bluuebunny/crossref_metadata_2025 huggingface dataset:
A note on analysing the multitrait‐multimethod matrix: An application of a generalized proximity function comparison
Authors: Hubert Lawrence J. , Baker Frank B.
Published: August 2011

Using the notion of a generalized proximity function comparison discussed by Hubert (1978), alternative indices are proposed for evaluating correlational pattern within a multitrait‐multimethod matrix. The measures that are presented and the inference paradigm based on random sampling only require the ordering of the correlations in the given multitrait‐multimethod matrix; consequently, they complement the original Campbell‐Fiske emphasis on ordinal comparison when assessing convergent and discriminant validity.
A simple comprehensive model for the analysis of covariance structures: Some remarks on applications
Authors: McDonald Roderick P.
Published: August 2011

To facilitate applications of a model for the analysis of covariance structures, some useful matrix identities and reparametorizations are given. Examples are given to illustrate the applicability of the model to longitudinal data, to treatments of ordered variables and to fitting the Rasch model for binary data.
Circularity and consistency in paired comparisons
Authors: Bezembinder Thorn G. G.
Published: August 2011

Let R be a linear order on a set Z = {x, y,…} of n objects. Let Dm and D(t) be systems of paired comparisons on Z such that in every one of the pairs with xRy the system Dm contains an observed proportion p = 0, 1/m,…, 1 of choices for x over y while D(t) contains a probability of choosing x over y as given by a choice theory (t) which also specifies R. For systems D1 a circularity index is proposed as an alternative to Kendall's and Slater's consistency indices. Some properties of these three indices are investigated in the sets of all possible D1 for some small n. If m > 1, Dm may be more or less compatible with D(t) and also give rise to a D1, estimating R. It is argued that the compatibility of Dm with D(t) may be regarded as an index of the external consistency of D1, with respect to R which is to be distinguished from its circularity or internal consistency. This distinction is corroborated by computer simulations of paired comparisons under Thurstone's case V model. The correlations between the three circularity indices and four indices of external consistency are essentially zero. Finally, the bearing of assessing circularity to the assessing and testing of the (in)transitivity of data systems is indicated.
A Bayesian approach for estimating the knowledge of the item pool in multiple choice tests
Authors: Wilmink F. W. , Nevels K.
Published: August 2011

Several models exist for the observed number Z of correct answers in a multiple choice test. One of these is the binomial error model which assumes that the conditional distribution of Z given the proportion‐correct true score is binomial. The specification of a beta distribution to the proportion‐correct true score has led to the development of the beta‐binomial model. Recently, extensions of the beta‐binomial model have been given that allow for guessing. Letting X be the number of known items in the test the regression of X on Z has received much attention. In the present paper it is argued that the number W of known items in the item pool is of interest rather than X, and the regression of W on Z is studied.
Correlation measures in item analysis
Authors: Cooper Colin
Published: August 2011

Henrysson (1963) has criticized the procedure of correlating an item with the sum of the remaining n − 1 items on the grounds that the criterion is a function of the items selected for analysis. Worst case distortions of the point biserial correlations are examined, and it is concluded that for many data sets such effects are likely to be negligible. In such cases it is argued that the corrected coefficients proposed by Henrysson (1963) should be avoided because of their strong assumptions concerning the factorial homogeneity of the test items.
Invariance in time series representations of 2‐input 2‐output psychophysical experiments
Authors: Gregson Robert A. M.
Published: August 2011

The dynamic representation of pairs of intensity judgement responses to two‐component odour mixtures, composed of various concentrations of bergamote and amyl acetate, is explored using multivariate time series analysis and the associated root locus diagrams derived from factoring a polynomial determinant of the matrix polynomial z‐transformation of the system transfer function.

The topology of the root loci is examined for both pseudocoupled and really coupled conditions, to see how the component odourants interact in determining the psychophysics of odour mixture perception. It is shown that most subjects show a loss in gain for both components, but that they are not dynamically homogeneous. Third‐order loop gain equations are a sufficient representation in nearly all cases.
The relativity of ‘absolute’ judgements
Authors: Laming Donald
Published: August 2011

Suppose that, with rather few exceptions, the assignment of a number to a stimulus on one trial of a magnitude estimation or category judgement experiment serves as the point of reference for choosing an appropriate assignment on the next trial. This principle of relative judgement—relative to the immediate context—is developed to generate models for both magnitude estimation and category judgement experiments. It is applied, in particular, to the explanation of three, hitherto unrelated, phenomena: these are (a) the limited transmission of information in category judgements; (b) sequential constraints on the resolving power of category judgements; and (c) the autocorrelation of successive numerical magnitude estimates. Finally, some comparison is made between the principle of relative judgement introduced here and other contemporary ideas which have been addressed to one or more of these three critical phenomena.
Agreement between observers when the categories are not specified in advance
Authors: Brook Richard J. , Stirling W. Douglas
Published: August 2011

To test the agreement between two observers who categorize a number of objects when the categories have not been specified in advance, Brennan & Light (1974) developed a statistic A′ and suggested a normal approximation for its distribution. In this paper it is shown that this approximation is inadequate particularly when one, or both, of the observers place a fairly equal number of objects in all of their categories. A chi‐squared approximation to the distribution of A′ is developed and is shown to work well in a variety of situations.

The relative powers of A′ and the ordinary X2 test for association are dependent on the type of ‘agreement between the observers’ that is assumed. However a simulation for a fairly general type of agreement indicates that the X2 test is more powerful. As the X2 test is also much easier to apply, it would seem preferable in most situations.
A regression model for recall order
Authors: Robertson Chris
Published: August 2011

A regression model for the order of recall of items in a free recall experiment which allows the effects of covariates to be measured is presented. The estimation of the parameters via Newton–Raphson iteration is discussed, as are methods of assessing the goodness of fit of the model. Diagnostic checks are illustrated on two sets of data and finally some extensions and drawbacks are considered.
Parsimony in the construction of diagnostic scales
Authors: Moran P. A. P.
Published: August 2011

Diagnostic scales are used for a variety of purposes. A widely used example is Goldberg's General Health Questionnaire (GHQ). Consider a scale consisting of n items, scored 0 or 1, and such that the total score is taken as a measure of some psychological attitude. It is natural to suppose that the more items are used, the more effective the scale. It is shown by simple examples that if a series of items is used in which the discriminating power of each is decreasing in order, and if the first n of these items are used to form the scale, the discriminating power of the sum, as measured by its correlation with an unobserved underlying variable, may increase and decrease as n increases in an almost arbitrary manner. This helps to explain why the 30‐item GHQ scale performs equally well with the 60‐item GHQ scale in practice. It also points to the need to use scales in which the items are weighted. If the weights are chosen in an optimal manner the efficiency of the scale will not decrease as the number of items increases.
Estimation of the KR20 reliability coefficient when data are incomplete
Authors: Huynh Huynh
Published: August 2011

Attention is focused on the estimation of the KR20 reliability coefficient when data are incomplete. In terms of point estimate, it is found that the analysis of variance procedure (Henderson's Method 1) would be most suitable among the three techniques studied. Confidence coefficients are provided for the KR20 when data are incomplete.
Choice basis: A model for multi‐attribute preference
Authors: Barthélemy J. P. , Mullet E.
Published: August 2011

This paper presents an illustration of the complementary use of the algebraic and the ‘information processing’ points of view in the domain of experts' choice. Our main proposition, supported by experimental results, is that the decision process itself can be represented by an algebraic rule. A systematization of this approach leads to the general notion of choice polynomials. Such polynomials are able to translate into mathematical terms psychological hypotheses and/or observations. They also give a new insight into the nature of the so‐called lexicographical rule.
Combining examination marks
Authors: Biggins J. D. , Loynes R. M. , Walker A. N.
Published: August 2011

In a set of examinations it is often the case that not every candidate takes every paper and yet a single overall mark must be assigned to each of the candidates. Some methods for tackling the problem of producing such marks, and difficulties they may lead to, are discussed. A fairly general framework into which many particular proposals can be fitted is described.
The economy of probabilistic stress: Interplay of controlling activity and threat reduction
Authors: Morrison Maxine S. , Neufeld Richard W. J. , Lefebvre Lorraine A.
Published: August 2011

In this paper, we examine salient properties of control in stressing situations; the degree of control varies with the number of alternatives available to an individual within a situation. Simulated conditions of control indicate that as alternatives become more available, so does potential reduction of the probability that aversive events will occur. The simulations indicate, further, that realizing this potential rests on predictive judgements surrounding the alternatives; such judgements represent ‘cognitive demands’ which are regarded as stressing in their own right. After being demonstrated quantitatively, the inverse relation between aversive‐event probability and requisite predictive judgements is examined empirically. Mathematical models of preference and choice are then used to identify implications of the inverse relation for the relative ‘appeal’ held by alternate conditions of control. Both strengths and limitations of the current formulation and its supporting evidence are noted. Finally, the present type of control regarding stressing events is compared to other types, followed by discussion of their respective roles.
Five decades of item response modelling
Authors: Goldstein Harvey , Wood Robert
Published: August 2011

An historical and theoretical review is provided of so called item response theory (IRT), more accurately described as item response modelling (IRM). This paper looks at 50 years of IRM and finds a disappointing lack of advance. It is shown how a linear model framework, involving different response transformations, unifies separate approaches to the study of test item responses.
The construction and assessment of mental maps
Authors: Gordon A. D. , Jupp P. E. , Byrne R. W.
Published: August 2011

In investigations into the manner in which people store spatial information, experimental subjects are often asked to estimate the distances and bearings between various landmarks. Methodology is described for constructing the mental map underlying a subject's matrix of distances, and the mental map underlying a subject's matrix of bearings. Also presented are methods of comparing matrices of distances or bearings, and the mental maps constructed from them, with the geographical map; this enables an assessment of differences between them. Some statistical models of disorientation are considered, and a method of choosing between them is described.
Aspects of the design and analysis of signal detection experiments
Authors: Robertson C. C. , Morgan B. J. T.
Published: August 2011

Guidelines are given for users of the simple Yes/No signal detection experiment, who want to design their experiments to ensure a given precision for estimators of d. Additionally, simulations of small‐scale Yes/No and rating‐method experiments are employed, to investigate when the use of asymptotic results is justified. Finally it is shown how the pay‐off matrix for the Yes/No experiment may be manipulated in order to optimize precision.

A general conclusion is that quite large experiments are needed in order to provide precise unbiased estimation of d, with sampling distributions which are not appreciably skewed.
Robustness and power of tests of variability on two independent groups
Authors: Ramsey Philip H. , Brailsford Eric A.
Published: August 2011

A number of procedures are investigated for testing differences in variability in seven population distributions. Some procedures, previously considered robust, are found to be robust only with certain sample sizes. Testing for kurtosis is found to be useful for increasing power provided N > 60. For equal sample sizes, maximum power is found to result from the application of one of Levene's procedures with platykurtic distributions and the Brown‐Forsythe procedure with leptokurtic distributions. No procedure is found to be adequately robust for all populations with unequal sample sizes. However, several methods are determined to be adequate if run at half the nominal alpha level.
Selection effects and unidimensionality in item response theory
Authors: Grayson D. A.
Published: August 2011

In the factor‐analytic perspective on unidimensional item response theory (IRT), the latent trait is construed as a single common factor to the items, each item having an independent residual which determines the item characteristic curve (ICC). It is possible that such residual terms have a component which is ‘stable’ and reflects some attribute of the subjects being measured other than the trait in common to all the items (the common factor). That is, heuristically, the ‘residual’ may consist of ‘specific’ and ‘error’ components. As such, comparison of subpopulations on such a test may confound selection effects on the common factor with selection effects on such stable components of the residuals, vitiating inference from manifest test response differences to common factor differences.

A technique for exploratory use in assessing the presence of such (undesirable) stable residuals using repeated measures data is discussed, together with applications. The technique is of broader potential application, allowing one to use repeated measures data to search for ‘user‐defined’ violations of unidimensionality. It assumes the existence of a sufficient score for the common factor, and is thus an exact technique when a Rasch model is assumed.
Relative improvement over chance (RIOC) for 2×2 tables
Authors: Copas John B. , Loeber Rolf
Published: August 2011

A novel index of association, called Relative Improvement Over Chance (RIOC), is described for 2×2 tables that corrects for chance and for limitations in maximum predictability due to unequal distributions of the marginals in such tables. Criteria for comparing the utility of this and existing indexes of association are reviewed. The theoretical distribution of RIOC for large and small sample sizes is presented, and tested against the results from computer generated tables. Methods are presented for calculating confidence intervals for RIOC, for testing the significance of individual values of RIOC, and for testing the difference between several values of RIOC from different studies.
Resolving mixtures of strategies in spatial visualization tasks
Authors: Mislevy Robert J. , Wingersky Marilyn S. , Irvine Sidney H. , Dann Peter L.
Published: August 2011

The models of standard test theory, having evolved under a trait‐oriented psychology, do not reflect the knowledge structures and the problem‐solving strategies now seen as central to understanding performance and learning. In some applications, however, key qualitative distinctions among persons as to structures and strategies can be expressed through mixtures of test theory models, drawing on substantive theory to delineate the components of the mixture. This approach is illustrated with response latencies to spatial visualization tasks that can be solved by mental rotation or by a non‐rotational rule‐based strategy. It is assumed that a subject employs the same strategy on all tasks, but the possibility of extending the approach to strategy‐switching is discussed.
The behaviour of three weighted least squares estimators for structured means analysis with non‐normal Likert variables
Authors: Kaplan David
Published: August 2011

A Monte Carlo framework is employed to examine the effects of non‐normality on three weighted least squares estimators for structured means analysis of Likert scaled variables. The GLS estimator is compared to Browne's (1984) ADF estimator for structured means (Muthen, 1989), and to the CVM estimator (Muthen, 1984) for a severely skewed case. Results show severe lack of robustness for the GLS chi‐square test, not found for ADF. Factor mean estimate bias is virtually non‐existent for both estimators, but some sampling variability bias was found for GLS and ADF with ADF performing slightly worse. The CVM estimator performs similar to ADF with respect to chi‐square and better than ADF with respect to sampling variability. Some problems of weight matrix calculations are noted. A discussion of the problem of mean and covariance structure distortion is discussed, and a case where such distortion exists is studied. Results lead to the conclusion that CVM may be the preferred estimator for structured means analysis of categorical variables.
Scaled test statistics and robust standard errors for non‐normal data in covariance structure analysis: A Monte Carlo study
Authors: Chou Chih‐Ping , Bentler P. M. , Satorra Albert
Published: August 2011

Research studying robustness of maximum likelihood (ML) statistics in covariance structure analysis has concluded that test statistics and standard errors are biased under severe non‐normality. An estimation procedure known as asymptotic distribution free (ADF), making no distributional assumption, has been suggested to avoid these biases. Corrections to the normal theory statistics to yield more adequate performance have also been proposed. This study compares the performance of a scaled test statistic and robust standard errors for two models under several non‐normal conditions and also compares these with the results from ML and ADF methods. Both ML and ADF test statistics performed rather well in one model and considerably worse in the other. In general, the scaled test statistic seemed to behave better than the ML test statistic and the ADF statistic performed the worst. The robust and ADF standard errors yielded more appropriate estimates of sampling variability than the ML standard errors, which were usually downward biased, in both models under most of the non‐normal conditions. ML test statistics and standard errors were found to be quite robust to the violation of the normality assumption when data had either symmetric and platykurtic distributions, or non‐symmetric and zero kurtotic distributions.
Robust nonlinear regression analysis
Authors: Verboon Peter
Published: August 2011

In the linear regression problem M‐estimators are frequently applied as an alternative to least squares estimators to obtain robustness, when there are outliers in the dependent variable. When we allow for nonlinear transformations of the variables (Young, 1981), the effects of outliers can still be large. In this paper it is shown that M‐estimators can also be used for nonlinear multiple regression. Two types of M‐estimators are used: the Huber and biweight estimator.

Permutation tests are applied to obtain significance levels for the multiple correlation coefficients. Furthermore, an exploratory procedure is proposed, which is useful in finding out which tuning constant is optimal for the given problem. In a Monte Carlo study the stability of the different solutions and the influence of the outliers is examined by using the jack‐knife. It was found that the biweight function was the most robust and eliminated the influence of the outliers.
Orthogonal Procrustes rotation for matrices with missing values
Authors: ten Berge Jos M. F. , Kiers Henk A. L. , Commandeur Jacques J. F.
Published: August 2011

A method is offered for orthogonal Procrustes rotation of two or more matrices with missing values, and an extension to Generalized Procrustes Analysis is given. The method is based on the idea that missing values, in arbitrary places, can be replaced by optimal values according to the least squares criterion. Commandeur has offered a method of orthogonal Procrustes rotation and Generalized Procrustes Analysis for the case where entire rows of the data matrices are missing. It is proved that our method yields essentially the same results as Commandeur's method, in that case. A simulation study for Procrustes rotation is described in which complete columns of matrices, derived from a common underlying structure, are deleted, and either replaced by zeros or estimated on the basis of the newly proposed method. In those conditions where the underlying structure can adequately be disentangled from the error, our method appears to recover the underlying structure more accurately than when the missing columns are replaced by zeros.
Subpopulation invariance of patterns in covariance matrices
Authors: Ellis Jules L.
Published: August 2011

A universal model is defined as a set of behavioural laws that hold for almost every subject of a given population. Universal models satisfy the principle of subpopulation invariance: If the model holds in a population, then the model and its predictions hold in every non‐negligible subpopulation. On basis of this principle it is shown that only one universal model, namely congenerity, can explain the ratio pattern of observed‐score covariance matrices. Similar results are obtained for the sign and order pattern of covariance matrices. More specifically, the necessary and sufficient conditions of these models can be formulated by the principle. Factor analysis representations can satisfy the principle, but do not necessarily do so. Multidimensional scaling distance representations, on the other hand, in general will violate the principle and are therefore not reducible to a universal model.
Regression analysis of multilevel data with measurement error
Authors: Longford N. T.
Published: August 2011

Multilevel data structures, such as data with individuals within groups, groups within areas, etc., arise in a variety of contexts. Regression models for such data allow for variation of the within‐group regression coefficients. Since some of the explanatory variables may be observed subject to measurement error, it is desirable to define models that combine within‐group correlation and measurement error. We discuss a general model formulation and a scoring algorithm for maximum likelihood estimation.
Some results on a Winsorized correlation coefficient
Authors: Wilcox Rand R.
Published: August 2011

Recent investigations indicate that psychometric measures often have distributions with very heavy tails, and that outliers are quite common. It has long been known that in terms of both power and Type I errors, even slight departures from normality can have serious consequences, and it is fairly evident that there are problems when using conventional measures of effect size, as is briefly illustrated in this paper. Similar problems arise when dealing with the usual correlation coefficient. Robust correlation coefficients have already been proposed that reflect the linear relationship between two random variables, but many have the unfortunate property of not always being equal to 0 under independence. One exception is the Winsorized correlation. The primary goal in this paper is to suggest a simple method for testing the hypothesis that the Winsorized correlation is equal to zero. A minor goal is to describe a formal definition of the Winsorized correlation coefficient in terms of Winsorized expected values.
Simplified interaction tests for non‐normal data in psychological research
Authors: Zimmerman Donald W.
Published: August 2011

This study examined three simple transformations which increase the power of F tests of main effects and interaction in 2 × 2 factorial designs under violation of normality. The study obtained Monte Carlo results from various heavy‐tailed densities, including mixed‐normal, exponential, Cauchy and Laplace densities, which are associated with grossly distorted probabilities of Type I and Type II errors. Transformation of scores to ranks made the F test for interaction robust and comparable in power to the Mann—Whitney‐Wilcoxon test for the same distributions. Transformation to ‘modular ranks’, having one‐fourth the number of values of conventional ranks, was equally effective. Detection and downweighting of outliers before performing the F test was more effective than rank methods for several distributions. Implications of these findings for the role of scales of measurement and nonparametric methods in psychological research are discussed.
A developmental path model and causal analysis of latent dichotomous variables
Authors: Eshima Nobuoki , Asano Chooichiro , Tabata Minoru
Published: August 2011

In a developmental study, it is reasonable to assume that a population is divided into several subpopulations according to developmental paths, i.e. each of the subpopulations depends on a developmental path of its own. Under this assumption, first, a latent structure model is proposed for explaining developmental paths in a population. Second, causal analysis of latent dichotomous variables indicating states of skill acquisition is discussed through the developmental paths. Basic measures of causal effects among the variables are defined. A numerical example illustrates the present approach.
Optimality criteria for principal component analysis and generalizations
Authors: ten Berge Jos M. F. , Kiers Henk A. L.
Published: August 2011

Principal components analysis can be derived from various criteria. Because these give essentially the same results, the question of which criterion should be used has not received much attention. Nevertheless, it can be argued that the approach of Pearson and Eckart & Young, based on variance explained by components, is more elegant and flexible than the (more popular) approach of Hotelling, which is concerned with variance that components have rather than explain. When two or more correlation or covariance matrices, based on the same variables, are to be analyzed in generalized component analysis, the question of which criterion is used becomes of utmost importance. A taxonomy of generalized principal component methods is given. It appears that generalized component analysis based on the Hotelling criterion coincides with one particular generalization based on the criterion of Pearson and Eckart & Young.
Measurement structures and invariant statistics
Authors: Chiang Ching‐Yuan
Published: August 2011

A suitable connection between measurement structures and statistical structures is suggested. It is pointed out that, under appropriate conditions, invariant statistics, which include invariant test statistics and equivariant estimators, are comparison invariant in the measurement‐theoretic sense. Examples of invariant functions used in statistics are discussed.
Multidimensional scaling with constrained dimensions: CONSCAL
Authors: Winsberg Suzanne , De Soete Geert
Published: August 2011

Multidimensional scaling is a technique used to represent pairwise dissimilarities among a set of objects in a Euclidean space of generally low dimensionality. The data determine the number of dimensions to retain, and in the case of the weighted Euclidean model the psychologically meaningful dimensions to interpret. However, it is often the case that it is difficult to determine the appropriate dimensionality based on goodness‐of‐fit statistics, and it is sometimes difficult to interpret each recovered dimension. Moreover, this problem may occur in situations where a small number of physical parameters may be used to describe the objects. Then it would appear useful to use this information and constrain the dimensions of the distance model to be monotone transformations of these physical dimensions. We therefore propose two models:

where djk is the distance between stimulus j and stimulus k;

there are R physical dimensions;

x(r)j is the coordinate of the jth object on the rth dimension;

fj is the vector of monotone transformations for the jth object, the rth component being f(r) (x(r)j);

A is an R × R symmetric matrix with 1s on the diagonal;

I is an R × R identity matrix with 1s on the diagonal, 0s elsewhere.

The monotone transformations are represented as I‐splines. Model one is a special case of model two for uncorrelated dimensions. Solutions may be compared with those obtained in the unconstrained case to choose the best representation of the data. Examples of real and artificial data will be presented.
Optimal test designs for polytomously scored items
Authors: Berger Martijn P. F. , Mathijssen Eric
Published: August 2011

As achievement testing gained currency in educational and psychological measurement, and item response theory (IRT) models were used more frequently to analyse such test data, the need for more efficient test designs became urgent. The results from the statistical theory on optimal design can be applied to the assembly of achievement tests by means of IRT models. Up till now, efficient test designs were considered only in relation to IRT models for dichotomous responses. In this paper the optimal assembly of tests will be considered for polytomously scored responses.
Testing equality of reliability and stability with simple linear constraints in multi‐wave, multi‐variable models
Authors: Alanen Erkki , Leskinen Esko , Kuusinen Jorma
Published: August 2011

Data from a longitudinal study on school achievement were used to develop new methods for analysing reliability of measurements and stability of behaviour over a long time interval. The proposed method of analysis makes it possible to test hypotheses about equality constraints on reliability and stability. It is known that the use of negative variances for imaginary latent variables with equality constraints between structural parameters produces standardized variances for endogenous latent variables and quality constraints for coefficients of stability. Reparameterization of random errors in measurement models allows equality constraints to be set for coefficients of cross‐sectional and of longitudinal reliability. This technique was applied to empirical longitudinal data by using reparameterized three‐wave, three‐variable models and simplex models.
Urine
TMPRSS2:ERG
Fusion Transcript Stratifies Prostate Cancer Risk in Men with Elevated Serum PSA
Authors: Tomlins Scott A. , Aubin Sheila M. J. , Siddiqui Javed , Lonigro Robert J. , Sefton-Miller Laurie , Miick Siobhan , Williamsen Sarah , Hodge Petrea , Meinke Jessica , Blase Amy , Penabella Yvonne , Day John R. , Varambally Radhika , Han Bo , Wood David , Wang Lei , Sanda Martin G. , Rubin Mark A. , Rhodes Daniel R. , Hollenbeck Brent , Sakamoto Kyoko , Silberstein Jonathan L. , Fradet Yves , Amberson James B. , Meyers Stephanie , Palanisamy Nallasivam , Rittenhouse Harry , Wei John T. , Groskopf Jack , Chinnaiyan Arul M.
Published: August 2011

Urine
TMPRSS2:ERG
gene fusion could be used for stratification of patients at higher risk for prostate cancer.
Cancer Returns
Authors: Emadi Ashkan
Published: August 2011

Genetic variants on chromosome 6 are associated with risk for second cancers after radiation therapy for childhood Hodgkin’s lymphoma.
Science Translational Medicine
Podcast: 3 August 2011
Authors: Klatzmann David , Colmone Angela
Published: August 2011

A conversation with David Klatzmann about a new vaccine platform to induce broadly neutralizing antibodies to hepatitis C virus.
Cross-Reactivity in the Histoplasma Antigen Enzyme Immunoassay Caused by Sporotrichosis
Authors: Assi Maha , Lakkis Iass E. , Wheat L. Joseph
Published: August 2011

Several endemic mycoses cause cross-reactions in theHistoplasmaantigen enzyme immunoassay. Herein, a positiveHistoplasmaantigen result has been recognized in a patient with sporotrichosis.
MassARRAY Spectrometry Is More Sensitive than PreTect HPV-Proofer and Consensus PCR for Type-Specific Detection of High-Risk Oncogenic Human Papillomavirus Genotypes in Cervical Cancer
Authors: Basu Partha , Chandna Puneet , Bamezai R. N. K. , Siddiqi Maqsood , Saranath Dhananjaya , Lear Adrian , Ratnam Sam
Published: August 2011

Type-specific detection of human papillomavirus (HPV) is indicated for better risk stratification and clinical management of women testing positive for HPV and for epidemiologic surveillance. MassARRAY spectrometry (MassARRAY; Sequenom) is a novel method for type-specific detection of 15 high-risk oncogenic HPV types: HPV-16, -18, -31, -33, -35, -39, -45, -51, -52, -56, -58, -59, -66, -68, and -73. PreTect HPV-Proofer (Proofer; Norchip) is a type-specific assay that detects E6/E7 mRNA from five high-risk oncogenic HPV types: HPV-16, -18, -31, -33, and -45. The performance of these tests for type-specific identification of HPV was assessed with cervical specimens from 192 cases of cervical cancer in comparison with consensus MY09/MY11 PCR followed by nucleotide sequencing (consensus PCR). The overall HPV detection rates were 94.8% (95% confidence interval [CI], 91.7, 97.9), 83.3% (95% CI, 78.1, 88.5), and 86.5% (95% CI, 81.7, 91.3) for MassARRAY, Proofer, and consensus PCR, respectively. All tests were negative in six (3.1%) of the 192 cases. Considering only the specimens that contained at least one of the five types targeted by Proofer, the detection rates were 96.6%, 91.4%, and 86.9% for MassARRAY, Proofer, and consensus PCR, respectively. MassARRAY detected multiple infections in 14.1%, Proofer detected multiple infections in 3.6%, and consensus PCR failed to detect any multiple infections. The agreement was highest at 86.0% (kappa = 0.76) between MassARRAY and Proofer and lowest at 81.8% (kappa = 0.69) between Proofer and consensus PCR. In conclusion, MassARRAY is a highly sensitive and accurate method for type-specific detection of oncogenic HPV in cervical cancer, with Proofer showing impressive performance.
Quadrupolar central transition (QCT) and13C NMR competition studies of metal ion binding to ovotransferrin
Authors: Saponja Jillian A. , Vogel Hans J.
Published: August 2011

The transferrins are a family of relatively large bilobal proteins that play a major role in the transport of Fe3+, as well as several other physiological and nonphysiological metal ions. Transferrins can also act as antimicrobial agents, by tightly sequestering iron and making it unavailable for bacterial growth. Using a combination of quadrupolar central transition (QCT) metal ion NMR (27Al,45Sc,51V, and71Ga) and13C NMR, the binding and displacement of a variety of metal ions to ovotransferrin was studied through direct metal ion competition experiments. The metal ions investigated (Al3+, Co3+, Fe3+, Ga3+, In3+, Sc3+, Y3+, and VO2+) were of differing ionic radius and charge, thus allowing for an assessment of how these factors contribute to metal ion affinity. The competition for the N- and C-terminal metal ion binding sites on ovotransferrin was directly followed by metal ion QCT NMR. Moreover,13C NMR was used to study the two protein-bound synergistic anions (13C-labeled carbonate), whose chemical shifts are distinct and dependent on the bound metal ion that is present in the binding sites. The observed order of decreasing affinity for the metal ions studied was Fe3+ ≈ In3+ ≥ Sc3+ ≥ Ga3+ > Al3+ > VO2+ > Y3+ ≥ Co3+. These results illustrate how a combination of multinuclear solution NMR methods can provide unique insights into the ligand binding properties of larger metalloproteins.
Improvements in MR imaging of solids through gradient waveform optimization
Authors: Gruwel Marco L.H. , Latta Peter , Tomanek Boguslaw
Published: August 2011

Magnetic resonance imaging (MRI) is known to provide a useful approach for the exploration of the chemistry and dynamics of a wide range of soft condensed materials. However, its application to solids has been limited to those materials with relatively narrow resonances. The time needed to obtain an image of a solid with a given resolution and signal-to-noise ratio (SNR) is directly proportional to the line width of the resonance. For MRI to become practical for the imaging of solids it will have to rely on the development and use of MR sequences that avoid the issues raised by line broadening of the resonance. In this paper we review the latest contributions towards MR imaging of solids from our laboratory, in particular, applications using optimized gradient waveforms. Acoustic noise reduction and SNR improvement obtained with modifications of the standard single-point imaging sequence are presented and discussed using examples.
Some Notes on Semiabelian Rings
Authors: Wei Junchao , Li Nanjie
Published: August 2011

It is proved that if a ring R is semiabelian, then so is
the skew polynomial ring R[x; σ], where σ is an endomorphism
of R satisfying σ(e) = e for all e ∈ E(R). Some characterizations
and properties of semiabelian rings are studied.
Total Least Squares Method for Robust Source Localization in Sensor Networks Using TDOA Measurements
Authors: Weng Yang , Xiao Wendong , Xie Lihua
Published: August 2011

The TDOA-based source localization problem in sensor networks is considered with sensor node location uncertainty. A total least squares (TLSs) algorithm is developed by a linear closed-form solution for this problem, and the uncertainty of the sensor location is formulated as a perturbation. The sensitivity of the TLS solution is also analyzed. Simulation results show its improved performance against the classic least squares approaches.
Peanut Seed Vigor Evaluation Using a Thermal Gradient
Authors: Grey Timothy L. , Beasley John P. , Webster Theodore M. , Chen Charles Y.
Published: August 2011

Experiments conducted from 2007 to 2009 evaluated germination of 11 peanut runner-type cultivars. Germination was evaluated in Petridishes incubated over a thermal gradient ranging from 14 to 30°C at 1.0 C increments. Beginning 24 hr after seeding, peanut was counted as germinated when radicles were greater than 5 mm long, with removal each day. Germination was counted daily for seven days after seeding. Growing-degree day (GDD) accumulation for each temperature increment was calculated based on daily mean temperature for that Petri dish. Two indices were obtained from a logistic growth curve used to elucidate seed germination by cultivar: (1) maximum indices of germination and (2) GDD value at 80% germination (Germ80), an indication of seed vigor the lower the Germ80value, the greater the seed lot vigor. Based on the two indices, seed lots “AT 3081R”, “AP-3”, “GA-06G”, and “Carver” had the strongest seed vigor (Germ8026 to 47 GDD) and a high maximum incidence of germination rate (80 to 94%). Seed lots of “C99-R”, “Georgia-01R”, “Georgia-02C”, and “Georgia-03L” had inconsistent seed performance, failing to achieve 80% germination in at least two of three years.
Open Reduction of Subcondylar Fractures Using a New Retractor
Authors: Sugamata Akira , Yoshizawa Naoki , Jimbo Yoshio
Published: August 2011

Many operative approaches have been described for the open reduction of subcondylar fractures and rigid fixation. However, fracture portions are deep and embedded among facial nerves so that visual surgery in this region is extremely limited. Once the operative field is exposed, the displacement of the condylar head is often dislocated by the anteromedial pull of the lateral pterygoid muscle and the fracture end of the condylar process is pulled up to the mandibular fossa by contraction of the masseter muscle. We made a new retractor to achieve a better field of view. It is possible to pull down the condylar process by opening the tips of the retractor using the specially made wrench system without special effort and keep the condylar process in the same position during reduction. In using this retractor, the fracture stumps were clearly exposed and more easily reposited.
Stability Analysis of Three‐Species Almost Periodic Competition Models with Grazing Rates and Diffusions
Authors: Wang Chang-you , Wang Rui-fang , Yi Ming , Li Rui
Published: August 2011

Almost periodic solution of a three‐species competition system with grazing rates and diffusions is investigated. By using the method of upper and lower solutions and Schauder fixed point theorem as well as Lyapunov stability theory, we give sufficient conditions to ensure the existence and globally asymptotically stable for the strictly positive space homogenous almost periodic solution, which extend and include corresponding results obtained by Q. C. Lin (1999), F. D. Chen and X. X. Chen (2003), and Y. Q. Liu, S. L, Xie, and Z. D. Xie (1996).
Targeting Human B-cell Malignancies through Ig Light Chain–Specific Cytotoxic T Lymphocytes
Authors: Weng Jinsheng , Cha Soung-Chul , Matsueda Satoko , Alatrash Gheath , Popescu Michael S. , Yi Qing , Molldrem Jeffrey J. , Wang Michael , Neelapu Sattva S. , Kwak Larry W.
Published: August 2011

Purpose: The variable regions of Ig (idiotype, Id) expressed by malignant B cells can be used as tumor-specific antigens that induce humoral and cellular immunity. However, epitopes derived from Id that stimulate human CD8+ T-cell immunity are incompletely characterized.

Experimental Design: The clonal Ig VL of human myeloma cell line U266 and five primary B-cell tumors were sequenced, and peptides corresponding to the Ig VL region were tested for their ability to stimulate CTLs from 10 HLA-A*0201–positive normal donors. The CTLs thus generated were tested against peptide-pulsed T2 cells and autologous tumor cells.

Results: Fourteen peptides derived from Ig light chain (VL) of U266 and primary B-cell tumors were used to generate 68 CTLs lines that specifically produced IFN-γ when cocultured with peptide-pulsed T2 cells. These CTLs lysed peptide-pulsed T2 cell as well as U266 or autologous tumor targets in an HLA class I–dependent manner. Sequence analysis revealed shared VL T-cell epitopes in U266 and primary B-cell tumors, not previously reported within Ig heavy chain (VH) sequences.

Conclusion: This study thus identifies novel immunogenic CTLs epitopes from Id VL, suggests that they are naturally presented on the surface of B-cell malignancies, and supports their inclusion in next-generation Id vaccines. The ability to prime T cells derived from normal HLA-matched donors, rather than patients, may also have direct application to current strategies, designed to generate allogeneic tumor-specific T cells for adoptive transfer. Clin Cancer Res; 17(18); 5945–52. ©2011 AACR.
Diagnostic Value of a Urine-Based Tumor Marker for Screening Lower Urinary Tract in Low-Risk Patients with Asymptomatic Microscopic Hematuria
Authors: Sagnak Levent , Ersoy Hamit , Gucuk Osman , Ozok Ugur , Topaloglu Hikmet
Published: August 2011

Background: To evaluate the use of NMP22 BladderChek® (NMP22BC) as an initial test in comparison to voided urine cytology for screening subjects with asymptomatic microscopic hematuria (AMH); those who are <40 years of age and have a low risk for bladder cancer based on a non-smoking history, and by discussing the guidelines on this subject. Methods: From October 2005 to September 2007, 164 patients (56 male, 108 female) were evaluated. Patients with risk factors according to AUA Best Practice Policy Recommendations on AMH were strictly excluded from the study. For upper urinary tract imaging, ultrasonography (USG) was performed and prior to the cystoscopic procedure freshly voided urine was sampled for urine cytology and NMP22BC assay in all patients. Biopsy was performed if suspicious lesions were seen or positive cytology was obtained. Results: The mean age was 30.8 years. As some benign urological pathologies were detected in 21 patients by USG, NMP22BC was positive in 26 patients where the cytology was confirmed as atypia in 5. Two TaG1 tumors were detected cystoscopically in a 39-year-old man and a 33-year-old woman where the NMP22BC test was positive and the cytology was negative in both patients. NMP22BC tests sensitivity, PPV and NPV values were detected to be higher compared to cytology and the likelihood ratio was 6.75. Conclusion: We recommend in evaluation of low-risk patients with AMH that, as an initial test, two non-invasive and cost-effective methods be chosen: an upper tract imaging by USG as recommended by guidelines, followed by an NMP22BC test for lower tract investigation instead of urine cytology.
Evidence for Using Lagged Climate Indices to Forecast Australian Seasonal Rainfall
Authors: Schepen Andrew , Wang Q. J. , Robertson David
Published: August 2011

Lagged oceanic and atmospheric climate indices are potentially useful predictors of seasonal rainfall totals. A rigorous Bayesian joint probability modeling approach is applied to find the cross-validation predictive densities of gridded Australian seasonal rainfall totals using lagged climate indices as predictors over the period of 1950–2009. The evidence supporting the use of each climate index as a predictor of seasonal rainfall is quantified by the pseudo-Bayes factor based on cross-validation predictive densities. The evidence strongly supports the use of climate indices from the Pacific region with weaker, but positive, evidence for the use of climate indices from the Indian region and the extratropical region. The spatial structure and seasonal variation of the evidence for each climate index is mapped and compared. Spatially, the strongest supporting evidence is found for forecasting in northern and eastern Australia. Seasonally, the strongest evidence is found from August–October to November–January and the weakest evidence is found from March–May to May–July. In some regions and seasons, there is little evidence supporting the use of climate indices for forecasting seasonal rainfall. Climate indices derived from sea surface temperature anomalies in the Pacific region show stronger persistence in the relationship with Australian seasonal rainfall totals than climate indices derived from sea surface temperature anomalies in the Indian region. Climate indices derived from atmospheric variables are also strongly supported, provided they represent the large-scale circulation. Many climate indices are found to show similar supporting evidence for forecasting Australian seasonal rainfall, leading to the prospect of combining climate indices in multiple predictor models and/or model averaging.