Sensitivity to initial conditions in the route-finder model

A model of stimulus generalization [Staddon, J.E.R., Reid, A.K., 1990. On the dynamics of generalization. Psychol. Rev. 97, 576-578] was extended by Reid and Staddon [Reid, A.K., Staddon, J.E.R., 1998. A dynamic route finder for the cognitive map. Psychol. Rev. 105, 585-601] to account for the route-finder issue in the Tolman-Guthrie discussion about cognitive maps. This deterministic model has been described as sensitive to initial conditions in terms of the parameters of a diffusion equation [Reid, A.K., Staddon, J.E.R., 1998. A dynamic route finder for the cognitive map. Psychol. Rev. 105, 585-601]. A simulation study was carried out to test this assertion, evaluating whether the pattern of variation in the model output resembled a chaotic pattern. Results indicate that the model is sensitive to initial conditions, suggesting that the spatial navigation task addressed by this model involves non-linear relationships and complexity beyond the apparent simplicity of the stimulus generalization process.     

Simulated neural dynamics of decision-making in an auditory delayed match-to-sample task

An important goal of research on the cognitive neuroscience of decision-making is to produce a comprehensive model of behavior that flows from perception to action with all of the intermediate steps defined. To understand the mechanisms of perceptual decision-making for an auditory discrimination experiment, we connected a large-scale, neurobiologically realistic auditory pattern recognition model to a three-layer decision-making model and simulated an auditory delayed match-to-sample (DMS) task. In each trial of our simulated DMS task, pairs of stimuli were compared each stimulus being a sequence of three frequency-modulated tonal-contour segments, and a "match" or "nonmatch" button was pressed. The model's simulated response times and the different patterns of neural responses (transient, sustained, increasing) are consistent with experimental data and the simulated neurophysiological activity provides insights into the neural interactions from perception to action in the auditory DMS task.     

Spontaneous eyeblinks are correlated with responses during the Stroop task

The timing and frequency of spontaneous eyeblinking is thought to be influenced by ongoing internal cognitive or neurophysiological processes, but how precisely these processes influence the dynamics of eyeblinking is still unclear. This study aimed to better understand the functional role of eyeblinking during cognitive processes by investigating the temporal pattern of eyeblinks during the performance of attentional tasks. The timing of spontaneous eyeblinks was recorded from 28 healthy subjects during the performance of both visual and auditory versions of the Stroop task, and the temporal distributions of eyeblinks were estimated in relation to the timing of stimulus presentation and vocal response during the tasks. We found that the spontaneous eyeblink rate increased during Stroop task performance compared with the resting rate. Importantly, the subjects (17/28 during the visual Stroop, 20/28 during the auditory Stroop) were more likely to blink before a vocal response in both tasks (150-250 msec) and the remaining subjects were more likely to blink soon after the vocal response (200-300 msec), regardless of the stimulus type (congruent or incongruent) or task difficulty. These findings show that spontaneous eyeblinks are closely associated with responses during the performance of the Stroop task on a short time scale and suggest that spontaneous eyeblinks likely signal a shift in the internal cognitive or attentional state of the subjects.     

IS EVOLVABILITY INVOLVED IN THE ORIGIN OF MODULAR VARIATION?

Abstract.— Lipson et al. (2002) presented an elegant linear algebraic formalism to define and study the evolution of modularity in an artificial evolving system. They employed simulation data to support their suggestion that modularity arises spontaneously in temporally fluctuating systems in response to selection for enhanced evolvability. We show analytically and by simulation that their correlate of modularity is itself under selection and so is not a reliable indicator of selection for modularity per se. In addition, we question the relation between modularity and evolvability in their simulations, suggesting that this modularity cannot confer enhanced evolvability.     

The timing of the cognitive cycle

We propose that human cognition consists of cascading cycles of recurring brain events. Each cognitive cycle senses the current situation, interprets it with reference to ongoing goals, and then selects an internal or external action in response. While most aspects of the cognitive cycle are unconscious, each cycle also yields a momentary "ignition" of conscious broadcasting. Neuroscientists have independently proposed ideas similar to the cognitive cycle, the fundamental hypothesis of the LIDA model of cognition. High-level cognition, such as deliberation, planning, etc., is typically enabled by multiple cognitive cycles. In this paper we describe a timing model LIDA's cognitive cycle. Based on empirical and simulation data we propose that an initial phase of perception (stimulus recognition) occurs 80-100 ms from stimulus onset under optimal conditions. It is followed by a conscious episode (broadcast) 200-280 ms after stimulus onset, and an action selection phase 60-110 ms from the start of the conscious phase. One cognitive cycle would therefore take 260-390 ms. The LIDA timing model is consistent with brain evidence indicating a fundamental role for a theta-gamma wave, spreading forward from sensory cortices to rostral corticothalamic regions. This posteriofrontal theta-gamma wave may be experienced as a conscious perceptual event starting at 200-280 ms post stimulus. The action selection component of the cycle is proposed to involve frontal, striatal and cerebellar regions. Thus the cycle is inherently recurrent, as the anatomy of the thalamocortical system suggests. The LIDA model fits a large body of cognitive and neuroscientific evidence. Finally, we describe two LIDA-based software agents: the LIDA Reaction Time agent that simulates human performance in a simple reaction time task, and the LIDA Allport agent which models phenomenal simultaneity within timeframes comparable to human subjects. While there are many models of reaction time performance, these results fall naturally out of a biologically and computationally plausible cognitive architecture.     

Self-synchronization and task fulfilment in ant colonies

Some authors have hypothesized that the observed self-synchronized activity in ant colonies provides some adaptive advantages, and, in particular, it has been suggested that task realization may benefit from this ordered temporal pattern of behaviour (Robinson, 1992, Ann. Rev. Entomol, 37, 637-702; Hatcher et al., 1992, Naturwissenschaften, 79, 32-34). In this paper, we use a model of self-synchronized activity (the fluid neural network) to suggest that with self-synchronized patterns of activity a task may be fulfiled more effectively than with non-synchronized activity, at the same average level of activity per individual.     

Exponential equilibration of genetic circuits using entropy methods

Journal of Mathematical Biology - We analyse a continuum model for genetic circuits based on a partial integro-differential equation initially proposed in Friedman et al. (Phys Rev Lett...     

Understanding decision-making deficits in neurological conditions: insights from models of natural action selection

Models of natural action selection implicate fronto-striatal circuits in both motor and cognitive 'actions'. Dysfunction of these circuits leads to decision-making deficits in various populations. We review how computational models provide insights into the mechanistic basis for these deficits in Parkinson's patients and those with ventromedial frontal damage. We then consider implications of the models for understanding behaviour and cognition in attention-deficit/hyperactivity disorder (ADHD). Incorporation of cortical noradrenaline function into the model improves action selection in noisy environments and accounts for response variability in ADHD. We close with more general clinical implications.     

No selection for cheating in a natural meta‐population of rhizobia

Whether natural selection favours ‘cheating’ in mutualisms is hotly debated. Gano‐Cohen et al. (2019a) report a negative correlation between fitness and mutualist quality in rhizobia, suggesting that rhizobia evolve to cheat. However, reanalysis of their data shows that the correlation is an artefact of unequal sampling across populations.     

Stroop effects from 3 to 10 years: the critical role of reading acquisition

We studied 241 nursery and primary school 3- to 10-year old children with a discrete-trial version of the Stroop Test, including both a Color-Naming and (for the 6- to 10-year olds only) a Word-Reading task. The classic Stroop effect was present across all the ages, with an inverted U-shaped pattern: increasing from 3- to 7-year olds, then decreasing. Preschool children who were able to read showed a Stroop effect larger than same-age, unable to read children. The reverse Stroop effect was present across all the studied ages but the 6-year-olds, who instead displayed some facilitation in reading congruent vs. black words. Since the acquisition of reading skills turned out to be crucial for the Stroop effects, the present research may be useful to study developmental reading impairments by providing normative data.     

Viral determinants of polarized assembly for the murine leukemia virus

Retrovirus transmission via direct cell-cell contact is more efficient than diffusion through the extracellular milieu. This is believed to be due to the ability of viruses to efficiently coordinate several steps of the retroviral life cycle at cell-cell contact sites (D. C. Johnson et al., J. Virol. 76:1-8, 2002; D. M. Phillips, AIDS 8:719-731, 1994; Q. Sattenau, Nat. Rev. Microbiol. 6:815-826, 2008). Using the murine leukemia virus (MLV) as a model retrovirus, we have previously shown that interaction between viral envelope (Env) and receptor directs viral assembly to cell-cell contact sites to promote efficient viral spreading (J. Jin et al., PLoS Biol. 7:e1000163, 2009). In addressing the underlying mechanism, we observed that Env cytoplasmic tail directs this contact-induced polarized assembly. We present here the viral determinants in the Env cytoplasmic tail and Gag that are important in this process. A tyrosine residue within the cytoplasmic tail of Env was identified, which directs polarized assembly. MLV matrix-mediated membrane targeting is required for Gag recruitment to sites of cell-cell contact. Our results suggest that MLV polarized assembly is mediated by a direct or indirect interaction between both domains, thereby coupling Gag recruitment and virus assembly to Env accumulation at the cell-cell interface. In contrast, HIV Gag that assembles outside of cell-cell interfaces can subsequently be drawn into contact zones mediated by MLV Env and receptor, a finding that is consistent with the previously observed lateral movement of HIV into the virological synapse (W. Hubner et al., Science 323:1743-1747, 2009; D. Rudnicka et al., J. Virol. 83:6234-6246, 2009). As such, we observed two distinct modes of virus cell-to-cell transmission that involve either polarized or nonpolarized assembly, but both result in virus transmission.     

Connexons and cell adhesion: a romantic phase

Recent evidence indicates, that gap junction forming proteins do not only contribute to intercellular communication (Kanno and Saffitz in Cardiovasc Pathol 10:169-177, 2001; Saez et al. in Physiol Rev 83:1359-1400, 2003), ion homeostasis and volume control (Goldberg et al. in J Biol Chem 277:36725-36730, 2002; Saez et al. in Physiol Rev 83:1359-1400, 2003). They also serve biological functions in a mechanical sense, supporting adherent connections between neighbouring cells of epithelial and non-epithelial tissues (Clair et al. in Exp Cell Res 314:1250-1265, 2008; Shaw et al. in Cell 128:547-560, 2007), where they stabilize migratory pathways in the developing central nervous system (Elias et al. in Nature 448:901-907, 2007; Malatesta et al. in Development 127:5253-5263, 2000; Noctor et al. in Nature 409:714-720, 2001; Rakic in Brain Res 33:471-476, 1971; J Comp Neurol 145:61-83 1972; Science 241:170-176, 1988), or mediate polarized movements and directionality of neural crest cells during organogenesis (Kirby and Waldo in Circ Res 77:211-215, 1995; Xu et al. in Development 133:3629-3639, 2006). Since, most data describing adhesive properties of gap junctions delt with connexin 43 (Cx43) (Beardslee et al. in Circ Res 83:629-635, 1998), we will focus our brief review on this isoform.     

Clarifying the roles of kinetics and diffusion in activated sludge filamentous bulking

We hypothesized that the growth rates of filaments and floc formers in activated sludge are affected by the combination of kinetic selection (Lou and de los Reyes, Biotechnol Bioeng 92(6): 729-739, 2005b) and substrate diffusion limitation (Martins et al., Water Res 37:2555-2570, 2003). To clarify the influence of these factors in explaining filamentous bulking, a conceptual framework was developed in this study. The framework suggests the existence of three different regions corresponding to bulking, non-bulking, and intermediate regions, based on substrate concentration. In the bulking and non-bulking regions, kinetic growth differences control the competition process, and filaments or floc formers dominate, respectively. In the intermediate region, substrate diffusion limitation, determined by the floc size, plays the major role in causing bulking. To test this framework, sequencing batch reactors (SBRs) were operated with influent COD of 100, 300, 600, and 1,000 mg/L, and the sludge settleability was measured at various floc size distributions that were developed using different mixing strengths. The experimental data in the bulking and intermediate regions supported the proposed framework. A model integrating the two factors was developed to simulate the substrate concentrations at different depths and floc sizes under intermittently feeding conditions. The modeling results confirmed that substrate diffusion limitation occurs inside the flocs at a certain range of activated sludge floc sizes over the operation cycle, and provided additional support for the proposed framework.     

Genomic evidence for parallel adaptation to cities

Urban evolutionary biology is the study of rapid evolutionary change in response to humans and our uses of land to support city dwellers. Because cities are relatively modern additions to the natural world, research on urban evolution tends to focus on microevolutionary change that has happened across a few to many hundreds of generations. These questions still fall under the broad purview of evolutionary ecology. However, the severity, rapidity and replication of environmental changes that drive evolution in this context make it worthy of specific attention. Urban evolution provides the opportunity to study the earliest stages of evolution in a context that is scientifically interesting and societally important. The newness of urban populations and their proximity to natural populations also creates challenges when trying to detect population genetic change. In a From the Cover article in this issue of Molecular Ecology, Mueller et al. use whole genome resequencing data to address some of these challenges while exploring genetic changes associated with urbanization in three replicate urban‐rural burrowing owl (Athene cunicularia) populations. Combining multiple approaches across these sample sites Mueller et al. find evidence for selection on genes whose function is related to synapses, neuron projections, brain connectivity and cognitive function in general. That selection was parallel suggests that phenotypes related to brain processes were probably particularly important for urban adaptation.     

Good genes go fisherian

It has been a common perception of the ‘good genes’ mechanism of sexual selection that mating with males affording the most extreme sexual ornaments should benefit females by increasing the survival of their progeny. The ‘sexy son’ mechanism, however, stressed the enhanced reproduction of highly ornamented male progeny. A new model developed by Kokko et al. now shows that both mechanisms belong to the same continuum of indirect selection, but their relative weights can vary depending on the costs of mate choice.     

Mutant EF-Tu increases missense error in vitro

Summary We have studied the consequences of mutational alteration in the structure of EF-Tu on the missense errors and proofreading activity of bacterial ribosomes in vitro. Our data show that the EF-Tu Bo mutant form of EF-Tu (van der Meide et al. 1983a) is inactive in polypeptide synthesis on the ribosome, even though it binds aminoacyl-tRNA. A second mutant form, EF-Tu Ar (van der Meide et al. 1983a), is active in polypeptide synthesis but supports a much higher messense incorporation with either leucine isoacceptor 2 or leucine isoacceptor 4 in the in vitro system. Further analysis of the kinetic basis of this enhanced missense frequency revealed that the mutation responsible for the alteration in EF-Tu Ar increases the errors at both the proofreading step and the initial selection. In this respect the effect of this particular mutation is similar to the mode of action of the antibiotic kanamycin (Jelenc and Kurland 1984).     

Biological effects due to weak electric and magnetic fields: the temperature variation threshold.

A large number of epidemiological and experimental studies suggest that prolonged (>100 s) weak 50-60-Hz electric and magnetic field (EMF) exposures may cause biological effects(NIEHS Working Group, NIH, 1998; Bersani, 1999). We show, however, that for typical temperature sensitivities of biochemical processes, realistic temperature variations during long exposures raise the threshold exposure by two to three orders of magnitude over a fundamental value, independent of the biophysical coupling mechanism. Temperature variations have been omitted in previous theoretical analyses of possible weak field effects, particularly stochastic resonance (Bezrukov and Vodyanoy 1997a. Nature. 385:319-321; Astumian et al., 1997 Nature. 338:632-633; Bezrukov and Vodyanoy, 1997b. Nature. 338:663; Dykman and McClintock, 1998. Nature. 391:344; McClintock, 1998;. Gammaitoni et al., 1998. Rev. Mod. Phys. 70:223-287). Although sensory systems usually respond to much shorter (approximately 1 s) exposures and can approach fundamental limits (Bialek, 1987 Annu. Rev. Biophys. Biophys. Chem. 16:455-468; Adair et al, 1998. Chaos. 8:576-587), our results significantly decrease the plausibility of effects for nonsensory biological systems due to prolonged, weak-field exposures.     

Limits of Data Analysis in Scientific Inference: Reply to Sleep et al.

ABSTRACT Statistical inference is an important element of science, but these inferences are constrained within the framework established by the objectives and design of a study. The choice of approach to data analysis, while important, has far less consequence on scientific inference than claimed by Sleep et al. (2007). Their principal assertion—that when model selection is used as the approach to data analysis, all studies provide a reliable foundation for distinguishing among mechanistic explanatory hypotheses—is incorrect and encourages faulty inferences. Sleep et al. (2007) overlook the critical distinction between inferences that result from studies designed a priori to discriminate among a set of candidate explanations versus inferences that result from exploring data post hoc from studies designed originally to meet pattern-based objectives. No approach to data analysis, including model selection, has the power to overcome fundamental limitations on inferences imposed by study design. The comments by Sleep et al. (2007) reinforce the need for scientists to understand clearly the inferential basis for their scientific claims, including the roles and limitations of data analysis.