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The analysis of multiple bivariate correlations is often carried out by conducting simple tests to check whether each of them is significantly different from zero. In addition, pairwise differences are often judged by eye or by comparing the p-values of the individual tests of significance despite the existence of statistical tests for differences between correlations. This paper uses simulation methods to assess the accuracy (empirical Type I error rate), power, and robustness of 10 tests designed to check the significance of the difference between two dependent correlations with overlapping variables (i.e., the correlation between X1 and Y and the correlation between X2 and Y). Five of the tests turned out to be inadvisable because their empirical Type I error rates under normality differ greatly from the nominal alpha level of .05 either across the board or within certain sub-ranges of the parameter space. The remaining five tests were acceptable and their merits were similar in terms of all comparison criteria, although none of them was robust across all forms of non-normality explored in the study. Practical recommendations are given for the choice of a statistical test to compare dependent correlations with overlapping variables., Ministerio de Ciencia e Innovación (España), Depto. de Psicobiología y Metodología en Ciencias del Comportamiento, Fac. de Psicología, TRUE, pub

Papillon-Lefèvre syndrome (PLS) has recently been shown to be caused by mutations in the cathepsin C gene resulting in periodontal disease and palmoplantar keratosis. Thirteen different homozygous mutations have been characterised in PLS patients of different ethnic origin. In the present paper, a PLS patient is described who carries two novel mutations (706G>T and 872G>A) in the paternal and maternal chromosomes, respectively. This is the first compound patient described so far. In addition, a novel symptomless mutation (458C>T) in the cathepsin C gene is described in three homozygous individuals. Thus, not all mutations should be considered as a cause of disease, whether case studies or general population screening is performed. Another already described mutation that provoked the Haim-Munk syndrome (HMS) in Indian Jews has also been found to give rise to PLS in a Spanish family from Madrid. On the other hand, PLS patients are ameliorated by retinoids, which indicates that retinoids may be used as therapeutic agents in this immune system deficiency., Depto. de Inmunología, Oftalmología y ORL, Fac. de Medicina, TRUE, pub

Summary: Three ataxia telangiectasia (AT) patients have been characterized immunologically and molecularly. Patient 1 presents two nondescribed splicing mutations which affect exons 15 and 21 of the ATM gene. The maternal defect consists of a G>A transition in the first nucleotide of the intron 21 donor splicing site which results in a complete deletion of exon 21. The paternal mutation consists of an A > C transversion in the intron 14 acceptor splicing site which produces a partial skipping of exon 15. Two abnormal alternative transcripts were found, respectively, 17 and 41 nucleotides shorter. Patient 2 presents a homozygous genomic deletion of 28 nucleotides in the last exon of the gene. This deletion changes the normal reading frame after residue 3003 of the protein and introduces a premature stop codon at residue 3008 that could originate a truncated ATM protein. Patient 3, a compound heterozygote, presents a defect which consists of a G > A transition in the first nucleotide of intron 62 donor splicing site which results in a complete deletion of exon 62. The results obtained during a three year period in the proliferation assays show an impaired PMA (phorbol myristate acetate) activation in specific T lymphocyte activation pathways (CD69, CD26, CD28, CD3, PHA, PWM and Con A mediated) but not in others (CD2, ionomycin, and Ig surface receptor). The possible link among specific ATM mutations and abnormal immune responses is unknown., Ministerio de Educación y Ciencia, Comunidad Autónoma de Madrid, Depto. de Inmunología, Oftalmología y ORL, Fac. de Medicina, TRUE, pub

Proportion correct in two-alternative forcedchoice (2AFC) detection tasks often varies when the stimulus is presented in the first or in the second interval.Reanalysis of published data reveals that these order effects (or interval bias) are strong and prevalent, refuting the standard difference model of signal detection theory. Order effects are commonly regarded as evidence that observers use an off-center criterion under the difference model with bias. We consider an alternative difference model with indecision whereby observers are occasionally undecided and guess with some bias toward one of the response options. Whether or not the data show order effects, the two models fit 2AFC data indistinguishably, but they yield meaningfully different estimates of sensory parameters. Under indeterminacy as to which model governs 2AFC performance, parameter estimates are suspect and potentially misleading. The indeterminacy can be circumvented by modifying the response format so that observers can express indecision when needed. Reanalysis of published data collected in this way lends support to the indecision model. We illustrate alternative approaches to fitting psychometric functions under the indecision model and discuss designs for 2AFC experiments that improve the accuracy of parameter estimates, whether or not order effects are apparent in the data., Ministerio de Ciencia e Innovación (MICINN), Depto. de Psicobiología y Metodología en Ciencias del Comportamiento, Fac. de Psicología, TRUE, pub

Temporal-order judgment (TOJ) and simultaneity judgment (SJ) tasks are used to study differences in speed of processing across sensory modalities, stimulus types, or experimental conditions. Matthews and Welch (2015) reported that observed performance in SJ and TOJ tasks is superior when visual stimuli are presented in the left visual field (LVF) compared to the right visual field (RVF), revealing an LVF advantage presumably reflecting attentional influences. Because observed performance reflects the interplay of perceptual and decisional processes involved in carrying out the tasks, analyses that separate out these influences are needed to determine the origin of the LVF advantage. We re-analyzed the data of Matthews and Welch (2015) using a model of performance in SJ and TOJ tasks that separates out these influences. Parameter estimates capturing the operation of perceptual processes did not differ between hemifields by these analyses, whereas parameter estimates capturing the operation of decisional processes differed. In line with other evidence, perceptual processing also did not differ between SJ and TOJ tasks. Thus, the LVF advantage occurs with identical speeds of processing in both visual hemifields. If attention is responsible for the LVF advantage, it does not exert its influence via prior entry., Ministerio de Economía y Competitividad (MINECO), Depto. de Psicobiología y Metodología en Ciencias del Comportamiento, Fac. de Psicología, TRUE, pub

Research on the perception of temporal order uses either temporal-order judgment (TOJ) tasks or synchrony judgment (SJ) tasks, in both of which two stimuli are presented with some temporal delay and observers must judge the order of presentation. Results generally differ across tasks, raising concerns about whether they measure the same processes. We present a model including sensory and decisional parameters that places these tasks in a common framework that allows studying their implications on observed performance. TOJ tasks imply specific decisional components that explain the discrepancy of results obtained with TOJ and SJ tasks. The model is also tested against published data on audiovisual temporal-order judgments, and the fit is satisfactory, although model parameters are more accurately estimated with SJ tasks. Measures of latent point of subjective simultaneity and latent sensitivity are defined that are invariant across tasks by isolating the sensory parameters governing observed performance, whereas decisional parameters vary across tasks and account for observed differences across them. Our analyses concur with other evidence advising against the use of TOJ tasks in research on perception of temporal order., Ministerio de Ciencia e Innovación (MICINN), Depto. de Psicobiología y Metodología en Ciencias del Comportamiento, Fac. de Psicología, TRUE, pub

The transducer function mu for contrast perception describes the nonlinear mapping of stimulus contrast onto an internal response. Under a signal detection theory approach, the transducer model of contrast perception states that the internal response elicited by a stimulus of contrast c is a random variable with mean mu(c). Using this approach, we derive the formal relations between the transducer function, the threshold-versus-contrast (TvC) function, and the psychometric functions for contrast detection and discrimination in 2AFC tasks. We show that the mathematical form of the TvC function is determined only by mu, and that the psychometric functions for detection and discrimination have a common mathematical form with common parameters emanating from, and only from, the transducer function mu and the form of the distribution of the internal responses. We discuss the theoretical and practical implications of these relations, which have bearings on the tenability of certain mathematical forms for the psychometric function and on the suitability of empirical approaches to model validation. We also present the results of a comprehensive test of these relations using two alternative forms of the transducer model: a three-parameter version that renders logistic psychometric functions and a five-parameter version using Foley's variant of the Naka-Rushton equation as transducer function. Our results support the validity of the formal relations implied by the general transducer model, and the two versions that were contrasted account for our data equally well., Ministerio de Educación y Ciencia (España), Depto. de Psicobiología y Metodología en Ciencias del Comportamiento, Fac. de Psicología, TRUE, pub

Ulrich and Vorberg (2009) presented a method that fits distinct functions for each order of presentation of standard and test stimuli in a two-alternative forced-choice (2AFC) discrimination task, which removes the contaminating influence of order effects from estimates of the difference limen. The two functions are fitted simultaneously under the constraint that their average evaluates to 0.5 when test and standard have the same magnitude, which was regarded as a general property of 2AFC tasks. This constraint implies that physical identity produces indistinguishability, which is valid when test and standard are identical except for magnitude along the dimension of comparison. However, indistinguishability does not occur at physical identity when test and standard differ on dimensions other than that along which they are compared (e.g., vertical and horizontal lines of the same length are not perceived to have the same length). In these cases, the method of Ulrich and Vorberg cannot be used. We propose a generalization of their method for use in such cases and illustrate it with data from a 2AFC experiment involving length discrimination of horizontal and vertical lines. The resultant data could be fitted with our generalization but not with the method of Ulrich and Vorberg. Further extensions of this method are discussed., Ministerio de Ciencia e Innovación (MICINN), Depto. de Psicobiología y Metodología en Ciencias del Comportamiento, Fac. de Psicología, TRUE, pub

We recently published an article (García-Pérez & Alcalá- Quintana, 2010) reanalyzing data presented by Lapid, Ulrich, and Rammsayer (2008) and discussing a theoretical argument developed by Ulrich and Vorberg (2009). The purpose of this note is to correct an error in our study that has some theoretical importance, although it does not affect the conclusion that was raised. The error lies in that asymptote parameters reflecting lapses or finger errors should not enter the constraint relating the psychometric functions that describe performance when the comparison stimulus in a two-alternative forced choice (2AFC) discrimination task is presented in the first or second interval., Depto. de Psicobiología y Metodología en Ciencias del Comportamiento, Fac. de Psicología, TRUE, pub

Morgan, Dillenburger, Raphael, and Solomon have shown that observers can use different response strategies when unsure of their answer, and, thus, they can voluntarily shift the location of the psychometric function estimated with the method of single stimuli (MSS; sometimes also referred to as the single-interval, two-alternative method). They wondered whether MSS could distinguish response bias from a true perceptual effect that would also shift the location of the psychometric function. We demonstrate theoretically that the inability to distinguish response bias from perceptual effects is an inherent shortcoming of MSS, although a three-response format including also an "undecided" response option may solve the problem under restrictive assumptions whose validity cannot be tested with MSS data. We also show that a proper two-alternative forced-choice (2AFC) task with the three-response format is free of all these problems so that bias and perceptual effects can easily be separated out. The use of a three-response 2AFC format is essential to eliminate a confound (response bias) in studies of perceptual effects and, hence, to eliminate a threat to the internal validity of research in this area., Ministerio de Ciencia e Innovación (MICINN), Depto. de Psicobiología y Metodología en Ciencias del Comportamiento, Fac. de Psicología, TRUE, pub

Fixed-step-size (FSS) and Bayesian staircases are widely used methods to estimate sensory thresholds in 2AFC tasks, although a direct comparison of both types of procedure under identical conditions has not previously been reported. A simulation study and an empirical test were conducted to compare the performance of optimized Bayesian staircases with that of four optimized variants of FSS staircase differing as to up-down rule. The ultimate goal was to determine whether FSS or Bayesian staircases are the best choice in experimental psychophysics. The comparison considered the properties of the estimates (i.e. bias and standard errors) in relation to their cost (i.e. the number of trials to completion). The simulation study showed that mean estimates of Bayesian and FSS staircases are dependable when sufficient trials are given and that, in both cases, the standard deviation (SD) of the estimates decreases with number of trials, although the SD of Bayesian estimates is always lower than that of FSS estimates (and thus, Bayesian staircases are more efficient). The empirical test did not support these conclusions, as (1) neither procedure rendered estimates converging on some value, (2) standard deviations did not follow the expected pattern of decrease with number of trials, and (3) both procedures appeared to be equally efficient. Potential factors explaining the discrepancies between simulation and empirical results are commented upon and, all things considered, a sensible recommendation is for psychophysicists to run no fewer than 18 and no more than 30 reversals of an FSS staircase implementing the 1-up/3-down rule., Ministerio de Educación, Cultura y Deporte, Ministerio de Ciencia y Tecnología, Depto. de Psicobiología y Metodología en Ciencias del Comportamiento, Fac. de Psicología, TRUE, pub

Recent studies have reported that flanking stimuli broaden the psychometric function and lower detection thresholds. In the present study, we measured psychometric functions for detection and discrimination with and without flankers to investigate whether these effects occur throughout the contrast continuum. Our results confirm that lower detection thresholds with flankers are accompanied by broader psychometric functions. Psychometric functions for discrimination reveal that discrimination thresholds with and without flankers are similar across standard levels, and that the broadening of psychometric functions with flankers disappears as standard contrast increases, to the point that psychometric functions at high standard levels are virtually identical with or without flankers. Threshold-versus-contrast (TvC) curves with flankers only differ from TvC curves without flankers in occasional shallower dippers and lower branches on the left of the dipper, but they run virtually superimposed at high standard levels. We discuss differences between our results and other results in the literature, and how they are likely attributed to the differential vulnerability of alternative psychophysical procedures to the effects of presentation order. We show that different models of flanker facilitation can fit the data equally well, which stresses that succeeding at fitting a model does not validate it in any sense., Ministerio Ciencia e Innovación (MICINN), Ministerio de Educación y Ciencia (MEC), Depto. de Psicobiología y Metodología en Ciencias del Comportamiento, Fac. de Psicología, TRUE, pub

Lapid, Ulrich, and Rammsayer (2008) reported that estimates of the difference limen (DL) from a two-alternative forced choice (2AFC) task are higher than those obtained from a reminder task. This article reanalyzes their data in order to correct an error in their estimates of the DL from 2AFC data. We also extend the psychometric functions fitted to data from both tasks to incorporate an extra parameter that has been shown to allow obtaining accurate estimates of the DL that are unaffected by lapses. Contrary to Lapid et al.'s conclusion, our reanalysis shows that DLs estimated with the 2AFC task are only minimally (and not always significantly) larger than those estimated with the reminder task. We also show that their data are contaminated by response bias, and that the small remaining difference between DLs estimated with 2AFC and reminder tasks can be reasonably attributed to the differential effects that response bias has in either task as they were defined in Lapid et al.'s experiments. Finally, we discuss a novel approach presented by Ulrich and Vorberg (2009) for fitting psychometric functions to 2AFC discrimination data., Ministerio de Ciencia e Innovación (MICINN), Depto. de Psicobiología y Metodología en Ciencias del Comportamiento, Fac. de Psicología, TRUE, pub

Research on temporal-order perception uses temporal-order judgment (TOJ) tasks or synchrony judgment (SJ) tasks in their binary SJ2 or ternary SJ3 variants. In all cases, two stimuli are presented with some temporal delay, and observers judge the order of presentation. Arbitrary psychometric functions are typically fitted to obtain performance measures such as sensitivity or the point of subjective simultaneity, but the parameters of these functions are uninterpretable. We describe routines in MATLAB and R that fit model-based functions whose parameters are interpretable in terms of the processes underlying temporal-order and simultaneity judgments and responses. These functions arise from an independent-channels model assuming arrival latencies with exponential distributions and a trichotomous decision space. Different routines fit data separately for SJ2, SJ3, and TOJ tasks, jointly for any two tasks, or also jointly for the three tasks (for common cases in which two or even the three tasks were used with the same stimuli and participants). Additional routines provide bootstrap p-values and confidence intervals for estimated parameters. A further routine is included that obtains performance measures from the fitted functions. An R package for Windows and source code of the MATLAB and R routines are available as Supplementary Files., Ministerio de Ciencia e Innovación (MICINN), Depto. de Psicobiología y Metodología en Ciencias del Comportamiento, Fac. de Psicología, TRUE, pub

Current interest in measuring quality of life is generating interest in the construction of computerized adaptive tests (CATs) with Likert-type items. Calibration of an item bank for use in CAT requires collecting responses to a large number of candidate items. However, the number is usually too large to administer to each subject in the calibration sample. The concurrent anchor-item design solves this problem by splitting the items into separate subtests, with some common items across subtests; then administering each subtest to a different sample; and finally running estimation algorithms once on the aggregated data array, from which a substantial number of responses are then missing. Although the use of anchor-item designs is widespread, the consequences of several configuration decisions on the accuracy of parameter estimates have never been studied in the polytomous case. The present study addresses this question by simulation, comparing the outcomes of several alternatives on the configuration of the anchor-item design. The factors defining variants of the anchor-item design are (a) subtest size, (b) balance of common and unique items per subtest, (c) characteristics of the common items, and (d) criteria for the distribution of unique items across subtests. The results of this study indicate that maximizing accuracy in item parameter recovery requires subtests of the largest possible number of items and the smallest possible number of common items; the characteristics of the common items and the criterion for distribution of unique items do not affect accuracy., Ministerio de Educación y Ciencia (España), Depto. de Psicobiología y Metodología en Ciencias del Comportamiento, Fac. de Psicología, TRUE, pub

Omnibus tests of significance in contingency tables use statistics of the chi-square type. When the null is rejected, residual analyses are conducted to identify cells in which observed frequencies differ significantly from expected frequencies. Residual analyses are thus conditioned on a significant omnibus test. Conditional approaches have been shown to substantially alter type I error rates in cases involving t tests conditional on the results of a test of equality of variances, or tests of regression coefficients conditional on the results of tests of heteroscedasticity. We show that residual analyses conditional on a significant omnibus test are also affected by this problem, yielding type I error rates that can be up to 6 times larger than nominal rates, depending on the size of the table and the form of the marginal distributions. We explored several unconditional approaches in search for a method that maintains the nominal type I error rate and found out that a bootstrap correction for multiple testing achieved this goal. The validity of this approach is documented for two-way contingency tables in the contexts of tests of independence, tests of homogeneity, and fitting psychometric functions. Computer code in MATLAB and R to conduct these analyses is provided as Supplementary Material., Ministerio de Ciencia e Innovación (MICINN), Ministerio de Economía y Competitividad (MINECO), Ministerio de Ciencia e Innovación and FEDER, Universidad del PaísVasco UPV/EHU, Departamento de Educación del Gobierno Vasco, UPV/EHU Econometrics Research Group, Depto. de Psicobiología y Metodología en Ciencias del Comportamiento, Fac. de Psicología, TRUE, pub

Threshold estimation with sequential procedures is justifiable on the surmise that the index used in the so-called dynamic stopping rule has diagnostic value for identifying when an accurate estimate has been obtained. The performance of five types of Bayesian sequential procedure was compared here to that of an analogous fixed-length procedure. Indices for use in sequential procedures were: (1) the width of the Bayesian probability interval, (2) the posterior standard deviation, (3) the absolute change, (4) the average change, and (5) the number of sign fluctuations. A simulation study was carried out to evaluate which index renders estimates with less bias and smaller standard error at lower cost (i.e. lower average number of trials to completion), in both yes–no and two-alternative forced-choice (2AFC) tasks. We also considered the effect of the form and parameters of the psychometric function and its similarity with themodel function assumed in the procedure. Our results show that sequential procedures do not outperform fixed-length procedures in yes–no tasks. However, in 2AFC tasks, sequential procedures not based on sign fluctuations all yield minimally better estimates than fixed-length procedures, although most of the improvement occurs with short runs that render undependable estimates and the differences vanish when the procedures run for a number of trials (around 70) that ensures dependability. Thus, none of the indices considered here (some of which are widespread) has the diagnostic value that would justify its use. In addition, difficulties of implementation make sequential procedures unfit as alternatives to fixed-length procedures., Ministerio de Educación, Cultura y Deporte (España), Ministerio de Ciencia y Tecnología (España), Depto. de Psicobiología y Metodología en Ciencias del Comportamiento, Fac. de Psicología, TRUE, pub