Native state of natural proteins optimizes local entropy

The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic stability. Building on the successful applications of physical concepts and sampling algorithms recently introduced in the study of disordered systems, in particular artificial neural networks, we quantitatively explore how well a quantity known as the local entropy describes the native state of model proteins. In lattice models and all-atom representations of proteins, we are able to efficiently sample high local entropy states and to provide a proof of concept of enhanced stability and folding rate. Our methods are based on simple and general statistical-mechanics arguments, and thus we expect that they are of very general use

From Display to Labelled Proofs for Tense Logics

We introduce an effective translation from proofs in the display calculus to proofs in the labelled calculus in the context of tense logics. We identify the labelled calculus proofs in the image of this translation as those built from labelled sequents whose underlying directed graph possesses certain properties. For the basic normal tense logic Kt, the image is shown to be the set of all proofs in the labelled calculus G3Kt

Asymmetrical copper root pruning may improve root traits for reforesting steep and/or windy sites

Our research demonstrates that plant material can be produced in the nursery with asymmetrical root systems, which may have utility for reforestation of difficult planting sites characterized by steep slopes and/or windy conditions. Such a root system can be generated using chemical root pruning by applying cupric carbonate (Cu) that can arrest the development of, or cause mortality to, root apical meristems resulting in the formation of new lateral roots with an overall increase in the biomass, length, and volume of the root system. Our objective was to investigate the effect of chemical root pruning on the morphological and architectural traits of adventitious roots produced by poplar cuttings (Populus nigra L.) grown in containers coated with Cu in various symmetrical (Side, Bottom, Side + Bottom) and asymmetrical (half side + half bottom) patterns. After six weeks, roots of the cuttings were extracted from different container depths (Top, Middle, and Bottom) and portions (non-coated, Cu-coated), and analyzed. The root systems reacted to all coating patterns by increasing length, biomass, volume, and average diameters, but magnitude of increase was further affected by depth. In particular, root growth was unaffected at the Top of the container, and length was the highest at the Bottom depth. The Middle depth had a significant increment in both biomass and volume. Also, the root population increased in diameter as a possible response to Cu exposure. Interestingly, in the asymmetrically coated containers this depth response in the non-coated portions was of higher magnitude than in the Cu-coated portions

Electricity from Wood: A Wood Quality and Energy Efficiency Approach to Small Scale Pyro-gasification

AbstractThe global demand for renewable energy in the last years is facing innovations like the co-generation of electricity and heat from wooden industrial residues and biomass. Wood gasification is a very promising technique for conversion of wood chemical energy into thermal energy and into electricity. A new generation of small scale, moderately priced and easy to install pyro-gasification plants became available on the market, being an opportunity for the SMEs. These systems are also characterized by a remarkable operational easiness and great versatility in the type of used biomass, which can range from industrial residues (sawdust, wood chips...) to biomass of forestry and non-forestry origin. This study performed an extensive testing of a small size pyro-gasification plant capable of producing 30kW of electricity and 30kW of thermal energy, both net to enter in the network of GSE (Energy Services Manager) via the feed-in tariff and in a small district heating network or other uses. The process of pyro-gasification is analyzed in its entirety by a characterization of input biomass, pyro-gasification process monitoring, analysis of the quality of the produced syngas, characterization of residues due to the process (washing water smoke, charcoal...) and verification of the total efficiency. The electric efficiency of the system, from hardwood to syngas to electricity is quantified in being 12%

Integrated stratigraphy and astrochronology of the Messinian GSSP at Oued Akrech (Atlantic Morocco)

A much improved high-resolution integrated stratigraphy (calcareous plankton biostratigraphy, magnetostratigraphy, cyclostratigraphy) is presented for the classic section of Oued Akrech (Atlantic Morocco) straddling the Tortonian^Messinian boundary. Magnetobiostratigraphic correlations with time-equivalent and astronomically dated sections in the Mediterranean indicate that cyclic alternations of indurated light beige coloured marls and softer, more clayey and reddish coloured marls are dominantly precession-controlled. Characteristic sedimentary cycle patterns, in particular those reflecting precession^obliquity interference, allow for one possible tuning, thus providing accurate astronomical ages for cycles, calcareous plankton events and magnetic reversals. The tuning further indicates that the reddish layers are the equivalent of sapropels in the Mediterranean. The Messinian Global boundary Stratotype Section and Point (GSSP) has recently been formally defined at the base of the reddish layer of cycle No. 15 in section Oued Akrech. This level coincides closely with the first regular occurrence of the Globorotalia miotumida group and is astronomically dated at 7.251 Ma. The global correlation potential is guaranteed by the straightforward calibration of the Oued Akrech magnetostratigraphy to the geomagnetic polarity time scale, locating the GSSP within C3Br.1r. In the marine realm the calcareous nannofossil genus Amaurolithus provides a series of extremely useful events to delimit the boundary on a global scale. The astronomical tuning guarantees a direct first-order calibration of the Messinian GSSP to the standard geological time scale once, as anticipated, the late Miocene part of the astronomical time scale has been incorporated

Region-Based Classification of PolSAR Data Using Radial Basis Kernel Functions With Stochastic Distances

Region-based classification of PolSAR data can be effectively performed by seeking for the assignment that minimizes a distance between prototypes and segments. Silva et al (2013) used stochastic distances between complex multivariate Wishart models which, differently from other measures, are computationally tractable. In this work we assess the robustness of such approach with respect to errors in the training stage, and propose an extension that alleviates such problems. We introduce robustness in the process by incorporating a combination of radial basis kernel functions and stochastic distances with Support Vector Machines (SVM). We consider several stochastic distances between Wishart: Bhatacharyya, Kullback-Leibler, Chi-Square, R\'{e}nyi, and Hellinger. We perform two case studies with PolSAR images, both simulated and from actual sensors, and different classification scenarios to compare the performance of Minimum Distance and SVM classification frameworks. With this, we model the situation of imperfect training samples. We show that SVM with the proposed kernel functions achieves better performance with respect to Minimum Distance, at the expense of more computational resources and the need of parameter tuning. Code and data are provided for reproducibility.Comment: Accepted for publication in the International Journal of Digital Eart

Genetic diversity and introgression by AFLP analisys in Phaseolus vulgaris L.

Phaseolus vulgaris L. is an economically important species whose origin is in the America continent where domestication took place and diverged in Mesoamerican and Andean gene pools. After Columbus’s voyage common bean was introduced into the Iberian Peninsula from which this species spread into the European countries and around the world. In this study investigate the extent of diversity of European germplasm compared to the American germplasm and to define the level of introgression between the European Mesoamerican and Andean gene pools are investigated. 68 accessions representative of Mesoamerican and Andean American gene pools and 241 accessions from 24 different countries belonging to an European bean core collection were analysed for three morphologic quantitative (length, height and width ) and 4 qualitative (shape, lighter colour, darker colour and coat pattern of seed) seed characters and for 4 AFLP primer combinations: E-AGT/MGAC, E-AGT/M-GTA, E-ACC/M-AGA and E-ACC/M-ATG. A total of 138 polymorphic bands were scored among the 309 accessions analysed. The European and the Mesoamerican gene pools had a number of common and very common AFLP polymorphic bands higher than the American and the Andean gene pools. The European accessions moreover were used for Structure and cpSSR analysis to identify pure and introgressed lines. These groups were compared for morphological traits and AFLP profiles. Results showed significative differences among diverse groups for morphological traits and for AFLP band frequencies, even though the diversity index were the same (He = 0.23). Hypothesis of introgression among American and European, Mesoamerican and Andean gene pools are discussed