The nature of the Cr-C bond: direct estimation of aromaticity in Fischer carbenes

Report for the scientific sojourn at the the Philipps-Universität Marburg, Germany, from september to december 2007. For the first, we employed the Energy-Decomposition Analysis (EDA) to investigate aromaticity on Fischer carbenes as it is related through all the reaction mechanisms studied in my PhD thesis. This powerful tool, compared with other well-known aromaticity indices in the literature like NICS, is useful not only for quantitative results but also to measure the degree of conjugation or hyperconjugation in molecules. Our results showed for the annelated benzenoid systems studied here, that electron density is more concentrated on the outer rings than in the central one. The strain-induced bond localization plays a major role as a driven force to keep the more substituted ring as the less aromatic. The discussion presented in this work was contrasted at different levels of theory to calibrate the method and ensure the consistency of our results. We think these conclusions can also be extended to arene chemistry for explaining aromaticity and regioselectivity reactions found in those systems.In the second work, we have employed the Turbomole program package and density-functionals of the best performance in the state of art, to explore reaction mechanisms in the noble gas chemistry. Particularly, we were interested in compounds of the form H--Ng--Ng--F (where Ng (Noble Gas) = Ar, Kr and Xe) and we investigated the relative stability of these species. Our quantum chemical calculations predict that the dixenon compound HXeXeF has an activation barrier for decomposition of 11 kcal/mol which should be large enough to identify the molecule in a low-temperature matrix. The other noble gases present lower activation barriers and therefore are more labile and difficult to be observable systems experimentally.

Efectes no intencionats de transgens i optimització de la producció de pèptids antimicrobians d'ús fitosanitari en plantes-biofactoria

Actualment s’està duent a terme el projecte de tesi consistent en estudiar la producció de pèptids antimicrobians d'ús fitosanitari en plantes-biofactoria. Durant aquest període de la tesi doctoral he realitzat la transformació (mitjançant Agrobacterium tumefaciens) de plantes d’arròs per a la síntesi massiva d’una sèrie de pèptids antimicrobians, BP188, BP183, BP183TAG, BP215, BP173 i BP178. Es tracta d’una sèrie de derivats de BP100 que presenta unes propietats fitosanitàries molt interessants: elevada activitat contra bacteris d’interès fitosanitari, toxicitat reduïda i estabilitat moderada. El treball que he realitzat per dur a terme aquesta tasca ha requerit inicialment realitzar els clonatges necessaris per a les transformacions; per a continuació realitzar les transformacions de calls d’arròs varietat Sènia, seleccionar les cèl•lules transformades, regenerar plantes transgèniques i analitzar-ne la presència del transgén.

Compositional amalgamations and balances: a critical approach

The amalgamation operation is frequently used to reduce the number of parts of compositional data but it is a non-linear operation in the simplex with the usual geometry,the Aitchison geometry. The concept of balances between groups, a particular coordinate system designed over binary partitions of the parts, could be an alternative to theamalgamation in some cases. In this work we discuss the proper application of bothconcepts using a real data set corresponding to behavioral measures of pregnant sows

La evaluación de la reducción de amenazas en el Parque Natural de la Zona Volcánica de la Garrotxa (Girona)

En este artículo se presenta la metodología y los resultados derivados de la aplicación de una adaptación del denominado modelo de evaluación de reducción de amenazas (Threat Reduction Assesment) en el Parque Natural de la Zona Volcánica de la Garrotxa (PNZVG). Endefinitiva, se pretende valorar la efectividad de la gestión a partir del grado de reducción de amenazas en el PNZVG. El estudio se realizó a partir de la elaboración de una evaluación externa e independiente, que ha contado a la vez con una estrecha colaboración de los órganos gestores y rectores del Parque, así como con una activa participación de distintos agentes sociales clave. Se concluye que, después de veinticinco años de existencia del Parque, muchas de las amenazas iniciales sólo se han reducido de forma modesta e incluso a partir del índice adaptado, considerado un enfoque más realista; con lo cual se llega a la preocupante conclusión de que algunas de las amenazas más importantes se han incrementado

Statistical treatment of grain-size curves and empirical distributions: densities as compositions?

The preceding two editions of CoDaWork included talks on the possible considerationof densities as infinite compositions: Egozcue and D´ıaz-Barrero (2003) extended theEuclidean structure of the simplex to a Hilbert space structure of the set of densitieswithin a bounded interval, and van den Boogaart (2005) generalized this to the setof densities bounded by an arbitrary reference density. From the many variations ofthe Hilbert structures available, we work with three cases. For bounded variables, abasis derived from Legendre polynomials is used. For variables with a lower bound, westandardize them with respect to an exponential distribution and express their densitiesas coordinates in a basis derived from Laguerre polynomials. Finally, for unboundedvariables, a normal distribution is used as reference, and coordinates are obtained withrespect to a Hermite-polynomials-based basis.To get the coordinates, several approaches can be considered. A numerical accuracyproblem occurs if one estimates the coordinates directly by using discretized scalarproducts. Thus we propose to use a weighted linear regression approach, where all k-order polynomials are used as predictand variables and weights are proportional to thereference density. Finally, for the case of 2-order Hermite polinomials (normal reference)and 1-order Laguerre polinomials (exponential), one can also derive the coordinatesfrom their relationships to the classical mean and variance.Apart of these theoretical issues, this contribution focuses on the application of thistheory to two main problems in sedimentary geology: the comparison of several grainsize distributions, and the comparison among different rocks of the empirical distribution of a property measured on a batch of individual grains from the same rock orsediment, like their composition

Hilbert space on probability density functions with Aitchison geometry

Compositional data analysis motivated the introduction of a complete Euclidean structure in the simplex of D parts. This was based on the early work of J. Aitchison (1986) and completed recently when Aitchinson distance in the simplex was associated with an inner product and orthonormal bases were identified (Aitchison and others, 2002; Egozcue and others, 2003). A partition of the support of a random variable generates a composition by assigning the probability of each interval to a part of the composition. One can imagine that the partition can be refined and the probability density would represent a kind of continuous composition of probabilities in a simplex of infinitely many parts. This intuitive idea would lead to a Hilbert-space of probability densitiesby generalizing the Aitchison geometry for compositions in the simplex into the set probability densities

Distributions on the simplex

The simplex, the sample space of compositional data, can be structured as a real Euclidean space. This fact allows to work with the coefficients with respect to an orthonormal basis. Over these coefficients we apply standard real analysis, inparticular, we define two different laws of probability trought the density function and we study their main properties

An R Library for Compositional Data Analysis in Archaeometry

Compositional data naturally arises from the scientific analysis of the chemicalcomposition of archaeological material such as ceramic and glass artefacts. Data of thistype can be explored using a variety of techniques, from standard multivariate methodssuch as principal components analysis and cluster analysis, to methods based upon theuse of log-ratios. The general aim is to identify groups of chemically similar artefactsthat could potentially be used to answer questions of provenance.This paper will demonstrate work in progress on the development of a documentedlibrary of methods, implemented using the statistical package R, for the analysis ofcompositional data. R is an open source package that makes available very powerfulstatistical facilities at no cost. We aim to show how, with the aid of statistical softwaresuch as R, traditional exploratory multivariate analysis can easily be used alongside, orin combination with, specialist techniques of compositional data analysis.The library has been developed from a core of basic R functionality, together withpurpose-written routines arising from our own research (for example that reported atCoDaWork'03). In addition, we have included other appropriate publicly availabletechniques and libraries that have been implemented in R by other authors. Availablefunctions range from standard multivariate techniques through to various approaches tolog-ratio analysis and zero replacement. We also discuss and demonstrate a smallselection of relatively new techniques that have hitherto been little-used inarchaeometric applications involving compositional data. The application of the libraryto the analysis of data arising in archaeometry will be demonstrated; results fromdifferent analyses will be compared; and the utility of the various methods discussed

Thermodynamics and log–contrast analysis in fluid geochemistry

There are two principal chemical concepts that are important for studying the naturalenvironment. The first one is thermodynamics, which describes whether a system is atequilibrium or can spontaneously change by chemical reactions. The second main conceptis how fast chemical reactions (kinetics or rate of chemical change) take place wheneverthey start. In this work we examine a natural system in which both thermodynamics andkinetic factors are important in determining the abundance of NH+4 , NO−2 and NO−3 insuperficial waters. Samples were collected in the Arno Basin (Tuscany, Italy), a system inwhich natural and antrophic effects both contribute to highly modify the chemical compositionof water. Thermodynamical modelling based on the reduction-oxidation reactionsinvolving the passage NH+4 -& NO−2 -& NO−3 in equilibrium conditions has allowed todetermine the Eh redox potential values able to characterise the state of each sample and,consequently, of the fluid environment from which it was drawn. Just as pH expressesthe concentration of H+ in solution, redox potential is used to express the tendency of anenvironment to receive or supply electrons. In this context, oxic environments, as thoseof river systems, are said to have a high redox potential because O2 is available as anelectron acceptor.Principles of thermodynamics and chemical kinetics allow to obtain a model that oftendoes not completely describe the reality of natural systems. Chemical reactions may indeedfail to achieve equilibrium because the products escape from the site of the rectionor because reactions involving the trasformation are very slow, so that non-equilibriumconditions exist for long periods. Moreover, reaction rates can be sensitive to poorly understoodcatalytic effects or to surface effects, while variables as concentration (a largenumber of chemical species can coexist and interact concurrently), temperature and pressurecan have large gradients in natural systems. By taking into account this, data of 91water samples have been modelled by using statistical methodologies for compositionaldata. The application of log–contrast analysis has allowed to obtain statistical parametersto be correlated with the calculated Eh values. In this way, natural conditions in whichchemical equilibrium is hypothesised, as well as underlying fast reactions, are comparedwith those described by a stochastic approach

Compositional analysis of archaeological glasses

At CoDaWork'03 we presented work on the analysis of archaeological glass composi-tional data. Such data typically consist of geochemical compositions involving 10-12variables and approximates completely compositional data if the main component, sil-ica, is included. We suggested that what has been termed `crude' principal componentanalysis (PCA) of standardized data often identi ed interpretable pattern in the datamore readily than analyses based on log-ratio transformed data (LRA). The funda-mental problem is that, in LRA, minor oxides with high relative variation, that maynot be structure carrying, can dominate an analysis and obscure pattern associatedwith variables present at higher absolute levels. We investigate this further using sub-compositional data relating to archaeological glasses found on Israeli sites. A simplemodel for glass-making is that it is based on a `recipe' consisting of two `ingredients',sand and a source of soda. Our analysis focuses on the sub-composition of componentsassociated with the sand source. A `crude' PCA of standardized data shows two clearcompositional groups that can be interpreted in terms of di erent recipes being used atdi erent periods, reected in absolute di erences in the composition. LRA analysis canbe undertaken either by normalizing the data or de ning a `residual'. In either case,after some `tuning', these groups are recovered. The results from the normalized LRAare di erently interpreted as showing that the source of sand used to make the glassdi ered. These results are complementary. One relates to the recipe used. The otherrelates to the composition (and presumed sources) of one of the ingredients. It seemsto be axiomatic in some expositions of LRA that statistical analysis of compositionaldata should focus on relative variation via the use of ratios. Our analysis suggests thatabsolute di erences can also be informative

Interpretation of wind components as compositional variables

The classical statistical study of the wind speed in the atmospheric surface layer is madegenerally from the analysis of the three habitual components that perform the wind data,that is, the component W-E, the component S-N and the vertical component,considering these components independent.When the goal of the study of these data is the Aeolian energy, so is when wind isstudied from an energetic point of view and the squares of wind components can beconsidered as compositional variables. To do so, each component has to be divided bythe module of the corresponding vector.In this work the theoretical analysis of the components of the wind as compositionaldata is presented and also the conclusions that can be obtained from the point of view ofthe practical applications as well as those that can be derived from the application ofthis technique in different conditions of weather

Alternative ways to estimate change points in multinomial sequences. An application to an authorship attribution problem

The statistical analysis of literary style is the part of stylometry that compares measurable characteristicsin a text that are rarely controlled by the author, with those in other texts. When thegoal is to settle authorship questions, these characteristics should relate to the author’s style andnot to the genre, epoch or editor, and they should be such that their variation between authors islarger than the variation within comparable texts from the same author.For an overview of the literature on stylometry and some of the techniques involved, see for exampleMosteller and Wallace (1964, 82), Herdan (1964), Morton (1978), Holmes (1985), Oakes (1998) orLebart, Salem and Berry (1998).Tirant lo Blanc, a chivalry book, is the main work in catalan literature and it was hailed to be“the best book of its kind in the world” by Cervantes in Don Quixote. Considered by writterslike Vargas Llosa or Damaso Alonso to be the first modern novel in Europe, it has been translatedseveral times into Spanish, Italian and French, with modern English translations by Rosenthal(1996) and La Fontaine (1993). The main body of this book was written between 1460 and 1465,but it was not printed until 1490.There is an intense and long lasting debate around its authorship sprouting from its first edition,where its introduction states that the whole book is the work of Martorell (1413?-1468), while atthe end it is stated that the last one fourth of the book is by Galba (?-1490), after the death ofMartorell. Some of the authors that support the theory of single authorship are Riquer (1990),Chiner (1993) and Badia (1993), while some of those supporting the double authorship are Riquer(1947), Coromines (1956) and Ferrando (1995). For an overview of this debate, see Riquer (1990).Neither of the two candidate authors left any text comparable to the one under study, and thereforediscriminant analysis can not be used to help classify chapters by author. By using sample textsencompassing about ten percent of the book, and looking at word length and at the use of 44conjunctions, prepositions and articles, Ginebra and Cabos (1998) detect heterogeneities that mightindicate the existence of two authors. By analyzing the diversity of the vocabulary, Riba andGinebra (2000) estimates that stylistic boundary to be near chapter 383.Following the lead of the extensive literature, this paper looks into word length, the use of the mostfrequent words and into the use of vowels in each chapter of the book. Given that the featuresselected are categorical, that leads to three contingency tables of ordered rows and therefore tothree sequences of multinomial observations.Section 2 explores these sequences graphically, observing a clear shift in their distribution. Section 3describes the problem of the estimation of a suden change-point in those sequences, in the followingsections we propose various ways to estimate change-points in multinomial sequences; the methodin section 4 involves fitting models for polytomous data, the one in Section 5 fits gamma modelsonto the sequence of Chi-square distances between each row profiles and the average profile, theone in Section 6 fits models onto the sequence of values taken by the first component of thecorrespondence analysis as well as onto sequences of other summary measures like the averageword length. In Section 7 we fit models onto the marginal binomial sequences to identify thefeatures that distinguish the chapters before and after that boundary. Most methods rely heavilyon the use of generalized linear models

News from compositions, the R package

The R-package “compositions”is a tool for advanced compositional analysis. Its basicfunctionality has seen some conceptual improvement, containing now some facilitiesto work with and represent ilr bases built from balances, and an elaborated subsys-tem for dealing with several kinds of irregular data: (rounded or structural) zeroes,incomplete observations and outliers. The general approach to these irregularities isbased on subcompositions: for an irregular datum, one can distinguish a “regular” sub-composition (where all parts are actually observed and the datum behaves typically)and a “problematic” subcomposition (with those unobserved, zero or rounded parts, orelse where the datum shows an erratic or atypical behaviour). Systematic classificationschemes are proposed for both outliers and missing values (including zeros) focusing onthe nature of irregularities in the datum subcomposition(s).To compute statistics with values missing at random and structural zeros, a projectionapproach is implemented: a given datum contributes to the estimation of the desiredparameters only on the subcompositon where it was observed. For data sets withvalues below the detection limit, two different approaches are provided: the well-knownimputation technique, and also the projection approach.To compute statistics in the presence of outliers, robust statistics are adapted to thecharacteristics of compositional data, based on the minimum covariance determinantapproach. The outlier classification is based on four different models of outlier occur-rence and Monte-Carlo-based tests for their characterization. Furthermore the packageprovides special plots helping to understand the nature of outliers in the dataset.Keywords: coda-dendrogram, lost values, MAR, missing data, MCD estimator,robustness, rounded zeros

La competència «El treball col·laboratiu» : una oportunitat per a incorporar les TIC en la didàctica universitària. Descripció de l'experiència amb la plataforma ACME (UdG)

L'article és una reflexió sobre els requisits de formació dels professionals que demana la societat del coneixement. Un dels objectius més importants que ha de tenir la universitat en la societat del coneixement és la formació de professionals competents que tinguin prou eines intel·lectuals per a enfrontar-se a la incertesa de la informació, a la consciència que aquesta té una data de caducitat a curt termini i a l'ansietat que això provoca. Però, a més, també han de ser capaços de definir i crear les eines de treball amb què donaran sentit i eficàcia a aquest coneixement mudable i mutant. Per això, l'espai europeu d'ensenyament superior prioritza la competència transversal del treball col·laboratiu amb l'objectiu de promoure un aprenentatge autònom, compromès i adaptat a les noves necessitats de l'empresa del segle xxi. En aquest context, es presenta l'entorn teòric que fonamenta el treball desenvolupat a la plataforma informàtica ACME, que uneix el treball col·laboratiu i l'aprenentatge semipresencial o blended learning. Així mateix, es descriuen amb detall alguns exemples de wikis, paradigma del treball col·laboratiu, fets en assignatures impartides per la Universitat de Girona en l'espai virtual ACME

L'ambient urbà i la criminalitat. Robatoris contra el patrimoni a la ciutat de Girona

L’estudi de la criminalitat és multifactorial, cal destriar en la mesura del possible els factorsambientals, d’entorn urbà, que poden jugar el paper de facilitadors de la delinqüència. Lestipologies delictives són diverses i amb motivacions "mòbils" diferenciats, el que confereixdificultats a l’estudi de la criminalitat, és per aquesta raó que es trien dues tipologies derobatoris contra el patrimoni per ser analitzats: robatoris amb força a interior de domicili(vivenda) i els furts, en un marc de ciutat petita-mitjana, com és el cas de Girona. Elconeixement per part de l’autor del marc urbà n’és un part essencial per desenvolupar l’estudi.Un dels objectius finalistes és aconseguir avançar en estudis de diagnosi criminal de les ciutats;així com en el coneixement dels patrons espaials que tenen les tipologies delictives i lainfluència de les característiques del disseny urbà sobre la criminalitat. La metodologia ques’implementarà serà: recerca bibliogràfica, estadística descriptiva i inferencial, sistemesd’informació geogràfica, així com la deducció a partir de la visualització de la cartografiagenerada i un treball de camp de les zones d’alta ocurrència delictiva dels delictes esmentats.Pel que fa a les hipòtesis principals: els robatoris contra el patrimoni no es concentren en àreesdegradades urbanísticament sinó ans el contrari en ambients urbans cuidats. Aquesta hipòtesies contraposa a la teoria criminal de la "Broken Windows", que esmenta que els espais urbansdegradats és on hi ha menys ocupació d’espai públic i més delinqüència. Una altra hipòtesiimportant és que els espais percebuts com a segurs, respecte les tipologies delictivesesmentades, són els més insegurs