Lie Markov models with purine/pyrimidine symmetry

Continuous-time Markov chains are a standard tool in phylogenetic inference. If homogeneity is assumed, the chain is formulated by specifying time-independent rates of substitutions between states in the chain. In applications, there are usually extra constraints on the rates, depending on the situation. If a model is formulated in this way, it is possible to generalise it and allow for an inhomogeneous process, with time-dependent rates satisfying the same constraints. It is then useful to require that there exists a homogeneous average of this inhomogeneous process within the same model. This leads to the definition of "Lie Markov models", which are precisely the class of models where such an average exists. These models form Lie algebras and hence concepts from Lie group theory are central to their derivation. In this paper, we concentrate on applications to phylogenetics and nucleotide evolution, and derive the complete hierarchy of Lie Markov models that respect the grouping of nucleotides into purines and pyrimidines -- that is, models with purine/pyrimidine symmetry. We also discuss how to handle the subtleties of applying Lie group methods, most naturally defined over the complex field, to the stochastic case of a Markov process, where parameter values are restricted to be real and positive. In particular, we explore the geometric embedding of the cone of stochastic rate matrices within the ambient space of the associated complex Lie algebra. The whole list of Lie Markov models with purine/pyrimidine symmetry is available at http://www.pagines.ma1.upc.edu/~jfernandez/LMNR.pdf.Comment: 32 page

Spatial and temporal variability of CO2 emisions in soils under conventional tillage and no-till farming

Agricultural soils can act as a carbon sink depending on the soil management practices employed. As a result of this functional duality, soil management systems are present in international documents relating to climate change mitigation. Agricultural practices are responsible for 14% of total greenhouse gas emissions (GHG’s) (MMA, 2009)(1). Conservation agriculture (CA) is one of the most effective agricultural systems for reducing CO2 emissions, as it increases the sequestration of atmospheric carbon in the soil. In order to assess the performance of CA in terms of CO2 emissions, a field trial was conducted comparing soil derived CO2 fluxes under No-till (NT) farming and under conventional tillage. Three pilot farms were selected in the cereal-growing area of southern Spain, located in Las Cabezas de San Juan (Seville), Carmona (Seville) and Cordoba. Each pilot farm comprises six experimental plots with an approximate area of five hectares; three of the six plots implement CA practices, while the other three use conventional tillage techniques. The subdivision of each tillage system into 3 plots allowed the simultaneous cropping of the three crops of the wheat-sunflower-legume rotation each year. Results showed that carbon dioxide emissions were 31 to 91% higher in tilled soils than in untilled soils, and that there was a great seasonal variability of CO2 emissions, as weather conditions also differed considerably for the different sampling periods. In all cases, the CO2 fluxes emitted into the atmosphere were always higher when soil was subject to conventional tillage

Perception of pupils of basic education about zoos: identifying different perspectives

Zoos are places often used by teachers, since they allow for both animalsóbservation and biodiversity contact. The Lisbon zoo opened in 1884 and is regularly visited by pupils of Basic Education, and only a few have never been there. In fact, many children only have the opportunity to see wildlife in zoos, where there is an attempt to combine scientific learning with entertainment, arguments that reveal an anthropocentric perspective. However, zoos are controversial places and are subject to strong criticism. Proponents of a biocentric perspective, centred on animals, highlight the following negative aspects: i) the use of animals as means to our ends; ii) the deprivation of freedom and conditioning of their behaviours; iii) the inculcation of the idea that Man is superior to other species. As for the advocates of an ecocentric perspective, centred on the value of ecosystems, they emphasize the fragmented view of nature that zoos transmit. Even so, in this perspective, there is recognition that zoos can play a role in the conservation of species. This study sought to determine how 124 pupils from a state school in Lisbon perceive zoos, in particularly the Lisbon zoo. The children, with an average age of 13, attended the 7th grade of schooling in 2014/15. To this end, a questionnaire with two parts was applied. In the first part, it was asked if the pupils had already visited the Lisbon zoo or other similar space; they also had to identify three positive and three negative aspects associated with this place; In the second part, after collection of the first one, the pupils were asked to express their level of agreement (1, strongly disagree, to 5, strongly agree) concerning 18 statements expressing different ideas about zoos: 6 of them had an anthropocentric content (supporting zoos); 6 others, an ecocentric content (supporting zoos under certain conditions); and the other 6, a biocentric content (opposing to these spaces). An average for each perspective was obtained and the averages were compared with a Multivariate Test (3 factors) within subjects. The results showed that only 4 (3.2%) pupils had never visited a zoo. Concerning the positive aspects of the Lisbon zoo, a large majority emphasized the contact with animals (75%), the offered services and entertainment (56.5%), as the cable car and the fast food restaurants, and the animal shows (35.5%). Only 8.9% of the children reported aspects focused on animals, like the fact that they are well treated or the appropriate spaces where they lived; in relation to the negative aspects, 42.7% of the respondents focused on the general space conditions, especially the smell and dirtiness, in the presence of less beloved animals and in the weak interaction with animals, 22.6%, and 26% even said that zoos have nothing negative. Only 8.1% of the pupils mentioned the inadequacy of the spaces for animals and the absence of freedom. Accordingly, the 6 biocentric statements were those that received less agreement while the others expressing the anthropocentric and ecocentric perspectives emerged with a closer and higher average, with statistically significant differences (p = 0.000). The participants also revealed a full consistency in the responses in both parts of the questionnaire. The results also suggest that children are slightly aware of the negative aspects of zoos, and indicate that the teachers that they had so far didn´t stimulate much a discussion on this subject, if at all.info:eu-repo/semantics/publishedVersio

Effects of the environment on galaxies in the Catalogue of Isolated Galaxies: physical satellites and large scale structure

We aim to identify and quantify the effects of the satellite distribution around a sample of galaxies in the Catalogue of Isolated Galaxies (CIG), as well as the effects of the Large Scale Structure (LSS) using the SDSS-DR9. To recover the physically bound galaxies we focus on the satellites which are within the escape speed of each CIG galaxy. We also propose a more conservative method using the stacked Gaussian distribution of the velocity difference of the neighbours. The tidal strengths affecting the primary galaxy are estimated to quantify the effects of the local and LSS environments. We also define the projected number density parameter at the 5$^{\rm th}$ nearest neighbour to characterise the LSS around the CIG galaxies. Out of the 386 CIG galaxies considered in this study, at least 340 (88\% of the sample) have no physically linked satellite. Out of the 386 CIG galaxies, 327 (85\% of the sample) have no physical companion within a projected distance of 0.3 Mpc. The CIG galaxies are distributed following the LSS of the local Universe, although presenting a large heterogeneity in their degree of connection with it. A clear segregation appears between early-type CIG galaxies with companions and isolated late-type CIG galaxies. Isolated galaxies are in general bluer, with likely younger stellar populations and rather high star formation with respect to older, redder CIG galaxies with companions. Reciprocally, the satellites are redder and with an older stellar populations around massive early-type CIG galaxies, while they have a younger stellar content around massive late-type CIG galaxies. This suggests that the CIG is composed of a heterogeneous population of galaxies, sampling from old to more recent, dynamical systems of galaxies.Comment: 19 pages, 10 figures, 1 table, accepted for publication in Astronomy & Astrophysic

Actualidad editorial de la historia conceptual

El artículo se incluye dentro de la revista en un dossier titulado 'Filosofía de la historia e historia conceptual II'. En consonancia con este epígrafe y bajo el lema de 'Actualidad editorial de la historia conceptual' se agrupan varias reseñas de publicaciones centradas en esta disciplina. En primer lugar, Lorena Rivera León se ocupa del monográfico 'Teoría y práctica de la historia conceptual' publicado por la revista 'Isegoría', nº 37 (2007), así como del volumen 'Teorías y prácticas de la historia conceptual' compilado por Faustino Oncina Coves y aparecido en CSIC-Plaza y Valdés en 2008. En segundo término, María G. Navarro presta atención a 'Conceptos. Revista de investigación graciana', nº 5 (2008). Por último, José Manuel Sánchez Fernández se detiene en el libro 'Historia conceptual, Ilustración y modernidad', escrito por Faustino Oncina Coves, que vio la luz en la editorial Anthropos en 2009

Improving the canolol amount and the yield of expressed canola oil applying combined pretreatments

Canolol is a potent natural antioxidant. It exhibits antimutagenic and anticarcinogenic properties, showing an even more potent antimutagenic activity than that of α-tocopherol and flavonoids. This compound is formed due to high temperatures during processing of some seeds of brassica family, like canola. The nutritional value of canola oil can be increased by increasing the content of canolol, subjecting the seeds to different pretreatments (steam, microwaves). The aim of this work was to study treatments applied to canola seeds in order to improve the quality of the expressed oil, increasing the amount of canolol, and also to obtain higher yields of oil by pressing. Canola seeds were subjected to different treatments: -Hydrothermal (HT), by exposing the grains to steam in an autoclave; -Microwave (MW), irradiation in a microwave oven; Combination of both treatments (HT-MW): exposing the seeds to water vapor and then microwave irradiating until grains reached a 7% moisture, dry basis. Oil was extracted from pretreated and untreated samples by pressing using a helical screw press. Oil yield was determined by evaluating the residual oil remaining in the press cake. Canolol content was determined in all samples by HPLC. The combined pretreatment HT-MW significantly increased the amount of canolol in oil (495ppm in contrast with 5ppm in untreated samples) and significantly improved its oxidative stability. Moreover, this pretreatment generated the highest oil yield by expression, extracting 86% of the total oil. While, by pressing untreated canola, 68% of the total oil in grains was obtained, in hydrothermally pretreated samples it was extracted a 76% of the oil and 8% in the case of only irradiated with microwaves samples. Furthermore, SEM micrographs showed a more open structure in samples treated by combined pretreatment HT-MW, which could have improved the availability of oil, favoring the oil expression process.Fil: Cortese, C.M.. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ingeniería Olavarría. Grupo Tecnologías de Semillas; ArgentinaFil: Portela, G.. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ingeniería Olavarría. Grupo Tecnologías de Semillas; ArgentinaFil: Sánchez, Ramiro Julián. Universidad Nacional del Centro de la Provincia de Buenos Aires. Centro de Investigaciones en Física e Ingeniería del Centro de la Provincia de Buenos Aires. - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Centro de Investigaciones en Física e Ingeniería del Centro de la Provincia de Buenos Aires. - Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Centro de Investigaciones en Física e Ingeniería del Centro de la Provincia de Buenos Aires; Argentina. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ingeniería Olavarría. Grupo Tecnologías de Semillas; ArgentinaFil: Fernández, María Belén. Universidad Nacional del Centro de la Provincia de Buenos Aires. Centro de Investigaciones en Física e Ingeniería del Centro de la Provincia de Buenos Aires. - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Centro de Investigaciones en Física e Ingeniería del Centro de la Provincia de Buenos Aires. - Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas. Centro de Investigaciones en Física e Ingeniería del Centro de la Provincia de Buenos Aires; Argentina. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ingeniería Olavarría. Grupo Tecnologías de Semillas; Argentin

Truth telling and terminal patient care

En el presente escrito, abordamos la cuestión de la verdad en la relación médico- paciente, concretamente en el caso de los enfermos terminales. Analizamos los problemas y actitudes acerca de decir la verdad cuando se trata de una enfermedad mortal, concluyendo lo importante que es que haya una comunicación fluida y veraz en la relación terapéutica. Así mismo, examinamos y destacamos el papel que pueden tener los médicos generales –el médico de cabecera– en la atención a enfermos terminales en el hogar y con sus familiares y/o amigos.The aim of this text is to examine the issue of truth telling in doctor-patient relationships, namely in the case of terminal patients. We analyze the problems and attitudes regarding truth telling that there are present when patients suffer from mortal diseases. We conclude that it is very important to keep a fluent and truthful communication in the doctor-patient relationship. We also examine and stress the role that general practitioners can play in the care of terminal patients at their home and with their friends and/or relatives

Especies de caza: procesos de extinción ocultos tras elevados tamaños de censo

Management of game species may involve a risk of alteration of their genetic properties. Local adaptations may be disrupted if artificially selected individuals from farms or those belonging to distant geographical areas are introduced to increase population density or trophy “quality”. In Spain, red deer (Cervus elaphus) from different European subspecies have been introduced to increase the size of trophies (antlers) of local populations. Legislation against these introductions is not effective for various reasons, and once the individuals are in the Iberian peninsula it is virtually impossible to prevent their spreading throughout the whole territory without a genetic tool to distinguish between autochthonous and foreign specimens. We have developed such a genetic test and propose a strategy to dissuade land–owners from importing foreign deer. Since deer are bred mainly for their antlers, our strategy is based on an agreement with the National Trophy Body in Spain which rejects trophies from foreign populations. Rejection decreases the value of the trophy so that it becomes more profitable to produce autochthonous deer. Using such a strategy at some critical step in the production or commercialization process may be a good model to apply in protecting genetic properties of exploited species.La gestión de las especies de caza puede conllevar riesgos de alteración de sus propiedades genéticas. Las adaptaciones locales pueden deteriorarse si ejemplares producidos mediante selección artificial en granjas o procedentes de áreas geográficas distantes, son introducidos para aumentar la densidad poblacional o la "calidad" de los trofeos de caza. En España, se han introducido ejemplares de ciervo ibérico (Cervus elaphus) procedentes de distintas subespecies europeas para aumentar así el tamaño de las cuernas (trofeos de caza) de las poblaciones autóctonas. La legislación contra este tipo de introducciones no es eficaz por diversos motivos y, una vez introducidos los ejemplares en la península ibérica, es prácticamente imposible prevenir su dispersión por todo el territorio sin contar con herramientas genéticas que permitan diferenciar los ejemplares autóctonos de los foráneos. Nosotros hemos desarrollado un test genético para este fin, y hemos propuesto una estrategia para disuadir a lospropietarios de llevar a cabo la importación de ejemplares foráneos. Puesto que los ciervos se crían fundamentalmente por su cornamenta como trofeo de caza, nuestra estrategia se ha basado en un acuerdo con la Junta Nacional de Homologación de Trofeos de Caza, para que ésta rechace los trofeos pertenecientes a ejemplares foráneos. Este rechazo reduce el valor de los ejemplares procedentes de otras poblaciones y favorece la producción de ciervo autóctono. Sugerimos que la utilización de estrategias de este tipo en puntos clave de procesos de producción o comercialización, puede ser un buen modelo a aplicar para proteger las propiedades genéticas de las especies sujetas a explotación por el hombre