Different ways of modeling spatial-frequency uncertainty in visual signal detection

Inferior human signal-detection behavior compared with that of ideal observers has been explained by intrinsic uncertainty of the human observer with respect to certain signal parameters. One way to model this uncertainty is to assume that the observer simultaneously monitors multiple channels, corresponding to possible parameters. However, it is also conceivable to assume that an observer, uncertain about which channel to monitor, chooses a suboptimally tuned single filter. Finally, uncertainty may also cause the filter underlying a single channel to broaden. In this paper these different models are investigated with respect to spatial-frequency uncertainty for matched filters detecting Gabor signals. All three mechanisms predict a decrease in detection performance. However, it is shown that the resulting psychometric functions are different. While the slopes increase with uncertainty for the multiple-channel models, they decrease for a randomly chosen single channel. Broadening a single filter leads to parallel psychometric functions.     

On analyzing circadian rhythms data using nonlinear mixed models with harmonic terms

Wang, Ke, and Brown (2003, Biometrics59, 804-812) developed a smoothing-based approach for modeling circadian rhythms with random effects. Their approach is flexible in that fixed and random covariates can affect both the amplitude and phase shift of a nonparametrically smoothed periodic function. In motivating their approach, Wang et al. stated that a simple sinusoidal function is too restrictive. In addition, they stated that "although adding harmonics can improve the fit, it is difficult to decide how many harmonics to include in the model, and the results are difficult to interpret." We disagree with the notion that harmonic models cannot be a useful tool in modeling longitudinal circadian rhythm data. In this note, we show how nonlinear mixed models with harmonic terms allow for a simple and flexible alternative to Wang et al.'s approach. We show how to choose the number of harmonics using penalized likelihood to flexibly model circadian rhythms and to estimate the effect of covariates on the rhythms. We fit harmonic models to the cortisol circadian rhythm data presented by Wang et al. to illustrate our approach. Furthermore, we evaluate the properties of our procedure with a small simulation study. The proposed parametric approach provides an alternative to Wang et al.'s semiparametric approach and has the added advantage of being easy to implement in most statistical software packages.     

Determination of the intrinsic redox potentials of FeS centers of respiratory complex I from experimental titration curves

Recently, Euro et al. [Biochem. 47, 3185 (2008) ] have reported titration data for seven of nine FeS redox centers of complex I from Escherichiacoli. There is a significant uncertainty in the assignment of the titration data. Four of the titration curves were assigned to N1a, N1b, N6b, and N2 centers; one curve either to N3 or N7; one more either to N4 or N5; and the last one denoted Nx could not be assigned at all. In addition, the assignment of the titration data to the N6b/N6a pair is also uncertain. In this paper, using our calculated interaction energies [Couch et al. BBA 1787, 1266 (2009)], we perform statistical analysis of these data, considering a variety of possible assignments, find the best fit, and determine the intrinsic redox potentials of the centers. The intrinsic potentials could be determined with an uncertainty of less than ± 10 mV at a 95% confidence level for best fit assignments. We also find that the best agreement between theoretical and experimental titration curves is obtained with the N6b-N2 interaction equal to 71 ± 14 or 96 ± 26 mV depending on the N6b/N6a titration data assignment, which is stronger than was expected and may indicate a close distance of the N2 center to the membrane surface.     

Characterisation of the alpha 1-protease inhibitor system in Thoroughbred horse plasma by horizontal two-dimensional (ISO-DALT) electrophoresis. 2. Protease inhibition

The protease inhibitory spectra of the eight homozygous Thoroughbred Pi types against trypsin, elastase and chymotrypsin have been determined. The alpha 1-protease inhibitor proteins exhibit three classes of inhibitory specificity towards these enzymes. The Pi types F, I, N and U exhibit class I (trypsin, elastase and chymotrypsin) and class II (trypsin and elastase) types of inhibition and fit Juneja et al.'s (1979) classification of two separate genetic systems Pi 1 and Pi 2 based on differences in the inhibitory spectra against trypsin and chymotrypsin. The remaining four Pi types are exceptions to Juneja et al.'s (1979) classification. Types G, L, S1 and S2 possess class I but not class II proteins. A third class of proteins (class III) which exclusively inhibit chymotrypsin was detected in all eight protease inhibitor types. Type G is well represented by class III proteins because two of the three major proteins of the ISO-DALT pattern inhibit only chymotrypsin and is thus an exception to Juneja et al.'s (1979) classification.     

The transducer model for contrast detection and discrimination: formal relations, implications, and an empirical test

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.     

Effects of Spatial Frequency Similarity and Dissimilarity on Contour Integration

We examined the effects of spatial frequency similarity and dissimilarity on human contour integration under various conditions of uncertainty. Participants performed a temporal 2AFC contour detection task. Spatial frequency jitter up to 3.0 octaves was applied either to background elements, or to contour and background elements, or to none of both. Results converge on four major findings. (1) Contours defined by spatial frequency similarity alone are only scarcely visible, suggesting the absence of specialized cortical routines for shape detection based on spatial frequency similarity. (2) When orientation collinearity and spatial frequency similarity are combined along a contour, performance amplifies far beyond probability summation when compared to the fully heterogenous condition but only to a margin compatible with probability summation when compared to the fully homogenous case. (3) Psychometric functions are steeper but not shifted for homogenous contours in heterogenous backgrounds indicating an advantageous signal-to-noise ratio. The additional similarity cue therefore not so much improves contour detection performance but primarily reduces observer uncertainty about whether a potential candidate is a contour or just a false positive. (4) Contour integration is a broadband mechanism which is only moderately impaired by spatial frequency dissimilarity.     

Psychometric curves of lateral facilitation

Visibility of an oriented stimulus may be enhanced by nearby stimuli that are co-aligned with the target. However, the underlying mechanism governing this facilitation is controversial. Here we measured the dependence of percent correct detection on the target's contrast (psychometric curve) with and without flankers, where flankers were either collinear with or orthogonal to the target. We find that the effect of collinear flankers can be described as a translation of the psychometric function along the linear contrast axis. This behavior is consistent, within experimental error, with two types of models: (1) non-linear transduction of target contrast with collinear flankers having additive effects on contrast, and (2) uncertainty reduction (Pelli, 1985) by collinear flankers. We discuss properties of collinear facilitation that can help deciding between these two models.     

A passive dynamic walking robot that has a deterministic nonlinear gait

There is a growing body of evidence that the step-to-step variations present in human walking are related to the biomechanics of the locomotive system. However, we still have limited understanding of what biomechanical variables influence the observed nonlinear gait variations. It is necessary to develop reliable models that closely resemble the nonlinear gait dynamics in order to advance our knowledge in this scientific field. Previously, Goswami et al. [1998. A study of the passive gait of a compass-like biped robot: symmetry and chaos. International Journal of Robotic Research 17(12)] and Garcia et al. [1998. The simplest walking model: stability, complexity, and scaling. Journal of Biomechanical Engineering 120(2), 281-288] have demonstrated that passive dynamic walking computer models can exhibit a cascade of bifurcations in their gait pattern that lead to a deterministic nonlinear gait pattern. These computer models suggest that the intrinsic mechanical dynamics may be at least partially responsible for the deterministic nonlinear gait pattern; however, this has not been shown for a physical walking robot. Here we use the largest Laypunov exponent and a surrogation analysis method to confirm and extend Garcia et al.'s and Goswami et al.'s original results to a physical passive dynamic walking robot. Experimental outcomes from our walking robot further support the notion that the deterministic nonlinear step-to-step variations present in gait may be partly governed by the intrinsic mechanical dynamics of the locomotive system. Furthermore the nonlinear analysis techniques used in this investigation offer novel methods for quantifying the nature of the step-to-step variations found in human and robotic gait.     

Seasonal variation in Plasmodium prevalence in a population of blue tits Cyanistes caeruleus

1. Seasonal variation in environmental conditions is ubiquitous and can affect the spread of infectious diseases. Understanding seasonal patterns of disease incidence can help to identify mechanisms, such as the demography of hosts and vectors, which influence parasite transmission dynamics. 2. We examined seasonal variation in Plasmodium infection in a blue tit Cyanistes caeruleus population over 3 years using sensitive molecular diagnostic techniques, in light of Beaudoin et al.'s (1971; Journal of Wildlife Diseases, 7, 5-13) model of seasonal variation in avian malaria prevalence in temperate areas. This model predicts a within-year bimodal pattern of spring and autumn peaks with a winter absence of infection. 3. Avian malaria infections were mostly Plasmodium (24.4%) with occasional Haemoproteus infections (0.8%). Statistical nonlinear smoothing techniques applied to longitudinal presence/absence data revealed marked temporal variation in Plasmodium prevalence, which apparently showed a within-year bimodal pattern similar to Beaudoin et al.'s model. However, of the two Plasmodium morphospecies accounting for most infections, only the seasonal pattern of Plasmodium circumflexum supported Beaudoin et al.'s model. On closer examination there was also considerable age structure in infection: Beaudoin et al.'s seasonal pattern was observed only in first year and not older birds. Plasmodium relictum prevalence was less seasonally variable. 4. For these two Plasmodium morphospecies, we reject Beaudoin et al.'s model as it does not survive closer scrutiny of the complexities of seasonal variation among Plasmodium morphospecies and host age classes. Studies of host-parasite interactions should consider seasonal variation whenever possible. We discuss the ecological and evolutionary implications of seasonal variation in disease prevalence.     

The use of map functions in multipoint mapping.

The analysis of multipoint data in humans involves detection of linkage, inferences about order, and estimation of map lengths. In order to calculate likelihoods, it is necessary to have predictive formulas for multiple recombination frequencies. In the present study the Markovian assumption of Morton and MacLean is generalized to give predictive formulas for multiple-region recombination using realistic map functions. The best-fitting map functions have been determined by fitting the nine-locus data of Morgan et al. and the seven-locus data of Weinstein on the Drosophila X chromosome. Two map functions fit the data better than other published functions: that of Rao et al. with a map parameter of P = .33 and a new function suggested in the present paper. The close agreement of the estimate of the mapping parameter with a previous estimate inferred from human male meiosis suggests that the map function is robust. A further improvement in the fit to the data can be obtained by the addition of a second parameter to reduce the expected number of multiple recombinants. By comparison with the map functions recommended in the present paper, the assumption of no interference gives a poor fit to the data.     

Four Theorems on the Psychometric Function

In a 2-alternative forced-choice (2AFC) discrimination task, observers choose which of two stimuli has the higher value. The psychometric function for this task gives the probability of a correct response for a given stimulus difference, . This paper proves four theorems about the psychometric function. Assuming the observer applies a transducer and adds noise, Theorem 1 derives a convenient general expression for the psychometric function. Discrimination data are often fitted with a Weibull function. Theorem 2 proves that the Weibull “slope” parameter, , can be approximated by , where is the of the Weibull function that fits best to the cumulative noise distribution, and depends on the transducer. We derive general expressions for and , from which we derive expressions for specific cases. One case that follows naturally from our general analysis is Pelli''s finding that, when , . We also consider two limiting cases. Theorem 3 proves that, as sensitivity improves, 2AFC performance will usually approach that for a linear transducer, whatever the actual transducer; we show that this does not apply at signal levels where the transducer gradient is zero, which explains why it does not apply to contrast detection. Theorem 4 proves that, when the exponent of a power-function transducer approaches zero, 2AFC performance approaches that of a logarithmic transducer. We show that the power-function exponents of 0.4–0.5 fitted to suprathreshold contrast discrimination data are close enough to zero for the fitted psychometric function to be practically indistinguishable from that of a log transducer. Finally, Weibull reflects the shape of the noise distribution, and we used our results to assess the recent claim that internal noise has higher kurtosis than a Gaussian. Our analysis of for contrast discrimination suggests that, if internal noise is stimulus-independent, it has lower kurtosis than a Gaussian.     

Set-size effects for spatial frequency change and discrimination in multiple targets

In visual search tasks with a near-threshold target amongst distracters, log detection thresholds rise in proportion to the log of the number of stimuli. Previous research has shown a very steep slope for this set-size effect where the target is a change in spatial frequency (SF) across an ISI, suggesting a low-level explanation for 'change blindness (Wright et al., 2000). Here, we analyse stimulus and task variables in order to determine the contributions of stimulus detection and attention processes. Stimuli consisted of two 150 ms frames each containing 1 to 4 Gabor targets, with an ISI of 250 ms. In a 2AFC detection task with uniform distracters, slopes of 0.23-0.52 were found, in line with visual search results. 2AFC SF discrimination tasks gave slopes of 0.68, 0.69 with homogeneous distracters and 0.76-0.96 with inhomogeneous distracters, consistent with averaging of stimuli within a frame. If the distracters were also made to change across ISI, averaging was impossible, and focal attention was required to solve the discrimination. This always gave set-size slopes > 1. It is concluded that, under conditions where a stimulus array can be analysed globally, change detection performance is limited by signal detection mechanisms, rather than limited capacity attention or memory mechanisms. However, where this is prevented, for example by changing more than one item, limitations due to attention or memory produce an even steeper set-size effect.     

Waiting to inhale: HIF-1 modulates aerobic respiration

The hypoxia-inducible factor HIF-1 is known to promote anaerobic respiration during low oxygen conditions (hypoxia). In this issue, Fukuda et al. (2007) expand the range of HIF-1's functions by showing that it modulates aerobic respiration as well.     

Body size changes in ground beetle assemblages – a reanalysis of Braun et al. (2004)'s data

Abstract.  1. Data in Braun et al .'s (2004) recent paper on size trends in ground beetles (Carabidae) are re-analysed, after re-classifying the species according to feeding categories.
2. When ground beetles are classified as predatory species, mixed feeders or herbivores, and evaluated separately, the size trends indicate group-specific differences. Most of these do not support the efficiency-specialisation hypothesis.
3. Taxonomic groups rarely fit into one ecological category and ecological analyses should explicitly consider this hurdle.     

A model of the single atrial cell: relation between calcium current and calcium release

The hypothesis that calcium release from the sarcoplasmic reticulum in cardiac muscle is induced by rises in free cytosolic calcium (Fabiato 1983, Am. J. Physiol 245) allows the possibility that the release could be at least partly regenerative. There would then be a non-linear relation between calcium current and calcium release. We have investigated this possibility in a single-cell version of the rabbit-atrial model developed by Hilgemann & Noble (1987, Proc. R. Soc. Lond. B 230). The model predicts different voltage ranges of activation for calcium-dependent processes (like the sodium-calcium exchange current, contraction or Fura-2 signals) and the calcium current, in agreement with the experimental results obtained by Earm et al. (1990, Proc. R. Soc. Lond. B 240) on exchange current tails, Cannell et al. (1987, Science, Wash. 238) by using Fura-2 signals, and Fedida et al. (1987, J. Physiol., Lond. 385) and Talo et al. (1988, Biology of isolated adult cardiac myocytes) by using contraction. However, when the Fura-2 concentration is sufficiently high (greater than 200 microM) the activation ranges become very similar as the buffering properties of Fura-2 are sufficient to remove the regenerative effect. It is therefore important to allow for the buffering properties of calcium indicators when investigating the correlation between calcium current and calcium release.     

Thresholds vary between spatial and temporal forced-choice paradigms: the case of lateral interactions in peripheral vision

Psychophysicists use spatial or temporal two-alternative forced-choice (2AFC) paradigms interchangeably. Thus, experiments with the same general goal are carried out using one or the other paradigm by distinct or even the same research groups. For example, this situation has occurred both in studies on visual sensitivity in dyslexia and in studies on lateral interactions in peripheral vision. Conflicting results in either field (e.g. whether or not dyslexics have a visual deficit and whether or not peripheral detection is facilitated by the presence of flankers) appear to be resolved on the surmise that spatial and temporal 2AFC paradigms indeed produce different results. We designed experiments in which peripheral detection thresholds for Gabor patches (in the presence or absence of suprathreshold flankers) could be measured using completely equivalent spatial and temporal 2AFC paradigms so that any resultant difference can be unequivocally attributed to the effect of the paradigms themselves. The results showed that spatial 2AFC renders significantly lower sensitivity than temporal 2AFC when the target is presented along with suprathreshold flankers, but about the same sensitivity as temporal 2AFC when the target is presented alone. In the end, this resulted in statistically significant facilitation in peripheral vision only when measured with temporal 2AFC. Separate experiments at each of several peripheral locations revealed that the presence and magnitude of this effect varies not only with psychophysical paradigm but also with retinal locus.     

Detection of aperiodic test patterns by pattern specific detectors revealed by subthreshold summation

The hypothesis that the visual system detects, under certain conditions, stimulus patterns by means of filters matched to these patterns (Hauske et al. 1976) may be challenged by the argument that other coding mechanisms like spatial frequency channels, Gabor or Hermite filters mimick the behaviour of matched filters, a view supported by the finding of non-linear contrast-interrelationship functions (CIFs), as determined in superposition experiments. In this paper we argue that an overall non-linear CIF does not contradict the hypothesis of detection by a single matched filter: we find that the sensitivity functions determined in our experiments can be separated into two components reflecting (i) a bandpass filter and (ii) a filter characterised by the spectrum of the test-pattern. Received: 16 December 1996 / Accepted in revised form: 9 June 1998     

Life tables and development of Bemisia argentifolii (Homoptera: Aleyrodidae) at different temperatures

The life history of Bemisia argentifolii Bellows & Perring (Homoptera: Aleyrodidae) on tomato (Lycopersicum spp.) was studied based on the age-stage, two-sex life table at 15, 20, 25, 28, 30, and 35 degrees C. The intrinsic rate of increase (r) at these temperatures is -0.0176, 0.0667, 0.1469, 0.1611, 0.1745, and 0.0989 d(-1), respectively. The relationship among the gross reproductive rate (GRR), the net reproductive rate (R0), and the preadult survivorship (l(a)) is consistent with GRR > l(a) x GRR > R0 for all results at different temperatures. The mean generation time is 81.9, 48.6, 28.4, 25.3, 22.1, and 18.2 d, respectively. The developmental rate of the egg stage at different temperatures fit a linear equation with a thermal summation 89.2 degree-days and a developmental threshold of 11.4 degrees C. The developmental rates of the nymphal stage fit the model of Stinner et al. and the parameters of C, Rmax, k1 and k2 were 0.085, 0.0833, 5.298, and -0.263, respectively.     

Spatial integration characteristics in motion detection and direction identification

Spatial integration characteristics were assessed with drifting gratings for both detection and direction-identification contrast thresholds. Thresholds were measured while stimulus width, length or both were varied. It was found that: (1) the shape of the size/sensitivity functions changes with spatial, but not with temporal, frequency; (2) direction-identification thresholds diverge from the detection thresholds below 1 cycle but can be reliably measured for stimulus widths as small as 0.1275 cycles; (3) the integration characteristics are slightly anisotropic for the identification but not for the detection process, and (4) the two-dimensional spatial integration cannot be directly predicted from its one-dimensional characteristics. Width/sensitivity detection functions are well fitted by predictions of Wilson and Bergen's four-channel model. Predictions from a temporal covariance model provide a poor fit to the identification data. It is argued that classes of detection and direction-identification models must involve identical nonlinearities prior to their respective thresholds. It is concluded that the hypothesis according to which both performances are determined by the same spatial integration stage cannot be rejected.     

Model cortical association fields account for the time course and dependence on target complexity of human contour perception

Can lateral connectivity in the primary visual cortex account for the time dependence and intrinsic task difficulty of human contour detection? To answer this question, we created a synthetic image set that prevents sole reliance on either low-level visual features or high-level context for the detection of target objects. Rendered images consist of smoothly varying, globally aligned contour fragments (amoebas) distributed among groups of randomly rotated fragments (clutter). The time course and accuracy of amoeba detection by humans was measured using a two-alternative forced choice protocol with self-reported confidence and variable image presentation time (20-200 ms), followed by an image mask optimized so as to interrupt visual processing. Measured psychometric functions were well fit by sigmoidal functions with exponential time constants of 30-91 ms, depending on amoeba complexity. Key aspects of the psychophysical experiments were accounted for by a computational network model, in which simulated responses across retinotopic arrays of orientation-selective elements were modulated by cortical association fields, represented as multiplicative kernels computed from the differences in pairwise edge statistics between target and distractor images. Comparing the experimental and the computational results suggests that each iteration of the lateral interactions takes at least ms of cortical processing time. Our results provide evidence that cortical association fields between orientation selective elements in early visual areas can account for important temporal and task-dependent aspects of the psychometric curves characterizing human contour perception, with the remaining discrepancies postulated to arise from the influence of higher cortical areas.