Hebb and the art of spine remodeling

The notion that synaptic remodeling underlies certain forms of learning is one of the main tenets of Hebb's inspiring theories dating from the 1940s. Until recently, however, direct evidence for tight relationships between synaptic remodeling and behavior has been scarce. Fascinating data from recent studies on the remodeling of postsynaptic structures known as dendritic spines indicates that such relationships might be more complex than initially expected

Relation between stress heterogeneity and aftershock rate in the rate-and-state model

We estimate the rate of aftershocks triggered by a heterogeneous stress change, using the rate-and-state model of Dieterich [1994].We show that an exponential stress distribution Pt(au) ~exp(-tautau_0) gives an Omori law decay of aftershocks with time ~1/t^p, with an exponent p=1-A sigma_n/tau_0, where A is a parameter of the rate-and-state friction law, and \sigma_n the normal stress. Omori exponent p thus decreases if the stress "heterogeneity" tau_0 decreases. We also invert the stress distribution P(tau) from the seismicity rate R(t), assuming that the stress does not change with time. We apply this method to a synthetic stress map, using the (modified) scale invariant "k^2" slip model [Herrero and Bernard, 1994]. We generate synthetic aftershock catalogs from this stress change.The seismicity rate on the rupture area shows a huge increase at short times, even if the stress decreases on average. Aftershocks are clustered in the regions of low slip, but the spatial distribution is more diffuse than for a simple slip dislocation. Because the stress field is very heterogeneous, there are many patches of positive stress changes everywhere on the fault.This stochastic slip model gives a Gaussian stress distribution, but nevertheless produces an aftershock rate which is very close to Omori's law, with an effective p<=1, which increases slowly with time. We obtain a good estimation of the stress distribution for realistic catalogs, when we constrain the shape of the distribution. However, there are probably other factors which also affect the temporal decay of aftershocks with time. In particular, heterogeneity of A\sigma_n can also modify the parameters p and c of Omori's law. Finally, we show that stress shadows are very difficult to observe in a heterogeneous stress context.Comment: In press in JG

Biological interaction networks are conserved at the module level

<p>Abstract</p> <p>Background</p> <p>Orthologous genes are highly conserved between closely related species and biological systems often utilize the same genes across different organisms. However, while sequence similarity often implies functional similarity, interaction data is not well conserved even for proteins with high sequence similarity. Several recent studies comparing high throughput data including expression, protein-protein, protein-DNA, and genetic interactions between close species show conservation at a much lower rate than expected.</p> <p>Results</p> <p>In this work we collected comprehensive high-throughput interaction datasets for four model organisms (<it>S. cerevisiae, S. pombe, C. elegans</it>, and <it>D. melanogaster</it>) and carried out systematic analyses in order to explain the apparent lower conservation of interaction data when compared to the conservation of sequence data. We first showed that several previously proposed hypotheses only provide a limited explanation for such lower conservation rates. We combined all interaction evidences into an integrated network for each species and identified functional modules from these integrated networks. We then demonstrate that interactions that are part of functional modules are conserved at much higher rates than previous reports in the literature, while interactions that connect between distinct functional modules are conserved at lower rates.</p> <p>Conclusions</p> <p>We show that conservation is maintained between species, but mainly at the module level. Our results indicate that interactions within modules are much more likely to be conserved than interactions between proteins in different modules. This provides a network based explanation to the observed conservation rates that can also help explain why so many biological processes are well conserved despite the lower levels of conservation for the interactions of proteins participating in these processes.</p> <p>Accompanying website: <url>http://www.sb.cs.cmu.edu/CrossSP</url></p

Efficient LZ78 factorization of grammar compressed text

We present an efficient algorithm for computing the LZ78 factorization of a text, where the text is represented as a straight line program (SLP), which is a context free grammar in the Chomsky normal form that generates a single string. Given an SLP of size $n$ representing a text $S$ of length $N$, our algorithm computes the LZ78 factorization of $T$ in $O(n\sqrt{N}+m\log N)$ time and $O(n\sqrt{N}+m)$ space, where $m$ is the number of resulting LZ78 factors. We also show how to improve the algorithm so that the $n\sqrt{N}$ term in the time and space complexities becomes either $nL$, where $L$ is the length of the longest LZ78 factor, or $(N - \alpha)$ where $\alpha \geq 0$ is a quantity which depends on the amount of redundancy that the SLP captures with respect to substrings of $S$ of a certain length. Since $m = O(N/\log_\sigma N)$ where $\sigma$ is the alphabet size, the latter is asymptotically at least as fast as a linear time algorithm which runs on the uncompressed string when $\sigma$ is constant, and can be more efficient when the text is compressible, i.e. when $m$ and $n$ are small.Comment: SPIRE 201

Dynamic Fluctuation Phenomena in Double Membrane Films

Dynamics of double membrane films is investigated in the long-wavelength limit including the overdamped squeezing mode. We demonstrate that thermal fluctuations essentially modify the character of the mode due to its nonlinear coupling to the transversal shear hydrodynamic mode. The corresponding Green function acquires as a function of the frequency a cut along the imaginary semi-axis. Fluctuations lead to increasing the attenuation of the squeezing mode it becomes larger than the `bare' value.Comment: 7 pages, Revte

Synapse integrity and function: Dependence on protein synthesis and identification of potential failure points

Synaptic integrity and function depend on myriad proteins - labile molecules with finite lifetimes that need to be continually replaced with freshly synthesized copies. Here we describe experiments designed to expose synaptic (and neuronal) properties and functions that are particularly sensitive to disruptions in protein supply, identify proteins lost early upon such disruptions, and uncover potential, yet currently underappreciated failure points. We report here that acute suppressions of protein synthesis are followed within hours by reductions in spontaneous network activity levels, impaired oxidative phosphorylation and mitochondrial function, and, importantly, destabilization and loss of both excitatory and inhibitory postsynaptic specializations. Conversely, gross impairments in presynaptic vesicle recycling occur over longer time scales (days), as does overt cell death. Proteomic analysis identified groups of potentially essential ‘early-lost’ proteins including regulators of synapse stability, proteins related to bioenergetics, fatty acid and lipid metabolism, and, unexpectedly, numerous proteins involved in Alzheimer’s disease pathology and amyloid beta processing. Collectively, these findings point to neuronal excitability, energy supply and synaptic stability as early-occurring failure points under conditions of compromised supply of newly synthesized protein copies

The potential impact of Brexit on the energy, water and food nexus in the UK: A fuzzy cognitive mapping approach

© 2017 The Authors. Energy is one of the cornerstones essential for human life, along with other services such as water and food. Understanding how the different services in the energy-water-food (EWF) nexus interact and are perceived by different actors is key to achieving sustainability. In this paper, we derive a model of the EWF nexus using fuzzy cognitive mapping (FCM). Data were collected in a two-step approach from workshops with researchers and stakeholders involved in the three focal sectors. Four FCMs were developed; one for each of the EWF sectors, and one for the interactions that create the nexus between EWF. The FCM represents the combined views of the groups who participated in the workshops, the importance and limitations of which is discussed. To demonstrate its effectiveness, the aggregated FCM was applied to predict the impacts on the EWF nexus of four scenarios under which the United Kingdom would depart from the European Union (i.e. Brexit). The FCM indicated that energy-related concepts had the largest influence on the EWF nexus and that EWF demand will decrease most under a 'hard-Brexit' scenario. The demand for energy was shown to decline relatively less than other services and was strongly associated with gross domestic product (GDP), whereas UK population size had a stronger effect on water and food demand. Overall, we found a threefold change across all concepts in scenarios without freedom of movement, contribution to the EU budget, and increased policy devolution to the UK