Identifying short motifs by means of extreme value analysis

The problem of detecting a binding site -- a substring of DNA where transcription factors attach -- on a long DNA sequence requires the recognition of a small pattern in a large background. For short binding sites, the matching probability can display large fluctuations from one putative binding site to another. Here we use a self-consistent statistical procedure that accounts correctly for the large deviations of the matching probability to predict the location of short binding sites. We apply it in two distinct situations: (a) the detection of the binding sites for three specific transcription factors on a set of 134 estrogen-regulated genes; (b) the identification, in a set of 138 possible transcription factors, of the ones binding a specific set of nine genes. In both instances, experimental findings are reproduced (when available) and the number of false positives is significantly reduced with respect to the other methods commonly employed.Comment: 6 pages, 5 figure

A note on drastic product logic

The drastic product $*_D$ is known to be the smallest $t$-norm, since $x *_D y = 0$ whenever $x, y < 1$. This $t$-norm is not left-continuous, and hence it does not admit a residuum. So, there are no drastic product $t$-norm based many-valued logics, in the sense of [EG01]. However, if we renounce standard completeness, we can study the logic whose semantics is provided by those MTL chains whose monoidal operation is the drastic product. This logic is called ${\rm S}_{3}{\rm MTL}$ in [NOG06]. In this note we justify the study of this logic, which we rechristen DP (for drastic product), by means of some interesting properties relating DP and its algebraic semantics to a weakened law of excluded middle, to the $\Delta$ projection operator and to discriminator varieties. We shall show that the category of finite DP-algebras is dually equivalent to a category whose objects are multisets of finite chains. This duality allows us to classify all axiomatic extensions of DP, and to compute the free finitely generated DP-algebras.Comment: 11 pages, 3 figure

D-brane Instantons on the T^6/Z_3 orientifold

We give a detailed microscopic derivation of gauge and stringy instanton generated superpotentials for gauge theories living on D3-branes at Z_3-orientifold singularities. Gauge instantons are generated by D(-1)-branes and lead to Affleck, Dine and Seiberg (ADS) like superpotentials in the effective N=1 gauge theories with three generations of bifundamental and anti/symmetric matter. Stringy instanton effects are generated by Euclidean ED3-branes wrapping four-cycles on T^6/\Z_3. They give rise to Majorana masses in one case and non-renormalizable superpotentials for the other cases. Finally we determine the conditions under which ADS like superpotentials are generated in N=1 gauge theories with adjoints, fundamentals, symmetric and antisymmetric chiral matter.Comment: 31 pages, no figure

BeppoSAX observations of Mrk 841 and Mrk335

We present and discuss BeppoSAX observations of Mrk841 and Mrk335, two Seyfert 1 galaxies in which previous observations have established the presence of soft excesses. We confirm the soft excess in both sources, even if for Mrk~841 a warm absorber provides a fit almost as good as the one with a true excess. As far as the hard X-ray continuum is concerned, a Comptonization model provides a fit as good as a power law and a physically sound solution for Mrk841. For Mrk335, the Comptonization model gives a result which is somewhat better on statistical ground, but rather problematic on physical ground. The most interesting results regard the reprocessing components. For Mrk841 we find a very large reflection continuum but an almost normal iron line equivalent width even if, within the errors, a solution in which both components are a factor ~2 larger than expected for an accretion disc is still marginally acceptable. If this is the case, an anisotropy of the primary emission seems the best explanation. On the contrary, in Mrk335 we find a very large iron line EW but a reflection component not accordingly large. In this case, the best solution seems to be in terms of reflection from an ionized disc.Comment: Accepted for publication in A&

Massive higher spins and holography

We review recent progress towards the understanding of higher spin gauge symmetry breaking in AdS space from a holographic vantage point. According to the AdS/CFT correspondence, N=4 SYM theory at vanishing coupling constant should be dual to a theory in AdS which exhibits higher spin gauge symmetry enhancement. When the SYM coupling is non-zero, all but a handful of HS currents are violated by anomalies, and correspondingly local higher spin symmetry in the bulk gets spontaneously broken. In agreement with previous results and holographic expectations, we find that, barring one notable exception (spin 1 eating spin 0), the Goldstone modes responsible for HS symmetry breaking in AdS have non-vanishing mass even in the limit in which the gauge symmetry is restored. We show that spontaneous breaking a' la Stueckelberg implies that the mass of the relevant spin s'=s-1 Goldstone field is exactly the one predicted by the correspondence.Comment: 8 pages, talk presented by M.B. at the "Fourth Meeting on Constrained Dynamics and Quantum gravity" held in Cala Gonone (Sardinia, Italy), September 12-16, 200

Self-Assembly of Patchy Particles into Polymer Chains: A Parameter-Free Comparison between Wertheim Theory and Monte Carlo Simulation

We numerically study a simple fluid composed of particles having a hard-core repulsion, complemented by two short-ranged attractive (sticky) spots at the particle poles, which provides a simple model for equilibrium polymerization of linear chains. The simplicity of the model allows for a close comparison, with no fitting parameters, between simulations and theoretical predictions based on the Wertheim perturbation theory, a unique framework for the analytic prediction of the properties of self-assembling particle systems in terms of molecular parameter and liquid state correlation functions. This theory has not been subjected to stringent tests against simulation data for ordering across the polymerization transition. We numerically determine many of the thermodynamic properties governing this basic form of self-assembly (energy per particle, order parameter or average fraction of particles in the associated state, average chain length, chain length distribution, average end-to-end distance of the chains, and the static structure factor) and find that predictions of the Wertheim theory accord remarkably well with the simulation results

Probing 3-D matter distribution at z~2 with QSO multiple lines of sight

We investigate the 3-D matter distribution at z~2 with high resolution (R ~ 40000) spectra of QSO pairs and groups obtained with the UVES spectrograph at ESO VLT. Our sample is unique for the number density of objects and the variety of separations, between 0.5 and 7 proper Mpc. We compute the real space cross-correlation function of the Lyman-alpha forest transmitted fluxes. There is a significant clustering signal up to ~2 proper Mpc, which is still present when absorption lines with high column density (log N > 13.8) are excluded.Comment: Poster paper presented at the IAU Colloquium #199 on "Probing Galaxies through Quasar Absorption Lines" held in Shanghai, China from March 14th to 18th, 200

Designing Urban Spaces to Enhance Active and Sustainable Mobility: An Analysis of Physical and Symbolic Affordances in School Squares in the Metropolitan Area of Milan, Italy

As thresholds to cities, public spaces adjacent to schools play an important role in children’s everyday mobilities, potentially shaping their future mobility habits and affective experiences. The purpose of this paper is to investigate the urban design conditions of such spaces, defined as “school squares”, and, with the aid of affordance theory, to analyze spatial features and characteristics that might encourage or hinder active and sustainable mobility practices. In the first part of the paper, we define sustainable mobility, conduct a literature review on affective responses to the urban environment, and discuss active school travel (AST) in relation to the design of school squares. By focusing on 416 primary and lower secondary schools in the metropolitan area of Milan, we present an assessment method that is composed of on-desk and on-site surveys. In particular, Phase 1 defines the type of school squares, Phase 2 investigates physical affordances (spatial features and characteristics that directly influence active mobility practices, such as bicycle racks, protective barriers, benches, and parked cars), and Phase 3 discusses symbolic affordances (elements and characteristics that might induce different affective responses to a school square with regard to active mobility, such as bicycle racks, parked cars, greenery, and dustbins). The results indicate that in most cases school squares are characterized by typological confusion that has nothing to do with the school environment: narrow sidewalks, disorder, and low levels of safety. In order to promote active and sustainable mobility choices and enhance children’s mobile experiences, it is necessary to address the aforementioned features. The ultimate goal of this paper is to provide insights for developing an urban regeneration framework that considers school squares a safe context and a starting point from which to perform sustainable mobility practices

Tomography of the intergalactic medium with Ly-alpha forests in close QSO pairs

We study the three-dimensional distribution of non virialised matter at z~2 using high resolution spectra of QSO pairs and simulated spectra drawn from cosmological hydrodynamical simulations. We have collected the largest sample of QSO pairs ever observed with UVES at the ESO-VLT, with angular separations between ~1 and 14 arcmin. The observed correlation functions of the transmitted flux in the HI Lyman alpha forest along and transverse to the lines of sight are in good agreement implying that the distortions in redshift space due to peculiar velocities are small. The clustering signal is significant up to velocity separations of ~200 km/s, or about 3 h^{-1} comoving Mpc. The regions at lower overdensity (rho/ < 6.5) are still clustered but on smaller scales (Delta v < 100 km/s). The observed and simulated correlation functions are compatible at the 3 sigma level. A better concordance is obtained when only the low overdensity regions are selected for the analysis or when the effective optical depth of the simulated spectra is increased artificially, suggesting a deficiency of strong lines in the simulated spectra. We found that also a lower value of the power-law index of the temperature-density relation for the Lyman alpha forest gas improves the agreement between observed and simulated results. If confirmed, this would be consistent with other observations favouring a late HeII reionization epoch (at z~3). We remark the detection of a significant clustering signal in the cross correlation coefficient at a transverse velocity separation Delta v_{\perp} ~500 km/s whose origin needs further investigation.Comment: Accepted for publication in MNRAS, revised version matching the accepted on