01988nas a2200133   4500008004100000245010500041210006900146260003000215520151100245100002101756700002201777700001901799856003601818       2013                        en  d00aEarly phase of plasticity-related gene regulation and SRF dependent transcription in the hippocampus0 aEarly phase of plasticityrelated gene regulation and SRF depende  bPublic Library of Science3 aHippocampal organotypic cultures are a highly reliable in vitro model for studying neuroplasticity: in this paper, we analyze the early phase of the transcriptional response induced by a 20 µM gabazine treatment (GabT), a GABA-Ar antagonist, by using Affymetrix oligonucleotide microarray, RT-PCR based time-course and chromatin-immuno-precipitation. The transcriptome profiling revealed that the pool of genes up-regulated by GabT, besides being strongly related to the regulation of growth and synaptic transmission, is also endowed with neuro-protective and pro-survival properties. By using RT-PCR, we quantified a time-course of the transient expression for 33 of the highest up-regulated genes, with an average sampling rate of 10 minutes and covering the time interval [10:90] minutes. The cluster analysis of the time-course disclosed the existence of three different dynamical patterns, one of which proved, in a statistical analysis based on results from previous works, to be significantly related with SRF-dependent regulation (p-value<0.05). The chromatin immunoprecipitation (chip) assay confirmed the rich presence of working CArG boxes in the genes belonging to the latter dynamical pattern and therefore validated the statistical analysis. Furthermore, an in silico analysis of the promoters revealed the presence of additional conserved CArG boxes upstream of the genes Nr4a1 and Rgs2. The chip assay confirmed a significant SRF signal in the Nr4a1 CArG box but not in the Rgs2 CArG box.1 aIacono, Giovanni1 aAltafini, Claudio1 aTorre, Vincent  uhttp://hdl.handle.net/1963/728701741nas a2200133   4500008004100000245007700041210006900118260001000187520130700197100002401504700002101528700002201549856003601571       2012                        en  d00aExploring the low-energy landscape of large-scale signed social networks0 aExploring the lowenergy landscape of largescale signed social ne  bSISSA3 aAnalogously to a spin glass, a large-scale signed social network is characterized by the presence of disorder, expressed in this context (and in the social network literature) by the concept of structural balance. If, as we have recently shown, the signed social networks currently available have a limited amount of true disorder (or frustration), it is also interesting to investigate how this frustration is organized, by exploring the landscape of near-optimal structural balance. What we obtain in this paper is that while one of the networks analyzed shows a unique valley of minima, and a funneled landscape that gradually and smoothly worsens as we move away from the optimum, another network shows instead several distinct valleys of optimal or near-optimal structural balance, separated by energy barriers determined by internally balanced subcommunities of users, a phenomenon similar to the replica-symmetry breaking of spin glasses. Multiple, essentially isoenergetic, arrangements of these communities are possible. Passing from one valley to another requires one to destroy the internal arrangement of these balanced subcommunities and then to reform it again. It is essentially this process of breaking the internal balance of the subcommunities which gives rise to the energy barriers.1 aFacchetti, Giuseppe1 aIacono, Giovanni1 aAltafini, Claudio  uhttp://hdl.handle.net/1963/650400980nas a2200121   4500008004300000245005900043210005800102260002800160520059200188100002000780700002200800856003600822       2009                        en_Ud  00aERNEST: a toolbox for chemical reaction network theory0 aERNEST a toolbox for chemical reaction network theory  bOxford University Press3 aSummary: ERNEST Reaction Network Equilibria Study Toolbox is a MATLAB package which, by checking various different criteria on the structure of a chemical reaction network, can exclude the multistationarity of the corresponding reaction system. The results obtained are independent of the rate constants of the reactions, and can be used for model discrimination.\\nAvailability and Implementation: The software, implemented in MATLAB, is available under the GNU GPL free software license from http://people.sissa.it/~altafini/papers/SoAl09/. It requires the MATLAB Optimization Toolbox.1 aSoranzo, Nicola1 aAltafini, Claudio  uhttp://hdl.handle.net/1963/382600739nas a2200109   4500008004100000245008000041210007100121260001300192520036600205100002200571856003600593       2005                        en  d00aExplicit Wei–Norman formulae for matrix Lie groups via Putzer\\\'s method0 aExplicit Wei–Norman formulae for matrix Lie groups via Putzers m  bElsevier3 aThe Wei–Norman formula locally relates the Magnus solution of a system of linear time-varying ODEs with the solution expressed in terms of products of exponentials by means of a set of nonlinear differential equations in the parameters of the two types of solutions. A closed form expression of such formula is proposed based on the use of Putzer\\\'s method.1 aAltafini, Claudio  uhttp://hdl.handle.net/1963/4538