Kernel-PCA data integration with enhanced interpretability

Background Nowadays, combining the different sources of information to improve the biological knowledge available is a challenge in bioinformatics. One of the most powerful methods for integrating heterogeneous data types are kernel-based methods. Kernel-based data integration approaches consist of two basic steps: firstly the right kernel is chosen for each data set; secondly the kernels from the different data sources are combined to give a complete representation of the available data for a given statistical task. Results We analyze the integration of data from several sources of information using kernel PCA, from the point of view of reducing dimensionality. Moreover, we improve the interpretability of kernel PCA by adding to the plot the representation of the input variables that belong to any dataset. In particular, for each input variable or linear combination of input variables, we can represent the direction of maximum growth locally, which allows us to identify those samples with higher/lower values of the variables analyzed. Conclusions The integration of different datasets and the simultaneous representation of samples and variables together give us a better understanding of biological knowledge.

Valoración social de las propiedades estéticas de los hayedos en Cataluña

Se aplican métodos ensayados en otros países (Scenic Beauty Estimation Method, SBE) para la determinación de las cualidades estéticas de masas forestales de interés recreativo a parcelas en diversas localizaciones del haya en Cataluña, abarcando diferencias significativas en estación, origen, edad y forma de masa. Las valoraciones se refieren a las cualidades estéticas de los rodales de haya vistos desde el interior del bosque, es decir, tal como son apreciados por parte de los visitantes de los montes. Las valoraciones se obtienen a través de paneles de observadores en sesiones fotográficas, se transforman a una escala común y se relacionan mediante análisis de regresión a las variables dasométricas tomadas en las parcelas de inventario. El desarrollo de modelos estadísticos que describen preferencias sociales permite medir la aportación de las diferentes variables dasométricas a la mejora estética de las masas de haya, y puede servir como guía en la ordenación de hayedos en que el uso público sea predominante o muy importante.

Autoecología de los hayedos catalanes

Este estudio está basado en el muestreo de campo y posterior análisis de 24 parcelas de hayedo seleccionadas mediante una estratificación de su área de distribución basada en la clasificación CLATERES de la Ecorregión Catalano-Aragonesa. En cada parcela se han evaluado 3 parámetros fisiográficos, 15 climáticos y 18 edáficos, a partir de los cuales se han establecido sus valores paramétricos centrales y marginales que permiten definir los hábitats fisiográfico, climático y edáfico de las masas de Fagus sylvatica L. en Cataluña. Los hayedos catalanes se presentan sobre substratos litológicos muy diversos (plutonitas, vulcanitas, metamorfitas y sedimentitas, tanto ácidas como básicas), con texturas predominantes francas, franco-arenosas o franco-limosas. Los suelos, según FAO, son mayoritariamente cambisoles. A pesar de que la capacidad de retención de agua de sus suelos es escasa, la sequía fisiológica es reducida. Los humus predominantemente pertenecen a los tipos mull forestal y mull cálcico. Además, se presentan una serie de parámetros selvícolas ( Densidad de pies y densidad de chirpiales, Area basimétrica, Altura Total dominante, Índices de Hart-Becking, Índice de Calidad de Estación y Edad de la masa) que al correlacionarlos con los ecológicos nos ha permitido comprobar que los mejores hayedos se encuentran en las localizaciones más térmicas, en las que incluso se podría producir sequía fisiológica si no fuera por que existen suficientes precipitaciones estivales.

Determination of the complexing capacity of synthetic and real wine for Zn using Absence of Gradients and Nerstian Equilibrium Stripping technique

The complexing capacity of synthetic (0.011 M tartrate in 13.5% ethanol) and real wine (Raimat Abadia) in titrations with added total Zn concentrations up to 0.03 M has been determined following the free Zn concentrations with AGNES (absence of gradients and Nernstian equilibrium stripping) technique. A correction to find the preconcentration factor or gain (Y1) really applied at each one of the ionic strengths reached due to Zn additions along the titration has been applied. The standard implementation of AGNES to real wine led to the observation of two anomalous behaviors: (a) an increasingly negative current in the deposition stage (labeled as “HER” effect) and (b) a minimum in the currents of the stripping stage plot (labeled as the “dip” effect). A practical strategy to apply AGNES avoiding the dip effect has been developed to quantify properly free Zn concentrations. The van den Berg–Ružic–Lee linearization method (assuming the existence of just 1:1 complexes) has been adapted to consider the dilution effect and the ionic strength changes. Aggregated stability constants and total ligand concentrations have been calculated from synthetic and wine titration data. The found complexing capacity in the studied wine (cT,L = 0.0179 ± 0.0007 M) indicates the contribution of ligands other than tartrate (which is confirmed to be the main one).

Geology of the Cerro-Quema Au-Cu deposit (Azuero Peninsula, Panama)

The Cerro Quema district, located on the Azuero Peninsula, Panama, is part of a large regional hydrothermal system controlled by regional faults striking broadly E-W, developed within the Río Quema Formation. This formation is composed of volcanic, sedimentary and volcano-sedimentary rocks indicating a submarine depositional environment, corresponding to the fore-arc basin of a Cretaceous-Paleogene volcanic arc. The structures observed in the area and their tectono-stratigraphic relationship with the surrounding formations suggest a compressive and/or transpressive tectonic regime, at least during Late Cretaceous-Oligocene times. The igneous rocks of the Río Quema Formation plot within the calc-alkaline field with trace and rare earth element (REE) patterns of volcanic arc affinity. This volcanic arc developed on the Caribbean large igneous province during subduction of the Farallon Plate. Mineralization consists of disseminations of pyrite and enargite as well as a stockwork of pyrite and barite with minor sphalerite, galena and chalcopyrite, hosted by a subaqueous dacitic lava dome of the Río Quema Formation. Gold is present as submicroscopic grains and associated with pyrite as invisible gold. A hydrothermal alteration pattern with a core of advanced argillic alteration (vuggy silica with alunite, dickite, pyrite and enargite) and an outer zone of argillic alteration (kaolinite, smectite and illite) has been observed. Supergene oxidation overprinted the hydrothermal alteration resulting in a thick cap of residual silica and iron oxides. The ore minerals, the alteration pattern and the tectono-volcanic environment of Cerro Quema are consistent with a high sulfidation epithermal system developed in the Azuero peninsula during pre-Oligocene times.

Assessing changes in Cd phytoavailability to tomato in amended calcareous soils.

A plot study was conducted to assess changes in Cd phytoavailability to a tomato cultivar in an agricultural soil in Southeastern Spain amended in two different ways (A and B), under controlled conditions. The experimental soil corresponded to a fine-loamy carbonatic thermic Calcidic Haploxeroll (Soil Survey Staff, 1998). A) Soil was amended with a single application of sewage sludge from a municipal source that had a total Cd concentration of 0.5 mg kg-1 at a rate that represented a final average concentration in the mixture of soil and sludge of less than 50 µg Cd kg-1. B) The amendment consisted of the addition of a mineral fertiliser with the same amount of NPK as in the sewage sludge application. The final levels of Cd were supposed to be negligible. A plot series without amendments was also performed (C). DTPA plus triethanolamine, and ammonium acetate extractable fractions in soils were analysed for all the plots. The time-dependent Cd accumulation in different parts of the tomato plants was studied by means of a Cd salt treatment. For each block (A, B, and C) four levels of Cd (0, 3, 30, 100 mg kg-1) were added as CdCl2. There was a significant increase in plant Cd after the initial cropping. Tomato stems, leaves and fruits were analysed separately for Cd determination. Differential Cd distribution and accumulation in tomato parts was detected.

Kernel-PCA data integration with enhanced interpretability

Background Nowadays, combining the different sources of information to improve the biological knowledge available is a challenge in bioinformatics. One of the most powerful methods for integrating heterogeneous data types are kernel-based methods. Kernel-based data integration approaches consist of two basic steps: firstly the right kernel is chosen for each data set; secondly the kernels from the different data sources are combined to give a complete representation of the available data for a given statistical task. Results We analyze the integration of data from several sources of information using kernel PCA, from the point of view of reducing dimensionality. Moreover, we improve the interpretability of kernel PCA by adding to the plot the representation of the input variables that belong to any dataset. In particular, for each input variable or linear combination of input variables, we can represent the direction of maximum growth locally, which allows us to identify those samples with higher/lower values of the variables analyzed. Conclusions The integration of different datasets and the simultaneous representation of samples and variables together give us a better understanding of biological knowledge.

Computational toolbox towards evolutionary domain mapping of membrane proteins

Membrane proteins account for about 20% to 30% of all proteins encoded in a typical genome. They play central roles in multiple cellular processes mediating the interaction of the cell with its surrounding. Over 60% of all drug targets contain a membrane domain. The experimental difficulties of obtaining a crystal structural severely limits our ability or understanding of membrane protein function. Computational evolutionary studies of proteins are crucial for the prediction of 3D structures. In this project, we construct a tool able to quantify the evolutionary positive selective pressure on each residue of membrane proteins through maximum likelihood phylogeny reconstruction. The conservation plot combined with a structural homology model is also a potent tool to predict those residues that have essentials roles in the structure and function of a membrane protein and can be very useful in the design of validation experiments.

Response of the Thermal Conductivity as a Function of Water Content of a Burnt Mediterranean Loam Soil

The purpose of this research is to explore the variability on the soil thermal conductivity -λ- after a prescribe fire, and to assess the effects of the ashes on the heat transfer once it"s were incorporated into the soil matrix. Sampling plot was located in the Montgrí Massif (NE of Spain). A set of 42 soil samples between surface and 5 cm depth was collected before and after the fire. To characterize the soil chemical and physical variables were analyzed. To determine the vari-ability on the soil λ a dry-out curve per scenario (before and after fire) was determined. SoilRho® method based on ASTM D-5334-08 which was validated by LabFerrer was used. Soil thermal conductivity has shown changes in their values. Indeed, in all moisture scenarios the values of soil λ decreased after soil was burnt. The critical point in the rela-tionship ϴ (λ) for the soil after fire which always was stronger than soil before to be burnt. Soil with"white" ashes showed a high thermal conductivity. An X-Ray diffractometry analysis allowed to clarify and to verify these results. To sum up, we could say that thermal conductivity presents changes when the scenario changes, i.e. before and after to be burnt. On the other hand, the volume of ashes incorporated on the soil increased the differences between no burnt and burnt soil, showing even some improvements on the heat transfer when water content started to govern the process.

A subalpine rangeland bird community before and after fire: prescribed burning in the Eastern Pyrenees

High mountain rangelands host important populations of threatened bird species, but can be affected by extensive changes in land use. I studied the breeding bird community of two shrubland plots at 1,850–2,100 m a.s.l. in the Pyrenees. Breeding territories were mapped for four years, before and after the prescribed burning, the aim of which was to increase the grazing value of the study area. The most abundant species (reaching ≥3 breeding pairs/10 ha in at least one plot and one year) were Dunnock Prunella modularis, Dartford Warbler Sylvia undata, Stonechat Saxicola torquatus, Rock Bunting Emberiza cia and Ortolan Bunting E. hortulana. The open-shrubland plot contained a similar number of breeding species (10 vs.9), but a lower overall density (23 vs. 28 breeding pairs/10 ha) than the dense-shrubland plot. Most breeding species alsooccurred in winter. After fire, the number of bird species, overall density and conservation value (an index that takes into account all species’ densities and their categories of conservation concern in Europe) decreased, but tended to recover afterwards. These results may help understand the composition and dynamics of bird assemblages in managed mountain areas

The effect of skewness and kurtosis on the Kenward-Roger approximation when group distributions differ

This study examined the independent effect of skewness and kurtosis on the robustness of the linear mixed model (LMM), with the Kenward-Roger (KR) procedure, when group distributions are different, sample sizes are small, and sphericity cannot be assumed. Methods: A Monte Carlo simulation study considering a split-plot design involving three groups and four repeated measures was performed. Results: The results showed that when group distributions are different, the effect of skewness on KR robustness is greater than that of kurtosis for the corresponding values. Furthermore, the pairings of skewness and kurtosis with group size were found to be relevant variables when applying this procedure. Conclusions: With sample sizes of 45 and 60, KR is a suitable option for analyzing data when the distributions are: (a) mesokurtic and not highly or extremely skewed, and (b) symmetric with different degrees of kurtosis. With total sample sizes of 30, it is adequate when group sizes are equal and the distributions are: (a) mesokurtic and slightly or moderately skewed, and sphericity is assumed; and (b) symmetric with a moderate or high/extreme violation of kurtosis. Alternative analyses should be considered when the distributions are highly or extremely skewed and samples sizes are small.

Las reglas de la mayoría y Borda: un ejercicio de simulación

En el presente documento se describe un ejercicio de simulación orientado a facilitar la comprensión y asimilación del funcionamiento de la votación por mayoría y la regla de Borda. El ejercicio consiste en proponer a los alumnos que escojan entre dos proyectos (un programa de becas y una ampliación de las aulas de estudio) que presuntamente se van a realizar en la facultad en la que estudian. Para determinar qué proyecto se debería llevar a cabo se utiliza las reglas de la mayoría y Borda. Los alumnos deben responder a diversas rondas de votaciones donde el orden de la votación o agenda ha sido determinada por el instructor. El ejercicio es útil para exponer y debatir las cuestiones que se explican en un curso estándar de Hacienda Pública sobre el uso de la regla de la mayoría y la regla de Borda, como por ejemplo, la existencia de ciclos en los resultados de una votación, la posibilidad de condicionar el resultado de las votaciones mediante la manipulación de la agenda, el comportamiento estratégico, la formación de coaliciones, las propiedades del teorema de Arrow y la eficiencia de la(s) diferentes alternativas escogidas. El ejercicio se enmarca como parte de las actividades realizadas por el Grupo de Innovación Docente (GID-HAL) de la Universidad de Barcelona.

Private micro-irrigation costs using reclaimed water

The cost of reusing water in micro-irrigation at the field level has not been studied in depth although the use of effluents in agriculture is a viable alternative in areas where water is scarce or there is intense competition for its use. The aim of the present study is to analyse the private costs of water reuse in micro-irrigation in an experimental plot. This analysis is intended to provide information about the decision a farmer would make when the choice to use conventional or reclaimed water is guided by cost criteria. The components of the total costs of different combinations of four types of filters and five emitters that can be installed in micro-irrigation systems using reclaimed water have been studied with the data obtained from an experimental plot in conditions similar to those of fruit orchards. Different scenarios that compared the costs of using conventional or reclaimed water in terms of water price and nutrient content were also studied. The results show that a proper combination of filters and emitters can save up to 33% in irrigation costs. Capital costs and maintenance costs were the most variable among the different combinations. Scenario analysis showed that the greater price of reclaimed water could be compensated by high nutrient contents, which would reduce fertilizer costs