01-01

    Three experiments designed to investigate the ability of naive observers to discriminate rotational velocities of two simultaneously viewed objects are described. Rotations are constrained to occur about the x and y axes, resulting in linear two-dimensional image trajectories. The results indicate that observers can discriminate angular velocities with a competence near that for linear velocities. However, perceived angular rate is influenced by structural aspects of the stimuli.

  5. The Sociology of Discrimination: Racial Discrimination in Employment, Housing, Credit, and Consumer Markets

    PubMed Central

    Pager, Devah; Shepherd, Hana

    2010-01-01

    Persistent racial inequality in employment, housing, and a wide range of other social domains has renewed interest in the possible role of discrimination. And yet, unlike in the pre–civil rights era, when racial prejudice and discrimination were overt and widespread, today discrimination is less readily identifiable, posing problems for social scientific conceptualization and measurement. This article reviews the relevant literature on discrimination, with an emphasis on racial discrimination in employment, housing, credit markets, and consumer interactions. We begin by defining discrimination and discussing relevant methods of measurement. We then provide an overview of major findings from studies of discrimination in each of the four domains; and, finally, we turn to a discussion of the individual, organizational, and structural mechanisms that may underlie contemporary forms of discrimination. This discussion seeks to orient readers to some of the key debates in the study of discrimination and to provide a roadmap for those interested in building upon this long and important line of research. PMID:20689680

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

    PubMed

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

    2011-08-02

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

  7. Dombrock genotyping in Brazilian blood donors reveals different regional frequencies of the HY allele

    PubMed Central

    Piassi, Fabiana Chagas Camargos; Santos, Silvana Maria Eloi; de Castilho, Lilian Maria; Baleotti Júnior, Wilson; Suzuki, Rodrigo Buzinaro; da Cunha, Débora Moura

    2013-01-01

    Background Dombrock blood group system genotyping has revealed various rearrangements of the Dombrock gene and identified new variant alleles in Brazil (i.e., DO*A-SH, DO*A-WL and DO*B-WL). Because of the high heterogeneity of the Brazilian population, interregional differences are expected during the investigation of Dombrock genotypes. Objective The present study aims to determine the frequencies of Dombrock genotypes in blood donors from Minas Gerais and compare the frequencies of the HY and JO alleles to those of another population in Brazil. Methods The frequencies of the DO alleles in Minas Gerais, a southeastern state of Brazil, were determined from the genotyping of 270 blood donors. Genotyping involved polymerase chain reaction and restriction fragment length polymorphism analysis to identify the 323G>T, 350C>T, 793A>G, and 898C>G mutations, which are related to the HY, JO, DO*A/DO*B, and DO*A-WL/DO*B-WL alleles, respectively. Moreover, the frequencies of rare HY and JO alleles were statistically compared using the chi-square test with data from another Brazilian region. Results The HY allele frequency in Minas Gerais (2.4%) was almost twice that of the JO allele (1.5%). The frequency of the HY allele was significantly higher (p-value = 0.001) than that in another Brazilian population and includes a rare homozygous donor with the Hy- phenotype. In addition, the DO*A-WL and DO*B-WL alleles, which were first identified in Brazil, were found in the state of Minas Gerais. Conclusions The data confirm that the frequencies of DO alleles differ between regions in Brazil. The population of Minas Gerais could be targeted in a screening strategy to identify the Hy- phenotype in order to develop a rare blood bank. PMID:24478605

  8. 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).

  9. Kernel Optimization in Discriminant Analysis

    PubMed Central

    You, Di; Hamsici, Onur C.; Martinez, Aleix M.

    2011-01-01

    Kernel mapping is one of the most used approaches to intrinsically derive nonlinear classifiers. The idea is to use a kernel function which maps the original nonlinearly separable problem to a space of intrinsically larger dimensionality where the classes are linearly separable. A major problem in the design of kernel methods is to find the kernel parameters that make the problem linear in the mapped representation. This paper derives the first criterion that specifically aims to find a kernel representation where the Bayes classifier becomes linear. We illustrate how this result can be successfully applied in several kernel discriminant analysis algorithms. Experimental results using a large number of databases and classifiers demonstrate the utility of the proposed approach. The paper also shows (theoretically and experimentally) that a kernel version of Subclass Discriminant Analysis yields the highest recognition rates. PMID:20820072

  10. Transformation of QTL genotypic effects to allelic effects

    PubMed Central

    Nagamine, Yoshitaka

    2005-01-01

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

  11. Fast spatial ancestry via flexible allele frequency surfaces

    PubMed Central

    Rañola, John Michael; Novembre, John; Lange, Kenneth

    2014-01-01

    Motivation: Unique modeling and computational challenges arise in locating the geographic origin of individuals based on their genetic backgrounds. Single-nucleotide polymorphisms (SNPs) vary widely in informativeness, allele frequencies change non-linearly with geography and reliable localization requires evidence to be integrated across a multitude of SNPs. These problems become even more acute for individuals of mixed ancestry. It is hardly surprising that matching genetic models to computational constraints has limited the development of methods for estimating geographic origins. We attack these related problems by borrowing ideas from image processing and optimization theory. Our proposed model divides the region of interest into pixels and operates SNP by SNP. We estimate allele frequencies across the landscape by maximizing a product of binomial likelihoods penalized by nearest neighbor interactions. Penalization smooths allele frequency estimates and promotes estimation at pixels with no data. Maximization is accomplished by a minorize–maximize (MM) algorithm. Once allele frequency surfaces are available, one can apply Bayes’ rule to compute the posterior probability that each pixel is the pixel of origin of a given person. Placement of admixed individuals on the landscape is more complicated and requires estimation of the fractional contribution of each pixel to a person’s genome. This estimation problem also succumbs to a penalized MM algorithm. Results: We applied the model to the Population Reference Sample (POPRES) data. The model gives better localization for both unmixed and admixed individuals than existing methods despite using just a small fraction of the available SNPs. Computing times are comparable with the best competing software. Availability and implementation: Software will be freely available as the OriGen package in R. Contact: ranolaj@uw.edu or klange@ucla.edu Supplementary information: Supplementary data are available at

  12. Discrimination Method of the Volatiles from Fresh Mushrooms by an Electronic Nose Using a Trapping System and Statistical Standardization to Reduce Sensor Value Variation

    PubMed Central

    Fujioka, Kouki; Shimizu, Nobuo; Manome, Yoshinobu; Ikeda, Keiichi; Yamamoto, Kenji; Tomizawa, Yasuko

    2013-01-01

    Electronic noses have the benefit of obtaining smell information in a simple and objective manner, therefore, many applications have been developed for broad analysis areas such as food, drinks, cosmetics, medicine, and agriculture. However, measurement values from electronic noses have a tendency to vary under humidity or alcohol exposure conditions, since several types of sensors in the devices are affected by such variables. Consequently, we show three techniques for reducing the variation of sensor values: (1) using a trapping system to reduce the infering components; (2) performing statistical standardization (calculation of z-score); and (3) selecting suitable sensors. With these techniques, we discriminated the volatiles of four types of fresh mushrooms: golden needle (Flammulina velutipes), white mushroom (Agaricus bisporus), shiitake (Lentinus edodes), and eryngii (Pleurotus eryngii) among six fresh mushrooms (hen of the woods (Grifola frondosa), shimeji (Hypsizygus marmoreus) plus the above mushrooms). Additionally, we succeeded in discrimination of white mushroom, only comparing with artificial mushroom flavors, such as champignon flavor and truffle flavor. In conclusion, our techniques will expand the options to reduce variations in sensor values. PMID:24233028

  13. Near-infrared reflectance spectroscopy as a method to predict chemical composition of breast meat and discriminate between different n-3 feeding sources.

    PubMed

    Berzaghi, P; Dalle Zotte, A; Jansson, L M; Andrighetto, I

    2005-01-01

    The objective of this study was to evaluate near-infrared reflectance spectroscopy (NIRS) as a tool to predict the physicochemical composition of breast meat samples of laying hens fed 4 different diets, a control and 3 diets enriched with different sources of n-3 polyunsaturated fatty acids: marine origin, extruded linseed, and ground linseed. Furthermore, NIRS was used as a tool to classify meat samples according to feeding regimen. Samples were analyzed chemically for DM, ash, protein, lipids, and fatty acid profile. Absorption spectra were collected in diffuse reflectance mode between 1,100 and 2,498 nm every 2 nm. The calibration results for the 72 meat samples were accurate in predicting DM, protein, lipids, and major fatty acids. Poor results were obtained for the calibration equations for ash, pH, color, and lipid oxidation parameters. Partial least squares discriminant analysis was developed to differentiate the breast meat samples that originated from hens fed the different diets. The performance of the discriminant models showed 100% correct classification between the control and the enriched diets. It was concluded that NIRS could be used for quality control predicting chemical composition of poultry meat and possibly some dietary treatments applied to the chickens.

  14. Rotary pin-in-maze discriminator

    DOEpatents

    Benavides, G.L.

    1997-05-06

    A discriminator apparatus and method that discriminates between a unique signal and any other (incorrect) signal are disclosed. The unique signal is a sequence of events; each event can assume one of two possible event states. Given the unique signal, a maze wheel is allowed to rotate fully in one direction. Given an incorrect signal, both the maze wheel and a pin wheel lock in position. 4 figs.

  15. Data mining methods in the prediction of Dementia: A real-data comparison of the accuracy, sensitivity and specificity of linear discriminant analysis, logistic regression, neural networks, support vector machines, classification trees and random forests

    PubMed Central

    2011-01-01

    Background Dementia and cognitive impairment associated with aging are a major medical and social concern. Neuropsychological testing is a key element in the diagnostic procedures of Mild Cognitive Impairment (MCI), but has presently a limited value in the prediction of progression to dementia. We advance the hypothesis that newer statistical classification methods derived from data mining and machine learning methods like Neural Networks, Support Vector Machines and Random Forests can improve accuracy, sensitivity and specificity of predictions obtained from neuropsychological testing. Seven non parametric classifiers derived from data mining methods (Multilayer Perceptrons Neural Networks, Radial Basis Function Neural Networks, Support Vector Machines, CART, CHAID and QUEST Classification Trees and Random Forests) were compared to three traditional classifiers (Linear Discriminant Analysis, Quadratic Discriminant Analysis and Logistic Regression) in terms of overall classification accuracy, specificity, sensitivity, Area under the ROC curve and Press'Q. Model predictors were 10 neuropsychological tests currently used in the diagnosis of dementia. Statistical distributions of classification parameters obtained from a 5-fold cross-validation were compared using the Friedman's nonparametric test. Results Press' Q test showed that all classifiers performed better than chance alone (p < 0.05). Support Vector Machines showed the larger overall classification accuracy (Median (Me) = 0.76) an area under the ROC (Me = 0.90). However this method showed high specificity (Me = 1.0) but low sensitivity (Me = 0.3). Random Forest ranked second in overall accuracy (Me = 0.73) with high area under the ROC (Me = 0.73) specificity (Me = 0.73) and sensitivity (Me = 0.64). Linear Discriminant Analysis also showed acceptable overall accuracy (Me = 0.66), with acceptable area under the ROC (Me = 0.72) specificity (Me = 0.66) and sensitivity (Me = 0.64). The remaining classifiers showed

  16. The Influence of Discrimination on Smoking Cessation among Latinos

    PubMed Central

    Kendzor, Darla E.; Businelle, Michael S.; Reitzel, Lorraine R.; Castro, Yessenia; Vidrine, Jennifer I.; Mazas, Carlos A.; Cinciripini, Paul M.; Lam, Cho Y.; Adams, Claire E.; Correa-Fernández, Virmarie; Cano, Miguel Ángel; Wetter, David W.

    2014-01-01

    Background: Although studies have shown a cross-sectional link between discrimination and smoking, the prospective influence of discrimination on smoking cessation has yet to be evaluated. Thus, the purpose of the current study was to determine the influence of everyday and major discrimination on smoking cessation among Latinos making a quit attempt. Methods: Participants were 190 Spanish speaking smokers of Mexican Heritage recruited from the Houston, TX metropolitan area who participated in the study between 2009 and 2012. Logistic regression analyses were conducted to evaluate the associations of everyday and major discrimination with smoking abstinence at 26 weeks post-quit. Results: Most participants reported at least some everyday discrimination (64.4%), and at least one major discrimination event (56%) in their lifetimes. Race/ethnicity/nationality was the most commonly perceived reason for both everyday and major discrimination. Everyday discrimination was not associated with post-quit smoking status. However, experiencing a greater number of major discrimination events was associated with a reduced likelihood of achieving 7-day point prevalence smoking abstinence, OR = .51, p = .004, and continuous smoking abstinence, OR = .29, p = .018, at 26 weeks post-quit. Conclusions: Findings highlight the high frequency of exposure to discrimination among Latinos, and demonstrate the negative impact of major discrimination events on a smoking cessation attempt. Efforts are needed to attenuate the detrimental effects of major discrimination events on smoking cessation outcomes. PMID:24485880

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

    SciTech Connect

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

    1997-02-01

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

  18. Allele specific-PCR and melting curve analysis showed relatively high frequency of β-casein gene A1 allele in Iranian Holstein, Simmental and native cows.

    PubMed

    Gholami, M; Hafezian, S H; Rahimi, G; Farhadi, A; Rahimi, Z; Kahrizi, D; Kiani, S; Karim, H; Vaziri, S; Muhammadi, S; Veisi, F; Ghadiri, K; Shetabi, H; Zargooshi, J

    2016-10-31

    There are two allelic forms of A1 and A2 of β-casein gene in dairy cattle. Proteolytic digestion of bovine β-casein A1 type produces bioactive peptide of β-casomorphin-7 known as milk devil. β-casomorphin-7 causes many diseases, including type 1 diabetes, cardiovascular disease syndrome, sudden death and madness. The aim of the present study was to determine the different allelic forms of β-casein gene in Iranian Holstein, Simmental and native cattle in order to identify A1 and A2 variants. The blood samples were collected randomly and DNA was extracted using modified salting out method. An 854 bp fragment including part of exon 7 and part of intron 6 of β-casein gene was amplified by allele specific polymerase chain reaction (AS-PCR). Also, the accuracy of AS-PCR genotyping has been confirmed by melting temperature curve analysis using Real-time PCR machinery. The comparison of observed allele and genotype frequency among the studied breeds was performed using the Fisher exact and Chi-squared test, respectively by SAS program. Obtained results showed the A1 allele frequencies of 50, 51.57, 54.5, 49.4 and 46.6% in Holstein, Simmental, Sistani, Taleshi and Mazandarani cattle populations, respectively. The chi-square test was shown that no any populations were in Hardy-Weinberg equilibrium for studied marker locus. Comparison and analysis of the test results for allelic frequency showed no any significant differences between breeds (P>0.05). The frequency of observed genotypes only differs significantly between Holstein and Taleshi breeds but no any statistically significant differences were found for other breeds (P>0.05). A relatively high frequency of β-casein A1 allele was observed in Iranian native cattle. Therefore, determine the genotypes and preference alleles A2 in these native and commercial cattle is recommended.

  19. Identification and DNA sequence analysis of 15 new {alpha}{sub 1}-antitrypsin variants, including two PI*QO alleles and one deficient PI*M allele

    SciTech Connect

    Faber, J.P.; Kirchgesser, M.; Schwaab, R.; Bidlingmaier, F.; Poller, W.; Weidinger, S.; Olek, K. |

    1994-12-01

    The authors have investigated the molecular basis of 15 new {alpha}{sub 1}-antitrypsin ({alpha}1AT) variants. Phenotyping by isoelectric focusing (IEF) was used as a screening method to detect {alpha}1AT variants at the protein level. Genotyping was then performed by sequence analysis of all coding exons, exon-intron junctions, and the hepatocyte-specific promotor region including exon Ic. Three of these rare variants are alleles of clinical relevance, associated with undetectable or very low serum levels of {alpha}1AT: the PI*Q0saarbruecken allele generated by a 1-bp C-nucleotide insertion within a stretch of seven cytosines spanning residues 360-362, resulting in a 3{prime} frameshift and the acquisition of a stop codon at residue 376; a point mutation in the PI*Q0lisbon allele, resulting in a single amino acid substitution Thr{sup 68}(ACC){yields}Ile(ATC); and an in-frame trinucleotide deletion {Delta}Phe{sup 51} (TTC) in the highly deficient PI*Mpalermo allele. The remaining 12 alleles are associated with normal {alpha}1AT serum levels and are characterized by point mutations causing single amino acid substitutions in all but one case. This exception is a silent mutation, which does not affect the amino acid sequence. The limitation of IEF compared with DNA sequence analysis, for identification of new variants, their generation by mutagenesis, and the clinical relevance of the three deficiency alleles are discussed.

  20. Binocular contrast discrimination needs monocular multiplicative noise

    PubMed Central

    Ding, Jian; Levi, Dennis M.

    2016-01-01

    The effects of signal and noise on contrast discrimination are difficult to separate because of a singularity in the signal-detection-theory model of two-alternative forced-choice contrast discrimination (Katkov, Tsodyks, & Sagi, 2006). In this article, we show that it is possible to eliminate the singularity by combining that model with a binocular combination model to fit monocular, dichoptic, and binocular contrast discrimination. We performed three experiments using identical stimuli to measure the perceived phase, perceived contrast, and contrast discrimination of a cyclopean sine wave. In the absence of a fixation point, we found a binocular advantage in contrast discrimination both at low contrasts (<4%), consistent with previous studies, and at high contrasts (≥34%), which has not been previously reported. However, control experiments showed no binocular advantage at high contrasts in the presence of a fixation point or for observers without accommodation. We evaluated two putative contrast-discrimination mechanisms: a nonlinear contrast transducer and multiplicative noise (MN). A binocular combination model (the DSKL model; Ding, Klein, & Levi, 2013b) was first fitted to both the perceived-phase and the perceived-contrast data sets, then combined with either the nonlinear contrast transducer or the MN mechanism to fit the contrast-discrimination data. We found that the best model combined the DSKL model with early MN. Model simulations showed that, after going through interocular suppression, the uncorrelated noise in the two eyes became anticorrelated, resulting in less binocular noise and therefore a binocular advantage in the discrimination task. Combining a nonlinear contrast transducer or MN with a binocular combination model (DSKL) provides a powerful method for evaluating the two putative contrast-discrimination mechanisms. PMID:26982370

  1. Binocular contrast discrimination needs monocular multiplicative noise.

    PubMed

    Ding, Jian; Levi, Dennis M

    2016-01-01

    The effects of signal and noise on contrast discrimination are difficult to separate because of a singularity in the signal-detection-theory model of two-alternative forced-choice contrast discrimination (Katkov, Tsodyks, & Sagi, 2006). In this article, we show that it is possible to eliminate the singularity by combining that model with a binocular combination model to fit monocular, dichoptic, and binocular contrast discrimination. We performed three experiments using identical stimuli to measure the perceived phase, perceived contrast, and contrast discrimination of a cyclopean sine wave. In the absence of a fixation point, we found a binocular advantage in contrast discrimination both at low contrasts (<4%), consistent with previous studies, and at high contrasts (≥34%), which has not been previously reported. However, control experiments showed no binocular advantage at high contrasts in the presence of a fixation point or for observers without accommodation. We evaluated two putative contrast-discrimination mechanisms: a nonlinear contrast transducer and multiplicative noise (MN). A binocular combination model (the DSKL model; Ding, Klein, & Levi, 2013b) was first fitted to both the perceived-phase and the perceived-contrast data sets, then combined with either the nonlinear contrast transducer or the MN mechanism to fit the contrast-discrimination data. We found that the best model combined the DSKL model with early MN. Model simulations showed that, after going through interocular suppression, the uncorrelated noise in the two eyes became anticorrelated, resulting in less binocular noise and therefore a binocular advantage in the discrimination task. Combining a nonlinear contrast transducer or MN with a binocular combination model (DSKL) provides a powerful method for evaluating the two putative contrast-discrimination mechanisms.

  2. A majority of Huntington's disease patients may be treatable by individualized allele-specific RNA interference.

    PubMed

    Lombardi, Maria Stella; Jaspers, Leonie; Spronkmans, Christine; Gellera, Cinzia; Taroni, Franco; Di Maria, Emilio; Donato, Stefano Di; Kaemmerer, William F

    2009-06-01

    Use of RNA interference to reduce huntingtin protein (htt) expression in affected brain regions may provide an effective treatment for Huntington disease (HD), but it remains uncertain whether suppression of both wild-type and mutant alleles in a heterozygous patient will provide more benefit than harm. Previous research has shown suppression of just the mutant allele is achievable using siRNA targeted to regions of HD mRNA containing single nucleotide polymorphisms (SNPs). To determine whether more than a minority of patients may be eligible for an allele-specific therapy, we genotyped DNA from 327 unrelated European Caucasian HD patients at 26 SNP sites in the HD gene. Over 86% of the patients were found to be heterozygous for at least one SNP among those tested. Because the sites are genetically linked, one cannot use the heterozygosity rates of the individual SNPs to predict how many sites (and corresponding allele-specific siRNA) would be needed to provide at least one treatment possibility for this percentage of patients. By computing all combinations, we found that a repertoire of allele-specific siRNA corresponding to seven sites can provide at least one allele-specific siRNA treatment option for 85.6% of our sample. Moreover, we provide evidence that allele-specific siRNA targeting these sites are readily identifiable using a high throughput screening method, and that allele-specific siRNA identified using this method indeed show selective suppression of endogenous mutant htt protein in fibroblast cells from HD patients. Therefore, allele-specific siRNA are not so rare as to be impractical to find and use therapeutically.

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

    PubMed Central

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

    2000-01-01

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

  4. 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.

  5. 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

  6. Effect of HLA-DPA1 alleles on chronic hepatitis B prognosis and treatment response

    PubMed Central

    Katrinli, Seyma; Enc, Feruze Yilmaz; Ozdil, Kamil; Ozturk, Oguzhan; Tuncer, Ilyas; Doganay, Gizem Dinler; Doganay, Levent

    2016-01-01

    OBJECTIVE: Chronic hepatitis B (CHB) is a major health problem. The outcome of hepatitis B virus (HBV) infection is associated with variations in HLA-DPA1 alleles. The aim of this study was to investigate possible associations of HLA-DPA1 alleles with treatment response and with hepatitis B virus e antigen (HBeAg) seroconversion. METHODS: Eight different HLA-DPA1 alleles from 246 CHB patients were genotyped by polymerase chain reaction with sequence-specific primers at high resolution to investigate the association of HLA-DPA1 alleles with treatment response, development of cirrhosis, HBeAg seroconversion, and disease reoccurrence upon HBeAg loss. RESULTS: There was no significant association between HLA-DPA1 alleles and treatment response, development of cirrhosis, or HBeAg seroconversion. However, HLA-DPA1*04:01 allele was significantly more frequently found in patients who redeveloped disease upon HBeAg seroconversion (100% vs 36.8%: p=0.037; Fisher’s exact test). CONCLUSION: HLA-DPA1*04:01 allele may be a risk factor for reoccurrence of CHB after HBeAg seroconversion. PMID:28275747

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

    PubMed

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

    2009-09-01

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

  8. Variable Selection Strategies in Discriminate Analysis.

    ERIC Educational Resources Information Center

    Tanguma, Jesus

    This paper presents three variable selection strategies in discriminate analysis (all variables in the model, use of stepwise methods, and all possible subsets). All three methods are illustrated through examples. Although the all variables in the model and the stepwise methods are the most widely used, B. Thompson (1996) and C. Huberty (1994)…

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

    PubMed

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

    2017-03-20

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

  10. Predictive long-range allele-specific mapping of regulatory variants and target transcripts.

    PubMed

    Lee, Kibaick; Lee, Seulkee; Bang, Hyoeun; Choi, Jung Kyoon

    2017-01-01

    Genome-wide association studies (GWASs) have identified a large number of noncoding associations, calling for systematic mapping to causal regulatory variants and their distal target genes. A widely used method, quantitative trait loci (QTL) mapping for chromatin or expression traits, suffers from sample-to-sample experimental variation and trans-acting or environmental effects. Instead, alleles at heterozygous loci can be compared within a sample, thereby controlling for those confounding factors. Here we introduce a method for chromatin structure-based allele-specific pairing of regulatory variants and target transcripts. With phased genotypes, much of allele-specific expression could be explained by paired allelic cis-regulation across a long range. This approach showed approximately two times greater sensitivity than QTL mapping. There are cases in which allele imbalance cannot be tested because heterozygotes are not available among reference samples. Therefore, we employed a machine learning method to predict missing positive cases based on various features shared by observed allele-specific pairs. We showed that only 10 reference samples are sufficient to achieve high prediction accuracy with a low sampling variation. In conclusion, our method enables highly sensitive fine mapping and target identification for trait-associated variants based on a small number of reference samples.

  11. Bias, discrimination, and obesity.

    PubMed

    Puhl, R; Brownell, K D

    2001-12-01

    This article reviews information on discriminatory attitudes and behaviors against obese individuals, integrates this to show whether systematic discrimination occurs and why, and discusses needed work in the field. Clear and consistent stigmatization, and in some cases discrimination, can be documented in three important areas of living: employment, education, and health care. Among the findings are that 28% of teachers in one study said that becoming obese is the worst thing that can happen to a person; 24% of nurses said that they are "repulsed" by obese persons; and, controlling for income and grades, parents provide less college support for their overweight than for their thin children. There are also suggestions but not yet documentation of discrimination occurring in adoption proceedings, jury selection, housing, and other areas. Given the vast numbers of people potentially affected, it is important to consider the research-related, educational, and social policy implications of these findings.

  12. Rapid Discrimination for Traditional Complex Herbal Medicines from Different Parts, Collection Time, and Origins Using High-Performance Liquid Chromatography and Near-Infrared Spectral Fingerprints with Aid of Pattern Recognition Methods

    PubMed Central

    Fu, Haiyan; Fan, Yao; Zhang, Xu; Lan, Hanyue; Yang, Tianming; Shao, Mei; Li, Sihan

    2015-01-01

    As an effective method, the fingerprint technique, which emphasized the whole compositions of samples, has already been used in various fields, especially in identifying and assessing the quality of herbal medicines. High-performance liquid chromatography (HPLC) and near-infrared (NIR), with their unique characteristics of reliability, versatility, precision, and simple measurement, played an important role among all the fingerprint techniques. In this paper, a supervised pattern recognition method based on PLSDA algorithm by HPLC and NIR has been established to identify the information of Hibiscus mutabilis L. and Berberidis radix, two common kinds of herbal medicines. By comparing component analysis (PCA), linear discriminant analysis (LDA), and particularly partial least squares discriminant analysis (PLSDA) with different fingerprint preprocessing of NIR spectra variables, PLSDA model showed perfect functions on the analysis of samples as well as chromatograms. Most important, this pattern recognition method by HPLC and NIR can be used to identify different collection parts, collection time, and different origins or various species belonging to the same genera of herbal medicines which proved to be a promising approach for the identification of complex information of herbal medicines. PMID:26345990

  13. Optical fiber phase discriminator.

    PubMed

    Danielson, B L

    1978-11-15

    Phase discriminators are devices widely used at rf and microwave frequencies to convert phase, or frequency, changes to amplitude changes. They find widespread use in generating audio feedback signals for frequency stabilization of oscillators and in angle demodulation applications. This paper demonstrates that similar devices, with similar functions, can be constructed in the visible region using optical fibers as delay-line elements. The operating principles of an optical-fiber delay-line phase discriminator are discussed. The sensitivity is shown to be proportional to the fiber propagation-delay time. A device working at 0.6328 microm is described and compared with predictions.

  14. Semiparametric Allelic Tests for Mapping Multiple Phenotypes: Binomial Regression and Mahalanobis Distance.

    PubMed

    Majumdar, Arunabha; Witte, John S; Ghosh, Saurabh

    2015-12-01

    Binary phenotypes commonly arise due to multiple underlying quantitative precursors and genetic variants may impact multiple traits in a pleiotropic manner. Hence, simultaneously analyzing such correlated traits may be more powerful than analyzing individual traits. Various genotype-level methods, e.g., MultiPhen (O'Reilly et al. []), have been developed to identify genetic factors underlying a multivariate phenotype. For univariate phenotypes, the usefulness and applicability of allele-level tests have been investigated. The test of allele frequency difference among cases and controls is commonly used for mapping case-control association. However, allelic methods for multivariate association mapping have not been studied much. In this article, we explore two allelic tests of multivariate association: one using a Binomial regression model based on inverted regression of genotype on phenotype (Binomial regression-based Association of Multivariate Phenotypes [BAMP]), and the other employing the Mahalanobis distance between two sample means of the multivariate phenotype vector for two alleles at a single-nucleotide polymorphism (Distance-based Association of Multivariate Phenotypes [DAMP]). These methods can incorporate both discrete and continuous phenotypes. Some theoretical properties for BAMP are studied. Using simulations, the power of the methods for detecting multivariate association is compared with the genotype-level test MultiPhen's. The allelic tests yield marginally higher power than MultiPhen for multivariate phenotypes. For one/two binary traits under recessive mode of inheritance, allelic tests are found to be substantially more powerful. All three tests are applied to two different real data and the results offer some support for the simulation study. We propose a hybrid approach for testing multivariate association that implements MultiPhen when Hardy-Weinberg Equilibrium (HWE) is violated and BAMP otherwise, because the allelic approaches assume HWE.

  15. Amyloid mediates the association of apolipoprotein E e4 allele to cognitive function in older people

    PubMed Central

    Bennett, D; Schneider, J; Wilson, R; Bienias, J; Berry-Kravis, E; Arnold, S

    2005-01-01

    Background: The neurobiological changes underlying the association of the apolipoprotein E (APOE) e4 allele with level of cognition are poorly understood. Objective: To test the hypothesis that amyloid load can account for (mediate) the association of the APOE e4 allele with level of cognition assessed proximate to death. Methods: There were 44 subjects with clinically diagnosed Alzheimer's disease and 50 without dementia, who had participated in the Religious Orders Study. They underwent determination of APOE allele status, had comprehensive cognitive testing in the last year of life, and brain autopsy at death. The percentage area of cortex occupied by amyloid beta and the density of tau positive neurofibrillary tangles were quantified from six brain regions and averaged to yield summary measures of amyloid load and neurofibrillary tangles. Multiple regression analyses were used to examine whether amyloid load could account for the effect of allele status on level of cognition, controlling for age, sex, and education. Results: Possession of at least one APOE e4 allele was associated with lower level of cognitive function proximate to death (p = 0.04). The effect of the e4 allele was reduced by nearly 60% and was no longer significant after controlling for the effect of amyloid load, whereas there was a robust inverse association between amyloid and cognition (p = 0.001). Because prior work had suggested that neurofibrillary tangles could account for the association of amyloid on cognition, we next examined whether amyloid could account for the effect of allele status on tangles. In a series of regression analyses, e4 was associated with density of tangles (p = 0.002), but the effect of the e4 allele was reduced by more than 50% and was no longer significant after controlling for the effect of amyloid load. Conclusion: These findings are consistent with a sequence of events whereby the e4 allele works through amyloid deposition and subsequent tangle formation to

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

    PubMed

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

    1995-01-01

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

  17. Max-Margin-Based Discriminative Feature Learning.

    PubMed

    Li, Changsheng; Liu, Qingshan; Dong, Weishan; Wei, Fan; Zhang, Xin; Yang, Lin

    2016-12-01

    In this brief, we propose a new max-margin-based discriminative feature learning method. In particular, we aim at learning a low-dimensional feature representation, so as to maximize the global margin of the data and make the samples from the same class as close as possible. In order to enhance the robustness to noise, we leverage a regularization term to make the transformation matrix sparse in rows. In addition, we further learn and leverage the correlations among multiple categories for assisting in learning discriminative features. The experimental results demonstrate the power of the proposed method against the related state-of-the-art methods.

  18. Education and Gender Discrimination

    ERIC Educational Resources Information Center

    Sumi, V. S.

    2012-01-01

    This paper discusses the status of women education in present education system and some measures to overcome the lags existing. Discrimination against girls and women in the developing world is a devastating reality. It results in millions of individual tragedies, which add up to lost potential for entire countries. Gender bias in education is an…

  19. Analytic boosted boson discrimination

    DOE PAGES

    Larkoski, Andrew J.; Moult, Ian; Neill, Duff

    2016-05-20

    Observables which discriminate boosted topologies from massive QCD jets are of great importance for the success of the jet substructure program at the Large Hadron Collider. Such observables, while both widely and successfully used, have been studied almost exclusively with Monte Carlo simulations. In this paper we present the first all-orders factorization theorem for a two-prong discriminant based on a jet shape variable, D2, valid for both signal and background jets. Our factorization theorem simultaneously describes the production of both collinear and soft subjets, and we introduce a novel zero-bin procedure to correctly describe the transition region between these limits.more » By proving an all orders factorization theorem, we enable a systematically improvable description, and allow for precision comparisons between data, Monte Carlo, and first principles QCD calculations for jet substructure observables. Using our factorization theorem, we present numerical results for the discrimination of a boosted Z boson from massive QCD background jets. We compare our results with Monte Carlo predictions which allows for a detailed understanding of the extent to which these generators accurately describe the formation of two-prong QCD jets, and informs their usage in substructure analyses. In conclusion, our calculation also provides considerable insight into the discrimination power and calculability of jet substructure observables in general.« less

  20. Analytic boosted boson discrimination

    SciTech Connect

    Larkoski, Andrew J.; Moult, Ian; Neill, Duff

    2016-05-20

    Observables which discriminate boosted topologies from massive QCD jets are of great importance for the success of the jet substructure program at the Large Hadron Collider. Such observables, while both widely and successfully used, have been studied almost exclusively with Monte Carlo simulations. In this paper we present the first all-orders factorization theorem for a two-prong discriminant based on a jet shape variable, D2, valid for both signal and background jets. Our factorization theorem simultaneously describes the production of both collinear and soft subjets, and we introduce a novel zero-bin procedure to correctly describe the transition region between these limits. By proving an all orders factorization theorem, we enable a systematically improvable description, and allow for precision comparisons between data, Monte Carlo, and first principles QCD calculations for jet substructure observables. Using our factorization theorem, we present numerical results for the discrimination of a boosted Z boson from massive QCD background jets. We compare our results with Monte Carlo predictions which allows for a detailed understanding of the extent to which these generators accurately describe the formation of two-prong QCD jets, and informs their usage in substructure analyses. In conclusion, our calculation also provides considerable insight into the discrimination power and calculability of jet substructure observables in general.

  1. Discrimination Learning in Children

    ERIC Educational Resources Information Center

    Ochocki, Thomas E.; And Others

    1975-01-01

    Examined the learning performance of 192 fourth-, fifth-, and sixth-grade children on either a two or four choice simultaneous color discrimination task. Compared the use of verbal reinforcement and/or punishment, under conditions of either complete or incomplete instructions. (Author/SDH)

  2. RISE TIME DELAY DISCRIMINATOR

    DOEpatents

    Johnstone, C.W.

    1959-09-29

    A pulse-height discriminator for generating an output pulse when the accepted input pulse is approximately at its maximum value is described. A gating tube and a negative bias generator responsive to the derivative of the input pulse and means for impressing the output of the bias generator to at least one control electrode of the gating tube are included.

  3. Aptitude Tests and Discrimination

    ERIC Educational Resources Information Center

    Coupland, D. E.

    1970-01-01

    Explains why in the United States the feeling is increasing that much of the aptitude testing now being done discriminates against minority group members seeking employment. Skeptical of eliminating the discriminatory aspects of testing, the article raises the question of eliminating testing itself. (DM)

  4. Sex Discrimination in Coaching.

    ERIC Educational Resources Information Center

    Dessem, Lawrence

    1980-01-01

    Even in situations in which the underpayment of girls' coaches is due to the sex of the students coached rather than to the sex of the coaches, the coaches and the girls coached are victims of unlawful discrimination. Available from Harvard Women's Law Journal, Harvard Law School, Cambridge, MA 02138. (Author/IRT)

  5. Discrimination. Opposing Viewpoints Series.

    ERIC Educational Resources Information Center

    Williams, Mary E., Ed.

    Books in the Opposing Viewpoints series challenge readers to question their own opinions and assumptions. By reading carefully balanced views, readers confront new ideas on the topic of interest. The Civil Rights Act of 1964, which prohibited job discrimination based on age, race, religion, gender, or national origin, provided the groundwork for…

  6. Noncontact discrimination of animal and human blood with vacuum blood vessel and factors affect the discrimination

    NASA Astrophysics Data System (ADS)

    Zhang, Linna; Zhang, Shengzhao; Sun, Meixiu; Li, Hongxiao; Li, Yingxin; Fu, Zhigang; Guan, Yang; Li, Gang; Lin, Ling

    2017-03-01

    Discrimination of human and nonhuman blood is crucial for import-export ports and inspection and quarantine departments. Current methods are usually destructive, complicated and time-consuming. We had previously demonstrated that visible diffuse reflectance spectroscopy combining PLS-DA method can successfully realize human blood discrimination. In that research, the spectra were measured with the fiber probe under the surface of blood samples. However, open sampling may pollute the blood samples. Virulence factors in blood samples can also endanger inspectors. In this paper, we explored the classification effect with the blood samples measured in the original containers-vacuum blood vessel. Furthermore, we studied the impact of different conditions of blood samples, such as coagulation and hemolysis, on the prediction ability of the discrimination model. The calibration model built with blood samples in different conditions displayed a satisfactory prediction result. This research demonstrated that visible and near-infrared diffuse reflectance spectroscopy method was potential for noncontact discrimination of human blood.

  7. 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.

  8. Comparison of allele frequencies of eight STR loci from Argentinian Amerindian and European populations.

    PubMed

    Sala, A; Penacino, G; Corach, D

    1998-10-01

    Eight STR systems (THO1, FABP, VWA, FES/FPS, HPRTB, F13A1, CSF1PO, and D6S366) were investigated in different ethnic groups of Argentina. Allele and genotype frequencies, power of exclusion, and discriminative power were investigated. Hardy-Weinberg expectations were calculated from heterozygosity levels. FST and G tests demonstrated that significant differences exist among the investigated populations for some of the eight STRs markers. The Wichi Indians are clearly separated from the Mapuche and Tehuelche, who in turn are closer to the European population, suggesting non-Amerindian admixture.

  9. Characterization and distribution of Mhc-DPB1 alleles in chimpanzee and rhesus macaque populations.

    PubMed

    Otting, N; Doxiadis, G G; Versluis, L; de Groot, N G; Anholts, J; Verduin, W; Rozemuller, E; Claas, F; Tilanus, M G; Bontrop, R E

    1998-10-01

    Allelic diversity at the nonhuman primate Mhc-DPB1 locus was studied by determining exon 2 nucleotide sequences. This resulted in the detection of 17 chimpanzee (Pan troglodytes), 2 orangutan (Pongo pygmaeus) and 16 rhesus macaque (Macaca mulatta) alleles. These were compiled with primate Mhc-DPB1 nucleotide sequences that were published previously. Based upon the results, a sequence specific oligotyping method was developed allowing us to investigate the distribution of Mhc-DPB1 alleles in distinct chimpanzee and rhesus macaque colonies. Like found in humans, chimpanzee and rhesus macaque populations originating from different geographic backgrounds appear to be characterized by the presence of a few dominant Mhc-DPB1 alleles.

  10. Do Heliconius butterfly species exchange mimicry alleles?

    PubMed Central

    Smith, Joel; Kronforst, Marcus R.

    2013-01-01

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

  11. Statistical Inference in the Wright-Fisher Model Using Allele Frequency Data.

    PubMed

    Tataru, Paula; Simonsen, Maria; Bataillon, Thomas; Hobolth, Asger

    2016-08-02

    The Wright-Fisher model provides an elegant mathematical framework for understanding allele frequency data. In particular, the model can be used to infer the demographic history of species and identify loci under selection. A crucial quantity for inference under the Wright-Fisher model is the distribution of allele frequencies (DAF). Despite the apparent simplicity of the model, the calculation of the DAF is challenging. We review and discuss strategies for approximating the DAF, and how these are used in methods that perform inference from allele frequency data. Various evolutionary forces can be incorporated in the Wright-Fisher model, and we consider these in turn. We begin our review with the basic bi-allelic Wright-Fisher model where random genetic drift is the only evolutionary force. We then consider mutation, migration, and selection. In particular, we compare diffusion-based and moment-based methods in terms of accuracy, computational efficiency, and analytical tractability. We conclude with a brief overview of the multi-allelic process with a general mutation model. [Allele frequency, diffusion, inference, moments, selection, Wright-Fisher.].

  12. 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.

  13. Allelic variation contributes to bacterial host specificity

    DOE PAGES

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

    2015-10-30

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

  14. Discrimination among Panax species using spectral fingerprinting

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Spectral fingerprints of samples of three Panax species (P. quinquefolius L., P. ginseng, and P. notoginseng) were acquired using UV, NIR, and MS spectrometry. With principal components analysis (PCA), all three methods allowed visual discrimination between all three species. All three methods wer...

  15. HLA-DRB1 and -DRB3 allele frequencies and haplotypic associations in Koreans.

    PubMed

    Song, Eun Young; Park, Hyejin; Roh, Eun Youn; Park, Myoung Hee

    2004-03-01

    We have investigated the frequencies of human leukocyte antigen-DRB1 (HLA-DRB1) and -DRB3 alleles and DRB1-DRB3 haplotypic associations in 800 Koreans. DRB1 genotyping was done using polymerase chain reaction-sequence-specific oligonucleotide (PCR-SSO) and PCR-single strand conformation polymorphism (SSCP) methods. DRB3 genotyping was done on 447 samples carrying DRB3-associated DRB1 alleles (DRB1*03, *11, *12, *13, and *14) using PCR-SSCP method. The allele frequencies of DRB3*0101, DRB3*0202, and DRB3*0301 were 0.073, 0.136, and 0.120, respectively, and we found one case of a probable new allele (DRB3*01new, 0.001). DRB1-DRB3 haplotypes with frequency (HF) > 0.005 exhibited strong associations between DRB3*0101 and DRB1*1201, *1301, and *1403; between DRB3*0301 and DRB1*1202 and *1302; between DRB3*0202 and DRB1*0301, *1101, *1401, *1405, and *1406 alleles. Most of the DRB1 alleles with frequency > 0.005 were exclusively associated with particular DRB3 alleles with relative linkage disequilibrium values of 1.0, except for DRB1*1201, *1202 and *1301; the rare presence (HF < 0.005) of DRB3*0202 associations were observed for these DRB1 alleles. We also investigated and presented rare DRB1-DRB3 associations in additional 6000 Koreans. Comparison with other ethnic groups revealed that DRB1*0301 and *1301 related DRB1-DRB3 haplotypes vary among different populations, in that Koreans and other Asian populations show less diversity compared with Caucasoids or African Americans.

  16. Psychophysical estimation of speed discrimination. I. Methodology.

    PubMed

    Lakshminarayanan, Vasudevan; Raghuram, Aparna; Khanna, Ritu

    2005-10-01

    Thresholds were assessed for a speed discrimination task with a pair of luminance-defined drifting gratings. The design and results of a series of experiments dealing in general with speed discrimination are described. Results show that for a speed discrimination task using drifting gratings, simultaneous presentation of the pair of gratings (spatially separated) was preferred over sequential presentation (temporally separated) in order to minimize the effects of eye movements and tracking. An interstimulus interval of at least 1000 ms was necessary to prevent motion aftereffects on subsequently viewed stimuli. For the two reference speeds tested of 2 and 8 deg/s using identical spatial frequency or randomizing spatial frequency for the pair of gratings did not affect speed discrimination thresholds. Implementing a staircase method of estimating thresholds was preferred over the method of constant stimuli or the method of limits. The results of these experiments were used to define the methodology for an investigation of aging and motion perception. These results will be of interest and use to psychophysicists designing and implementing speed discrimination paradigms.

  17. A novel technique for detecting single nucleotide polymorphisms by analyzing consumed allele-specific primers.

    PubMed

    Watanabe, G; Umetsu, K; Yuasa, I; Sato, M; Sakabe, M; Naito, E; Yamanouchi, H; Suzuki, T

    2001-02-01

    We present a simple and rapid polymerase chain reaction (PCR)-based technique, termed consumed allele-specific primer analysis (CASPA), as a new strategy for single nucleotide polymorphism (SNP) analysis. The method involves the use of labeled allele-specific primers, differing in length, with several noncomplementary nucleotides added in the 5'-terminal region. After PCR amplification, the amounts of the remaining primers not incorporated into the PCR products are determined. Thus, nucleotide substitutions are identified by measuring the consumption of primers. In this study, the CASPA method was successfully applied to ABO genotyping. In the present method, the allele-specific primer only anneals with the target polymorphic site on the DNA, so it is not necessary to analyze the PCR products. Therefore, this method is only little affected by modification of the PCR products. The CASPA method is expected to be a useful tool for typing of SNPs.

  18. Lifetime Discrimination Associated with Greater Likelihood of Premenstrual Dysphoric Disorder

    PubMed Central

    Desai, Rani; Kasl, Stanislav; Levy, Becca R.

    2011-01-01

    Abstract Objectives To evaluate whether the stressor of perceived discrimination was associated with premenstrual dysphoric disorder (PMDD) and premenstrual symptoms among minority women. This study builds on previous research that found perceived discrimination was positively associated with other psychiatric illnesses. Methods Participants were 2718 Asian, Latina, and black premenopausal women aged 18–40 years who completed the World Mental Health Composite International Diagnostic Interview for the National Latino and Asian American Survey or the National Survey of American Life. Perceived discrimination was assessed with the Everyday Discrimination Scale. DSM-IV-based diagnostic algorithms generated a provisional lifetime diagnosis of PMDD. Results Eighty-three percent of the participants reported experiencing discrimination (due to race, gender, age, height or weight, or other reasons) in their lifetimes. The frequency of perceived discrimination was positively associated with PMDD (odds ratio [OR] 1.08, 95% confidence interval [CI] 1.05-1.10) and premenstrual symptoms (OR 1.04, 95% CI 1.02-1.05), independent of demographic covariates and social desirability. Women reporting gender discrimination (OR 5.18, 95% CI 1.80-14.90), race discrimination (OR 4.14, 95% CI 1.54-11.11), and other forms of discrimination (OR 6.43, 95% CI 2.11-19.65) were significantly more likely than women without experiences of discrimination to have PMDD. Subtle discrimination was more strongly associated with PMDD (OR 1.12, 95% CI 1.01-1.23) than was blatant discrimination (OR 1.04, 95% CI 0.94-1.15). Conclusions This study is the first to demonstrate that perceived discrimination is associated with PMDD and premenstrual symptoms. These findings suggest that the prevalence of these conditions may be lessened by reducing discrimination in women's lives. PMID:21671777

  19. The Struggle against Sex Discrimination.

    ERIC Educational Resources Information Center

    Williamson, Jane

    1982-01-01

    Provides overview of laws, policies, and regulations available to women to secure their job rights when faced with sex discrimination. Equal pay, sexual harassment, pregnancy discrimination, and affirmative action are discussed, noting procedures involved in filing a complaint. (EJS)

  20. The Case for Positive Discrimination

    ERIC Educational Resources Information Center

    Miller, S. M.

    1973-01-01

    Discusses both three basic strategies, preferences, allocational priorities, and incentives--and four principles of positive discrimination--compensation and rectification, appropriate meritocratic criteria, the development of the discriminated, and fairness. (JM)

  1. Genetic discrimination in the workplace.

    PubMed

    Miller, P S

    1998-01-01

    Author argues that the Americans with Disabilities Act prohibits discrimination against workers based on their genetic makeup. He also examines state legislation and recently proposed federal legislation prohibiting genetic discrimination.

  2. Stimulus Structure, Discrimination, and Interference

    ERIC Educational Resources Information Center

    Runquist, Willard N.

    1975-01-01

    The general purpose of this experiment was to determine whether differences in stimulus discrimination, as determined by the MIR (missing-item recognition) test, are correlated with interference in recall, as demanded by the discriminative coding hypothesis. (Author/RK)

  3. Object discrimination reversal as a method to assess cognitive impairment in nonhuman primate enhanced pre- and postnatal developmental (ePPND) studies: statistical power analysis.

    PubMed

    Cappon, Gregg D; Bowman, Christopher J; Hurtt, Mark E; Grantham, Lonnie E

    2012-10-01

    An important aspect of the enhanced pre- and postnatal developmental (ePPND) toxicity study in nonhuman primates (NHP) is that it combines in utero and postnatal assessments in a single study. However, it is unclear if NHP ePPND studies are suitable to perform all of the evaluations incorporated into rodent PPND studies. To understand the value of including cognitive assessment in a NHP ePPND toxicity study, we performed a power analysis of object discrimination reversal task data using a modified Wisconsin General Testing Apparatus (ODR-WGTA) from two NHP ePPND studies. ODR-WGTA endpoints evaluated were days to learning and to first reversal, and number of reversals. With α = 0.05 and a one-sided t-test, a sample of seven provided 80% power to predict a 100% increase in all three of the ODR-WGTA endpoints; a sample of 25 provided 80% power to predict a 50% increase. Similar power analyses were performed with data from the Cincinnati Water Maze (CWM) and passive avoidance tests from three rat PPND toxicity studies. Groups of 5 and 15 in the CWM and passive avoidance test, respectively, provided 80% power to detect a 100% change. While the power of the CWM is not far superior to the NHP ODR-WGTA, a clear advantage is the routine use of larger sample size, with a group of 20 rats the CWM provides ~90% power to detect a 50% change. Due to the limitations on the number of animals, the ODR-WGTA may not be suitable for assessing cognitive impairment in NHP ePPND studies.

  4. Probabilistic models for semisupervised discriminative motif discovery in DNA sequences.

    PubMed

    Kim, Jong Kyoung; Choi, Seungjin

    2011-01-01

    Methods for discriminative motif discovery in DNA sequences identify transcription factor binding sites (TFBSs), searching only for patterns that differentiate two sets (positive and negative sets) of sequences. On one hand, discriminative methods increase the sensitivity and specificity of motif discovery, compared to generative models. On the other hand, generative models can easily exploit unlabeled sequences to better detect functional motifs when labeled training samples are limited. In this paper, we develop a hybrid generative/discriminative model which enables us to make use of unlabeled sequences in the framework of discriminative motif discovery, leading to semisupervised discriminative motif discovery. Numerical experiments on yeast ChIP-chip data for discovering DNA motifs demonstrate that the best performance is obtained between the purely-generative and the purely-discriminative and the semisupervised learning improves the performance when labeled sequences are limited.

  5. Transgender Discrimination and the Law

    ERIC Educational Resources Information Center

    Trotter, Richard

    2010-01-01

    An emerging area of law is developing regarding sex/gender identity discrimination, also referred to as transgender discrimination, as distinguished from discrimination based on sexual orientation. A transgendered individual is defined as "a person who has a gender-identity disorder which is a persistent discomfort about one?s assigned sex or…

  6. Price Discrimination: A Classroom Experiment

    ERIC Educational Resources Information Center

    Aguiló, Paula; Sard, Maria; Tugores, Maria

    2016-01-01

    In this article, the authors describe a classroom experiment aimed at familiarizing students with different types of price discrimination (first-, second-, and third-degree price discrimination). During the experiment, the students were asked to decide what tariffs to set as monopolists for each of the price discrimination scenarios under…

  7. Price Discrimination: Lessons for Consumers.

    ERIC Educational Resources Information Center

    Maynes, E. Scott

    1990-01-01

    Explains price and product discrimination, showing how intelligent consumers can achieve increased purchasing power of their income and discusses how consumer educators can explain this discrimination. Evaluates the pros and cons of price/product discrimination from the social viewpoint. (Author/JOW)

  8. 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...

  9. 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.

  10. 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.

  11. FET Frequency Discriminator.

    DTIC Science & Technology

    1982-03-01

    conversion . characteristic of the frequency discriminator is significant and :ending upon the specific system - may be the limiting factor in the accu of...the results obtained did not .-" allow for the accurate determinat ion of the change in impedance, addit ional 14 -~ 12V - - Figure 7. Impedance plot...44*. -. 7 ’I -- -..- ,. -, 4., /-.,’ .3 8 V ............... ... .. .$, L- 12v - Figure 9. Impedance plot tor five diodes inl parallel. A circuit was

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

    PubMed

    Remington, David L

    2015-12-01

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

  13. Symmetry impedes symmetry discrimination.

    PubMed

    Tjan, Bosco S; Liu, Zili

    2005-12-16

    Objects in the world, natural and artificial alike, are often bilaterally symmetric. The visual system is likely to take advantage of this regularity to encode shapes for efficient object recognition. The nature of encoding a symmetric shape, and of encoding any departure from it, is therefore an important matter in visual perception. We addressed this issue of shape encoding empirically, noting that a particular encoding scheme necessarily leads to a specific profile of sensitivity in perceptual discriminations. We studied symmetry discrimination using human faces and random dots. Each face stimulus was a frontal view of a three-dimensional (3-D) face model. The 3-D face model was a linearly weighted average (a morph) between the model of an original face and that of the corresponding mirror face. Using this morphing technique to vary the degree of asymmetry, we found that, for faces and analogously generated random-dot patterns alike, symmetry discrimination was worst when the stimuli were nearly symmetric, in apparent opposition to almost all studies in the literature. We analyzed the previous work and reconciled the old and new results using a generic model with a simple nonlinearity. By defining asymmetry as the minimal difference between the left and right halves of an object, we found that the visual system was disproportionately more sensitive to larger departures from symmetry than to smaller ones. We further demonstrated that our empirical and modeling results were consistent with Weber-Fechner's and Stevens's laws.

  14. Discrimination in lexical decision

    PubMed Central

    Feldman, Laurie Beth; Ramscar, Michael; Hendrix, Peter; Baayen, R. Harald

    2017-01-01

    In this study we present a novel set of discrimination-based indicators of language processing derived from Naive Discriminative Learning (ndl) theory. We compare the effectiveness of these new measures with classical lexical-distributional measures—in particular, frequency counts and form similarity measures—to predict lexical decision latencies when a complete morphological segmentation of masked primes is or is not possible. Data derive from a re-analysis of a large subset of decision latencies from the English Lexicon Project, as well as from the results of two new masked priming studies. Results demonstrate the superiority of discrimination-based predictors over lexical-distributional predictors alone, across both the simple and primed lexical decision tasks. Comparable priming after masked corner and cornea type primes, across two experiments, fails to support early obligatory segmentation into morphemes as predicted by the morpho-orthographic account of reading. Results fit well with ndl theory, which, in conformity with Word and Paradigm theory, rejects the morpheme as a relevant unit of analysis. Furthermore, results indicate that readers with greater spelling proficiency and larger vocabularies make better use of orthographic priors and handle lexical competition more efficiently. PMID:28235015

  15. Workplace discrimination and cancer.

    PubMed

    McKenna, Maureen A; Fabian, Ellen; Hurley, Jessica E; McMahon, Brian T; West, Steven L

    2007-01-01

    Data from the Equal Employment Opportunity Commission (EEOC) Integrated Mission System database were analyzed with specific reference to allegations of workplace discrimination filed by individuals with cancer under ADA Title One. These 6,832 allegations, filed between July 27, 1992 and September 30, 2003, were compared to 167,798 allegations from a general disability population on the following dimensions: type of workplace discrimination; demographic characteristics of the charging parties (CPs); the industry designation, location, and size of employers; and the outcome or resolution of EEOC investigations. Results showed allegations derived from CPs with cancer were more likely than those in the general disability population to include issues involving discharge, terms and conditions of employment, lay-off, wages, and demotion. Compared to the general disability group, CPs with cancer were more likely to be female, older, and White. Allegations derived from CPs with cancer were also more likely to be filed against smaller employers (15-100 workers) or those in service industries. Finally, the resolution of allegations by CPs with cancer were more likely to be meritorious than those filed from the general disability population; that is, actual discrimination is more likely to have occurred.

  16. [Comment on] Statistical discrimination

    NASA Astrophysics Data System (ADS)

    Chinn, Douglas

    In the December 8, 1981, issue of Eos, a news item reported the conclusion of a National Research Council study that sexual discrimination against women with Ph.D.'s exists in the field of geophysics. Basically, the item reported that even when allowances are made for motherhood the percentage of female Ph.D.'s holding high university and corporate positions is significantly lower than the percentage of male Ph.D.'s holding the same types of positions. The sexual discrimination conclusion, based only on these statistics, assumes that there are no basic psychological differences between men and women that might cause different populations in the employment group studied. Therefore, the reasoning goes, after taking into account possible effects from differences related to anatomy, such as women stopping their careers in order to bear and raise children, the statistical distributions of positions held by male and female Ph.D.'s ought to be very similar to one another. Any significant differences between the distributions must be caused primarily by sexual discrimination.

  17. PCR Strategies for Complete Allele Calling in Multigene Families Using High-Throughput Sequencing Approaches.

    PubMed

    Marmesat, Elena; Soriano, Laura; Mazzoni, Camila J; Sommer, Simone; Godoy, José A

    2016-01-01

    The characterization of multigene families with high copy number variation is often approached through PCR amplification with highly degenerate primers to account for all expected variants flanking the region of interest. Such an approach often introduces PCR biases that result in an unbalanced representation of targets in high-throughput sequencing libraries that eventually results in incomplete detection of the targeted alleles. Here we confirm this result and propose two different amplification strategies to alleviate this problem. The first strategy (called pooled-PCRs) targets different subsets of alleles in multiple independent PCRs using different moderately degenerate primer pairs, whereas the second approach (called pooled-primers) uses a custom-made pool of non-degenerate primers in a single PCR. We compare their performance to the common use of a single PCR with highly degenerate primers using the MHC class I of the Iberian lynx as a model. We found both novel approaches to work similarly well and better than the conventional approach. They significantly scored more alleles per individual (11.33 ± 1.38 and 11.72 ± 0.89 vs 7.94 ± 1.95), yielded more complete allelic profiles (96.28 ± 8.46 and 99.50 ± 2.12 vs 63.76 ± 15.43), and revealed more alleles at a population level (13 vs 12). Finally, we could link each allele's amplification efficiency with the primer-mismatches in its flanking sequences and show that ultra-deep coverage offered by high-throughput technologies does not fully compensate for such biases, especially as real alleles may reach lower coverage than artefacts. Adopting either of the proposed amplification methods provides the opportunity to attain more complete allelic profiles at lower coverages, improving confidence over the downstream analyses and subsequent applications.

  18. Combination of Eight Alleles at Four Quantitative Trait Loci Determines Grain Length in Rice.

    PubMed

    Zeng, Yuxiang; Ji, Zhijuan; Wen, Zhihua; Liang, Yan; Yang, Changdeng

    2016-01-01

    Grain length is an important quantitative trait in rice (Oryza sativa L.) that influences both grain yield and exterior quality. Although many quantitative trait loci (QTLs) for grain length have been identified, it is still unclear how different alleles from different QTLs regulate grain length coordinately. To explore the mechanisms of QTL combination in the determination of grain length, five mapping populations, including two F2 populations, an F3 population, an F7 recombinant inbred line (RIL) population, and an F8 RIL population, were developed from the cross between the U.S. tropical japonica variety 'Lemont' and the Chinese indica variety 'Yangdao 4' and grown under different environmental conditions. Four QTLs (qGL-3-1, qGL-3-2, qGL-4, and qGL-7) for grain length were detected using both composite interval mapping and multiple interval mapping methods in the mapping populations. In each locus, there was an allele from one parent that increased grain length and another allele from another parent that decreased it. The eight alleles in the four QTLs were analyzed to determine whether these alleles act additively across loci, and lead to a linear relationship between the predicted breeding value of QTLs and phenotype. Linear regression analysis suggested that the combination of eight alleles determined grain length. Plants carrying more grain length-increasing alleles had longer grain length than those carrying more grain length-decreasing alleles. This trend was consistent in all five mapping populations and demonstrated the regulation of grain length by the four QTLs. Thus, these QTLs are ideal resources for modifying grain length in rice.

  19. Is the Ala12 variant of the PPARG gene an "unthrifty allele"?

    PubMed Central

    Ruiz-Narvaez, E

    2005-01-01

    Background: The thrifty genotype hypothesis proposes that genetic susceptibility to type 2 diabetes results from the positive selection of "thrifty" alleles in the past. A corollary of this hypothesis is that genetic variants protecting against the development of diabetes are "unthrifty" and thus subject to negative selection during human evolution. Methods: It was assessed whether age estimates of the diabetes protective PPARG Ala12 allele indicate effects of natural selection. Based on published data from four populations, the date of origin of the diabetes protective PPARG Ala12 variant was estimated using both allele frequency and linkage disequilibrium (LD) with the C1431T single nucleotide polymorphism in exon 6 of the PPARG gene. Results: The best LD based estimate of the age of the Ala12 allele gave an average of ∼32 000 years with a maximum upper bound of ∼58 000 years. Assuming a population with a growth rate of r = 0.01 per generation, the frequency based estimate of the age of the Ala12 variant gave an average of ∼27 000 years with a maximum upper bound of ∼42 000 years. Discussion: The similarity of both time estimates is consistent with selective equivalence of the diabetes protective PPARG Ala12 allele and the diabetes susceptible PPARG Pro12 allele. PMID:15994875

  20. Early detection of nonnative alleles in fish populations: When sample size actually matters

    USGS Publications Warehouse

    Croce, Patrick Della; Poole, Geoffrey C.; Payne, Robert A.; Gresswell, Bob

    2017-01-01

    Reliable detection of nonnative alleles is crucial for the conservation of sensitive native fish populations at risk of introgression. Typically, nonnative alleles in a population are detected through the analysis of genetic markers in a sample of individuals. Here we show that common assumptions associated with such analyses yield substantial overestimates of the likelihood of detecting nonnative alleles. We present a revised equation to estimate the likelihood of detecting nonnative alleles in a population with a given level of admixture. The new equation incorporates the effects of the genotypic structure of the sampled population and shows that conventional methods overestimate the likelihood of detection, especially when nonnative or F-1 hybrid individuals are present. Under such circumstances—which are typical of early stages of introgression and therefore most important for conservation efforts—our results show that improved detection of nonnative alleles arises primarily from increasing the number of individuals sampled rather than increasing the number of genetic markers analyzed. Using the revised equation, we describe a new approach to determining the number of individuals to sample and the number of diagnostic markers to analyze when attempting to monitor the arrival of nonnative alleles in native populations.

  1. Allelic diversity of metallothionein in Orchesella cincta (L.): traces of natural selection by environmental pollution.

    PubMed

    Timmermans, M J T N; Ellers, J; Van Straalen, N M

    2007-05-01

    The advances made in statistical methods to detect selection from DNA sequence variation has resulted in an enormous increase in the number of studies reporting positive selection. However, a disadvantage of such statistical tests is that often no insight into the actual source of selection is obtained. Finer understanding of evolution can be obtained when those statistical tests are combined with field observations on allele frequencies. We assessed whether the metallothionein (mt) gene of Orchesella cincta (Collembola), which codes for a metal-binding protein, is subject to selection, by investigating alleles and allele frequencies among European metal-stressed and reference populations. Eight highly divergent alleles were resolved in Northwest Europe. At the nucleotide level, a total of 51 polymorphic sites (five of them implying amino-acid changes) were observed. Although statistical tests applied to the sequences alone showed no indication of selection, a G-test rejected the null hypothesis that alleles are homogeneously distributed over metal-stressed and reference populations. Analysis of molecular variance assigned a small, but significant amount of the total variance to differences between metal-stressed and non-stressed populations. In addition, it was shown that metal-stressed populations tend to be more genetically diversified at this locus than non-stressed ones. These results suggest that the mt gene and its surrounding DNA region are affected by environmental metal contamination. This study illustrates that, in addition to statistical tests, field observations on allele frequencies are needed to gain understanding of selection and adaptive evolution.

  2. Unexpectedly high allelic diversity at the KIT locus causing dominant white color in the domestic pig.

    PubMed Central

    Pielberg, G; Olsson, C; Syvänen, A C; Andersson, L

    2002-01-01

    Mutations in KIT encoding the mast/stem cell growth factor receptor (MGF) are responsible for coat color variation in domestic pigs. The dominant white phenotype is caused by two mutations, a gene duplication and a splice mutation in one of the copies leading to skipping of exon 17. Here we applied minisequencing and pyrosequencing for quantitative analysis of the number of copies with the splice form. An unexpectedly high genetic diversity was revealed in white pigs. We found four different KIT alleles in a small sample of eight Large White females used as founder animals in a wild boar intercross. A similar number of KIT alleles was found in commercial populations of white Landrace and Large White pigs. We provide evidence for at least two new KIT alleles in pigs, both with a triplication of the gene. The results imply that KIT alleles with the duplication are genetically unstable and new alleles are most likely generated by unequal crossing over. This study provides an improved method for genotyping the complicated Dominant white/KIT locus in pigs. The results also suggest that some alleles may be associated with negative pleiotropic effects on other traits. PMID:11805065

  3. Self-incompatibility alleles in Polish wild pear (Pyrus pyraster (L.) Burgsd.): a preliminary analysis.

    PubMed

    Wolko, Ł; Antkowiak, W; Sips, M; Słomski, R

    2010-01-01

    Wild pear (Pyrus pyraster, syn. P. communis var. pyraster) is thought to be one of the species that gave rise to all other members of the genus Pyrus, although intraspecific hybridizations with cultivated varieties could cause the disappearance of original species characteristics. S-RNase alleles from 7 different wild pear individuals, collected from various regions of Poland, were cloned on the basis of the PCR method and nucleotide sequence analyses. The hypervariable (HV) region is responsible for allele-specific S-RNase activity in the self-incompatibility mechanism. The high level of polymorphism of its sequences may constitute a source of valuable phylogenetic information. From all individuals, 14 sequences were obtained successfully, and 9 of them were novel alleles. Phylogenetic analysis of these alleles was based on the amino acid sequence interpretation of coding regions and intron nucleotide sequences. The research conducted on a limited pool of available P. pyraster alleles gives only an initial insight into possible S-RNase allele polymorphisms in wild populations. At this stage, the results do not confirm a strong influence of cultivated pear species on the wild pear.

  4. 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.

  5. Experiences of mental health discrimination in New Zealand.

    PubMed

    Peterson, Deborah; Pere, Lynne; Sheehan, Nancy; Surgenor, Gael

    2007-01-01

    Discrimination against people with experience of mental illness is a recognised problem, and there is a lack of information in New Zealand regarding the nature of this discrimination. The Like Minds, Like Mine project is a New Zealand initiative to combat the stigma and discrimination associated with mental illness. This paper reports on a study undertaken as part of this initiative, and describes the nature of discrimination that people with experience of mental illness face in New Zealand. A written survey was undertaken with people with experience of mental illness from throughout New Zealand, using a mixture of qualitative and quantitative questions. This questionnaire was distributed throughout the country in 2003, using a variety of distribution methods, and 785 responses were received and analysed from people self-identifying as having experienced mental illness. Respondents reported discrimination in all areas of their lives. The most commonly reported areas were discrimination by friends and family (59%), a fear of being discriminated against (46%), and discrimination in looking for employment (34%) and mental health services (34%). Discrimination can limit the participation of people with experience of mental illness in our society. We all need to examine our own attitudes and behaviours and take responsibility for discrimination.

  6. 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.

  7. 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

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

    PubMed

    Lachance, Joseph; Tishkoff, Sarah A

    2014-10-02

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

  9. Perceptual learning in maze discriminations.

    PubMed

    Trobalon, J B; Sansa, J; Chamizo, V D; Mackintosh, N J

    1991-11-01

    In Experiment 1, rats were trained on a discrimination between rubber- and sandpaper-covered arms of a maze after one group had been pre-exposed to these intra-maze cues. Pre-exposure facilitated subsequent discrimination learning, unless the discrimination was made easier by adding further discriminative stimuli, when it now significantly retarded learning. In Experiment 2, rats were trained on an extra-maze spatial discrimination, again after one group, but not another, had been pre-exposed to the extra-maze landmarks. Here too, pre-exposure facilitated subsequent discrimination learning, unless the discrimination was made substantially easier by arranging that the two arms between which rats had to choose were always separated by 135 degrees. The results of both experiments can be explained by supposing that perceptual learning depends on the presence of features common to S+ and S-.

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

    PubMed Central

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

    1998-01-01

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

  11. Uncommon HLA alleles identified by hemizygous ultra-high Sanger sequencing: haplotype associations and reconsideration of their assignment in the Common and Well-Documented catalogue.

    PubMed

    Voorter, Christina E M; Groeneweg, Mathijs; Groeneveld, Lisette; Tilanus, Marcel G J

    2016-02-01

    Although the number of HLA alleles still increases, many of them have been reported being uncommon. This is partly due to lack of full length gene sequencing, especially for those alleles belonging to an allele ambiguity in which the first discovered allele has been assigned as the most frequent one. As members of the working group on Common and Well Documented (CWD) alleles and since we implemented full length group-specific sequencing as standard method routinely, we have investigated the presence of presumably rare alleles in our collection of HLA typing data. We identified 50 alleles, that were not previously encountered as Common or Well Documented. Sixteen of them should be added to the CWD catalogue, since we encountered them in 5 or more unrelated individuals. Another 11 could be added, based upon our results and the data present in the IMGT database and the rare allele section of the allele frequencies database. Furthermore, tight associations were observed between several different alleles even at the level of synonymous and non-coding sequences. In addition, in several cases the uncommon allele was found to be more frequent than its common counterpart.

  12. HLA B27 allele types in homogeneous groups of juvenile idiopathic arthritis patients in Latvia

    PubMed Central

    2010-01-01

    Juvenile idiopathic arthritis (JIA) is a heterogeneous condition and therapeutic strategies vary in different JIA types. The routinely accepted practice to start with Sulphasalazine (SS) as the first line treatment in patients with HLA B27 positive JIA proves to be ineffective in a large proportion of children. Objective to investigate HLA B27 positive JIA patients clinical characteristics, determined HLA B27 allele types and their connection with antirheumatic treatment in homogenous patient groups. Materials and methods 56 patients diagnosed with JIA and observed over the period 2006 to 2009 included in the study. HLAB27 allele types were determined using PCR method. Results In HLA B27 positive JIA patients mean disease onset was 12.34 ± 3.3 years. Most common (44%) JIA type was enthesitis related arthritis. Positive response to the treatment with SS was found in 32% of patients, Methotrexate (MTX) - in 43%, combined treatment - SS with MTX was effective in 12.5%. 12.5% of patients required combination MTX with Enbrel. Eight HLA B27 allele types were found in JIA patients in Latvia: *2702, *2703, *2704, *2705, *2710, *2715, *2717, *2728. The most common was *2705 - in 55% of cases. Among all the patients enthesitis related arthritis most commonly occurred in patients with HLAB*2705 allele (OR = 2.01, p < 0.02), oligoarthritis in patients with *2710 allele (OR = 3.0, p < 0.04) and polyarthritis with *2717 allele (OR = 3.0, p < 0.05). In patients with *2705 allele effective treatment was MTX (OR = 1.13, p < 0.03) and MTX with SS (OR = 2.02, p < 0.05), but in patients having *2703 allele - MTX with Enbrel (OR = 2.94, p < 0.02). Conclusions There are 8 different HLA B27 alleles in JIA patients in Latvia and the most common is *2705, but in order to assert them to be disease associated alleles, more extensive studies are needed, including control group of HLA B27 positive healthy individuals. Standard treatment approach with SS proves to be unsatisfactory in the

  13. Allele frequency distribution for 15 autosomal STR loci in Afridi Pathan population of Uttar Pradesh, India.

    PubMed

    Noor, Sabahat; Ali, Shahnaz; Eaaswarkhanth, Muthukrishnan; Haque, Ikramul

    2009-11-01

    Allele frequencies of the 15 autosomal short tandem repeat (STR) loci D8S1179, D21S11, D7S820, CSF1PO D19S433, vWA, TPOX, D18S51, D3S1358, THO1, D13S317, D16S539, D2S1338, D5S818 and FGA were determined in Afridi Pathan population of Uttar Pradesh, India. All the 15 STR loci studied were found to be highly polymorphic with respect to observed heterozygosity values. Adherence to the expectations of the Hardy-Weinberg equilibrium (HWE) was confirmed for all the loci with an exception of TPOX and FGA. The allele 12 in CSF1PO was found to be most frequent. The power of discrimination was found to be high ranging from a minimum of 0.858 for the locus CSFIPO to maximum of 0.962 for the locus FGA, thereby facilitating the validation and efficiency of these STR markers in human identification. Population differentiation test between the studied and neighboring populations revealed significant differences at several loci suggesting the endogamous nature of the studied population. To the best of our knowledge, Afridi Pathan population has not been explored genetically for generating forensic data on STR markers. Therefore, STR allele frequency data of this unique population is a valuable contribution to the existing DNA database on Indian populations.

  14. Forensic Spanish allele and haplotype database for a 17 X-STR panel.

    PubMed

    Prieto-Fernández, Endika; Núñez, Carolina; Baeta, Miriam; Jiménez-Moreno, Susana; Martínez-Jarreta, Begoña; de Pancorbo, Marian M

    2016-09-01

    The currently developed 17 X-STR panel (DXS8378, DXS9898, DXS7133, GATA31E08, GATA172D05, DXS6801, DXS7423, DXS6809, DXS6799, DXS7132, DXS9902, DXS6800, DXS6789, DXS10075, DXS10079, DXS6807, and DXS6803) offers a highly discriminative tool for forensic identification and kinship testing. With the aim of providing a global Spanish population X-STR database, we present haplotype and allele frequencies and parameters of forensic interest for the 17 X-STR panel obtained from 593 unrelated individuals from Alicante, Aragon, the Basque Country, Andalusia, Galicia, Madrid, and Barcelona that represent the most populated regions of the Spanish Peninsular territory. The seven populations were compared to test possible population genetic substructures. The lack of significant differences among the studied Spanish populations supports the use of the allele and haplotype frequency database presented herein as a global Spanish population sample useful for statistical evaluation in forensic casework. After conducting the LD plots derived from HapMap and pairwise linkage disequilibrium tests, DXS7132, DXS10075, and DXS10079 markers were included in a cluster and haplotype frequencies were calculated. The improvement in the forensic parameters for the Spanish population using 17 X-STRs in comparison to the previous 10 X-STR allele frequencies database is also shown.

  15. Assessing Predictive Accuracy in Discriminant Analysis.

    ERIC Educational Resources Information Center

    Huberty, Carl J.; And Others

    1987-01-01

    Three estimates of the probabilities of correct classification in predictive discriminant analysis were computed using mathematical formulas, resubstitution, and external analyses: (1) optimal hit rate; (2) actual hit rate; and (3) expected actual hit rate. Methods were compared using Monte Carlo sampling from two data sets. (Author/GDC)

  16. Optimal Experimental Design for Model Discrimination

    ERIC Educational Resources Information Center

    Myung, Jay I.; Pitt, Mark A.

    2009-01-01

    Models of a psychological process can be difficult to discriminate experimentally because it is not easy to determine the values of the critical design variables (e.g., presentation schedule, stimulus structure) that will be most informative in differentiating them. Recent developments in sampling-based search methods in statistics make it…

  17. Novel Acoustic Scattering Processes for Target Discrimination

    DTIC Science & Technology

    2007-09-30

    acoustic signal using algorithms originally developed for high-frequency acoustical holography [11]. Data is only acquired by scanning a hydrophone ...by the application of a back-propagation algorithm based on the methods of acoustic holography . Selected results relevant to the interpretation of...Novel Acoustic Scattering Processes for Target Discrimination Philip L. Marston Physics and Astronomy Dept., Washington State University, Pullman

  18. Novel microsatellite markers for the oriental fruit moth Grapholita molesta (Lepidoptera: Tortricidae) and effects of null alleles on population genetics analyses.

    PubMed

    Song, W; Cao, L-J; Wang, Y-Z; Li, B-Y; Wei, S-J

    2016-11-07

    The oriental fruit moth (OFM) Grapholita molesta (Lepidoptera: Tortricidae) is an important economic pest of stone and pome fruits worldwide. We sequenced the OFM genome using next-generation sequencing and characterized the microsatellite distribution. In total, 56,674 microsatellites were identified, with 11,584 loci suitable for primer design. Twenty-seven polymorphic microsatellites, including 24 loci with trinucleotide repeat and three with pentanucleotide repeat, were validated in 95 individuals from four natural populations. The allele numbers ranged from 4 to 40, with an average value of 13.7 per locus. A high frequency of null alleles was observed in most loci developed for the OFM. Three marker panels, all of the loci, nine loci with the lowest null allele frequencies, and nine loci with the highest null allele frequencies, were established for population genetics analyses. The null allele influenced estimations of genetic diversity parameters but not the OFM's genetic structure. Both a STRUCTURE analysis and a discriminant analysis of principal components, using the three marker panels, divided the four natural populations into three groups. However, more individuals were incorrectly assigned by the STRUCTURE analysis when the marker panel with the highest null allele frequency was used compared with the other two panels. Our study provides empirical research on the effects of null alleles on population genetics analyses. The microsatellites developed will be valuable markers for genetic studies of the OFM.

  19. Discrimination, Mastery, and Depressive Symptoms among African American Men

    ERIC Educational Resources Information Center

    Watkins, Daphne C.; Hudson, Darrell L.; Caldwell, Cleopatra Howard; Siefert, Kristine; Jackson, James S.

    2011-01-01

    Purpose: This study examines the influence of discrimination and mastery on depressive symptoms for African American men at young (18-34), middle (35-54), and late (55+) adulthood. Method: Analyses are based on responses from 1,271 African American men from the National Survey of American Life (NSAL). Results: Discrimination was significantly…

  20. Perceptual Adaptation of Voice Gender Discrimination with Spectrally Shifted Vowels

    ERIC Educational Resources Information Center

    Li, Tianhao; Fu, Qian-Jie

    2011-01-01

    Purpose: To determine whether perceptual adaptation improves voice gender discrimination of spectrally shifted vowels and, if so, which acoustic cues contribute to the improvement. Method: Voice gender discrimination was measured for 10 normal-hearing subjects, during 5 days of adaptation to spectrally shifted vowels, produced by processing the…

  1. Odour-based kin discrimination in the cooperatively breeding meerkat.

    PubMed

    Leclaire, Sarah; Nielsen, Johanna F; Thavarajah, Nathan K; Manser, Marta; Clutton-Brock, Tim H

    2013-02-23

    Kin recognition is a useful ability for animals, facilitating cooperation among relatives and avoidance of excessive kin competition or inbreeding. In meerkats, Suricata suricatta, encounters between unfamiliar kin are relatively frequent, and kin recognition by phenotype matching is expected to avoid inbreeding with close relatives. Here, we investigate whether female meerkats are able to discriminate the scent of unfamiliar kin from unfamiliar non-kin. Dominant females were presented with anal gland secretion from unfamiliar individuals that varied in their relatedness. Our result indicates that females spent more time investigating the scent of related than unrelated unfamiliar individuals, suggesting that females may use a phenotype matching mechanism (or recognition alleles) to discriminate the odour of their kin from the odour of their non-kin. Our study provides a key starting point for further investigations into the use of kin recognition for inbreeding avoidance in the widely studied meerkat.

  2. Odour-based kin discrimination in the cooperatively breeding meerkat

    PubMed Central

    Leclaire, Sarah; Nielsen, Johanna F.; Thavarajah, Nathan K.; Manser, Marta; Clutton-Brock, Tim H.

    2013-01-01

    Kin recognition is a useful ability for animals, facilitating cooperation among relatives and avoidance of excessive kin competition or inbreeding. In meerkats, Suricata suricatta, encounters between unfamiliar kin are relatively frequent, and kin recognition by phenotype matching is expected to avoid inbreeding with close relatives. Here, we investigate whether female meerkats are able to discriminate the scent of unfamiliar kin from unfamiliar non-kin. Dominant females were presented with anal gland secretion from unfamiliar individuals that varied in their relatedness. Our result indicates that females spent more time investigating the scent of related than unrelated unfamiliar individuals, suggesting that females may use a phenotype matching mechanism (or recognition alleles) to discriminate the odour of their kin from the odour of their non-kin. Our study provides a key starting point for further investigations into the use of kin recognition for inbreeding avoidance in the widely studied meerkat. PMID:23234867

  3. 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.

  4. Kernel Partial Least Squares for Nonlinear Regression and Discrimination

    NASA Technical Reports Server (NTRS)

    Rosipal, Roman; Clancy, Daniel (Technical Monitor)

    2002-01-01

    This paper summarizes recent results on applying the method of partial least squares (PLS) in a reproducing kernel Hilbert space (RKHS). A previously proposed kernel PLS regression model was proven to be competitive with other regularized regression methods in RKHS. The family of nonlinear kernel-based PLS models is extended by considering the kernel PLS method for discrimination. Theoretical and experimental results on a two-class discrimination problem indicate usefulness of the method.

  5. Haplotypic Background of a Private Allele at High Frequency in the Americas

    PubMed Central

    Schroeder, Kari B.; Jakobsson, Mattias; Crawford, Michael H.; Schurr, Theodore G.; Boca, Simina M.; Conrad, Donald F.; Tito, Raul Y.; Osipova, Ludmilla P.; Tarskaia, Larissa A.; Zhadanov, Sergey I.; Wall, Jeffrey D.; Pritchard, Jonathan K.; Malhi, Ripan S.; Smith, David G.; Rosenberg, Noah A.

    2009-01-01

    Recently, the observation of a high-frequency private allele, the 9-repeat allele at microsatellite D9S1120, in all sampled Native American and Western Beringian populations has been interpreted as evidence that all modern Native Americans descend primarily from a single founding population. However, this inference assumed that all copies of the 9-repeat allele were identical by descent and that the geographic distribution of this allele had not been influenced by natural selection. To investigate whether these assumptions are satisfied, we genotyped 34 single nucleotide polymorphisms across ∼500 kilobases (kb) around D9S1120 in 21 Native American and Western Beringian populations and 54 other worldwide populations. All chromosomes with the 9-repeat allele share the same haplotypic background in the vicinity of D9S1120, suggesting that all sampled copies of the 9-repeat allele are identical by descent. Ninety-one percent of these chromosomes share the same 76.26 kb haplotype, which we call the “American Modal Haplotype” (AMH). Three observations lead us to conclude that the high frequency and widespread distribution of the 9-repeat allele are unlikely to be the result of positive selection: 1) aside from its association with the 9-repeat allele, the AMH does not have a high frequency in the Americas, 2) the AMH is not unusually long for its frequency compared with other haplotypes in the Americas, and 3) in Latin American mestizo populations, the proportion of Native American ancestry at D9S1120 is not unusual compared with that observed at other genomewide microsatellites. Using a new method for estimating the time to the most recent common ancestor (MRCA) of all sampled copies of an allele on the basis of an estimate of the length of the genealogy descended from the MRCA, we calculate the mean time to the MRCA of the 9-repeat allele to be between 7,325 and 39,900 years, depending on the demographic model used. The results support the hypothesis that all

  6. A Self-Affine Multi-Fractal Wave/Turbulence Discrimination Method Using Data from Single Point Fast Response Sensors in a Nocturnal Atmospheric Boundary Layer

    DTIC Science & Technology

    1992-04-10

    and passive tracer concentrations, and their cross correlations have generally been used to estimate the magnitude of dispersive atmospheric transport...of gravity waves and turbulence. . 10 III. METHODS .......... ........................ 12 A. Data .......... ........................ 12 B. Analysis ...unstable, i.e., strange. For waves or even limit cycle motion about fixed attractors, self-similarity does not occur. Pertinent to time series analysis , this

  7. Natural Selection VS. Random Drift: Evidence from Temporal Variation in Allele Frequencies in Nature

    PubMed Central

    Mueller, Laurence D.; Barr, Lorraine G.; Ayala, Francisco J.

    1985-01-01

    We have obtained monthly samples of two species, Drosophila pseudoobscura and Drosophila persimilis, in a natural population from Napa County, California. In each species, about 300 genes have been assayed by electrophoresis for each of seven enzyme loci in each monthly sample from March 1972 to June 1975. Using statistical methods developed for the purpose, we have examined whether the allele frequencies at different loci vary in a correlated fashion. The methods used do not detect natural selection when it is deterministic (e.g., overdominance or directional selection), but only when alleles at different loci vary simultaneously in response to the same environmental variations. Moreover, only relatively large fitness differences (of the order of 15%) are detectable. We have found strong evidence of correlated allele frequency variation in 13–20% of the cases examined. We interpret this as evidence that natural selection plays a major role in the evolution of protein polymorphisms in nature. PMID:4054608

  8. Discrimination against Muslim American adolescents.

    PubMed

    Aroian, Karen J

    2012-06-01

    Although there is ample evidence of discrimination toward Muslim Americans in general, there is limited information specific to Muslim American adolescents. The few existing studies specific to this age group suggest that Muslim American adolescents encounter much discrimination from teachers, school administrators, and classmates. This descriptive qualitative study complements the few existing studies on Muslim American adolescents by obtaining in-depth description of the discrimination they encounter. The sample was 14 Muslim American adolescents who participated in one of two gender-specific focus groups about their discrimination experiences. Findings identified school settings as rife with discrimination toward Muslims, portrayed Muslim girls as at risk for harassment by strangers in public places, and illustrated how Muslim youth cope with discrimination. The study findings sensitize school nurses to the nature of the problem and provide direction for intervention.

  9. Analysis of clinical laboratory data by biplot methods using a three-dimensional display: discrimination of renal stone-patients with idiopathic hypercalciuria and primary hyperparathyroidism.

    PubMed

    Tschöpe, W; Schmidt-Gayk, H; Ritz, E; Weber, E; Berger, J

    1979-08-01

    The biplot technique is a very useful graphical method to display the relationships between row and column characteristics in two-way tables. This method is applicable as long as the rank-2 approximation explains a large part (e.g. 95%) of the whole variability. However, since in large tables only a rank-3 approximation will yield such a high degree of explanation, a three-dimensional biplot technique has been introduced, using a 3d-screen as a matter of presentation of clinical laboratory data. The value of such a procedure is illustrated using as a clinical example a patient population with recurrent renal stone formation due either to primary hyperparathyroidism or to idiopathic hypercalciuria.

  10. Group-specific PCR-RFLP and real-time PCR methods for detection and tentative discrimination of strictly anaerobic beer-spoilage bacteria of the class Clostridia.

    PubMed

    Juvonen, Riikka; Koivula, Teija; Haikara, Auli

    2008-07-15

    The strictly anaerobic brewery contaminants of the genera Pectinatus, Megasphaera, Selenomonas and Zymophilus in the class Clostridia constitute an important group of spoilage bacteria of unpasteurised, packaged beers. The aim of this study was to develop and evaluate group-specific PCR methods to detect and differentiate these bacteria in beer. A group-specific primer pair targeting a 342-bp variable region of the 16S rRNA gene was designed and evaluated in end-point PCR with gel electrophoresis and in real-time PCR with SYBR Green I dye. Significant cross-reactions with DNAs from any of the forty-two brewery-related, non-target microbes or from real brewery samples were not detected in either PCR system. The group-specific end-point and real-time PCR products could be differentiated according to species/genus and spoilage potential using restriction fragment length polymorphism (KpnI, XmnI, BssHII, ScaI) and melting point curve analysis, respectively. In combination with a rapid DNA extraction method, the PCR reactions detected ca 10(0)-10(3) CFU per 25 ml of beer depending on the strain and on the PCR system. The end-point and real-time PCR analysis took 6-7 h and 2-3 h, respectively. Pre-PCR enrichment of beer samples for 1-3 days ensured the detection of even a single cultivable cell. The PCR and cultivation results of real brewery samples were mostly congruent but the PCR methods were occasionally more sensitive. The PCR methods developed allow the detection of all the nine beer-spoilage Pectinatus, Megasphaera, Selenomonas and Zymophilus species in a single reaction and their differentiation below group level and reduce the analysis time for testing of their presence in beer samples by 1-2 days. The methods can be applied for brewery routine quality control and for studying occurrence, diversity and numbers of the strictly anaerobic beer spoilers in the brewing process.

  11. Interpreting past religious discrimination today.

    PubMed

    Schumm, Walter R

    2003-10-01

    Much of modern western law now presupposes opposition to discrimination based on race, religion, sex, national origin, and other factors. However, ancient religious Scriptures may have sanctioned certain types of discrimination. Whether those who are inclined to accept literal interpretations of their Scriptures will condone certain forms of discrimination could be evaluated to contrast the effects of modernization versus religious indoctrination on various kinds of prejudice.

  12. PCR Strategies for Complete Allele Calling in Multigene Families Using High-Throughput Sequencing Approaches

    PubMed Central

    Marmesat, Elena; Soriano, Laura; Mazzoni, Camila J.; Sommer, Simone

    2016-01-01

    The characterization of multigene families with high copy number variation is often approached through PCR amplification with highly degenerate primers to account for all expected variants flanking the region of interest. Such an approach often introduces PCR biases that result in an unbalanced representation of targets in high-throughput sequencing libraries that eventually results in incomplete detection of the targeted alleles. Here we confirm this result and propose two different amplification strategies to alleviate this problem. The first strategy (called pooled-PCRs) targets different subsets of alleles in multiple independent PCRs using different moderately degenerate primer pairs, whereas the second approach (called pooled-primers) uses a custom-made pool of non-degenerate primers in a single PCR. We compare their performance to the common use of a single PCR with highly degenerate primers using the MHC class I of the Iberian lynx as a model. We found both novel approaches to work similarly well and better than the conventional approach. They significantly scored more alleles per individual (11.33 ± 1.38 and 11.72 ± 0.89 vs 7.94 ± 1.95), yielded more complete allelic profiles (96.28 ± 8.46 and 99.50 ± 2.12 vs 63.76 ± 15.43), and revealed more alleles at a population level (13 vs 12). Finally, we could link each allele’s amplification efficiency with the primer-mismatches in its flanking sequences and show that ultra-deep coverage offered by high-throughput technologies does not fully compensate for such biases, especially as real alleles may reach lower coverage than artefacts. Adopting either of the proposed amplification methods provides the opportunity to attain more complete allelic profiles at lower coverages, improving confidence over the downstream analyses and subsequent applications. PMID:27294261

  13. Analytical method for total chromium and nickel in urine using an inductively coupled plasma-universal cell technology-mass spectrometer (ICP-UCT-MS) in kinetic energy discrimination (KED) mode.

    PubMed

    Quarles, C Derrick; Jones, Deanna R; Jarrett, Jeffery M; Shakirova, Gulchekhra; Pan, Yi; Caldwell, Kathleen L; Jones, Robert L

    Biomonitoring and emergency response measurements are an important aspect of the Division of Laboratory Sciences of the National Center for Environmental Health, Centers for Disease Control and Prevention (CDC). The continuing advancement in instrumentation allows for enhancements to existing analytical methods. Prior to this work, chromium and nickel were analyzed on a sector field inductively coupled plasma-mass spectrometer (SF-ICP-MS). This type of instrumentation provides the necessary sensitivity, selectivity, accuracy, and precision but due to the higher complexity of instrumentation and operation, it is not preferred for routine high throughput biomonitoring needs. Instead a quadrupole based method has been developed on a PerkinElmer NexION(™) 300D ICP-MS. The instrument is operated using 6.0 mL min(-1) helium as the collision cell gas and in kinetic energy discrimination mode, interferences are successfully removed for the analysis of (52)Cr ((40)Ar(12)C and (35)Cl(16)O(1)H) and (60)Ni ((44)Ca(16)O). The limits of detection are 0.162 μg L(-1) Cr and 0.248 μg L(-1) Ni. Method accuracy using NIST SRM 2668 level 1 (1.08 μg L(-1) Cr and 2.31μg L(-1) Ni) and level 2 (27.7 μg L(-1) Cr and 115 μg L(-1) Ni) was within the 95% confidence intervals reported in the NIST certificate. Among-run precision is less than 10% RSDs (N = 20) for in house quality control and NIST SRM urine samples. While the limits of detection (LOD) for the new quadrupole ICP-UCT-MS with KED method are similar to the SF-ICP-MS method, better measurement precision is observed for the quadrupole method. The new method presented provides fast, accurate, and more precise results on a less complex and more robust ICP-MS platform.

  14. Determination of arylsulfatase A pseudodeficiency allele and haplotype frequency in the Tunisian population.

    PubMed

    Ben Halim, Nizar; Dorboz, Imen; Kefi, Rym; Kharrat, Najla; Eymard-Pierre, Eleonore; Nagara, Majdi; Romdhane, Lilia; Ben Alaya-Bouafif, Nissaf; Rebai, Ahmed; Miladi, Najoua; Boespflug-Tanguy, Odile; Abdelhak, Sonia

    2016-03-01

    Arylsulfatase A (ASA) is a lysosomal enzyme involved in the catabolism of cerebroside sulfate. ASA deficiency is associated with metachromatic leukodystrophy (MLD). Low ASA activities have also been reported in a more common condition with no apparent clinical consequences termed ASA pseudo-deficiency (ASA-PD) which is associated with two linked mutations in the ASA gene (c.1049A>G and c.*96A>G). This study aimed to investigate the frequency of the two ASA-PD variants and their linkage disequilibrium (LD) among Tunisians. ASA-PD variants were detected in 129 healthy Tunisians and their frequencies were compared to those described worldwide. The frequency of the PD allele was estimated at 17.4% for the overall sample, with c.1049A>G and c.*96A>G frequencies of 25.6 and 17.4%, respectively. This study also revealed a high LD between the two ASA-PD variants (r(2) = 0.61). Inter-population analysis revealed similarities in the ASA-PD genetic structure between Tunisians and populations from Middle East with c.*96A>G frequencies being the highest in the world. A significant North vs. South genetic differentiation in the ASA-PD frequency was also observed in Tunisian population who seems genetically intermediate between Africans, Middle-Easterners and Europeans. This is the first report on the allele frequency of the ASA-PD in North Africa, revealing a relatively high frequency of the PD allele among Tunisians. This study gives also evidence on the importance of discriminating ASA-PD allele from pathological mutations causing MLD and supporting enzymatic activity testing with both sulfatiduria determination and genetic testing in the differential diagnosis of MLD in the Tunisian population.

  15. Lower Frequency of HLA-DRB1 Type 1 Diabetes Risk Alleles in Pediatric Patients with MODY

    PubMed Central

    López-Euba, Tamara; Velayos, Teresa; Martínez de LaPiscina, Idoia; Bilbao, José Ramón; Rica, Itxaso; Castaño, Luis

    2017-01-01

    Objective The aim of this study was to determine the frequency of susceptible HLA-DRB1 alleles for type 1 diabetes in a cohort of pediatric patients with a confirmed genetic diagnosis of MODY. Materials and Methods 160 families with a proband diagnosed with type 1 diabetes and 74 families with a molecular diagnosis of MODY (61 GCK-MODY and 13 HNF1A-MODY) were categorized at high definition for HLA-DRB1 locus. According to the presence or absence of the susceptible HLA-DRB1 alleles for type 1 diabetes, we considered three different HLA-DRB1 genotypes: 0 risk alleles (no DR3 no DR4); 1 risk allele (DR3 or DR4); 2 risk alleles (DR3 and/or DR4). Results Compared with type 1 diabetes, patients with MODY carried higher frequency of 0 risk alleles, OR 22.7 (95% CI: 10.7–48.6) and lower frequency of 1 or 2 risk alleles, OR 0.53 (95% CI: 0.29–0.96) and OR 0.06 (95% CI: 0.02–0.18), respectively. Conclusions The frequency of HLA-DRB1 risk alleles for type 1 diabetes is significantly lower in patients with MODY. In children and adolescents with diabetes, the presence of 2 risk alleles (DR3 and/or DR4) reduces the probability of MODY diagnosis, whereas the lack of risk alleles increases it. Therefore, we might consider that HLA-DRB1 provides additional information for the selection of patients with high probability of monogenic diabetes. PMID:28052112

  16. Identification of β-globin haplotypes linked to sickle hemoglobin (Hb S) alleles in Mazandaran province, Iran.

    PubMed

    Aghajani, Faeghe; Mahdavi, Mohammad Reza; Kosaryan, Mehrnoush; Mahdavi, Mehrad; Hamidi, Mohaddese; Jalali, Hossein

    2016-12-21

    Carrier frequency of the β(S) allele has been reported to be 0.19% in Mazandaran province, northern Iran. Haplotype analysis of the β(S) allele helps trace the origin of its encoded hemoglobin (Hb) variant, Hb S, in a region. The aim of this study was to investigate the haplotypes associated with β(S) alleles in Mazandaran province. Capillary electrophoresis was carried out to detect individuals suspected to have a βS allele(s). DNA analysis (PCR-RFLP) was used for final confirmation. To identify 5\\' to 3\\' β-globin gene cluster haplotypes associated with β(S) alleles, family linkage analysis was applied. Six polymorphic sites (HincII 5' to ε, XmnI 5' to (G)γ, HindIII in (G)γ, HindIII in (A)γ, HincII 3' to ψβ and AvaII in β) were investigated using the PCR-RFLP method. Five different haplotypes were linked to β(S) alleles, while β(A) alleles were associated with nine haplotypes. Among the β(S) alleles, 53.9% were associated with the Benin (----++) haplotype, and the Arab-Indian (+++-++) haplotype had the second-highest frequency (23%). Unlike southern provinces, where the Arab-Indian haplotype is prominent, the Benin haplotype is the most frequent haplotype in northern Iran, and this may represent a founder effect. Since the Benin haplotype does not carry the XmnI polymorphism 5' to the (G)γ gene, which is responsible for high expression of Hb F, a severe form of sickle cell disease can be anticipated in patients that are homozygous for the β(S) allele in the northern region.

  17. Racial Discrimination, Cultural Resilience, and Stress

    PubMed Central

    Wells, Samantha; Graham, Kathryn; George, Julie

    2016-01-01

    Objective: Racial discrimination is a social determinant of health for First Nations people. Cultural resilience has been regarded as a potentially positive resource for social outcomes. Using a compensatory model of resilience, this study sought to determine if cultural resilience (compensatory factor) neutralized or offset the detrimental effect of racial discrimination (social risk factor) on stress (outcome). Methods: Data were collected from October 2012 to February 2013 (N = 340) from adult members of the Kettle and Stony Point First Nation community in Ontario, Canada. The outcome was perceived stress; risk factor, racial discrimination; and compensatory factor, cultural resilience. Control variables included individual (education, sociability) and family (marital status, socioeconomic status) resilience resources and demographics (age and gender). The model was tested using sequential regression. Results: The risk factor, racial discrimination, increased stress across steps of the sequential model, while cultural resilience had an opposite modest effect on stress levels. In the final model with all variables, age and gender were significant, with the former having a negative effect on stress and women reporting higher levels of stress than males. Education, marital status, and socioeconomic status (household income) were not significant in the model. The model had R2 = 0.21 and adjusted R2 = 0.18 and semipartial correlation (squared) of 0.04 and 0.01 for racial discrimination and cultural resilience, respectively. Conclusions: In this study, cultural resilience compensated for the detrimental effect of racial discrimination on stress in a modest manner. These findings may support the development of programs and services fostering First Nations culture, pending further study. PMID:27254805

  18. Group-specific amplification of cDNA from DRB1 genes. Complete coding sequences of partially defined alleles and identification of the new alleles DRB1*040602, DRB1*111102, DRB1*080103, and DRB1*0113.

    PubMed

    Balas, Antonio; Vilches, Carlos; Rodríguez, Miguel A; Fernández, Begoña; Martinez, Maria Paz; de Pablo, Rosario; García-Sánchez, Félix; Vicario, Jose L

    2006-12-01

    We present here the complete coding sequences, previously unavailable, of the DRB1 alleles DRB1*030102, *0306, *040701, *0408, *1327, *1356, *1411, *1446, *1503, *1504, *0806, *0813, and *0818. For cDNA isolation, new group-specific primers located at the 5'UT and 3'UT regions were used to carry out allele-specific amplification and a convenient method for determining full-length sequences for DRB1 alleles. Complete coding sequencing of samples previously typed as DRB1*0406, DRB1*080101, and DRB1*1111 revealed new alleles with noncoding nucleotide changes at exons 1 and 3. In addition, we found a novel allele, DRB1*0113, whose second exon carries a sequence motif characteristic of DRB1*07 alleles. The predicted class II haplotypic associations of all alleles are reported and discussed.

  19. Optical methods and differential scanning calorimetry as a potential tool for discrimination of olive oils (extra virgin and mix with vegetable oils)

    NASA Astrophysics Data System (ADS)

    Nikolova, Kr.; Yovcheva, T.; Marudova, M.; Eftimov, T.; Bodurov, I.; Viraneva, A.; Vlaeva, I.

    2016-03-01

    Eleven samples from olive oil have been investigated using four physical methods - refractive index measurement, fluorescence spectra, color parameters and differential scanning colorimetry. In pomace olive oil (POO) and extra virgin olive oil (EVOO) the oleic acid (65.24 %-78.40 %) predominates over palmitic (10.47 %-15.07 %) and linoleic (5.26 %-13.92 %) acids. The fluorescence spectra contain three peaks related to oxidation products at about λ = (500-540) nm, chlorophyll content at about λ = (675-680) nm and non determined pigments at λ = (700-750) nm. The melting point for EVOO and POO is between -1 °C and -6 °C. In contrast, the salad olive oils melt between -24 °C and -30 °C. The refractive index for EVOO is lower than that for mixed olive oils. The proposed physical methods could be used for fast and simple detection of vegetable oils in EVOO without use of chemical substances. The experimental results are in accordance with those obtained by chemical analysis.

  20. Initial frequency of alleles conferring resistance to Bacillus thuringiensis poplar in a field population of Chrysomela tremulae.

    PubMed Central

    Génissel, Anne; Augustin, Sylvie; Courtin, Claudine; Pilate, Gilles; Lorme, Philippe; Bourguet, Denis

    2003-01-01

    Globally, the estimated total area planted with transgenic plants producing Bacillus thuringiensis (Bt) toxins was 12 million hectares in 2001. The risk of target pests becoming resistant to these toxins has led to the implementation of resistance-management strategies. The efficiency and sustainability of these strategies, including the high-dose plus refuge strategy currently recommended for North American maize, depend on the initial frequency of resistance alleles. In this study, we estimated the initial frequencies of alleles conferring resistance to transgenic Bt poplars producing Cry3A in a natural population of the poplar pest Chrysomela tremulae (Coleoptera: Chrysomelidae). We used the F(2) screen method developed for detecting resistance alleles in natural pest populations. At least three parents of the 270 lines tested were heterozygous for a major Bt resistance allele. We estimated mean resistance-allele frequency for the period 1999-2001 at 0.0037 (95% confidence interval = 0.00045-0.0080) with a detection probability of 90%. These results demonstrate that (i) the F(2) screen method can be used to detect major alleles conferring resistance to Bt-producing plants in insects and (ii) the initial frequency of alleles conferring resistance to Bt toxin can be close to the highest theoretical values that are expected prior to the use of Bt plants if considering fitness costs and typical mutation rates. PMID:12737656

  1. Weight discrimination and bullying.

    PubMed

    Puhl, Rebecca M; King, Kelly M

    2013-04-01

    Despite significant attention to the medical impacts of obesity, often ignored are the negative outcomes that obese children and adults experience as a result of stigma, bias, and discrimination. Obese individuals are frequently stigmatized because of their weight in many domains of daily life. Research spanning several decades has documented consistent weight bias and stigmatization in employment, health care, schools, the media, and interpersonal relationships. For overweight and obese youth, weight stigmatization translates into pervasive victimization, teasing, and bullying. Multiple adverse outcomes are associated with exposure to weight stigmatization, including depression, anxiety, low self-esteem, body dissatisfaction, suicidal ideation, poor academic performance, lower physical activity, maladaptive eating behaviors, and avoidance of health care. This review summarizes the nature and extent of weight stigmatization against overweight and obese individuals, as well as the resulting consequences that these experiences create for social, psychological, and physical health for children and adults who are targeted.

  2. The ever-expanding list of HLA alleles: changing HLA nomenclature and its relevance to clinical transplantation.

    PubMed

    Tait, Brian D

    2011-01-01

    Since the discovery of the HLA system 51 years ago, both the techniques for the detection of HLA antigens and the method of nomenclature for cataloguing them have changed dramatically. Initially serology was the sole technological tool available to describe the polymorphism of the class 1 and later the class 2 loci. Numbers were assigned to antigens as they were described and as serologic techniques that improved "subtypes" of the original antigens were described. With sequencing of HLA alleles, further polymorphisms were described, and it became evident that the degree of polymorphism was much greater than had hitherto been realized. Sequence differences were detected between alleles, which did not appear to provoke antibody responses but were clearly recognized by responding T cells. A new method of nomenclature was devised, which assigned 2 sets of numbers to each allele. The first 2 numbers indicated the serologic group to which the allele belonged, whereas the second set of 2 numbers was assigned in a numerical progression as each new allele was described. In addition, letters were introduced at the end of each allele where they were known to be nonexpressed or have low levels of cell expression. The limitation of this system is that it only caters for 99 alleles in each serologic group, and this has now been exceeded in some cases. The World Health Organization Nomenclature Committee for factors of the HLA system introduced a modification of the current nomenclature in April 2010 which uses colons to separate the numbers that has the effect of delimiting the number of alleles, which can be assigned to each serologic group. Due to the extensive polymorphism of the HLA genes, sequencing frequently results in ambiguous combinations of alleles and also "strings" of possible alleles due to polymorphisms in nonsequenced gene locations. The reporting in such instances has been simplified to some extent by the introduction of a lettering system to indicate a

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

    PubMed

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

    2009-03-01

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

  4. A DNA Barcoding Method to Discriminate between the Model Plant Brachypodium distachyon and Its Close Relatives B. stacei and B. hybridum (Poaceae)

    PubMed Central

    López-Alvarez, Diana; López-Herranz, Maria Luisa; Betekhtin, Alexander; Catalán, Pilar

    2012-01-01

    Background Brachypodium distachyon s. l. has been widely investigated across the world as a model plant for temperate cereals and biofuel grasses. However, this annual plant shows three cytotypes that have been recently recognized as three independent species, the diploids B. distachyon (2n = 10) and B. stacei (2n = 20) and their derived allotetraploid B. hybridum (2n = 30). Methodology/Principal Findings We propose a DNA barcoding approach that consists of a rapid, accurate and automatable species identification method using the standard DNA sequences of complementary plastid (trnLF) and nuclear (ITS, GI) loci. The highly homogenous but largely divergent B. distachyon and B. stacei diploids could be easily distinguished (100% identification success) using direct trnLF (2.4%), ITS (5.5%) or GI (3.8%) sequence divergence. By contrast, B. hybridum could only be unambiguously identified through the use of combined trnLF+ITS sequences (90% of identification success) or by cloned GI sequences (96.7%) that showed 5.4% (ITS) and 4% (GI) rate divergence between the two parental sequences found in the allopolyploid. Conclusion/Significance Our data provide an unbiased and effective barcode to differentiate these three closely-related species from one another. This procedure overcomes the taxonomic uncertainty generated from methods based on morphology or flow cytometry identifications that have resulted in some misclassifications of the model plant and its allies. Our study also demonstrates that the allotetraploid B. hybridum has resulted from bi-directional crosses of B. distachyon and B. stacei plants acting either as maternal or paternal parents. PMID:23240000

  5. Evaluation of the standard normal variate method for Laser-Induced Breakdown Spectroscopy data treatment applied to the discrimination of painting layers

    NASA Astrophysics Data System (ADS)

    Syvilay, D.; Wilkie-Chancellier, N.; Trichereau, B.; Texier, A.; Martinez, L.; Serfaty, S.; Detalle, V.

    2015-12-01

    Nowadays, Laser-Induced Breakdown Spectroscopy (LIBS) is frequently used for in situ analyses to identify pigments from mural paintings. Nonetheless, in situ analyses require a robust instrumentation in order to face to hard experimental conditions. This may imply variation of fluencies and thus inducing variation of LIBS signal, which degrades spectra and then results. Usually, to overcome these experimental errors, LIBS signal is processed. Signal processing methods most commonly used are the baseline subtraction and the normalization by using a spectral line. However, the latter suggests that this chosen element is a constant component of the material, which may not be the case in paint layers organized in stratigraphic layers. For this reason, it is sometimes difficult to apply this normalization. In this study, another normalization will be carried out to throw off these signal variations. Standard normal variate (SNV) is a normalization designed for these conditions. It is sometimes implemented in Diffuse Reflectance Infrared Fourier Transform Spectroscopy and in Raman Spectroscopy but rarely in LIBS. The SNV transformation is not newly applied on LIBS data, but for the first time the effect of SNV on LIBS spectra was evaluated in details (energy of laser, shot by shot, quantification). The aim of this paper is the quick visualization of the different layers of a stratigraphic painting sample by simple data representations (3D or 2D) after SNV normalization. In this investigation, we showed the potential power of SNV transformation to overcome undesired LIBS signal variations but also its limit of application. This method appears as a promising way to normalize LIBS data, which may be interesting for in-situ depth analyses.

  6. Perceived weight discrimination and obesity.

    PubMed

    Sutin, Angelina R; Terracciano, Antonio

    2013-01-01

    Weight discrimination is prevalent in American society. Although associated consistently with psychological and economic outcomes, less is known about whether weight discrimination is associated with longitudinal changes in obesity. The objectives of this research are (1) to test whether weight discrimination is associated with risk of becoming obese (Body Mass Index≥30; BMI) by follow-up among those not obese at baseline, and (2) to test whether weight discrimination is associated with risk of remaining obese at follow-up among those already obese at baseline. Participants were drawn from the Health and Retirement Study, a nationally representative longitudinal survey of community-dwelling US residents. A total of 6,157 participants (58.6% female) completed the discrimination measure and had weight and height available from the 2006 and 2010 assessments. Participants who experienced weight discrimination were approximately 2.5 times more likely to become obese by follow-up (OR = 2.54, 95% CI = 1.58-4.08) and participants who were obese at baseline were three times more likely to remain obese at follow up (OR = 3.20, 95% CI = 2.06-4.97) than those who had not experienced such discrimination. These effects held when controlling for demographic factors (age, sex, ethnicity, education) and when baseline BMI was included as a covariate. These effects were also specific to weight discrimination; other forms of discrimination (e.g., sex, race) were unrelated to risk of obesity at follow-up. The present research demonstrates that, in addition to poorer mental health outcomes, weight discrimination has implications for obesity. Rather than motivating individuals to lose weight, weight discrimination increases risk for obesity.

  7. CYP2D6 allele distribution in Macedonians, Albanians and Romanies in the Republic of Macedonia

    PubMed Central

    Kuzmanovska, M; Dimishkovska, M; Maleva Kostovska, I; Noveski, P; Sukarova Stefanovska, E

    2015-01-01

    Abstract Cytochrome P450 2D6 (CYP2D6) is an enzyme of great importance for the metabolism of clinically used drugs. More than 100 variants of the CYP2D6 gene have been identified so far. The aim of this study was to investigate the allele distribution of CYP2D6 gene variants in 100 individuals of each of the Macedonian, Albanian and Romany population, by genotyping using long range polymerase chain reaction (PCR) and a multiplex single base extension method. The most frequent variants and almost equally distributed in the three groups were the fully functional alleles *1 and *2. The most common non functional allele in all groups was *4 that was found in 22.5% of the Albanians. The most common allele with decreased activity was *41 which was found in 23.0% of the Romany ethnic group, in 11.0% of the Macedonians and in 10.5% of the Albanians. Seven percent of the Albanians, 6.0% of the Romani and 4.0% of the Macedonians were poor metabolizers, while 5.0% of the Macedonians, 1.0% of Albanians and 1.0% of the Romanies were ultrarapid metabolizers. We concluded that the CYP2D6 gene locus is highly heterogeneous in these groups and that the prevalence of the CYP2D6 allele variants and genotypes in the Republic of Macedonia is in accordance with that of other European populations. PMID:27785397

  8. CYP2D6 allele distribution in Macedonians, Albanians and Romanies in the Republic of Macedonia.

    PubMed

    Kuzmanovska, M; Dimishkovska, M; Maleva Kostovska, I; Noveski, P; Sukarova Stefanovska, E; Plaseska-Karanfilska, D

    2015-12-01

    Cytochrome P450 2D6 (CYP2D6) is an enzyme of great importance for the metabolism of clinically used drugs. More than 100 variants of the CYP2D6 gene have been identified so far. The aim of this study was to investigate the allele distribution of CYP2D6 gene variants in 100 individuals of each of the Macedonian, Albanian and Romany population, by genotyping using long range polymerase chain reaction (PCR) and a multiplex single base extension method. The most frequent variants and almost equally distributed in the three groups were the fully functional alleles *1 and *2. The most common non functional allele in all groups was *4 that was found in 22.5% of the Albanians. The most common allele with decreased activity was *41 which was found in 23.0% of the Romany ethnic group, in 11.0% of the Macedonians and in 10.5% of the Albanians. Seven percent of the Albanians, 6.0% of the Romani and 4.0% of the Macedonians were poor metabolizers, while 5.0% of the Macedonians, 1.0% of Albanians and 1.0% of the Romanies were ultrarapid metabolizers. We concluded that the CYP2D6 gene locus is highly heterogeneous in these groups and that the prevalence of the CYP2D6 allele variants and genotypes in the Republic of Macedonia is in accordance with that of other European populations.

  9. Detection of nucleotide-specific CRISPR/Cas9 modified alleles using multiplex ligation detection

    PubMed Central

    KC, R.; Srivastava, A.; Wilkowski, J. M.; Richter, C. E.; Shavit, J. A.; Burke, D. T.; Bielas, S. L.

    2016-01-01

    CRISPR/Cas9 genome-editing has emerged as a powerful tool to create mutant alleles in model organisms. However, the precision with which these mutations are created has introduced a new set of complications for genotyping and colony management. Traditional gene-targeting approaches in many experimental organisms incorporated exogenous DNA and/or allele specific sequence that allow for genotyping strategies based on binary readout of PCR product amplification and size selection. In contrast, alleles created by non-homologous end-joining (NHEJ) repair of double-stranded DNA breaks generated by Cas9 are much less amenable to such strategies. Here we describe a novel genotyping strategy that is cost effective, sequence specific and allows for accurate and efficient multiplexing of small insertion-deletions and single-nucleotide variants characteristic of CRISPR/Cas9 edited alleles. We show that ligation detection reaction (LDR) can be used to generate products that are sequence specific and uniquely detected by product size and/or fluorescent tags. The method works independently of the model organism and will be useful for colony management as mutant alleles differing by a few nucleotides become more prevalent in experimental animal colonies. PMID:27557703

  10. A pseudodeficiency allele (D152N) of the human beta-glucuronidase gene.

    PubMed

    Vervoort, R; Islam, M R; Sly, W; Chabas, A; Wevers, R; de Jong, J; Liebaers, I; Lissens, W

    1995-10-01

    We present evidence that a 480G-->A transition in the coding region of the beta-glucuronidase gene, which results in an aspartic-acid-to-asparagine substitution at amino acid position 152 (D152N), produces a pseudodeficiency allele (GUSBp) that leads to greatly reduced levels of beta-glucuronidase activity without apparent deleterious consequences. The 480G-->A mutation was found initially in the pseudodeficient mother of a child with mucopolysaccharidosis VII (MPSVII), but it was not on her disease-causing allele, which carried the L176F mutation. The 480G-->A change was also present in an unrelated individual with another MPSVII allele who had unusually low beta-glucuronidase activity, but whose clinical symptoms were probably unrelated to beta-glucuronidase deficiency. This individual also had an R357X mutation, probably on his second allele. We screened 100 unrelated normal individuals for the 480G-->A mutation with a PCR method and detected one carrier. Reduced beta-glucuronidase activity following transfection of COS cells with the D152N cDNA supported the causal relationship between the D152N allele and pseudodeficiency. The mutation reduced the fraction of expressed enzyme that was secreted. Pulse-chase experiments indicated that the reduced activity in COS cells was due to accelerated intracellular turnover of the D152N enzyme. They also suggested that a potential glycosylation site created by the mutation is utilized in approximately 50% of the enzyme expressed.

  11. Rapid, efficient and precise allele replacement in the fission yeast Schizosaccharomyces pombe

    PubMed Central

    Gao, Jun; Kan, Fengling; Wagnon, Jacy L.; Storey, Aaron J.; Protacio, Reine M.; Davidson, Mari K.; Wahls, Wayne P.

    2013-01-01

    Gene targeting provides a powerful tool to modify endogenous loci to contain specific mutations, insertions and deletions. Precise allele replacement, with no other chromosomal changes (e.g., insertion of selectable markers or heterologous promoters), maintains physiologically relevant context. Established methods for precise allele replacement in fission yeast employ two successive rounds of transformation and homologous recombination and require genotyping at each step. The relative efficiency of homologous recombination is low and a high rate of false positives during the second round of gene targeting further complicates matters. We report that pop-in, pop-out allele replacement circumvents these problems. We present data for 39 different allele replacements, involving simple and complex modifications at seven different target loci, that illustrate the power and utility of the approach. We also developed and validated a rapid, efficient process for precise allele replacement that requires only one round each of transformation and genotyping. We show that this process can be applied in population scale to an individual target locus, without genotyping, to identify clones with an altered phenotype (targeted forward genetics). It is therefore suitable for saturating, in situ, locus-specific mutation screens (e.g., of essential or non-essential genes and regulatory DNA elements) within normal chromosomal context. PMID:24026504

  12. Study of MICA alleles in 201 African Americans by multiplexed single nucleotide extension (MSNE) typing.

    PubMed

    Zhang, Yanzheng; Han, Mei; Vorhaben, Robert; Giang, Chris; Lavingia, Bhavna; Stastny, Peter

    2003-01-01

    We have developed a method for major histocompatibility complex class I chain-related gene A (MICA) genotyping using multiplexed single nucleotide extension (MSNE) and flow cytometric analysis of an array of fluorescent microspheres. This technique employs a polymerase chain reaction-derived target DNA containing all the polymorphic sites of MICA, synthetic complementary primers, biotinylated dideoxynucleotide triphosphate, fluorescent reporter molecules (streptavidin-phycoerythrin), and thermophilic DNA polymerase. Genomic DNA was amplified by MICA locus-specific primers and the MSNE reactions were carried out in the presence of 30 MSNE primers used to assay polymorphisms in exons 2, 3, and 4 of the MICA genes. Thirty-two previously typed cell lines were used as reference material. The MICA gene frequencies among 201 African-American unrelated donors were determined. Of 51 previously known alleles, 18 were observed in African-Americans, compared to 16 that were found in North American Caucasians and 9 in South American Indians, suggesting a more diversified allelic distribution in African-Americans. MICA*00201 and MICA*00801 were the two most frequent alleles in African-Americans. We observed a high degree of linkage disequilibrium between certain alleles of MICA and of human leukocyte antigen-B in the African-American population. The methodology described here offers a powerful new approach to DNA typing of the MICA alleles.

  13. Allele-specific copy number profiling by next-generation DNA sequencing.

    PubMed

    Chen, Hao; Bell, John M; Zavala, Nicolas A; Ji, Hanlee P; Zhang, Nancy R

    2015-02-27

    The progression and clonal development of tumors often involve amplifications and deletions of genomic DNA. Estimation of allele-specific copy number, which quantifies the number of copies of each allele at each variant loci rather than the total number of chromosome copies, is an important step in the characterization of tumor genomes and the inference of their clonal history. We describe a new method, falcon, for finding somatic allele-specific copy number changes by next generation sequencing of tumors with matched normals. falcon is based on a change-point model on a bivariate mixed Binomial process, which explicitly models the copy numbers of the two chromosome haplotypes and corrects for local allele-specific coverage biases. By using the Binomial distribution rather than a normal approximation, falcon more effectively pools evidence from sites with low coverage. A modified Bayesian information criterion is used to guide model selection for determining the number of copy number events. Falcon is evaluated on in silico spike-in data and applied to the analysis of a pre-malignant colon tumor sample and late-stage colorectal adenocarcinoma from the same individual. The allele-specific copy number estimates obtained by falcon allows us to draw detailed conclusions regarding the clonal history of the individual's colon cancer.

  14. Genetically Determined Amerindian Ancestry Correlates with Increased Frequency of Risk Alleles for Systemic Lupus Erythematosus

    PubMed Central

    Sanchez, E; Webb, R; Rasmussen, A.; Kelly, J.A; Riba, L.; Kaufman, K.M.; Garcia-de la Torre, I.; Moctezuma, J.F.; Maradiaga-Ceceña, M.A.; Cardiel, M.; Acevedo, E.; Cucho-Venegas, M.; Garcia, M.A.; Gamron, S.; Pons-Estel, B.A.; Vasconcelos, C.; Martin, J.; Tusié-Luna, T.; Harley, J.B.; Richardson, B.; Sawalha, A.H.; Alarcón-Riquelme, M.E.

    2011-01-01

    Objectives To analyze if genetically determined Amerindian ancestry predicts the increased presence of risk alleles of known susceptibility genes for systemic lupus erythematosus. Methods Single nucleotide polymorphisms within 16 confirmed genetic susceptibility loci for SLE were genotyped in a set of 804 Mestizo lupus patients and 667 Mestizo normal healthy controls. In addition, 347 admixture informative markers were genotyped. Individual ancestry proportions were determined using STRUCTURE. Association analysis was performed using PLINK, and correlation of the presence of risk alleles with ancestry was done using linear regression. Results A meta-analysis of the genetic association of the 16 SNPs across populations showed that TNFSF4, STAT4, PDCD1, ITGAM, and IRF5 were associated with lupus in a Hispanic-Mestizo cohort enriched for European and Amerindian ancestry. In addition, two SNPs within the MHC region, previously associated in a genome-wide association study in Europeans, were also associated in Mestizos. Using linear regression we predict an average increase of 2.34 risk alleles when comparing a lupus patient with 100% Amerindian ancestry to an SLE patient with 0% American Indian Ancestry (p<0.0001). SLE patients with 43% more Amerindian ancestry are predicted to carry one additional risk allele. Conclusion Amerindian ancestry increased the number of risk alleles for lupus. PMID:20848568

  15. Allelic diversity associated with aridity gradient in wild emmer wheat populations.

    PubMed

    Peleg, Zvi; Saranga, Yehoshua; Krugman, Tamar; Abbo, Shahal; Nevo, Eviatar; Fahima, Tzion

    2008-01-01

    The association between allelic diversity and ecogeographical variables was studied in natural populations of wild emmer wheat [Triticum turgidum ssp. dicoccoides (Körn.) Thell.], the tetraploid progenitor of cultivated wheat. Patterns of allelic diversity in 54 microsatellite loci were analyzed in a collection of 145 wild emmer wheat accessions representing 25 populations that were sampled across naturally occurring aridity gradient in Israel and surrounding regions. The obtained results revealed that 56% of the genetic variation resided among accessions within populations, while only 44% of the variation resided between populations. An unweighted pair-group method analysis (UPGMA) tree constructed based on the microsatellite allelic diversity divided the 25 populations into six major groups. Several groups were comprised of populations that were collected in ecologically similar but geographically remote habitats. Furthermore, genetic differentiation between populations was independent of the geographical distances. An interesting evolutionary phenomenon is highlighted by the unimodal relationship between allelic diversity and annual rainfall (r = 0.74, P < 0.0002), indicating higher allelic diversity in populations originated from habitats with intermediate environmental stress (i.e. rainfall 350-550 mm year(-1)). These results show for the first time that the 'intermediate-disturbance hypothesis', explaining biological diversity at the ecosystem level, also dominates the genetic diversity within a single species, the lowest hierarchical element of the biological diversity.

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

    PubMed

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

    1998-07-01

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

  17. 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.

  18. Estimating Allele Age and Selection Coefficient from Time-Serial Data

    PubMed Central

    Malaspinas, Anna-Sapfo; Malaspinas, Orestis; Evans, Steven N.; Slatkin, Montgomery

    2012-01-01

    Recent advances in sequencing technologies have made available an ever-increasing amount of ancient genomic data. In particular, it is now possible to target specific single nucleotide polymorphisms in several samples at different time points. Such time-series data are also available in the context of experimental or viral evolution. Time-series data should allow for a more precise inference of population genetic parameters and to test hypotheses about the recent action of natural selection. In this manuscript, we develop a likelihood method to jointly estimate the selection coefficient and the age of an allele from time-serial data. Our method can be used for allele frequencies sampled from a single diallelic locus. The transition probabilities are calculated by approximating the standard diffusion equation of the Wright–Fisher model with a one-step process. We show that our method produces unbiased estimates. The accuracy of the method is tested via simulations. Finally, the utility of the method is illustrated with an application to several loci encoding coat color in horses, a pattern that has previously been linked with domestication. Importantly, given our ability to estimate the age of the allele, it is possible to gain traction on the important problem of distinguishing selection on new mutations from selection on standing variation. In this coat color example for instance, we estimate the age of this allele, which is found to predate domestication. PMID:22851647

  19. Direct micro-haplotyping by multiple double PCR amplifications of specific alleles (MD-PASA)

    PubMed Central

    Eitan, Yuval; Kashi, Yechezkel

    2002-01-01

    Analysis of haplotypes is an important tool in population genetics, familial heredity and gene mapping. Determination of haplotypes of multiple single nucleotide polymorphisms (SNPs) or other simple mutations is time consuming and expensive when analyzing large populations, and often requires the help of computational and statistical procedures. Based on double PCR amplification of specific alleles, described previously, we have developed a simple, rapid and low-cost method for direct haplotyping of multiple SNPs and simple mutations found within relatively short specific regions or genes (micro-haplotypes). Using this method, it is possible to directly determine the physical linkage of multiple heterozygous alleles, by conducting a series of double allele-specific PCR amplification sets with simple analysis by gel electrophoresis. Application of the method requires prior information as to the sequence of the segment to be haplotyped, including the polymorphic sites. We applied the method to haplotyping of nine sites in the chicken HSP108 gene. One of the haplotypes in the population apparently arose by recombination between two existing haplotypes, and we were able to locate the point of recombination within a segment of 19 bp. We anticipate rapidly growing needs for SNP haplotyping in human (medical and pharmacogenetics), animal and plant genetics; in this context, the multiple double PCR amplifications of specific alleles (MD-PASA) method offers a useful haplotyping tool. PMID:12060700

  20. Estimating allele age and selection coefficient from time-serial data.

    PubMed

    Malaspinas, Anna-Sapfo; Malaspinas, Orestis; Evans, Steven N; Slatkin, Montgomery

    2012-10-01

    Recent advances in sequencing technologies have made available an ever-increasing amount of ancient genomic data. In particular, it is now possible to target specific single nucleotide polymorphisms in several samples at different time points. Such time-series data are also available in the context of experimental or viral evolution. Time-series data should allow for a more precise inference of population genetic parameters and to test hypotheses about the recent action of natural selection. In this manuscript, we develop a likelihood method to jointly estimate the selection coefficient and the age of an allele from time-serial data. Our method can be used for allele frequencies sampled from a single diallelic locus. The transition probabilities are calculated by approximating the standard diffusion equation of the Wright-Fisher model with a one-step process. We show that our method produces unbiased estimates. The accuracy of the method is tested via simulations. Finally, the utility of the method is illustrated with an application to several loci encoding coat color in horses, a pattern that has previously been linked with domestication. Importantly, given our ability to estimate the age of the allele, it is possible to gain traction on the important problem of distinguishing selection on new mutations from selection on standing variation. In this coat color example for instance, we estimate the age of this allele, which is found to predate domestication.

  1. 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.

  2. PCR method for the rapid detection and discrimination of Legionella spp. based on the amplification of pcs, pmtA, and 16S rRNA genes.

    PubMed

    Janczarek, Monika; Palusińska-Szysz, Marta

    2016-05-01

    Legionella bacteria are organisms of public health interest due to their ability to cause pneumonia (Legionnaires' disease) in susceptible humans and their ubiquitous presence in water supply systems. Rapid diagnosis of Legionnaires' disease allows the use of therapy specific for the disease. L. pneumophila serogroup 1 is the most common cause of infection acquired in community and hospital environments. The non-L. pneumophila infections are likely under-detected because of a lack of effective diagnosis. In this work, simplex and duplex PCR assays with the use of new molecular markers pcs and pmtA involved in phosphatidylcholine synthesis were specified for rapid and cost-efficient identification and distinguishing Legionella species. The sets of primers developed were found to be sensitive and specific for reliable detection of Legionella belonging to the eight most clinically relevant species. Among these, four primer sets I, II, VI, and VII used for duplex-PCRs proved to have the highest identification power and reliability in the detection of the bacteria. Application of this PCR-based method should improve detection of Legionella spp. in both clinical and environmental settings and facilitate molecular typing of these organisms.

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

    PubMed Central

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

    2015-01-01

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

  4. A novel chiral stationary phase HPLC-MS/MS method to discriminate between enzymatic oxidation and auto-oxidation of phosphatidylcholine.

    PubMed

    Ito, Junya; Nakagawa, Kiyotaka; Kato, Shunji; Hirokawa, Takafumi; Kuwahara, Shigefumi; Nagai, Toshiharu; Miyazawa, Teruo

    2016-11-01

    To elucidate the role of enzymatic lipid peroxidation in disease pathogenesis and in food deterioration, we recently achieved stereoselective analysis of phosphatidylcholine hydroperoxide (PCOOH) possessing 13S-hydroperoxy-9Z,11E-octadecadienoic acid (13(S)-9Z,11E-HPODE) using HPLC-MS/MS with a CHIRALPAK OP (+) column. Because enzymatic oxidation progresses concurrently with auto-oxidation, we need to distinguish them further. Here, we attempted such an analysis. First, we used lipoxygenase, linoleic acid, and lysophosphatidylcholine (LPC) to synthesize the enzymatic oxidation product 13(S)-9Z,11E-HPODE PC, and the auto-oxidation products 13(RS)-9Z,11E-HPODE PC and 13(RS)-9E,11E-HPODE PC, which were used as standards to test the ability of various columns to separate the enzymatic oxidation product from auto-oxidation products. Separation was achieved by connecting in series two columns with different properties: CHIRALPAK OP (+) and CHIRALPAK IB-3. The CHIRALPAK OP (+) column separated 13(R)-9Z,11E-HPODE PC and 13(S)-9Z,11E-HPODE PC, whereas CHIRALPAK IB-3 enabled separation of 13(S)-9Z,11E-HPODE PC and 13(RS)-9E,11E-HPODE PC. The results for the analysis of both enzymatically oxidized and auto-oxidized lecithin (an important phospholipid mixture in vivo and in food) indicate that our method would be useful for distinguishing enzymatic oxidation and auto-oxidation reactions. Such information will be invaluable for elucidating the involvement of PCOOH in disease pathogenesis and in food deterioration.

  5. Vibrotactile Discrimination of Musical Timbre

    ERIC Educational Resources Information Center

    Russo, Frank A.; Ammirante, Paolo; Fels, Deborah I.

    2012-01-01

    Five experiments investigated the ability to discriminate between musical timbres based on vibrotactile stimulation alone. Participants made same/different judgments on pairs of complex waveforms presented sequentially to the back through voice coils embedded in a conforming chair. Discrimination between cello, piano, and trombone tones matched…

  6. THE HIGH COST OF DISCRIMINATION.

    ERIC Educational Resources Information Center

    ROPER, ELMO

    ON THE BASIS OF EMPLOYEE SURVEYS AND IN-PLANT RESEARCH, THE TOTAL COST OF DISCRIMINATION TO AMERICAN BUSINESS AND INDUSTRY IN ACTUAL DOLLARS IS ESTIMATED AT ROUGHLY $30 BILLION ANNUALLY. DISCRIMINATION IN INDUSTRY BEGINS AT THE HIRING GATE WHERE MINORITY GROUPS ARE REFUSED EMPLOYMENT BECAUSE OF RACE, COLOR, RELIGION, NATIONALITY, POLITICAL…

  7. Memory Retrieval as Temporal Discrimination

    ERIC Educational Resources Information Center

    Brown, Gordon D. A.; Vousden, Janet I.; McCormack, Teresa

    2009-01-01

    Temporal distinctiveness models of memory retrieval claim that memories are organised partly in terms of their positions along a temporal dimension, and suggest that memory retrieval involves temporal discrimination. According to such models the retrievability of memories should be related to the discriminability of their temporal distances at the…

  8. Addressing Discrimination in School Matters!

    ERIC Educational Resources Information Center

    Sullivan, Amanda L.

    2009-01-01

    Every student has the right to an education free from discrimination that provides high-quality, equitable opportunities to learn. Unfortunately, sometimes individuals or systems may act in ways that violate this right. Discrimination occurs when people are treated unequally or less favorably than others because of some real or perceived…

  9. Discrimination against Muslim American Adolescents

    ERIC Educational Resources Information Center

    Aroian, Karen J.

    2012-01-01

    Although there is ample evidence of discrimination toward Muslim Americans in general, there is limited information specific to Muslim American adolescents. The few existing studies specific to this age group suggest that Muslim American adolescents encounter much discrimination from teachers, school administrators, and classmates. This…

  10. Invidious Discrimination: Second Generation Issues

    ERIC Educational Resources Information Center

    Simpson, Robert J.; Dee, Paul

    1976-01-01

    Discusses school law issues dealing with various forms of invidious discrimination. Considers discrimination based on forms of involuntary association (ethnicity, economic status, primary language, and maturity) and forms of voluntary association (sexual proclivity, marital status, pregnancy and parenthood, self-expression and appearance, religion…

  11. Gender Discrimination in Jessica's Career.

    ERIC Educational Resources Information Center

    Cook, Ellen Piel

    1997-01-01

    Focuses on the sexual harassment and other gender-related difficulties faced by a Chinese-American woman. Profiles her encounters with gender discrimination and how it hindered career advancement and led to professional isolation. Relates how this case study can be used to sensitize workers to gender discrimination. (RJM)

  12. Disability Discrimination in Higher Education.

    ERIC Educational Resources Information Center

    Weber, Mark C.

    2002-01-01

    Reviews developments in 2000 in the law of disability discrimination as it relates to higher education, which falls into five categories: (1) definition of a qualified individual; (2) accommodations, access, undue burden, and fundamental alteration of programs; (3) intentional discrimination, harassment, and retaliation; (4) Eleventh Amendment…

  13. Employment Discrimination in Higher Education.

    ERIC Educational Resources Information Center

    Hustoles, Thomas P.; Griffin, Oren R.

    2000-01-01

    Reviews court decisions related to employment discrimination in higher education. The most significant development was a series of cases affirming that Eleventh Amendment immunity from private money damage claims brought pursuant to various federal employment discrimination statutes applied to state colleges and universities. (SLD)

  14. Perceptions of Discrimination during Downsizing.

    ERIC Educational Resources Information Center

    Larkey, Linda Kathryn

    1993-01-01

    Demonstrates that perceptions of ethnic discrimination during layoffs are moderately correlated with perceptions of selection fairness and information access during the layoff process. Shows that, in the company studied, both minority and majority ethnic group members felt equally discriminated against. (SR)

  15. Price Discrimination in Academic Journals.

    ERIC Educational Resources Information Center

    Joyce, Patrick; Merz, Thomas E.

    1985-01-01

    Analysis of price discrimination (charging different prices to different customers for same product) for 89 academic journals in 6 disciplines reveals: incidence of price discrimination rose between 1974 and 1984, increase in mean institutional (library) subscription price exceeded increase in mean individual subscription price. Journal list…

  16. Allelic drop-out and preferential amplification in single cells and human blastomeres: implications for preimplantation diagnosis of sex and cystic fibrosis.

    PubMed

    Findlay, I; Ray, P; Quirke, P; Rutherford, A; Lilford, R

    1995-06-01

    Previously the diagnosis of sex and cystic fibrosis status has been studied on single cells using the polymerase chain reaction (PCR). It has been suggested that allelic drop-out (PCR failure of one allele) and/or preferential amplification (hypo-amplification of one allele) may contribute to poor reliability and misdiagnosis, although this remains controversial as some reports suggest that allelic drop-out does not occur. We investigated an improved method of diagnosing sex and cystic fibrosis in single cells using a new technology (fluorescent PCR) to determine the base level of PCR artefacts (allelic drop-out and preferential amplification) which, in combination with improved sensitivity, should improve PCR reliability and accuracy. Fluorescent PCR gives high reliability (approximately 97%) and accuracy rates (approximately 97%) in somatic cells for both sex and cystic fibrosis diagnosis and its lower detection threshold allows allelic drop-out and preferential amplification to be easily distinguished. We also achieved high reliability and accuracy in diagnosing cystic fibrosis in human blastomeres. This study confirms earlier reports of both allelic drop-out and preferential amplification in single cell analysis. We demonstrate that both allelic drop-out and preferential amplification occur in somatic cells and suggest these are separate phenomena. Preferential amplification appeared common in single cell PCR while allelic drop-out apparently occurred at random in each allele. Preferential amplification was mainly amplification of the larger allele. We suggest that some inaccuracy/misdiagnosis may be due to both preferential amplification as well as allelic drop-out. Other findings were variability in drop-out between PCR and that amplification of signals from human blastomeres may be linked to embryo quality. We suggest that allelic drop-out is dependent on the number of cells within the sample.

  17. Discriminant Multitaper Component Analysis of EEG

    NASA Astrophysics Data System (ADS)

    Dyrholm, Mads; Sajda, Paul

    2011-06-01

    This work extends Bilinear Discriminant Component Analysis to the case of oscillatory activity with allowed phase-variability across trials. The proposed method learns a spatial profile together with a multitaper basis which can integrate oscillatory power in a band-limited fashion. We demonstrate the method for predicting the handedness of a subject's button press given multivariate EEG data. We show that our method learns multitapers sensitive to oscillatory activity in the 8-12 Hz range with spatial filters selective for lateralized motor cortex. This finding is consistent with the well-known mu-rhythm, whose power is known to modulate as a function of which hand a subject plans to move, and thus is expected to be discriminative (predictive) of the subject's response.

  18. Vibrotactile discrimination of musical timbre.

    PubMed

    Russo, Frank A; Ammirante, Paolo; Fels, Deborah I

    2012-08-01

    Five experiments investigated the ability to discriminate between musical timbres based on vibrotactile stimulation alone. Participants made same/different judgments on pairs of complex waveforms presented sequentially to the back through voice coils embedded in a conforming chair. Discrimination between cello, piano, and trombone tones matched for F0, duration, and magnitude was above chance with white noise masking the sound output of the voice coils (Experiment 1), with additional masking to control for bone-conducted sound (Experiment 2), and among a group of deaf individuals (Experiment 4a). Hearing (Experiment 3) and deaf individuals (Experiment 4b) also successfully discriminated between dull and bright timbres varying only with regard to spectral centroid. We propose that, as with auditory discrimination of musical timbre, vibrotactile discrimination may involve the cortical integration of filtered output from frequency-tuned mechanoreceptors functioning as critical bands.

  19. Recovering frequencies of known haplotype blocks from single-nucleotide polymorphism allele frequencies.

    PubMed Central

    Pe'er, Itsik; Beckmann, Jacques S

    2004-01-01

    Prospects for large-scale association studies rely on economical methods and powerful analysis. Representing available SNPs by small subsets and measuring allele frequencies on pooled DNA samples each improve genotyping cost effectiveness, while haplotype analysis may highlight associations in otherwise underpowered studies. This manuscript provides the mathematical framework to integrate these methodologies. PMID:15126415

  20. HLA class II alleles and risk for peripheral neuropathy in type 2 diabetes patients

    PubMed Central

    Marzban, Ahmad; Kiani, Javad; Hajilooi, Mehrdad; Rezaei, Hamzeh; Kahramfar, Zohreh; Solgi, Ghasem

    2016-01-01

    The potential impact of human leukocyte antigen (HLA) genotype variations on development of diabetic peripheral neuropathy (DPN) is not well determined. This study aimed to identify the association of HLA class II alleles with DPN in type 2 diabetes (T2D) patients. Totally 106 T2D patients, 49 with DPN and 57 without DPN, and 100 ethnic-matched healthy controls were analyzed. Both groups of the patients were matched based on sex, age, body mass index (BMI) and duration of T2D. Polyneuropathy was diagnosed using electrodiagnostic methods. HLA-DRB1 and DQB1 genotyping was performed in all subjects by the polymerase chain reaction with sequence-specific primers (PCR-SSP) method. T2D patients with DPN showed higher frequencies of HLA-DRB1*10 and DRB1*12 alleles compared to control group (P = 0.04). HLA-DQB1*02 allele and HLA-DRB1*07-DQB1*02 haplotype were associated with a decreased risk for developing DPN in T2D patients (P = 0.02 and P = 0.05 respectively). Also, patients with severe neuropathy showed higher frequencies of DRB1*07 (P = 0.003) and DQB1*02 (P = 0.02) alleles than those with mild-to-moderate form of neuropathy. The distribution of DRB1 and DQB1 alleles and haplotypes were not statistically different between all patients and healthy controls. Our findings implicate a possible protective role of HLA-DQB1*02 allele and HLA-DRB1*07-DQB1*02 haplotype against development of peripheral neuropathy in T2D patients. Therefore, variations in HLA genotypes might be used as genetic markers for prediction and potentially management of neuropathy in T2D patients. PMID:28123430

  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.

  3. Studies in genetic discrimination. Final progress report

    SciTech Connect

    Not Available

    1994-06-01

    We have screened 1006 respondents in a study of genetic discrimination. Analysis of these responses has produced evidence of the range of institutions engaged in genetic discrimination and demonstrates the impact of this discrimination on the respondents to the study. We have found that both ignorance and policy underlie genetic discrimination and that anti-discrimination laws are being violated.

  4. STRait Razor: a length-based forensic STR allele-calling tool for use with second generation sequencing data.

    PubMed

    Warshauer, David H; Lin, David; Hari, Kumar; Jain, Ravi; Davis, Carey; Larue, Bobby; King, Jonathan L; Budowle, Bruce

    2013-07-01

    Recent studies have demonstrated the capability of second generation sequencing (SGS) to provide coverage of short tandem repeats (STRs) found within the human genome. However, there are relatively few bioinformatic software packages capable of detecting these markers in the raw sequence data. The extant STR-calling tools are sophisticated, but are not always applicable to the analysis of the STR loci commonly used in forensic analyses. STRait Razor is a newly developed Perl-based software tool that runs on the Linux/Unix operating system and is designed to detect forensically-relevant STR alleles in FASTQ sequence data, based on allelic length. It is capable of analyzing STR loci with repeat motifs ranging from simple to complex without the need for extensive allelic sequence data. STRait Razor is designed to interpret both single-end and paired-end data and relies on intelligent parallel processing to reduce analysis time. Users are presented with a number of customization options, including variable mismatch detection parameters, as well as the ability to easily allow for the detection of alleles at new loci. In its current state, the software detects alleles for 44 autosomal and Y-chromosome STR loci. The study described herein demonstrates that STRait Razor is capable of detecting STR alleles in data generated by multiple library preparation methods and two Illumina(®) sequencing instruments, with 100% concordance. The data also reveal noteworthy concepts related to the effect of different preparation chemistries and sequencing parameters on the bioinformatic detection of STR alleles.

  5. HLA-C locus allelic dropout in Sanger sequence-based typing due to intronic single nucleotide polymorphism.

    PubMed

    Cheng, Christopher; Kashi, Zahra Mehdizadeh; Martin, Russell; Woodruff, Gillian; Dinauer, David; Agostini, Tina

    2014-12-01

    We report a novel HLA-C allele that was identified during routine HLA typing using sequence-based methods. The patient was initially typed as a C*06:02, 06:04 with two nucleotide mismatches in exon 3, (C to T and T to G changes) which would have resulted in a non-synonymous mutation of a leucine residue being replaced with tryptophan. Further resolution of the patient's type by using sequence-specific primers (SSP) revealed that the companion allele to C*06:02 was a novel C*17:01. Confirmation of the existence of the new allele was performed across multiple platforms: Sanger sequencing, SSP, and Next Generation Sequencing (NGS) on the original sample and allele-specific clones for the entire HLA-C locus. The investigation revealed a single nucleotide mismatch within the Sanger sequencing primer binding site in intron 3. The mutation caused the initial C*17 dropout in exons 2 and 3. Further analysis of the Sanger and NGS data revealed that the C*17 had two additional unique positions in introns 2 and 7. The companion C*06:02 allele also possessed a novel position at intron 3. On August 31, 2013, the WHO nomenclature committee officially named the novel C*17:01 allele sequence as C*17:01:01:03 and the novel C*06:02 allele sequence as C*06:02:01:03.

  6. Resolving microsatellite genotype ambiguity in populations of allopolyploid and diploidized autopolyploid organisms using negative correlations between allelic variables.

    PubMed

    Clark, Lindsay V; Schreier, Andrea Drauch

    2016-11-21

    A major limitation in the analysis of genetic marker data from polyploid organisms is non-Mendelian segregation, particularly when a single marker yields allelic signals from multiple, independently segregating loci (isoloci). However, with markers such as microsatellites that detect more than two alleles, it is sometimes possible to deduce which alleles belong to which isoloci. Here, we describe a novel mathematical property of codominant marker data when it is recoded as binary (presence/absence) allelic variables: under random mating in an infinite population, two allelic variables will be negatively correlated if they belong to the same locus, but uncorrelated if they belong to different loci. We present an algorithm to take advantage of this mathematical property, sorting alleles into isoloci based on correlations, then refining the allele assignments after checking for consistency with individual genotypes. We demonstrate the utility of our method on simulated data, as well as a real microsatellite data set from a natural population of octoploid white sturgeon (Acipenser transmontanus). Our methodology is implemented in the R package polysat version 1.6.

  7. Relation between minimum-error discrimination and optimum unambiguous discrimination

    SciTech Connect

    Qiu Daowen; Li Lvjun

    2010-09-15

    In this paper, we investigate the relationship between the minimum-error probability Q{sub E} of ambiguous discrimination and the optimal inconclusive probability Q{sub U} of unambiguous discrimination. It is known that for discriminating two states, the inequality Q{sub U{>=}}2Q{sub E} has been proved in the literature. The main technical results are as follows: (1) We show that, for discriminating more than two states, Q{sub U{>=}}2Q{sub E} may not hold again, but the infimum of Q{sub U}/Q{sub E} is 1, and there is no supremum of Q{sub U}/Q{sub E}, which implies that the failure probabilities of the two schemes for discriminating some states may be narrowly or widely gapped. (2) We derive two concrete formulas of the minimum-error probability Q{sub E} and the optimal inconclusive probability Q{sub U}, respectively, for ambiguous discrimination and unambiguous discrimination among arbitrary m simultaneously diagonalizable mixed quantum states with given prior probabilities. In addition, we show that Q{sub E} and Q{sub U} satisfy the relationship that Q{sub U{>=}}(m/m-1)Q{sub E}.

  8. New organic crystals for pulse shape discrimination

    SciTech Connect

    Hull, G; Zaitseva, N; Cherepy, N; Newby, J; Stoeffl, W; Payne, S

    2008-07-16

    Efficient, readily-available, low-cost, high-energy neutron detectors can play a central role in detecting illicit nuclear weapons since neutrons are a strong indication for the presence of fissile material such as Plutonium and Highly-Enriched Uranium. The main challenge in detecting fast neutrons consists in the discrimination of the signal from the gamma radiation background. At present, the only well-investigated organic crystal scintillator for fast neutron detection, in a n/{gamma} mixed field, is stilbene, which while offering good pulse shape discrimination, is not widely used because of its limited availability and high cost. In this work we report the results of our studies made with a number of new organic crystals, which exhibit pulse shape discrimination for detection of fast neutrons. In particular 1,1,4,4-tetraphenyl-1,3-butadiene features a light yield higher than anthracene and a Figure of Merit (FOM) for the pulse shape discrimination better than stilbene. New crystals are good candidates for the low-cost solution growth method, thus representing promising organic scintillators for widespread deployment for high-energy neutron detection.

  9. Age-related changes in wavelength discrimination

    PubMed Central

    Shinomori, Keizo; Schefrin, Brooke E.; Werner, John S.

    2008-01-01

    Wavelength discrimination functions (420 to 620–650 nm) were measured for four younger (mean 30.9 years) and four older (mean 72.5 years) observers. Stimuli consisted of individually determined isoluminant monochromatic lights (10 Td) presented in each half of a 2° circular bipartite field with use of a Maxwellian-view optical system. A spatial two-alternative forced-choice method was used in combination with a staircase procedure to determine discrimination thresholds across the spectrum. Small but consistent elevations in discrimination thresholds were found for older compared with younger observers. Because the retinal illuminance of the stimuli was equated across all observers, these age-related losses in discrimination are attributable to neural changes. Analyses of these data reveal a significant change in Weber fraction across adulthood for a chromatically opponent pathway receiving primarily antagonistic signals from middle-wavelength-sensitive and long-wavelength-sensitive cones but not for a short-wavelength-sensitive cone pathway. PMID:11205976

  10. Obstacles and foliage discrimination using lidar

    NASA Astrophysics Data System (ADS)

    Morris, Daniel D.

    2016-05-01

    A central challenge to autonomous off-road navigation is discriminating between obstacles that are safe to drive over and those that pose a hazard to navigation and so must be circumnavigated. Foliage, which can often be safely driven over, presents two important perception problems. First, foliage can appear as a large impenetrable obstacle, and so must be discriminated from other objects. Second, real obstacles are much harder to detect when adjacent to or occluded by foliage and many detection methods fail to detect them due to additional clutter and partial occlusions from foliage. This paper addresses both the discrimination of foliage, and the detection of obstacles in and near foliage using Lidar. Our approach uses neighboring pixels in a depth image to construct features at each pixel that provide local surface properites. A generative model for obstacles is used to accumulate probabilistic evidence for obstacles and foliage in the vicinity of a moving platform. Detection of obstacles is then based on evidence within overlapping cells of a map without the need to segment segment obstacles and foliage. High accuracy obstacle and foliage discrimination is obtained and compared with the use of a point scatter measure.

  11. Fluid discrimination based on rock physics templates

    NASA Astrophysics Data System (ADS)

    Liu, Qian; Yin, Xingyao; Li, Chao

    2015-10-01

    Reservoir fluid discrimination is an indispensable part of seismic exploration. Reliable fluid discrimination helps to decrease the risk of exploration and to increase the success ratio of drilling. There are many kinds of fluid indicators that are used in fluid discriminations, most of which are single indicators. But single indicators do not always work well under complicated reservoir conditions. Therefore, combined fluid indicators are needed to increase accuracies of discriminations. In this paper, we have proposed an alternative strategy for the combination of fluid indicators. An alternative fluid indicator, the rock physics template-based indicator (RPTI) has been derived to combine the advantages of two single indicators. The RPTI is more sensitive to the contents of fluid than traditional indicators. The combination is implemented based on the characteristic of the fluid trend in the rock physics template, which means few subjective factors are involved. We also propose an inversion method to assure the accuracy of the RPTI input data. The RPTI profile is an intuitionistic interpretation of fluid content. Real data tests demonstrate the applicability and validity.

  12. Genetic parameters and allele frequencies of five new European Standard Set STR loci (D10S1248, D22S1045, D2S441, D1S1656, D12S391) in the population of Romania

    PubMed Central

    Stanciu, Florin; Vladu, Simona; Cuţăr, Veronica; Cocioabă, Daniela; Iancu, Florentina; Cotolea, Adnana; Stoian, Ionel Marius

    2013-01-01

    Aim To establish allele frequencies and genetic parameters for 5 new European Standard Set short tandem repeat (STR) loci in the population of Romania and to compare them with those in other populations. Methods DNA was isolated using QIAamp 96 DNA Swab BioRobot Kit and Chelex 100 methods. Polymerase chain reaction amplification was done using Investigator ESSplexPlus Kit (D1S1656, D2S441, D2S1338, D3S1358, D8S1179, D10S1248, D12S391, D16S539, D18S51, D19S433, D21S11, D22S1045, FGA, TH01, and vWA). For DNA typing, Applied Biosystems 3500/3500xL Genetic Analyzer was used. Statistical analysis was done using Powerstats, GDA, and Arlequin software. Results Power of discrimination and polymorphism information content was highest for two new ESS loci, D1S1656 and D12S391. Comparison of allele frequencies for 5 new ESS loci in Romanian population with previously published population data showed significant differences for all compared populations, with the exception of Hungary. Geographically more distant populations, such as Spain, Sweden, United Kingdom, Germany, and Portugal differed more than closer populations. Conclusion New ESS STR loci are very useful for the analysis of forensic samples (persons or traces) due to their characteristics (shortness and high polymorphism). In comparisons with other common STR markers, they have a higher power of discrimination and also higher polymorphism information content, and could be used in any national DNA database. PMID:23771753

  13. Observations Suggesting Allelism of the Achondroplasia and Hypochondroplasia Genes

    PubMed Central

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

    1973-01-01

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

  14. Comparison of X-ray powder diffraction and solid-state nuclear magnetic resonance in estimating crystalline fraction of tacrolimus in sustained-release amorphous solid dispersion and development of discriminating dissolution method.

    PubMed

    Rahman, Ziyaur; Bykadi, Srikant; Siddiqui, Akhtar; Khan, Mansoor A

    2015-05-01

    The focus of present investigation was to explore X-ray powder diffraction (XRPD) and solid-state nuclear magnetic resonance (ssNMR) techniques for amorphous and crystalline tacrolimus quantification in the sustained-release amorphous solid dispersion (ASD), and to propose discriminating dissolution method that can detect crystalline drug. The ASD and crystalline physical mixture was mixed in various proportions to make sample matrices containing 0%-100% crystalline-amorphous tacrolimus. Partial-least-square regression and principle component regression were applied to the spectral data. Dissolution of the ASD in the US FDA recommended dissolution medium with and without surfactant was performed. R(2) > 0.99 and slope was close to one for all the models. Root-mean-square of prediction, standard error of prediction, and bias were higher in ssNMR-based models when compared with XRPD data models. Dissolution of the ASD decreased with an increase in the crystalline tacrolimus in the formulations. Furthermore, detection of crystalline tacrolimus in the ASD was progressively masked with an increase in the surfactant level in the dissolution medium. XRPD and ssNMR can be used equally to quantitate the crystalline and amorphous fraction of tacrolimus in the ASD with good accuracy; however, ssNMR data collection time is excessively long, and minimum surfactant level in the dissolution medium maximizes detection of crystalline reversion in the formulation.

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

    PubMed

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

    2016-12-01

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

  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. 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.

  18. Mining the human phenome using allelic scores that index biological intermediates.

    PubMed

    Evans, David M; Brion, Marie Jo A; Paternoster, Lavinia; Kemp, John P; McMahon, George; Munafò, Marcus; Whitfield, John B; Medland, Sarah E; Montgomery, Grant W; Timpson, Nicholas J; St Pourcain, Beate; Lawlor, Debbie A; Martin, Nicholas G; Dehghan, Abbas; Hirschhorn, Joel; Smith, George Davey

    2013-10-01

    It is common practice in genome-wide association studies (GWAS) to focus on the relationship between disease risk and genetic variants one marker at a time. When relevant genes are identified it is often possible to implicate biological intermediates and pathways likely to be involved in disease aetiology. However, single genetic variants typically explain small amounts of disease risk. Our idea is to construct allelic scores that explain greater proportions of the variance in biological intermediates, and subsequently use these scores to data mine GWAS. To investigate the approach's properties, we indexed three biological intermediates where the results of large GWAS meta-analyses were available: body mass index, C-reactive protein and low density lipoprotein levels. We generated allelic scores in the Avon Longitudinal Study of Parents and Children, and in publicly available data from the first Wellcome Trust Case Control Consortium. We compared the explanatory ability of allelic scores in terms of their capacity to proxy for the intermediate of interest, and the extent to which they associated with disease. We found that allelic scores derived from known variants and allelic scores derived from hundreds of thousands of genetic markers explained significant portions of the variance in biological intermediates of interest, and many of these scores showed expected correlations with disease. Genome-wide allelic scores however tended to lack specificity suggesting that they should be used with caution and perhaps only to proxy biological intermediates for which there are no known individual variants. Power calculations confirm the feasibility of extending our strategy to the analysis of tens of thousands of molecular phenotypes in large genome-wide meta-analyses. We conclude that our method represents a simple way in which potentially tens of thousands of molecular phenotypes could be screened for causal relationships with disease without having to expensively measure

  19. Three new HLA-G alleles and their linkage disequilibria with HLA-A.

    PubMed

    Morales, P; Corell, A; Martínez-Laso, J; Martín-Villa, J M; Varela, P; Paz-Artal, E; Allende, L M; Arnaiz-Villena, A

    1993-01-01

    Three new allelic forms of the HLA-G DNA sequence (HLA-G*II, HLA-G*III, and HLA-G*IV) have been identified. With the HLA-G*I sequence (previously designated HLA 6.0) as a reference, HLA-G*II shows a silent (G-->A) mutation at the third base of codon 57, HLA-G*III bears a non-synonymous (A-->T), but conservative, (Thr-->Ser) substitution at the first base of codon 31, and HLA-G*IV shows two silent substitutions: (A-->T) at the third base of codon 107 and (G-->A) at the third base of codon 57. A rapid method of singling out each allele on genomic DNA has been developed by using polymerase chain reaction amplification followed by restriction endonuclease treatment. Also, more or less strong linkage disequilibria has been found between most HLA-A alleles and either HLA-G*I or *II, both being the most prevalent alleles in the population, with a genotypic frequency of 0.55 and 0.38, respectively; HLA-G*III is very rare and HLA-G*IV has a genotypic frequency of 0.07. An evolutive classification of HLA-A alleles results according to their association with either HLA-G*I or HLA-G*II, which does not correlate with the classical serological cross-reacting groups classification. The finding of a strong and selective A/G linkage disequilibria with most HLA-A alleles, together with the existence of less frequent random A/G associations, may suggest that there exist in different haplotypes true and varied A/G genetic distances (and not a recombinational hotspot). It may be inferred from preliminary data that in primates HLA-A/G haplotypes bearing G*II may have appeared later than those bearing G*I.

  20. Lesbians still face job discrimination.

    PubMed

    Ryniker, Margaret R

    2008-01-01

    This article examines continued discrimination against lesbians in the workplace. A number of cases from various jurisdictions in the United States are highlighted. The paper studies two common forms of discrimination: denial of employment benefits to same sex partners, and sexual harassment. On the first front, the case law suggests that health insurance coverage for one's partner is becoming the norm. On the question of sexual harassment in the workplace, the case law did not provide protection for lesbians. Finally, U.S. employment policies related to sexual orientation are contrasted with those in Israel, which provides much greater protection from discrimination.

  1. The animal farm philosophy of genetic discrimination.

    PubMed

    Wolbring, Gregor

    2004-01-01

    The paper by Dr. Gregor Wolbring addresses the issue of genetic discrimination from disabled people's rights perspective asking a) what the interpretation of genetic discrimination and the scope of Anti Genetic discrimination laws and law proposals is and b) whether the scope and interpretation of genetic discrimination and Anti Genetic discrimination laws and law proposal lead to more protection for-or increased discrimination against- disabled people"

  2. Manual discrimination of force

    NASA Technical Reports Server (NTRS)

    Pang, Xiao-Dong; Tan, HONG-Z.; Durlach, Nathaniel I.

    1991-01-01

    Optimal design of human-machine interfaces for teleoperators and virtual-environment systems which involve the tactual and kinesthetic modalities requires knowledge of the human's resolving power in these modalities. The resolution of the interface should be appropriately matched to that of the human operator. We report some preliminary results on the ability of the human hand to distinguish small differences in force under a variety of conditions. Experiments were conducted on force discrimination with the thumb pushing an interface that exerts a constant force over the pushing distance and the index finger pressing against a fixed support. The dependence of the sensitivity index d' on force increment can be fit by a straight line through the origin and the just-noticeable difference (JND) in force can thus be described by the inverse of the slope of this line. The receiver operating characteristic (ROC) was measured by varying the a priori probabilities of the two alternatives, reference force and reference force plus an increment, in one-interval, two-alternative, forced-choice experiments. When plotted on normal deviate coordinates, the ROC's were roughly straight lines of unit slope, thus supporting the assumption of equal-variance normal distributions and the use of the conventional d' measure. The JND was roughly 6-8 percent for reference force ranging from 2.5 to 10 newtons, pushing distance from 5 to 30 mm, and initial finger-span from 45 to 125 mm. Also, the JND remained the same when the subjects were instructed to change the average speed of pushing from 23 to 153 mm/sec. The pushing was terminated by reaching either a wall or a well, and the JND's were essentially the same in both cases.

  3. 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.

  4. Quantum process discrimination with information from environment

    NASA Astrophysics Data System (ADS)

    Wang, Yuan-Mei; Li, Jun-Gang; Zou, Jian; Xu, Bao-Ming

    2016-12-01

    In quantum metrology we usually extract information from the reduced probe system but ignore the information lost inevitably into the environment. However, K. Mølmer [Phys. Rev. Lett. 114, 040401 (2015)] showed that the information lost into the environment has an important effect on improving the successful probability of quantum process discrimination. Here we reconsider the model of a driven atom coupled to an environment and distinguish which of two candidate Hamiltonians governs the dynamics of the whole system. We mainly discuss two measurement methods, one of which obtains only the information from the reduced atom state and the other obtains the information from both the atom and its environment. Interestingly, for the two methods the optimal initial states of the atom, used to improve the successful probability of the process discrimination, are different. By comparing the two methods we find that the partial information from the environment is very useful for the discriminations. Project supported by the National Natural Science Foundation of China (Grant Nos. 11274043, 11375025, and 11005008).

  5. Damage Identification with Linear Discriminant Operators

    SciTech Connect

    Farrar, C.R.; Nix, D.A.; Duffey, T.A.; Cornwell, P.J.; Pardoen, G.C.

    1999-02-08

    This paper explores the application of statistical pattern recognition and machine learning techniques to vibration-based damage detection. First, the damage detection process is described in terms of a problem in statistical pattern recognition. Next, a specific example of a statistical-pattern-recognition-based damage detection process using a linear discriminant operator, ''Fisher's Discriminant'', is applied to the problem of identifying structural damage in a physical system. Accelerometer time histories are recorded from sensors attached to the system as that system is excited using a measured input. Linear Prediction Coding (LPC) coefficients are utilized to convert the accelerometer time-series data into multi-dimensional samples representing the resonances of the system during a brief segment of the time series. Fisher's discriminant is then used to find the linear projection of the LPC data distributions that best separates data from undamaged and damaged systems. The method i s applied to data from concrete bridge columns as the columns are progressively damaged. For this case, the method captures a clear distinction between undamaged and damaged vibration profiles. Further, the method assigns a probability of damage that can be used to rank systems in order of priority for inspection.

  6. Cooperation of Adhesin Alleles in Salmonella-Host Tropism

    PubMed Central

    De Masi, Leon; Yue, Min; Hu, Changmin; Rakov, Alexey V.; Rankin, Shelley C.

    2017-01-01

    ABSTRACT Allelic combinations and host specificities for three fimbrial adhesins, FimH, BcfD, and StfH, were compared for 262 strains of Salmonella enterica serovar Newport, a frequent human and livestock pathogen. Like FimH, BcfD had two major alleles (designated A and B), whereas StfH had two allelic groups, each with two alleles (subgroup A1 and A2 and subgroup B1 and B2). The most prevalent combinations of FimH/BcfD/StfH alleles in S. Newport were A/A/A1 and B/B/B1. The former set was most frequently found in bovine and porcine strains, whereas the latter combination was most frequently found in environmental and human isolates. Bacteria genetically engineered to express Fim, Bcf, or Stf fimbriae on their surface were tested with the different alleles for binding to human, porcine, and bovine intestinal epithelial cells. The major allelic combinations with bovine and porcine strains (A/A/A1) or with human isolates (B/B/B1) provided at least two alleles capable of binding significantly better than the other alleles to an intestinal epithelial cell line from the respective host(s). However, each combination of alleles kept at least one allele mediating binding to an intestinal epithelial cell from another host. These findings indicated that allelic variation in multiple adhesins of S. Newport contributes to bacterial adaptation to certain preferential hosts without losing the capacity to maintain a broad host range. IMPORTANCE Salmonella enterica remains a leading foodborne bacterial pathogen in the United States; infected livestock serve often as the source of contaminated food products. A study estimated that over a billion Salmonella gastroenteritis cases and up to 33 million typhoid cases occur annually worldwide, with 3.5 million deaths. Although many Salmonella strains with a broad host range present preferential associations with certain host species, it is not clear what determines the various levels of host adaptation. Here, causal properties of host

  7. Oligonucleotide Frequencies of Barcoding Loci Can Discriminate Species across Kingdoms

    PubMed Central

    Shukla, Virendra; Tuli, Rakesh

    2010-01-01

    Background DNA barcoding refers to the use of short DNA sequences for rapid identification of species. Genetic distance or character attributes of a particular barcode locus discriminate the species. We report an efficient approach to analyze short sequence data for discrimination between species. Methodology and Principal Findings A new approach, Oligonucleotide Frequency Range (OFR) of barcode loci for species discrimination is proposed. OFR of the loci that discriminates between species was characteristic of a species, i.e., the maxima and minima within a species did not overlap with that of other species. We compared the species resolution ability of different barcode loci using p-distance, Euclidean distance of oligonucleotide frequencies, nucleotide-character based approach and OFR method. The species resolution by OFR was either higher or comparable to the other methods. A short fragment of 126 bp of internal transcribed spacer region in ribosomal RNA gene was sufficient to discriminate a majority of the species using OFR. Conclusions/Significance Oligonucleotide frequency range of a barcode locus can discriminate between species. Ability to discriminate species using very short DNA fragments may have wider applications in forensic and conservation studies. PMID:20808837

  8. Allelic gene expression imbalance of bovine IGF2, LEP and CCL2 genes in liver, kidney and pituitary.

    PubMed

    Olbromski, R; Siadkowska, E; Zelazowska, B; Zwierzchowski, L

    2013-02-01

    Allelic expression imbalance (AEI) is an important genetic factor being the cause of differences in phenotypic traits that can be heritable. Studying AEI can be useful in searching for factors that modulate gene expression and help to understand molecular mechanisms underlying phenotypic changes. Although it was commonly recognized in many species and we know many genes show allelic expression imbalance, this phenomena was not studied on a larger scale in cattle. Using the pyrosequencing method we analyzed a set of 29 bovine genes in order to find those that have preferential allelic expression. The study was conducted in three tissues: liver, pituitary and kindey. Out of the studied group of genes 3 of them-LEP (leptin), IGF2 (insulin-like growth factor 2), CCL2 (chemokine C-C motif ligand 2) showed allelic expression imbalance.

  9. Molecular identification of rare FY*Null and FY*X alleles in Caucasian thalassemic family from Sardinia.

    PubMed

    Manfroi, Silvia; Scarcello, Antonio; Pagliaro, Pasqualepaolo

    2015-10-01

    Molecular genetic studies on Duffy blood group antigens have identified mutations underlying rare FY*Null and FY*X alleles. FY*Null has a high frequency in Blacks, especially from sub-Saharan Africa, while its frequency is not defined in Caucasians. FY*X allele, associated with Fy(a-b+w) phenotype, has a frequency of 2-3.5% in Caucasian people while it is absent in Blacks. During the project of extensive blood group genotyping in patients affected by hemoglobinopathies, we identified FY*X/FY*Null and FY*A/FY*Null genotypes in a Caucasian thalassemic family from Sardinia. We speculate on the frequency of FY*X and FY*Null alleles in Caucasian and Black people; further, we focused on the association of FY*X allele with weak Fyb antigen expression on red blood cells and its identification performing high sensitivity serological typing methods or genotyping.

  10. On the maintenance of genetic variation: global analysis of Kimura's continuum-of-alleles model.

    PubMed

    Bürger, R

    1986-01-01

    Methods of functional analysis are applied to provide an exact mathematical analysis of Kimura's continuum-of-alleles model. By an approximate analysis, Kimura obtained the result that the equilibrium distribution of allelic effects determining a quantitative character is Gaussian if fitness decreases quadratically from the optimum and if production of new mutants follows a Gaussian density. Lande extended this model considerably and proposed that high levels of genetic variation can be maintained by mutation even when there is strong stabilizing selection. This hypothesis has been questioned recently by Turelli, who published analyses and computer simulations of some multiallele models, approximating the continuum-of-alleles model, and reviewed relevant data. He found that the Kimura and Lande predictions overestimate the amount of equilibrium variance considerably if selection is not extremely weak or mutation rate not extremely high. The present analysis provides the first proof that in Kimura's model an equilibrium in fact exists and, moreover, that it is globally stable. Finally, using methods from quantum mechanics, estimates of the exact equilibrium variance are derived which are in best accordance with Turelli's results. This shows that continuum-of-alleles models may be excellent approximations to multiallele models, if analysed appropriately.

  11. Influence of HLA DRB1 alleles in the susceptibility of rheumatoid arthritis and the regulation of antibodies against citrullinated proteins and rheumatoid factor

    PubMed Central

    2010-01-01

    Introduction The purpose of this study was to investigate the association between HLA-DRB1 alleles with susceptibility to rheumatoid arthritis (RA) and production