394 research outputs found
Neutral coding - A report based on an NRP work session
Neural coding by impulses and trains on single and multiple channels, and representation of information in nonimpulse carrier
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Mice produce ultrasonic vocalizations by intra-laryngeal planar impinging jets
Rodent ultrasonic vocalizations (USVs) are a vital tool for linking gene mutations to behavior in mouse models of communication disorders, such as autism [1. However, we currently lack an understanding of how physiological and physical mechanisms combine to generate acoustic features of the vocalizations, and thus cannot meaningfully relate those features to experimental treatments. Here we test and provide evidence against the two leading hypotheses explaining USV production: superficial vocal fold vibrations [2, and a hole-tone whistle [3. Instead, we propose and provide theoretical and experimental evidence for an alternative and novel vocal production mechanism: a glottal jet impinging onto the laryngeal inner planar wall. Our data provide a framework for future research on the neuromuscular control of mouse vocal production and for interpreting mouse vocal behavior phenotypes.National Science Foundation (Grant ID: IOS 1257768), Danish Research Council, Carlsberg Foundatio
Expansion of layouts of complete binary trees into grids
AbstractLet Th be the complete binary tree of height h. Let M be the infinite grid graph with vertex set Z2, where two vertices (x1,y1) and (x2,y2) of M are adjacent if and only if |x1−x2|+|y1−y2|=1. Suppose that T is a tree which is a subdivision of Th and is also isomorphic to a subgraph of M. Motivated by issues in optimal VLSI design, we show that the point expansion ratio n(T)/n(Th)=n(T)/(2h+1−1) is bounded below by 1.122 for h sufficiently large. That is, we give bounds on how many vertices of degree 2 must be inserted along the edges of Th in order that the resulting tree can be laid out in the grid. Concerning the constructive end of VLSI design, suppose that T is a tree which is a subdivision of Th and is also isomorphic to a subgraph of the n×n grid graph. Define the expansion ratio of such a layout to be n2/n(Th)=n2/(2h+1−1). We show constructively that the minimum possible expansion ratio over all layouts of Th is bounded above by 1.4656 for sufficiently large h. That is, we give efficient layouts of complete binary trees into square grids, making improvements upon the previous work of others. We also give bounds for the point expansion and expansion problems for layouts of Th into extended grids, i.e. grids with added diagonals
Weak pairwise correlations imply strongly correlated network states in a neural population
Biological networks have so many possible states that exhaustive sampling is
impossible. Successful analysis thus depends on simplifying hypotheses, but
experiments on many systems hint that complicated, higher order interactions
among large groups of elements play an important role. In the vertebrate
retina, we show that weak correlations between pairs of neurons coexist with
strongly collective behavior in the responses of ten or more neurons.
Surprisingly, we find that this collective behavior is described quantitatively
by models that capture the observed pairwise correlations but assume no higher
order interactions. These maximum entropy models are equivalent to Ising
models, and predict that larger networks are completely dominated by
correlation effects. This suggests that the neural code has associative or
error-correcting properties, and we provide preliminary evidence for such
behavior. As a first test for the generality of these ideas, we show that
similar results are obtained from networks of cultured cortical neurons.Comment: Full account of work presented at the conference on Computational and
Systems Neuroscience (COSYNE), 17-20 March 2005, in Salt Lake City, Utah
(http://cosyne.org
Transfer RNA-derived small RNAs in the cancer transcriptome
The cellular lifetime includes stages such as differentiation, proliferation, division, senescence and apoptosis.These stages are driven by a strictly ordered process of transcription dynamics. Molecular disruption to RNA polymerase assembly, chromatin remodelling and transcription factor binding through to RNA editing, splicing, post-transcriptional regulation and ribosome scanning can result in significant costs arising from genome instability. Cancer development is one example of when such disruption takes place. RNA silencing is a term used to describe the effects of post-transcriptional gene silencing mediated by a diverse set of small RNA molecules. Small RNAs are crucial for regulating gene expression and microguarding genome integrity.RNA silencing studies predominantly focus on small RNAs such as microRNAs, short-interfering RNAs and piwi-interacting RNAs. We describe an emerging renewal of inter-est in a‘larger’small RNA, the transfer RNA (tRNA).Precisely generated tRNA-derived small RNAs, named tRNA halves (tiRNAs) and tRNA fragments (tRFs), have been reported to be abundant with dysregulation associated with cancer. Transfection of tiRNAs inhibits protein translation by displacing eukaryotic initiation factors from messenger RNA (mRNA) and inaugurating stress granule formation.Knockdown of an overexpressed tRF inhibits cancer cell proliferation. Recovery of lacking tRFs prevents cancer metastasis. The dual oncogenic and tumour-suppressive role is typical of functional small RNAs. We review recent reports on tiRNA and tRF discovery and biogenesis, identification and analysis from next-generation sequencing data and a mechanistic animal study to demonstrate their physiological role in cancer biology. We propose tRNA-derived small RNA-mediated RNA silencing is an innate defence mechanism to prevent oncogenic translation. We expect that cancer cells are percipient to their ablated control of transcription and attempt to prevent loss of genome control through RNA silencing
Synchronization of Integrate and Fire oscillators with global coupling
In this article we study the behavior of globally coupled assemblies of a
large number of Integrate and Fire oscillators with excitatory pulse-like
interactions. On some simple models we show that the additive effects of pulses
on the state of Integrate and Fire oscillators are sufficient for the
synchronization of the relaxations of all the oscillators. This synchronization
occurs in two forms depending on the system: either the oscillators evolve ``en
bloc'' at the same phase and therefore relax together or the oscillators do not
remain in phase but their relaxations occur always in stable avalanches. We
prove that synchronization can occur independently of the convexity or
concavity of the oscillators evolution function. Furthermore the presence of
disorder, up to some level, is not only compatible with synchronization, but
removes some possible degeneracy of identical systems and allows new mechanisms
towards this state.Comment: 37 pages, 19 postscript figures, Latex 2
Frequency decoding of periodically timed action potentials through distinct activity patterns in a random neural network
Frequency discrimination is a fundamental task of the auditory system. The
mammalian inner ear, or cochlea, provides a place code in which different
frequencies are detected at different spatial locations. However, a temporal
code based on spike timing is also available: action potentials evoked in an
auditory-nerve fiber by a low-frequency tone occur at a preferred phase of the
stimulus-they exhibit phase locking-and thus provide temporal information about
the tone's frequency. In an accompanying psychoacoustic study, and in agreement
with previous experiments, we show that humans employ this temporal information
for discrimination of low frequencies. How might such temporal information be
read out in the brain? Here we demonstrate that recurrent random neural
networks in which connections between neurons introduce characteristic time
delays, and in which neurons require temporally coinciding inputs for spike
initiation, can perform sharp frequency discrimination when stimulated with
phase-locked inputs. Although the frequency resolution achieved by such
networks is limited by the noise in phase locking, the resolution for realistic
values reaches the tiny frequency difference of 0.2% that has been measured in
humans.Comment: 16 pages, 5 figures, and supplementary informatio
An associative memory of Hodgkin-Huxley neuron networks with Willshaw-type synaptic couplings
An associative memory has been discussed of neural networks consisting of
spiking N (=100) Hodgkin-Huxley (HH) neurons with time-delayed couplings, which
memorize P patterns in their synaptic weights. In addition to excitatory
synapses whose strengths are modified after the Willshaw-type learning rule
with the 0/1 code for quiescent/active states, the network includes uniform
inhibitory synapses which are introduced to reduce cross-talk noises. Our
simulations of the HH neuron network for the noise-free state have shown to
yield a fairly good performance with the storage capacity of for the low neuron activity of . This
storage capacity of our temporal-code network is comparable to that of the
rate-code model with the Willshaw-type synapses. Our HH neuron network is
realized not to be vulnerable to the distribution of time delays in couplings.
The variability of interspace interval (ISI) of output spike trains in the
process of retrieving stored patterns is also discussed.Comment: 15 pages, 3 figures, changed Titl
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‘Our newsroom in the cloud’: Slack, virtual newsrooms and journalistic practice
Virtual newsrooms have enormous potential: enabling journalists around the world to pool their knowledge, skills and perspectives within joint projects, such as the Panama Papers. These virtual newsrooms are supported by Online Collaborative Software (OCS), the most popular of which is Slack. But although many of the world’s top news organisations now use Slack, there is no empirical research examining its impact on workplace processes or culture. This article presents the results of a year-long ethnographic study of a global digital news outlet, whose remote journalists collaborate, almost exclusively, via Slack. We found that the platform deepened relationships and enabled new creative practices across geographic regions. However, it also contributed to the erasure of the line between private and professional spheres for workers, and introduced new opportunities for management to shape newsroom culture. We argue that the concept of ‘space’ as developed by Harvey can helpfully frame the analysis of these new, important digital platforms
Microguards and micromessengers of the genome
The regulation of gene expression is of fundamental importance to maintain organismal function and integrity and requires a multifaceted and highly ordered sequence of events. The cyclic nature of gene expression is known as ‘transcription dynamics’. Disruption or perturbation of these dynamics can result in significant fitness costs arising from genome instability, accelerated ageing and disease. We review recent research that supports the idea that an important new role for small RNAs, particularly microRNAs (miRNAs), is in protecting the genome against short-term transcriptional fluctuations, in a process we term ‘microguarding’. An additional emerging role for miRNAs is as ‘micromessengers’—through alteration of gene expression in target cells to which they are trafficked within microvesicles. We describe the scant but emerging evidence that miRNAs can be moved between different cells, individuals and even species, to exert biologically significant responses. With these two new roles, miRNAs have the potential to protect against deleterious gene expression variation from perturbation and to themselves perturb the expression of genes in target cells. These interactions between cells will frequently be subject to conflicts of interest when they occur between unrelated cells that lack a coincidence of fitness interests. Hence, there is the potential for miRNAs to represent both a means to resolve conflicts of interest, as well as instigate them. We conclude by exploring this conflict hypothesis, by describing some of the initial evidence consistent with it and proposing new ideas for future research into this exciting topic
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