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.

Germination, senescence and pathogenic attack in soybean (Glycine max. L.): Identification of the cytosolic aconitase participating in the glyoxylate cycle

During our study of the glyoxylate cycle in soybean (Glycine max. L. var. Maple arrow), two mitochondrial and three cytosolic aconitase molecular species (EC 4.2.1.3) were detected, designated as M1, M2, C1, C2 and C3 isoforms, respectively, according to their intracellular locations and electrophoretic mobilities. Using the glyoxylate cycle marker enzymes isocitrate lyase (ICL, EC 4.1.3.1) and malate synthase (MS, EC 4.1.3.2), the activity of this pathway providing the essential link between P-oxidation and gluconeogenesis was confirmed during germination (cotyledons) and senescence (leaves). It was then established that, in both cases, the activity of the CI aconitase isoform developed concomitantly with the transcription and translation levels of the icl and ms genes. This strongly suggests that C1 aconitase is constitutive of the glyoxylate cycle. In addition, the same isoform was found to be active during pathogenic attack as well (hypocotyls). It might be assumed that in such a case the glyoxylate cycle is reinitiated as a part of a carbon reallocation system feeding on the diseased tissue cellular components.

Pathogenic attack and carbon reallocation in soybean leaves (Glycine max. L.): Reinitiation of the glyoxylate cycle as a defence reaction

Pathogenic attack by the fungus Botrytis cinerea (primary pathogen) on soybean leaves (Glycine max. L.; cv. Maple arrow) results in a hypersensitive response (necrotising infected leaves), in the establishment of local acquired resistance, as well as in the systemic induction of genes coding for pathogenesis-related proteins. It now appears that, concomitantly with these already well documented defence reactions, the pathogenic attack also induces the carbon reallocation mechanism based on the reinitiation of the glyoxylate cycle (pseudo-senescence of the infected leaves).

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.

General Equilibrium Analysis. A Century after Walras

2010 marks the hundredth anniversary of the death of Léon Walras, the brilliant originator and first formaliser of general equilibrium theory - one of the pillars of modern economic theory. In advancing much derided practical solutions Walras also displayed more concern for the problems of living in a second best world than is common in modern pure theories of the invisible hand, efficient market hypothesis, DSGE macroeconomics or the thinking of some contemporary free market admirers all based on general equilibrium theory. This book brings contributions from the likes of Kenneth Arrow, Alan Kirman, Richard Posner, Amartya Sen and Robert Solow to share their thoughts and reflections on the theoretical heritage of Léon Walras. Some authors reminisce on the part they played in the development of modern general economics theory; others reflect on the crucial part played by general equilibrium in the development of macroeconomics, microeconomics, growth theory, welfare economics and the theory of justice; others still complain about the wrong path economic theory took under the influence of post 1945 developments in general equilibrium theory.

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.

Lempitutkimukseni

Tutkimus sisältyy teokseen "Film theory goes to the movies"

La fureur divine et son détournement en Nb 25

The story Numbers of 25 which reports the incident of Baal Peor is one among several texts in the book of Numbers focusing on divine wrath, its cause and its consequences. The present article offers a detailed analysis of the account which is difficult to understand because of certain jumps in the plot and because of its allusive style. Scholars mostly agree with the idea that the story grew in two or three stages. A lot of commentators believe that the original story contains only the apostasy of Peor caused by the Moabites (vv. 1-5). A subsequent story would focus on Pinchas' action against Zimri and Kospi, and a third layer is linked to the story of the war between Israel and Midian (Numbers 31). The problem of this theory however is that it seems impossible to reconstruct an original story about the matter of Peor; one does not find a satisfying end within vv. 1-5. Furthermore, v. 5, which belongs to the first, "Moabite", section, is already linked to the theme of Midian which dominates the second and the third passage. Moreover, the assemblage of different themes and motifs seem having been done with care: Regarding the two abuses of Israel reported in the story--idolatry and intermarriage--, they often go together in late polemical Deuteronomistic and post-Deuteronomistic layers (Ezra-Nehemiah). The double focus on Midian and Moab could both be polemically directed against certain Moses traditions found in the books of Exodus and Deuteronomy (concerning Moses' marriage with a Midianite women on the one hand and his stay and death and burial in Moab - in the vicinity of Beth Peor - on the other hand). As in several ANE traditions also in the Hebrew Bible the motif of "divine wrath" serves to interpret fatal historical events; in Num 25 as in other Biblical stories however it is doubtful whether the alleged incident (the plague) really have taken place and the story's plot is anchored in ancient Israel's history.

Transgression et initiation : tendances idéologiques et développement littéraire du récit de Genèse 2-3

Several questions about the story of Gen 2-3 remain unresolved in current scholarship. For instance, the implications and manifold consequences of the transgression act - the consumption of the forbidden fruit - are much debated. Interpreters generally agree that the story is connected to several "J" / "non-P" narratives of the primeval history. Besides the use of the tetragrammaton as the designation for God, a common characteristic of these stories is the strong opposition between Yhwh as a harsh deity on one hand and disobedient and transgressing humankind on the other. This paper reconsiders several open questions as well as the aforementioned consensus. The analysis of important motifs in Gen 2-3 leads to the conclusion that this story differs in theologically important ways from the postulated "J"-narrative in Genesis. This indicates that it was not composed as an integral part of that narrative. There are, in Gen 2-3, ideological features and linguistic elements typical of the "J" stratum, but they are all found in the sections that present Yhwh God's investigation and punishment of the couple (3,8-19.24). Since these verses are in tension with or even contradict their immediate context, it should be assigned to a redactional ("J") layer. According to this analysis, the transgression in Gen 2-3 should not be considered a sin. Rather, it is an important step in human evolution towards a self-conscious and autonomous being. The plot has a structure similar to some episodes in ancient Near Eastern myths. 'Initiation' functions as a central theme. Finally, the article discusses the literary milieu of the story. Because of several linguistic and thematic similarities with Gen 1, with P-texts in general, and with the book of Ezekiel, the relationship of Gen 2-3 to these literary entities needs to be reconsidered.

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

Conseqüências da análise incorreta de experimentos blocados

Errors are always present in experimental measurements so, it is important to identify them and understand how they affect the results of experiments. Statistics suggest that the execution of experiments should follow random order, but unfortunately the complete randomization of experiments is not always viable for practical reasons. One possible simplification is blocked experiments within which the levels of certain factors are maintained fixed while the levels of others are randomized. However this has a cost. Although the experimental part is simplified, the statistical analysis becomes more complex.

Determinação dos parâmetros de arrhenius da reação de sorção do dióxido de enxofre por calcário

Sulfur emission in coal power generation is a matter of great environmental concern and limestone sorbents are widely used for reducing such emissions. Thermogravimetry was applied to determine the effects of the type of limestone (calcite and dolomite), particle size (530 and 650 µm) and atmosphere (air and nitrogen) on the kinetics of SO2 sorption by limestone. Isothermal experiments were performed for different temperatures (650 to 950 ºC), at local atmospheric pressure. The apparent activation energies, as indicated by the slope of the Arrhenius plot, resulted between 3.03 and 4.45 kJ mol-1 for the calcite, and 11.24 kJ mol-1 for the dolomite.