Improved RNA pseudoknots prediction and classification using a new topological invariant

We propose a new topological characterization of RNA secondary structures with pseudoknots based on two topological invariants. Starting from the classic arc-representation of RNA secondary structures, we consider a model that couples both I) the topological genus of the graph and II) the number of crossing arcs of the corresponding primitive graph. We add a term proportional to these topological invariants to the standard free energy of the RNA molecule, thus obtaining a novel free energy parametrization which takes into account the abundance of topologies of RNA pseudoknots observed in RNA databases.Comment: 9 pages, 6 figure

Passive exercise of the hind limbs after complete thoracic transection of the spinal cord promotes cortical reorganization.

Physical exercise promotes neural plasticity in the brain of healthy subjects and modulates pathophysiological neural plasticity after sensorimotor loss, but the mechanisms of this action are not fully understood. After spinal cord injury, cortical reorganization can be maximized by exercising the non-affected body or the residual functions of the affected body. However, exercise per se also produces systemic changes - such as increased cardiovascular fitness, improved circulation and neuroendocrine changes - that have a great impact on brain function and plasticity. It is therefore possible that passive exercise therapies typically applied below the level of the lesion in patients with spinal cord injury could put the brain in a more plastic state and promote cortical reorganization. To directly test this hypothesis, we applied passive hindlimb bike exercise after complete thoracic transection of the spinal cord in adult rats. Using western blot analysis, we found that the level of proteins associated with plasticity - specifically ADCY1 and BDNF - increased in the somatosensory cortex of transected animals that received passive bike exercise compared to transected animals that received sham exercise. Using electrophysiological techniques, we then verified that neurons in the deafferented hindlimb cortex increased their responsiveness to tactile stimuli delivered to the forelimb in transected animals that received passive bike exercise compared to transected animals that received sham exercise. Passive exercise below the level of the lesion, therefore, promotes cortical reorganization after spinal cord injury, uncovering a brain-body interaction that does not rely on intact sensorimotor pathways connecting the exercised body parts and the brain

Enumeration of RNA structures by Matrix Models

We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for the simple case of an RNA molecule with an infinitely flexible backbone, in which any arbitrary pair of bases is allowed. We analyze the distribution of the genus of pseudoknots as a function of the total number of nucleotides along the phosphate-sugar backbone.Comment: RevTeX, 4 pages, 2 figure

Unbiased estimates of galaxy scaling relations from photometric redshift surveys

Many physical properties of galaxies correlate with one another, and these correlations are often used to constrain galaxy formation models. Such correlations include the color-magnitude relation, the luminosity-size relation, the Fundamental Plane, etc. However, the transformation from observable (e.g. angular size, apparent brightness) to physical quantity (physical size, luminosity), is often distance-dependent. Noise in the distance estimate will lead to biased estimates of these correlations, thus compromising the ability of photometric redshift surveys to constrain galaxy formation models. We describe two methods which can remove this bias. One is a generalization of the V_max method, and the other is a maximum likelihood approach. We illustrate their effectiveness by studying the size-luminosity relation in a mock catalog, although both methods can be applied to other scaling relations as well. We show that if one simply uses photometric redshifts one obtains a biased relation; our methods correct for this bias and recover the true relation

Il censimento delle strade appartenenti alla rete extraurbana: aspetti metodologici e normativi

La mancata classificazione della rete comporta da un lato la quasi impossibile realizzazione dei Piani del Traffico della Viabilità Extraurbana (PTVE) e dall???altro determina la quasi impossibile definizione delle priorità in termini di manutenzione e ottimizzazione delle infrastrutture esistenti. A questi si aggiungono altri due aspetti: le Amministrazioni sono chiamate a perseguire l???innalzamento dei livelli di sicurezza stradale e dall???altro lato devono assicurare la totale accessibilità dei territori, il tutto in un contesto di totale contenimento della spesa

Vibrational properties of inclusion complexes: the case of indomethacin-cyclodextrin

Vibrational properties of inclusion complexes with cyclodextrins are studied by means of Raman spectroscopy and numerical simulation. In particular, Raman spectra of the non-steroidal, anti-inflammatory drug indomethacin undergo notable changes in the energy range between 1600 and 1700 cm$^{-1}$ when inclusion complexes with cyclodextrins are formed. By using both \emph{ab initio} quantum chemical calculations and molecular dynamics, we studied how to relate such changes to the geometry of the inclusion process, disentangling single-molecule effects, from changes in the solid state structure or dimerization processes.Comment: 14 file figure

Legacy and shockwaves: A spatial analysis of strengthening resilience of the power grid in Connecticut

Grid resilience and reliability are pivotal in the transition to low and zero carbon energy systems. Tree-trimming operations (TTOs) have become a pivotal tool for increasing the resilience power grids, especially in highly forested regions. Building on recent literature, we aim at assessing the temporal and spatial extents of the benefits that TTOs produce on the grid from three perspectives: the frequency, extent, and duration of outages. We use a unique dataset provided by Eversource Energy, New England's largest utility company, with outage events from 2009 to 2015. We employ spatial econometrics to investigate both the legacy and spatial extent of TTOs. Our results show TTOs benefits occur for all three metrics for at least 4 years, and benefits spillover to up to 2 km throughout the treated areas, with significant spatial spillovers across the state greater than direct effects. Implications lead to supporting TTOs as part of the hardening policies for utility companies, especially as home-based activities increase in importance in a post-COVID19 world

Market Power and Patent Strategies: Evidence from Renaissance Venice

This paper exploits the introduction of the first regularized patent system, which appeared in the Venetian Republic in 1474, to examine the factors shaping inventors\u2019 propensity to use a new form of intellectual property. We combine detailed information on craft guilds and patents in Renaissance Venice and show a negative association between patenting activity and guild statutory norms that strongly restricted entry and price competition. Our analysis shows that the heterogeneity in patenting activity documented by the industrial organization literature is not a special feature of modern technologies, but is rather a persistent phenomenon affected by market power

Consciousness Explained or Described?

Consciousness is an unusual phenomenon to study scientifically. It is defined as a subjective, first-person phenomenon, and science is an objective, third-person endeavor. This misalignment between the means—science—and the end—explaining consciousness—gave rise to what has become a productive workaround: the search for ‘neural correlates of consciousness’ (NCCs). Science can sidestep trying to explain consciousness and instead focus on characterizing the kind(s) of neural activity that are reliably correlated with consciousness. However, while we have learned a lot about consciousness in the bargain, the NCC approach was not originally intended as the foundation for a true explanation of consciousness. Indeed, it was proposed precisely to sidestep the, arguably futile, attempt to find one. So how can an account, couched in terms of neural correlates, do the work that a theory is supposed to do: explain consciousness? The answer is that it cannot, and in fact most modern accounts of consciousness do not pretend to. Thus, here, we challenge whether or not any modern accounts of consciousness are in fact theories at all. Instead we argue that they are (competing) laws of consciousness. They describe what they cannot explain, just as Newton described gravity long before a true explanation was ever offered. We lay out our argument using a variety of modern accounts as examples and go on to argue that at least one modern account of consciousness, attention schema theory, goes beyond describing consciousness-related brain activity and qualifies as an explanatory theory