Selective advantage of diffusing faster

We study a stochastic spatial model of biological competition in which two species have the same birth and death rates, but different diffusion constants. In the absence of this difference, the model can be considered as an off-lattice version of the Voter model and presents similar coarsening properties. We show that even a relative difference in diffusivity on the order of a few percent may lead to a strong bias in the coarsening process favoring the more agile species. We theoretically quantify this selective advantage and present analytical formulas for the average growth of the fastest species and its fixation probability.Comment: 8 pages, 5 figures (Main Text + Supplementary Information). Accepted versio

Blended numerical schemes for the advection equation and conservation laws

In this paper we propose a method to couple two or more explicit numerical schemes approximating the same time-dependent PDE, aiming at creating new schemes which inherit advantages of the original ones. We consider both advection equations and nonlinear conservation laws. By coupling a macroscopic (Eulerian) scheme with a microscopic (Lagrangian) scheme, we get a new kind of multiscale numerical method

Symmetric polarization insensitive directional couplers fabricated by femtosecond laser waveguide writing

We study analytically the polarization behaviour of directional couplers composed of birefringent waveguides, showing that they can induce polarization transformations that depend on the specific input-output path considered. On the basis of this study, we propose and demonstrate experimentally, by femtosecond laser writing, directional couplers that are free from this problem and also yield a polarization independent power-splitting ratio. More in detail, we devise two different approaches to realize such devices: the first one is based on local birefringence engineering, while the second one exploits ultra-low birefringence waveguides obtained by thermal annealing

VerbAtlas: a novel large-scale verbal semantic resource and its application to semantic role labeling

We present VerbAtlas, a new, hand-crafted lexical-semantic resource whose goal is to bring together all verbal synsets from WordNet into semantically-coherent frames. The frames define a common, prototypical argument structure while at the same time providing new concept-specific information. In contrast to PropBank, which defines enumerative semantic roles, VerbAtlas comes with an explicit, cross-frame set of semantic roles linked to selectional preferences expressed in terms of WordNet synsets, and is the first resource enriched with semantic information about implicit, shadow, and default arguments. We demonstrate the effectiveness of VerbAtlas in the task of dependency-based Semantic Role Labeling and show how its integration into a high-performance system leads to improvements on both the in-domain and out-of-domain test sets of CoNLL-2009. VerbAtlas is available at http://verbatlas.org

Exact results for the low energy AdS(4)XCP(3) string theory

We derive the Thermodynamic Bethe Ansatz equations for the relativistic sigma model describing the AdS(4)XCP(3) string II A theory at strong coupling (i.e. in the Alday-Maldacena decoupling limit). The corresponding Y-system involves an infinite number of Y functions and is of a new type, although it shares a peculiar feature with the Y-system for AdS(4)XCP(3). A truncation of the equations at level p and a further generalisation to generic rank N allow us an alternative description of the theory as the N=4, p= \infty representative in an infinite family of models corresponding to the conformal cosets CP(N-1)_p X U(1), perturbed by a relevant composite field \phi(N,p) =\phi_[CP(N-1)_p] X \phi[U(1)] that couples the two independent conformal field theories. The calculation of the ultraviolet central charge confirms the conjecture by Basso and Rej and the conformal dimension of the perturbing operator, at every N and p, is obtained using the Y-system periodicity. The conformal dimension of \phi[CP(N-1)_p] matches that of the field identified by Fendley while discussing integrability issues for the purely bosonic CP(N-1) sigma model.Comment: Latex fil

T-branes through 3d mirror symmetry

T-branes are exotic bound states of D-branes, characterized by mutually non-commuting vacuum expectation values for the worldvolume scalars. The M/F-theory geometry lifting D6/D7-brane configurations is blind to the T-brane data. In this paper, we make this data manifest, by probing the geometry with an M2-brane. We find that the effect of a T-brane is to deform the membrane worldvolume superpotential with monopole operators, which partially break the three-dimensional flavor symmetry, and reduce supersymmetry from N=4 to N=2. Our main tool is 3d mirror symmetry. Through this language, a very concrete framework is developed for understanding T-branes in M-theory. This leads us to uncover a new class of N=2 quiver gauge theories, whose Higgs branches mimic those of membranes at ADE singularities, but whose Coulomb branches differ from their N=4 counterparts.Comment: 36 page

New approaches to unveil the Transcriptional landscape of dopaminergic neurons

Recent advances in studying the mammalian transcriptome arised new questions about how genes are organized and what is the function of noncoding RNAs. Furthermore, the discovery of large amounts of polyA- transcripts and antisense transcription proved that a portion of the transcriptome has still to be characterized. The complex anatomo-functional organization of the brain has prevented a comprehensive analysis of the transcriptional landscape of this tissue. New techniques must be developed to approach neuronal heterogeneity. In this study we combined Laser Capture Microdissection (LCM) and nanoCAGE, based on Cap Analysis of Gene Expression (CAGE), to describe expressed genes and map their transcription start sites (TSS) in two specific populations, A9 and A10, of mouse mesencephalic dopaminergic cells. Although sharing common dopaminergic marker genes, these two populations are part of different midbrain anatomical structures, substantia nigra (SN) for A9 and ventral tegmental area (VTA) for A10, project to relatively distinct areas, participate to distinct ascending dopaminergic pathways, exhibit different electrophysiological properties and different susceptibility to neurodegeneration in Parkinson`s disease. Specific neurons were identified by the expression of Green Fluorescent Protein driven by a celltype specific promoter in transgenic mice. High-quality RNAs were purified from 1000-2500 cells collected by LCM. We adapted the CAGE technique to analyze limiting amounts of RNAs (nanoCAGE). We took advantage of the cap-switching properties of the reverse transcriptase to specifically tag the 5`end of transcripts with a sequence containing a class III restriction site for EcoP15I. By creating 32bp 5`tags, we considerably improved the TSS mapping rate on the genome. A semi-suppressive PCR strategy was used to prevent primer dimers formation. The use of random priming in the 1st strand synthesis allowed to capture poly(A)- RNAs. 5`tags were sequenced with Illumina-Solexa platform. Here we show that this new nanoCAGE technology ensures a true high-throughput coverage of the transcriptome of a small number of identified neurons and can be used as an effective mean for gene discovery in the noncoding RNAs, to uncover putative alternative promoters associated to variants of protein coding transcripts and to detect potentially regulatory antisense transcripts. A further experimental validation by 5`RACE (Rapid Amplification of cDNA Ends) and RT-PCR on few candidate genes, have confirmed the existence in vivo of alternative TSS in the case of key regulatory genes involved in specifying and maintaining the dopaminergic phenotype of these neurons such as \u3b1-synuclein (Snca), dopamine transporter (Dat), vescicular monoamine transporter 2 (Vmat2), catechol-O-methyltransferase (Comt). Furthermore the differential expression of an antisense transcript overlapping to the polyubiquitin (Ubc) gene was detected as potentially interesting candidate gene accounting for differences in the ubiquitin-proteasome system (UPS) function in the two neuron populations. The potential implications deriving from these newly discovered alternative promoters and transcripts are discussed, considering also the potential consequences for the corresponding protein isoforms

Compressive Sensing for Dynamic XRF Scanning

X-Ray Fluorescence (XRF) scanning is a widespread technique of high importance and impact since it provides chemical composition maps crucial for several scientific investigations. There are continuous requirements for larger, faster and highly resolved acquisitions in order to study complex structures. Among the scientific applications that benefit from it, some of them, such as wide scale brain imaging, are prohibitively difficult due to time constraints. However, typically the overall XRF imaging performance is improving through technological progress on XRF detectors and X-ray sources. This paper suggests an additional approach where XRF scanning is performed in a sparse way by skipping specific points or by varying dynamically acquisition time or other scan settings in a conditional manner. This paves the way for Compressive Sensing in XRF scans where data are acquired in a reduced manner allowing for challenging experiments, currently not feasible with the traditional scanning strategies. A series of different compressive sensing strategies for dynamic scans are presented here. A proof of principle experiment was performed at the TwinMic beamline of Elettra synchrotron. The outcome demonstrates the potential of Compressive Sensing for dynamic scans, suggesting its use in challenging scientific experiments while proposing a technical solution for beamline acquisition software.Comment: 16 pages, 7 figures, 1 tabl