Efficient on the fly calculation of time correlation functions in computer simulations

Time correlation functions yield profound information about the dynamics of a physical system and hence are frequently calculated in computer simulations. For systems whose dynamics span a wide range of time, currently used methods require significant computer time and memory. In this paper, we discuss the multiple-tau correlator method for the efficient calculation of accurate time correlation functions on the fly during computer simulations. The multiple-tau correlator is efficacious in terms of computational requirements and can be tuned to the desired level of accuracy. Further, we derive estimates for the error arising from the use of the multiple-tau correlator and extend it for use in the calculation of mean-square particle displacements and dynamic structure factors. The method described here, in hardware implementation, is routinely used in light scattering experiments but has not yet found widespread use in computer simulations.

Multiscale evolving complex network model of functional connectivity in neuronal cultures

Cultures of cortical neurons grown on multielectrode arrays exhibit spontaneous, robust and recurrent patterns of highly synchronous activity called bursts. These bursts play a crucial role in the development and topological selforganization of neuronal networks. Thus, understanding the evolution of synchrony within these bursts could give insight into network growth and the functional processes involved in learning and memory. Functional connectivity networks can be constructed by observing patterns of synchrony that evolve during bursts. To capture this evolution, a modelling approach is adopted using a framework of emergent evolving complex networks and, through taking advantage of the multiple time scales of the system, aims to show the importance of sequential and ordered synchronization in network function.

Efficiency of pseudo-spectral algorithms with Anderson mixing for the SCFT of periodic block-copolymer phases

This study examines the numerical accuracy, computational cost, and memory requirements of self-consistent field theory (SCFT) calculations when the diffusion equations are solved with various pseudo-spectral methods and the mean field equations are iterated with Anderson mixing. The different methods are tested on the triply-periodic gyroid and spherical phases of a diblock-copolymer melt over a range of intermediate segregations. Anderson mixing is found to be somewhat less effective than when combined with the full-spectral method, but it nevertheless functions admirably well provided that a large number of histories is used. Of the different pseudo-spectral algorithms, the 4th-order one of Ranjan, Qin and Morse performs best, although not quite as efficiently as the full-spectral method.

Curcumin protects organotypic hippocampal slice cultures 4 from Ab1–42 -induced synaptic toxicity

Increasing evidence demonstrates that beta-amyloid (Ab) is toxic to synapses, resulting in the progressive dismantling of neuronal circuits. Counteract the synaptotoxic effects of Ab could be particularly relevant for providing effective treatments for Alzheimer’s disease (AD). Curcumin was recently reported to improve learning and memory in animal models of AD. Little is currently known about the specific mechanisms by which Ab affects neuronal excitability and curcumin ameliorates synaptic transmission in the hippocampus. Organotypic hippocampal slice cultures exposed to Ab1–42 were used to study the neuroprotective effects of curcumin through a spectral analysis of multi-electrode array (MEA) recordings of spontaneous neuronal activity. Curcumin counteracted both deleterious effects of Ab; the initial synaptic dysfunction and the later neuronal death. The analysis of MEA recordings of spontaneous neuronal activity showed an attenuation of signal propagation induced by Ab before cell death and curcumin-induced alterations to local field potential (LFP) phase coherence. Curcumin-mediated attenuation of Ab-induced synaptic dysfunction involved regulation of synaptic proteins, namely phospho-CaMKII and phosphosynapsin I. Taken together, our results expand the neuroprotective role of curcumin to a synaptic level. The identification of these mechanisms underlying the effects of curcumin may lead to new targets for future therapies for AD.

Type-1 error inflation in the traditional by-participant analysis to metamemory accuracy: a generalized mixed-effects model perspective

In order to examine metacognitive accuracy (i.e., the relationship between metacognitive judgment and memory performance), researchers often rely on by-participant analysis, where metacognitive accuracy (e.g., resolution, as measured by the gamma coefficient or signal detection measures) is computed for each participant and the computed values are entered into group-level statistical tests such as the t-test. In the current work, we argue that the by-participant analysis, regardless of the accuracy measurements used, would produce a substantial inflation of Type-1 error rates, when a random item effect is present. A mixed-effects model is proposed as a way to effectively address the issue, and our simulation studies examining Type-1 error rates indeed showed superior performance of mixed-effects model analysis as compared to the conventional by-participant analysis. We also present real data applications to illustrate further strengths of mixed-effects model analysis. Our findings imply that caution is needed when using the by-participant analysis, and recommend the mixed-effects model analysis.

Age differences in brain activity during emotion processing: reflections of age-Related decline or increased emotion regulation?

Despite the fact that physical health and cognitive abilities decline with aging, the ability to regulate emotion remains stable and in some aspects improves across the adult life span. Older adults also show a positivity effect in their attention and memory, with diminished processing of negative stimuli relative to positive stimuli compared with younger adults. The current paper reviews functional magnetic resonance imaging studies investigating age-related differences in emotional processing and discusses how this evidence relates to two opposing theoretical accounts of older adults’ positivity effect. The aging-brain model [Cacioppo et al. in: Social Neuroscience: Toward Understanding the Underpinnings of the Social Mind. New York, Oxford University Press, 2011] proposes that older adults’ positivity effect is a consequence of age-related decline in the amygdala, whereas the cognitive control hypothesis [Kryla-Lighthall and Mather in: Handbook of Theories of Aging, ed 2. New York, Springer, 2009; Mather and Carstensen: Trends Cogn Sci 2005;9:496–502; Mather and Knight: Psychol Aging 2005;20:554–570] argues that the positivity effect is a result of older adults’ greater focus on regulating emotion. Based on evidence for structural and functional preservation of the amygdala in older adults and findings that older adults show greater prefrontal cortex activity than younger adults while engaging in emotion-processing tasks, we argue that the cognitive control hypothesis is a more likely explanation for older adults’ positivity effect than the aging-brain model.

The organization of emotionally autobiographical memories: How emotional knowledge for personal events is represented in autobiographical knowledge base?

The present study aimed to investigate the organization of autobiographical memory and to reveal how emotional knowledge for personal events is represented in autobiographical knowledge base. For these purposes, the event-cueing technique was employed (Brown & Schopflocher, 1998). Forty-six participants were provided eight retrieval cues and asked to generate a personal event related to each of them (i.e., cueing events). Following this, they responded to each cueing event by retrieving two personal episodes (i.e., cued events). The results indicated that cued events shared the life themes with cueing events, suggesting the thematic organization of autobiographical memory. We also found that the life themes of each personal episode determined types of emotional states with which they were associated. The implications for the affect and memory literature and the emotion regulation literature were discussed.

Profiling text comprehension impairments in aphasia

Background: Research in aphasia has focused on acquired dyslexias at the single word level, with a paucity of assessment techniques and rehabilitation approaches for individuals with difficulty at the text level. A rich literature from research with paediatric populations and healthy non-brain damaged, skilled adult readers allows the component processes that are important for text reading to be defined and more appropriate assessments to be devised. Aims: To assess the component processes of text reading in a small group of individuals with aphasia who report difficulties reading at the text level. Do assessments of component processes in reading comprehension reveal distinct profiles of text comprehension? To what extent are text comprehension difficulties caused by underlying linguistic and/or cognitive deficits? Methods & Procedures: Four individuals with mild aphasia who reported difficulties reading at the text level took part in a case-series study. Published assessments were used to confirm the presence of text comprehension impairment. Participants completed a range of assessments to provide a profile of their linguistic and cognitive skills, focusing on processes known to be important for text comprehension. We identified the following areas for assessment: reading speed, language skills (single word and sentence), inferencing, working memory and metacognitive skills (monitoring and strategy use). Outcomes & Results: Performance was compared against age-matched adult control data. One participant presented with a trend for impaired abilities in inferencing, with all other assessed skills being within normal limits. The other three had identified linguistic and working memory difficulties. One presented with a residual deficit in accessing single word meaning that affected text comprehension. The other two showed no clear link between sentence processing difficulties and text comprehension impairments. Across these three, data suggested a link between verbal working memory capacity and specific inferencing skills. Conclusions: Successful text reading relies on a number of component processes. In this paper we have made a start in defining those component processes and devising tasks suitable to assess them. From our results, assessment of verbal working memory and inferencing appears to be critical for understanding text comprehension impairments in aphasia. It is possible that rehabilitation input can capitalize on key meta-cognitive skills (monitoring, strategy use) to support functional reading in the face of existing linguistic, text comprehension and memory impairments.

Signaling via NF-kappaB in the nervous system

Nuclear factor kappa B (NF-kappaB) is an inducible transcription factor present in neurons and glia. Recent genetic models identified a role for NF-kappaB in neuroprotection against various neurotoxins. Furthermore, genetic evidence for a role in learning and memory is now emerging. This review highlights our current understanding of neuronal NF-kappaB in response to synaptic transmission and summarizes potential physiological functions of NF-kappaB in the nervous system. This article contains a listing of NF-kappaB activators and inhibitors in the nervous system, furthermore specific target genes are discussed. Synaptic NF-kappaB activated by glutamate and Ca2+ will be presented in the context of retrograde signaling. A controversial role of NF-kappaB in neurodegenerative diseases will be discussed. A model is proposed explaining this paradox as deregulated physiological NF-kappaB activity, where novel results are integrated, showing that p65 could be turned from an activator to a repressor of anti-apoptotic genes.

Transcription factor NF-kappaB is transported to the nucleus via cytoplasmic dynein/dynactin motor complex in hippocampal neurons

Background Long-term changes in synaptic plasticity require gene transcription, indicating that signals generated at the synapse must be transported to the nucleus. Synaptic activation of hippocampal neurons is known to trigger retrograde transport of transcription factor NF-κB. Transcription factors of the NF-κB family are widely expressed in the nervous system and regulate expression of several genes involved in neuroplasticity, cell survival, learning and memory. Principal Findings In this study, we examine the role of the dynein/dynactin motor complex in the cellular mechanism targeting and transporting activated NF-κB to the nucleus in response to synaptic stimulation. We demonstrate that overexpression of dynamitin, which is known to dissociate dynein from microtubules, and treatment with microtubule-disrupting drugs inhibits nuclear accumulation of NF-κB p65 and reduces NF-κB-dependent transcription activity. In this line, we show that p65 is associated with components of the dynein/dynactin complex in vivo and in vitro and that the nuclear localization sequence (NLS) within NF-κB p65 is essential for this binding. Conclusion This study shows the molecular mechanism for the retrograde transport of activated NF-κB from distant synaptic sites towards the nucleus.

Latent learning in end stage renal disease (ESRD)

Cognitive functions such as attention and memory are known to be impaired in End Stage Renal Disease (ESRD), but the sites of the neural changes underlying these impairments are uncertain. Patients and controls took part in a latent learning task, which had previously shown a dissociation between patients with Parkinson’s disease and those with medial temporal damage. ESRD patients (n=24) and age and education-matched controls (n=24) were randomly assigned to either an exposed or unexposed condition. In Phase 1 of the task, participants learned that a cue (word) on the back of a schematic head predicted that the subsequently seen face would be smiling. For the exposed (but not unexposed) condition, an additional (irrelevant) colour cue was shown during presentation. In Phase 2, a different association, between colour and facial expression, was learned. Instructions were the same for each phase: participants had to predict whether the subsequently viewed face was going to be happy or sad. No difference in error rate between the groups was found in Phase 1, suggesting that patients and controls learned at a similar rate. However, in Phase 2, a significant interaction was found between group and condition, with exposed controls performing significantly worse than unexposed (therefore demonstrating learned irrelevance). In contrast, exposed patients made a similar number of errors to unexposed in Phase 2. The pattern of results in ESRD was different from that previously found in Parkinson’s disease, suggesting a different neural origin.

La adquisición de las cláusulas relativas en niños hispanohablantes: un proceso dependiente de múltiples factores

Diessel and Tomasello (2000, 2005) propose that relative clauses (RC) are acquired in a piecemeal-fashion in which children initially produce relatively simple RCs. According to their hypothesis, several factors are involved in the process of mastering these sentences: i) similarities between RCs and simpler constructions; ii) semantic and pragmatic factors; iii) children processing limitations; and iv) RC´s frequency of use in the input. We study the RCs produced by 44 Spanish speaking children, from 1;07 to 5;00 years old in order to validate Diessel and Tomasello´s hypothesis in the acquisition of Spanish RCs. Results show that i) the first RCs to appear have just one proposition; ii) first RCs do not interrupt the main clause, they are rather attached at the end of it; iii) the first RCs with two propositions are predominantly intransitives, with a relative pronoun in the subject syntactic role; iv) during first periods, factors such as semantic and syntactic processing, and memory seem to play a more determinant role than input and pragmatic factors. Input factor could be indeed involved in the acquisition of RC but in late periods, when children are older than 4;00 years old; and v) transitive RCs appear in late periods. Diessel and Tomasello´s hypothesis seem to explain our results.