Effect of Correlated Lateral Geniculate Nucleus Firing Rates on Predictions for Monocular Eye Closure Versus Monocular Retinal Inactivation

Monocular deprivation experiments can be used to distinguish between different ideas concerning properties of cortical synaptic plasticity. Monocular deprivation by lid suture causes a rapid disconnection of the deprived eye connected to cortical neurons whereas total inactivation of the deprived eye produces much less of an ocular dominance shift. In order to understand these results one needs to know how lid suture and retinal inactivation affect neurons in the lateral geniculate nucleus (LGN) that provide the cortical input. Recent experimental results by Linden et al. showed that monocular lid suture and monocular inactivation do not change the mean firing rates of LGN neurons but that lid suture reduces correlations between adjacent neurons whereas monocular inactivation leads to correlated firing. These, somewhat surprising, results contradict assumptions that have been made to explain the outcomes of different monocular deprivation protocols. Based on these experimental results we modify our assumptions about inputs to cortex during different deprivation protocols and show their implications when combined with different cortical plasticity rules. Using theoretical analysis, random matrix theory and simulations we show that high levels of correlations reduce the ocular dominance shift in learning rules that depend on homosynaptic depression (i.e., Bienenstock-Cooper-Munro type rules), consistent with experimental results, but have the opposite effect in rules that depend on heterosynaptic depression (i.e., Hebbian/principal component analysis type rules)

Selectivity and Metaplasticity in a Unified Calcium-Dependent Model

A unified, biophysically motivated Calcium-Dependent Learning model has been shown to account for various rate-based and spike time-dependent paradigms for inducing synaptic plasticity. Here, we investigate the properties of this model for a multi-synapse neuron that receives inputs with different spike-train statistics. In addition, we present a physiological form of metaplasticity, an activity-driven regulation mechanism, that is essential for the robustness of the model. A neuron thus implemented develops stable and selective receptive fields, given various input statistic

Recovery From Monocular Deprivation Using Binocular Deprivation: Experimental Observations and Theoretical Analysis

Ocular dominance (OD) plasticity is a robust paradigm for examining the functional consequences of synaptic plasticity. Previous experimental and theoretical results have shown that OD plasticity can be accounted for by known synaptic plasticity mechanisms, using the assumption that deprivation by lid suture eliminates spatial structure in the deprived channel. Here we show that in the mouse, recovery from monocular lid suture can be obtained by subsequent binocular lid suture but not by dark rearing. This poses a significant challenge to previous theoretical results. We therefore performed simulations with a natural input environment appropriate for mouse visual cortex. In contrast to previous work we assume that lid suture causes degradation but not elimination of spatial structure, whereas dark rearing produces elimination of spatial structure. We present experimental evidence that supports this assumption, measuring responses through sutured lids in the mouse. The change in assumptions about the input environment is sufficient to account for new experimental observations, while still accounting for previous experimental results

Sound and Relaxed Behavioural Inheritance

Object-oriented (OO) inheritance establishes taxonomies of OO classes. Behavioural inheritance (BI), a strong version, emphasises substitutability: objects of child classes replace objects of their ascendant classes without any observable effect difference on the system. BI is related to data refinement, but refinement's constrictions rule out many useful OO subclassings. This paper revisits BI at the light of Z and the theory of data refinement. It studies existing solutions to this problem, criticises them, and proposes improved relaxations. The results are applicable to any OO language that supports design-by-contract (DbC). The paper's contributions include three novel BI relaxations supported by a mathematical model with proofs carried out in the Isabelle proof assistant, and an examination of BI in the DbC languages Eiffel, JML and Spec#

Basic, simple and extendable kinetic model of protein synthesis

Protein synthesis is one of the most fundamental biological processes, which consumes a significant amount of cellular resources. Despite existence of multiple mathematical models of translation, varying in the level of mechanistical details, surprisingly, there is no basic and simple chemical kinetic model of this process, derived directly from the detailed kinetic model. One of the reasons for this is that the translation process is characterized by indefinite number of states, thanks to existence of polysomes. We bypass this difficulty by applying a trick consisting in lumping multiple states of translated mRNA into few dynamical variables and by introducing a variable describing the pool of translating ribosomes. The simplest model can be solved analytically under some assumptions. The basic and simple model can be extended, if necessary, to take into account various phenomena such as the interaction between translating ribosomes, limited amount of ribosomal units or regulation of translation by microRNA. The model can be used as a building block (translation module) for more complex models of cellular processes. We demonstrate the utility of the model in two examples. First, we determine the critical parameters of the single protein synthesis for the case when the ribosomal units are abundant. Second, we demonstrate intrinsic bi-stability in the dynamics of the ribosomal protein turnover and predict that a minimal number of ribosomes should pre-exists in a living cell to sustain its protein synthesis machinery, even in the absence of proliferation.Comment: 22 pages, 9 figure

An Integrated Framework for Multiprocessor, Multimoded Real-Time Applications

The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-642-30598-6_2In this paper we propose an approach for building real-time systems under a combination of requirements: specification and handling of operating modes and mode changes; implementation on top of a multiprocessor platform; integration of both aspects within a common framework; and connection with schedulability analysis procedures. The proposed approach uses finite state machines to describe operating modes and transitions, and a framework of real-time utilities that implements the required behaviour in Ada 2012. Automatic code generation plays an important role: the system is derived from the functional and timing specification, and implemented according to the abstractions provided by the framework. Response time analysis enables assessing the schedulability of the different operating modes and the transitions between modes.This work was partially supported by the Vicerrectorado de Investigación of the UPV (PAID-06-10-2397), Ministerio de Ciencia e Innovación (TIN2011-28567-C03- 03) and European Union (FP7-ICT-287702)Sáez Barona, S.; Real Sáez, JV.; Crespo, A. (2012). An Integrated Framework for Multiprocessor, Multimoded Real-Time Applications. En Reliable Software Technologies – Ada-Europe 2012. Springer. 18-34. https://doi.org/10.1007/978-3-642-30598-6_21834Wellings, A.J., Burns, A.: A Framework for Real-Time Utilities for Ada 2005. Ada Letters XXVII(2) (August 2007)Real, J., Crespo, A.: Incorporating Operating Modes to an Ada Real-Time Framework. Ada Letters 30(1) (April 2010)Sáez, S., Terrasa, S., Crespo, A.: A Real-Time Framework for Multiprocessor Platforms Using Ada 2012. In: Romanovsky, A., Vardanega, T. (eds.) Ada-Europe 2011. LNCS, vol. 6652, pp. 46–60. Springer, Heidelberg (2011)Joseph, M., Pandya, P.: Finding response times in a real-time system. British Computer Society Computer Journal 29(5), 390–395 (1986)Audsley, N., Burns, A., Richardson, M., Tindell, K., Wellings, A.J.: Applying new scheduling theory to static priority pre-emptive scheduling. Software Engineering Journal 8(5), 284–292 (1993)Real, J., Crespo, A.: Mode Change Protocols for Real-Time Systems: A Survey and a new Proposal. Real-Time Systems 26(2), 161–197 (2004)Harel, D.: Statecharts: A visual formalism for complex systems. The Science of Computer Programming 8(3), 231–274 (1987)Object Management Group: Unified Modeling Language (OMG UML) V2.4 (August 2011), http://www.omg.org/spec/UML/2.4.1Sáez, S., Terrasa, S., Lorente, V., Crespo, A.: Implementing Reactive Systems with UML State Machines and Ada 2005. In: Kordon, F., Kermarrec, Y. (eds.) Ada-Europe 2009. LNCS, vol. 5570, pp. 149–163. Springer, Heidelberg (2009)Burns, A., Wellings, A.J.: Dispatching Domains for Multiprocessor Platforms and their Representation in Ada. In: Real, J., Vardanega, T. (eds.) Ada-Europe 2010. LNCS, vol. 6106, pp. 41–53. Springer, Heidelberg (2010)Barnett, J.: State Chart XML (SCXML): State Machine Notation for Control Abstraction (May 2008), http://www.w3.org/TR/scxml

The Languages Spoken in the Water Body (or the Biological Role of Cyanobacterial Toxins)

Although intensification of toxic cyanobacterial blooms over the last decade is a matter of growing concern due to bloom impact on water quality, the biological role of most of the toxins produced is not known. In this critical review we focus primarily on the biological role of two toxins, microcystins and cylindrospermopsin, in inter- and intra-species communication and in nutrient acquisition. We examine the experimental evidence supporting some of the dogmas in the field and raise several open questions to be dealt with in future research. We do not discuss the health and environmental implications of toxin presence in the water body