Attention and time estimation in 5- and 8-year-old children: a dual-task procedure

This experiment tested the effect of a dual-task on time reproduction in 5- and 8-year-olds. Children had to reproduce a stimulus duration lasting for 6 or 12 s, during which they either did or did not perform a concurrent non-temporal task (i.e. picture naming) both in low (LA) and high (HA) attentional demand conditions. The results showed that children reproduced shorter durations in the dual-task than in the single-task condition, whatever the duration value used. However, this shortening effect was greater in the 5-year-olds than in the 8-year-olds. Furthermore, in the 5-year-olds, temporal reproductions were significantly shorter in both dual-tasks (LA or HA) than in the single-task, whereas, in the 8-year-olds, differences reached significance only between the HA dual-task and the single-task. In the non-temporal task, the proportion of naming errors was also greater in the dual-task than in the single-task, especially under high attentional demand, but it did not significantly differ between the two age groups tested.     

Avoiding costly mistakes in groups: The evolution of error management in collective decision making

Individuals continuously have to balance the error costs of alternative decisions. A wealth of research has studied how single individuals navigate this, showing that individuals develop response biases to avoid the more costly error. We, however, know little about the dynamics in groups facing asymmetrical error costs and when social influence amplifies either safe or risky behavior. Here, we investigate this by modeling the decision process and information flow with a drift–diffusion model extended to the social domain. In the model individuals first gather independent personal information; they then enter a social phase in which they can either decide early based on personal information, or wait for additional social information. We combined the model with an evolutionary algorithm to derive adaptive behavior. We find that under asymmetric costs, individuals in large cooperative groups do not develop response biases because such biases amplify at the collective level, triggering false information cascades. Selfish individuals, however, undermine the group’s performance for their own benefit by developing higher response biases and waiting for more information. Our results have implications for our understanding of the social dynamics in groups facing asymmetrical errors costs, such as animal groups evading predation or police officers holding a suspect at gunpoint.     

Lighter: fast and memory-efficient sequencing error correction without counting

Lighter is a fast, memory-efficient tool for correcting sequencing errors. Lighter avoids counting k-mers. Instead, it uses a pair of Bloom filters, one holding a sample of the input k-mers and the other holding k-mers likely to be correct. As long as the sampling fraction is adjusted in inverse proportion to the depth of sequencing, Bloom filter size can be held constant while maintaining near-constant accuracy. Lighter is parallelized, uses no secondary storage, and is both faster and more memory-efficient than competing approaches while achieving comparable accuracy.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0509-9) contains supplementary material, which is available to authorized users.     

Modelling species distributions without using species distributions: the cane toad in Australia under current and future climates

Accurate predictions of the potential distribution of range-shifting species are required for effective management of invasive species, and for assessments of the impact of climate change on native species. Range-shifting species pose a challenge for traditional correlative approaches to range prediction, often requiring the extrapolation of complex statistical associations into novel environmental space. Here we take an alternative approach that does not use species occurrence data, but instead captures the fundamental niche of a species by mechanistically linking key organismal traits with spatial data using biophysical models. We demonstrate this approach with a major invasive species, the cane toad Bufo marinus in Australia, assessing the direct climatic constraints on its ability to move, survive, and reproduce. We show that the current range can be explained by thermal constraints on the locomotor potential of the adult stage together with limitations on the availability of water for the larval stage. Our analysis provides a framework for biologically grounded predictions of the potential for cane toads to expand their range under current and future climate scenarios. More generally, by quantifying spatial variation in physiological constraints on an organism, trait-based approaches can be used to investigate the range-limits of any species. Assessments of spatial variation in the physiological constraints on an organism may also provide a mechanistic basis for forecasting the rate of range expansion and for understanding a species' potential to evolve at range-edges. Mechanistic approaches thus have broad application to process-based ecological and evolutionary models of range-shift.     

Perceptual dominance time distributions in multistable visual perception

Perceptual multistability, alternative perceptions of an unchanging stimulus, gives important clues to neural dynamics. The present study examined 56 perceptual dominance time series for a Necker cube stimulus, for ambiguous motion, and for binocular rivalry. We made histograms of the perceptual dominance times, based on from 307 to 2478 responses per time series (median=612), and compared these histograms to gamma, lognormal and Weibull fitted distributions using the Kolmogorov–Smirnov goodness-of-fit test. In 40 of the 56 tested cases a lognormal distribution provided an acceptable fit to the histogram (in 24 cases it was the only fit). In 16 cases a gamma distribution, and in 11 cases a Weibull distribution, were acceptable but never as the only fit in either case. Any of the three distributions were acceptable in three cases and none provided acceptable fits in 12 cases. Considering only the 16 cases in which a lognormal distribution was rejected (p<0.05) revealed that minor adjustments to the fourth-moment term of the lognormal characteristic function restored good fits. These findings suggest that random fractal theory might provide insight into the underlying mechanisms of multistable perceptions.     

Liquid residence time distributions in immobilized cell bioreactors

Previous work has demonstrated that high ethanol productivities can be achieved using yeast or bacterial cells adsorbed onto the surface of ion exchange resin in vertical packed bed bioreactors. The present work quantitatively characterizes the overall degree of backmixing in such reactors at two scales of operation: 2.0 and 8.0 L. Stimulus-response experiments, using two solvents (2,3-butanediol and 2-ethoxyethanol) as tracers, were performed to measure the liquid phase residence time distribution (RTD) during continuous ethanol fermentations using the yeast Saccharomyces cerevisiae and the bacterium Zymomonas mobilis at the 2-L scale, and with S. cerevisiae at the 8-L scale. In order to separately determine the effects of liquid flow rate and gas evolution on the degree of mixing, stimulus-response experiments were also performed in the systems without microbial cells present. The evolution of CO(2) was found to dramatically increase the extent of mixing; however, the tanks-in-series model for non-ideal flow represented the systems adequately. The packed beds were equivalent to over 70 tanks-in-series during abiotic operation while during fermentations, with similar liquid flow rates, they ranged in equivalence from 35 to 15 tanks-in-series. This increased knowledge of the overall degree of mixing in packed bed, immobilized cell bioreactors will allow for more accurate kinetic modelling and efficient scale up of the process.     

Coalescent time distributions in trees of arbitrary size

The relationship between speciation times and the corresponding times of gene divergence is of interest in phylogenetic inference as a means of understanding the past evolutionary dynamics of populations and of estimating the timing of speciation events. It has long been recognized that gene divergence times might substantially pre-date speciation events. Although the distribution of the difference between these has previously been studied for the case of two populations, this distribution has not been explicitly computed for larger species phylogenies. Here we derive a simple method for computing this distribution for trees of arbitrary size. A two-stage procedure is proposed which (i) considers the probability distribution of the time from the speciation event at the root of the species tree to the gene coalescent time conditionally on the number of gene lineages available at the root; and (ii) calculates the probability mass function for the number of gene lineages at the root. This two-stage approach dramatically simplifies numerical analysis, because in the first step the conditional distribution does not depend on an underlying species tree, while in the second step the pattern of gene coalescence prior to the species tree root is irrelevant. In addition, the algorithm provides intuition concerning the properties of the distribution with respect to the various features of the underlying species tree. The methodology is complemented by developing probabilistic formulae and software, written in R. The method and software are tested on five-taxon species trees with varying levels of symmetry. The examples demonstrate that more symmetric species trees tend to have larger mean coalescent times and are more likely to have a unimodal gamma-like distribution with a long right tail, while asymmetric trees tend to have smaller mean coalescent times with an exponential-like distribution. In addition, species trees with longer branches generally have shorter mean coalescent times, with branches closest to the root of the tree being most influential.     

Modeling multicellular response to nonuniform distributions of radioactivity: differences in cellular response to self-dose and cross-dose

Radiopharmaceuticals are distributed nonuniformly in tissue. While distributions of radioactivity often appear uniform at the organ level, in fact, microscopic examination reveals that only a fraction of the cells in tissue are labeled. Labeled cells and unlabeled cells often receive different absorbed doses depending on the extent of the nonuniformity and the characteristics of the emitted radiations. The labeled cells receive an absorbed dose from radioactivity within the cell (self-dose) as well as an absorbed dose from radioactivity in surrounding labeled cells (cross-dose). Unlabeled cells receive only a cross-dose. In recent communications, a multicellular cluster model was used to investigate the lethality of microscopic nonuniform distributions of 131I iododeoxyuridine (131IdU). For a given mean absorbed dose to the tissue, the dose response depended on the percentage of cells that were labeled. Specifically, when 1, 10 and 100% of the cells were labeled, a D37 of 6.4, 5.7 and 4.5 Gy, respectively, was observed. The reason for these differences was recently traced to differences in the cellular response to the self- and cross-doses delivered by 131IdU. Systematic isolation of the effects of self-dose resulted in a D37 of 1.2 +/- 0.3 Gy. The cross-dose component yielded a D37 of 6.4 +/- 0.5 Gy. In the present work, the overall survival of multicellular clusters containing 1, 10 and 100% labeled cells is modeled using a semi-empirical approach that uses the mean lethal self- and cross-doses and the fraction of cells labeled. There is excellent agreement between the theoretical model and the experimental data when the surviving fraction is greater than 1%. Therefore, when the distribution of 131I in tissue is nonuniform at the microscopic level, and the cellular response to self- and cross-doses differs, multicellular dosimetry can be used successfully to predict biological response, whereas the mean absorbed dose fails in this regard.     

Distinguishing error from chaos in ecological time series

Over the years, there has been much discussion about the relative importance of environmental and biological factors in regulating natural populations. Often it is thought that environmental factors are associated with stochastic fluctuations in population density, and biological ones with deterministic regulation. We revisit these ideas in the light of recent work on chaos and nonlinear systems. We show that completely deterministic regulatory factors can lead to apparently random fluctuations in population density, and we then develop a new method (that can be applied to limited data sets) to make practical distinctions between apparently noisy dynamics produced by low-dimensional chaos and population variation that in fact derives from random (high-dimensional) noise, such as environmental stochasticity or sampling error. To show its practical use, the method is first applied to models where the dynamics are known. We then apply the method to several sets of real data, including newly analysed data on the incidence of measles in the United Kingdom. Here the additional problems of secular trends and spatial effects are explored. In particular, we find that on a city-by-city scale measles exhibits low-dimensional chaos (as has previously been found for measles in New York City), whereas on a larger, country-wide scale the dynamics appear as a noisy two-year cycle. In addition to shedding light on the basic dynamics of some nonlinear biological systems, this work dramatizes how the scale on which data is collected and analysed can affect the conclusions drawn.     

Phycomyces: discovery of the aiming error in the avoidance response

Vacuoles were prepared from germinating castor bean endosperm (Ricinus communis var Hale) and purified by filtration through a cotton layer under physiological osmolarity. The purity of vacuoles prepared by this method was comparable with that prepared by a sucrose step gradient centrifugation reported in a previous paper (Nishimura, Beevers 1978 Plant Physiol 62: 44-48). It was shown by assays of marker enzymes that the final preparation contained trace contamination of other organelles (glyoxysomes, mitochondria, and endoplasmic reticulum) and the cytosol. The isolated vacuoles were stained with neutral red, indicating that the intravacuolar pH is acidic. Intravacuolar pH of isolated vacuoles was determined by measuring the distribution of [¹⁴C]methylamine in the vacuoles and by directly measuring the pH of vacuolar extracts. The pH of isolated vacuolar extracts was 5.7 to 5.9. Similar values were obtained by the methylamine method and it was shown that intravacuolar pH increased as the pH of the medium was increased.     

Detecting multimodality in saccadic reaction time distributions in gap and overlap tasks

In many cases the distribution of saccadic reaction times (SRT) deviates considerably from a unimodal distribution and may often exhibit several peaks. We present a statistical approach to determining the number and form of the individual peaks. The overall density of the reaction times f _i (t), i=1…M obtained in M different experiments with the same subject is described as the sum of K basis functions x _k (t),k=1…K with different weights and an error term. A change in the experimental conditions is assumed to cause a change in the weights, not in the basis functions. We minimize the square of the difference (measured data minus approximation), divided by the error of the data. Incrementing K step by step we determine the necessary number of basis functions. This method is applied to data of six subjects tested in different saccade tasks. We detect five different modes: two in the range 80–140 ms (express modes), two in the range 145–190 ms (fast-regular mode) and one at about 230 ms (slow-regular mode). These modes are located at about the same positions for different subjects. The method presented here not only proves statistically the existence of several modes in SRT distributions but also allows the distributions to be described by a few characteristic numbers that go beyond the mean values and standard deviations. Received: 24 March 1997 / Accepted: 5 December 1997     

Moments of physiological transit time distributions and the time course of drug disposition in the body

Characterizing the tissue distribution kinetics of drugs by physiological and physico-chemical parameters and using a circulatory model the time course of blood concentration after intravenous injection is predicted for linear pharmacokinetic systems. The interrelationships between the first three (zero to second) moments of the distribution functions of organ transfer times, circulation times and residence times of drug molecules in the body are described. Utilizing literature data the model is applied to the analysis of lidocain kinetics in humans.     

Biocalcification through time: environmental challenge and cellular response

A concept explaining biocalcification as a form of calcium detoxification is advanced using geochemical and paleontological criteria. The first appearence of calcareous skeletons at the turn of the Precambrian/Cambrian is interpreted as a biotic response to a gradual rise of Ca²⁺ in world ocean resulting in Ca²⁺ stress environments in shelf areas. Periodic appearance in the Phanerozoic record of heavily calcified marine biota, absent or relic in modern seas, suggests considerable temporal fluctuations of calcium concentrations in the ancient ocean. Temporal changes in Ca²⁺ and mineral nutrient contents in the environment can thus be seen as overriding factors in the evolution of organisms.     

Costly mistakes: translational infidelity and protein homeostasis

Protein misfolding is increasingly being recognized as a key process in organismal health and disease. Drummond and Wilke (2008) show that misfolding caused by mistakes during the translation of RNA into proteins (mistranslation) also results in a strong selection pressure to optimize translational fidelity, especially for proteins that are highly expressed.     

Dynamics of the central bottleneck: dual-task and task uncertainty

Why is the human brain fundamentally limited when attempting to execute two tasks at the same time or in close succession? Two classical paradigms, psychological refractory period (PRP) and task switching, have independently approached this issue, making significant advances in our understanding of the architecture of cognition. Yet, there is an apparent contradiction between the conclusions derived from these two paradigms. The PRP paradigm, on the one hand, suggests that the simultaneous execution of two tasks is limited solely by a passive structural bottleneck in which the tasks are executed on a first-come, first-served basis. The task-switching paradigm, on the other hand, argues that switching back and forth between task configurations must be actively controlled by a central executive system (the system controlling voluntary, planned, and flexible action). Here we have explicitly designed an experiment mixing the essential ingredients of both paradigms: task uncertainty and task simultaneity. In addition to a central bottleneck, we obtain evidence for active processes of task setting (planning of the appropriate sequence of actions) and task disengaging (suppression of the plan set for the first task in order to proceed with the next one). Our results clarify the chronometric relations between these central components of dual-task processing, and in particular whether they operate serially or in parallel. On this basis, we propose a hierarchical model of cognitive architecture that provides a synthesis of task-switching and PRP paradigms.     

Prospective timing under dual-task paradigms: attentional and contextual-change mechanisms

The effect of a concurrent memory task on prospective time estimates by human participants was investigated in two experiments. The objective was to isolate task effects from those of participant timing strategy (self-paced counting) and number of contextual changes during the temporal stimulus. Accordingly, self-paced counting was suppressed by requiring participants to perform a word-reading task during the temporal stimuli, while number of stimulus changes presented during temporal stimuli was controlled. Presence versus absence of the concurrent memory task was manipulated in Experiment 1, and instruction to focus on timing or to focus on memory was manipulated in Experiment 2. There was no significant effect of presence versus absence of the concurrent memory task on time estimates; however, time estimates were shorter when participants were instructed to focus on memory versus timing. In both experiments, time estimates were positively correlated with participants' estimates of the number of words presented during the interval, even though number of words presented was invariant. These findings were generally consistent with resource-allocation attentional accounts of concurrent task effects; however, support for a contextual-change model of timing was also obtained.