WePreserve 2009: DPE/Planets/CASPAR/nestor Joint Training Event: The Preservation challenge: basic concepts and practical applications (Barcelona, 23-27 març 2009)

Reseña del congreso WePreserve 2009 que tuvo lugar los pasados 23 al 27 de marzo en Barcelona, organizadopor la Facultad de Biblioteconomía y Documentación de la Universitat de Barcelona, con la colaboración del Institut d'Estudis Catalans, la Biblioteca de Catalunya y el Consorci de Biblioteques de Barcelona. El seminario 2009 WePreserve se celebra anualmente desde el año 2007 y participan todas las figuras de referencia europeas en materia de investigación en sistemas y metodologías que garantizan la preservación digital de los documentos: Digital Preservation Europe (DPE), Preservation and Long-term Access Through Networked Services (Planets), Cultural Artistic and Scientific Knowledge for Preservation, Access and Retrieval (CASPAR), y Network of expertise in Digital long-term preservation (nestor).

Practical applications of quantum molecular similarity measures (QMSM): programs and examples

Es descriu l'aproximació de Capes Atòmiques dins de la teoria de la Semblança Molecular Quàntica. Partint només de dades teòriques, s'ha trobat una relació entre estructura molecular i activitat biològica per a diversos conjunts de molècules. Es descriuen els aspectes teòrics de la Semblança Molecular Quàntica i alguns exemples d'aplicació

Mixing compositions and other scales

Theory of compositional data analysis is often focused on the composition only. However in practical applications we often treat a composition together with covariableswith some other scale. This contribution systematically gathers and develop statistical tools for this situation. For instance, for the graphical display of the dependenceof a composition with a categorical variable, a colored set of ternary diagrams mightbe a good idea for a first look at the data, but it will fast hide important aspects ifthe composition has many parts, or it takes extreme values. On the other hand colored scatterplots of ilr components could not be very instructive for the analyst, if theconventional, black-box ilr is used.Thinking on terms of the Euclidean structure of the simplex, we suggest to set upappropriate projections, which on one side show the compositional geometry and on theother side are still comprehensible by a non-expert analyst, readable for all locations andscales of the data. This is e.g. done by defining special balance displays with carefully-selected axes. Following this idea, we need to systematically ask how to display, explore,describe, and test the relation to complementary or explanatory data of categorical, real,ratio or again compositional scales.This contribution shows that it is sufficient to use some basic concepts and very fewadvanced tools from multivariate statistics (principal covariances, multivariate linearmodels, trellis or parallel plots, etc.) to build appropriate procedures for all these combinations of scales. This has some fundamental implications in their software implementation, and how might they be taught to analysts not already experts in multivariateanalysis

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

Quantifying rock fabrics: a test of autocorrelation of the spatial distribution of cristals

A novel test of spatial independence of the distribution of crystals or phases in rocksbased on compositional statistics is introduced. It improves and generalizes the commonjoins-count statistics known from map analysis in geographic information systems.Assigning phases independently to objects in RD is modelled by a single-trial multinomialrandom function Z(x), where the probabilities of phases add to one and areexplicitly modelled as compositions in the K-part simplex SK. Thus, apparent inconsistenciesof the tests based on the conventional joins{count statistics and their possiblycontradictory interpretations are avoided. In practical applications we assume that theprobabilities of phases do not depend on the location but are identical everywhere inthe domain of de nition. Thus, the model involves the sum of r independent identicalmultinomial distributed 1-trial random variables which is an r-trial multinomialdistributed random variable. The probabilities of the distribution of the r counts canbe considered as a composition in the Q-part simplex SQ. They span the so calledHardy-Weinberg manifold H that is proved to be a K-1-affine subspace of SQ. This isa generalisation of the well-known Hardy-Weinberg law of genetics. If the assignmentof phases accounts for some kind of spatial dependence, then the r-trial probabilitiesdo not remain on H. This suggests the use of the Aitchison distance between observedprobabilities to H to test dependence. Moreover, when there is a spatial uctuation ofthe multinomial probabilities, the observed r-trial probabilities move on H. This shiftcan be used as to check for these uctuations. A practical procedure and an algorithmto perform the test have been developed. Some cases applied to simulated and realdata are presented.Key words: Spatial distribution of crystals in rocks, spatial distribution of phases,joins-count statistics, multinomial distribution, Hardy-Weinberg law, Hardy-Weinbergmanifold, Aitchison geometry

Modeling of hybrid systems by piecewise decomposition

Piecewise linear models systems arise as mathematical models of systems in many practical applications, often from linearization for nonlinear systems. There are two main approaches of dealing with these systems according to their continuous or discrete-time aspects. We propose an approach which is based on the state transformation, more particularly the partition of the phase portrait in different regions where each subregion is modeled as a two-dimensional linear time invariant system. Then the Takagi-Sugeno model, which is a combination of local model is calculated. The simulation results show that the Alpha partition is well-suited for dealing with such a system

From MuSIASEM theory to practice: report and reflections from field research in Kampot province, Cambodia

This document contains a report and summary of the field research activities in a rural community of rice farmers in Kampot province, Cambodia in 2011, which I conducted within the context of my PhD research at ICTA-UAB (Institute of Environmental Science and Technology, Autonomous University of Barcelona, Spain). The purpose of the field research was to gather data for a MuSIASEM analysis (Multi-Scale Integrated Analysis of Societal and Ecosystem Metabolism) at the village and household level, in order to analyze the multidimensional challenges that small farmers may face nowadays within the context of global rural change and declining access to land. While the literature on MuSIASEM offers a great variety of theoretical explanations and practical applications, there is little information available for students regarding the practical steps required for doing a MuSIASEM analysis at the local level. Within this context, this report offers not only a documentation of the field research design and data collection methods, but further provides a general overview on some organizational and preparative aspects, including some personal reflections, that one may face when preparing and conducting field research for MuSIASEM analysis. In summary, this document thus serves three objectives: (i) to assure methodological transparency for the future work, based on the collected data during field research, (ii) to share my personal experience on the preparative and practical steps required for field research and data collection for a MuSIASEM analysis at the local level, and (iii) to make available for the further interested reader some more detailed background information on the case study village.

Suitability of GRIND-based principal properties for the description of molecular similarity and ligand-based virtual screening

The information provided by the alignment-independent GRid Independent Descriptors (GRIND) can be condensed by the application of principal component analysis, obtaining a small number of principal properties (GRIND-PP), which is more suitable for describing molecular similarity. The objective of the present study is to optimize diverse parameters involved in the obtention of the GRIND-PP and validate their suitability for applications, requiring a biologically relevant description of the molecular similarity. With this aim, GRIND-PP computed with a collection of diverse settings were used to carry out ligand-based virtual screening (LBVS) on standard conditions. The quality of the results obtained was remarkable and comparable with other LBVS methods, and their detailed statistical analysis allowed to identify the method settings more determinant for the quality of the results and their optimum. Remarkably, some of these optimum settings differ significantly from those used in previously published applications, revealing their unexplored potential. Their applicability in large compound database was also explored by comparing the equivalence of the results obtained using either computed or projected principal properties. In general, the results of the study confirm the suitability of the GRIND-PP for practical applications and provide useful hints about how they should be computed for obtaining optimum results.

Synthesis of triheptanoin and formulation as a solid diet for rodents

Triheptanoin-enriched diets have been successfully used in the experimental treatment of various metabolic disorders. Maximal therapeutic effect is achieved in the context of a ketogenic diet where triheptanoin oil provides 3040% of the daily caloric intake. However, pre-clinical studies using triheptanoin-rich diets are hindered by the difficulty of administering to laboratory animals as a solid foodstuff. In the present study, we successfully synthesized triheptanoin to the highest standards of purity from glycerol and heptanoic acid, using sulfonated charcoal as a catalyst. Triheptanoin oil was then formulated as a solid, stable and palatable preparation using a ketogenic base and a combination of four commercially available formulation agents: hydrophilic fumed silica, hydrophobic fumed silica, microcrystalline cellulose, and talc. Diet compliance and safety was tested on C57Bl/6 mice over a 15-week period, comparing overall status and body weight change. Practical applications: This work provides a complete description of (i) an efficient and cost-effective synthesis of triheptanoin and (ii) its formulation as a solid, stable, and palatable ketogenic diet (triheptanoin-rich; 39% of the caloric intake) for rodents. Triheptanoin-rich diets will be helpful on pre-clinical experiments testing the therapeutic efficacy of triheptanoin in different rodent models of human diseases. In addition, using the same solidification procedure, other oils could be incorporated into rodent ketogenic diet to study their dosage and long-term effects on mammal health and development. This approach could be extremely valuable as ketogenic diet is widely used clinically for epilepsy treatment.

Synthesis of triheptanoin and formulation as a solid diet for rodents

Triheptanoin-enriched diets have been successfully used in the experimental treatment of various metabolic disorders. Maximal therapeutic effect is achieved in the context of a ketogenic diet where triheptanoin oil provides 3040% of the daily caloric intake. However, pre-clinical studies using triheptanoin-rich diets are hindered by the difficulty of administering to laboratory animals as a solid foodstuff. In the present study, we successfully synthesized triheptanoin to the highest standards of purity from glycerol and heptanoic acid, using sulfonated charcoal as a catalyst. Triheptanoin oil was then formulated as a solid, stable and palatable preparation using a ketogenic base and a combination of four commercially available formulation agents: hydrophilic fumed silica, hydrophobic fumed silica, microcrystalline cellulose, and talc. Diet compliance and safety was tested on C57Bl/6 mice over a 15-week period, comparing overall status and body weight change. Practical applications: This work provides a complete description of (i) an efficient and cost-effective synthesis of triheptanoin and (ii) its formulation as a solid, stable, and palatable ketogenic diet (triheptanoin-rich; 39% of the caloric intake) for rodents. Triheptanoin-rich diets will be helpful on pre-clinical experiments testing the therapeutic efficacy of triheptanoin in different rodent models of human diseases. In addition, using the same solidification procedure, other oils could be incorporated into rodent ketogenic diet to study their dosage and long-term effects on mammal health and development. This approach could be extremely valuable as ketogenic diet is widely used clinically for epilepsy treatment.

Synthesis of triheptanoin and formulation as a solid diet for rodents

Triheptanoin-enriched diets have been successfully used in the experimental treatment of various metabolic disorders. Maximal therapeutic effect is achieved in the context of a ketogenic diet where triheptanoin oil provides 3040% of the daily caloric intake. However, pre-clinical studies using triheptanoin-rich diets are hindered by the difficulty of administering to laboratory animals as a solid foodstuff. In the present study, we successfully synthesized triheptanoin to the highest standards of purity from glycerol and heptanoic acid, using sulfonated charcoal as a catalyst. Triheptanoin oil was then formulated as a solid, stable and palatable preparation using a ketogenic base and a combination of four commercially available formulation agents: hydrophilic fumed silica, hydrophobic fumed silica, microcrystalline cellulose, and talc. Diet compliance and safety was tested on C57Bl/6 mice over a 15-week period, comparing overall status and body weight change. Practical applications: This work provides a complete description of (i) an efficient and cost-effective synthesis of triheptanoin and (ii) its formulation as a solid, stable, and palatable ketogenic diet (triheptanoin-rich; 39% of the caloric intake) for rodents. Triheptanoin-rich diets will be helpful on pre-clinical experiments testing the therapeutic efficacy of triheptanoin in different rodent models of human diseases. In addition, using the same solidification procedure, other oils could be incorporated into rodent ketogenic diet to study their dosage and long-term effects on mammal health and development. This approach could be extremely valuable as ketogenic diet is widely used clinically for epilepsy treatment.

On the tractability of the piecewise-linear approximation for general discrete-choice network revenue management

The choice network revenue management (RM) model incorporates customer purchase behavioras customers purchasing products with certain probabilities that are a function of the offeredassortment of products, and is the appropriate model for airline and hotel network revenuemanagement, dynamic sales of bundles, and dynamic assortment optimization. The underlyingstochastic dynamic program is intractable and even its certainty-equivalence approximation, inthe form of a linear program called Choice Deterministic Linear Program (CDLP) is difficultto solve in most cases. The separation problem for CDLP is NP-complete for MNL with justtwo segments when their consideration sets overlap; the affine approximation of the dynamicprogram is NP-complete for even a single-segment MNL. This is in contrast to the independentclass(perfect-segmentation) case where even the piecewise-linear approximation has been shownto be tractable. In this paper we investigate the piecewise-linear approximation for network RMunder a general discrete-choice model of demand. We show that the gap between the CDLP andthe piecewise-linear bounds is within a factor of at most 2. We then show that the piecewiselinearapproximation is polynomially-time solvable for a fixed consideration set size, bringing itinto the realm of tractability for small consideration sets; small consideration sets are a reasonablemodeling tradeoff in many practical applications. Our solution relies on showing that forany discrete-choice model the separation problem for the linear program of the piecewise-linearapproximation can be solved exactly by a Lagrangian relaxation. We give modeling extensionsand show by numerical experiments the improvements from using piecewise-linear approximationfunctions.

Integrative analysis of the Regulatory Region of the FGFR3 Oncogene

The study of transcriptional regulation often needs the integration of diverse yet independent data. In the present work, sequence conservation, predic-tion of transcription factor binding sites (TFBS) and gene expression analysis have been applied to the detection of putative transcription factor (TF) modules in the regulatory region of the FGFR3 oncogene. Several TFs with conserved binding sites in the FGFR3 regulatory region have shown high positive or negative corre-lation with FGFR3 expression both in urothelial carcinoma and in benign nevi. By means of conserved TF cluster analysis, two different TF modules have been iden-tified in the promoter and first intron of FGFR3 gene. These modules contain acti-vating AP2, E2F, E47 and SP1 binding sites plus motifs for EGR with possible repressor function.

Improving a leaves automatic recognition process using PCA

In this work we present a simulation of a recognition process with perimeter characterization of a simple plant leaves as a unique discriminating parameter. Data coding allowing for independence of leaves size and orientation may penalize performance recognition for some varieties. Border description sequences are then used, and Principal Component Analysis (PCA) is applied in order to study which is the best number of components for the classification task, implemented by means of a Support Vector Machine (SVM) System. Obtained results are satisfactory, and compared with [4] our system improves the recognition success, diminishing the variance at the same time.

A priori parameterisation of the CERES soil-crop models and tests against several European data sets

Mechanistic soil-crop models have become indispensable tools to investigate the effect of management practices on the productivity or environmental impacts of arable crops. Ideally these models may claim to be universally applicable because they simulate the major processes governing the fate of inputs such as fertiliser nitrogen or pesticides. However, because they deal with complex systems and uncertain phenomena, site-specific calibration is usually a prerequisite to ensure their predictions are realistic. This statement implies that some experimental knowledge on the system to be simulated should be available prior to any modelling attempt, and raises a tremendous limitation to practical applications of models. Because the demand for more general simulation results is high, modellers have nevertheless taken the bold step of extrapolating a model tested within a limited sample of real conditions to a much larger domain. While methodological questions are often disregarded in this extrapolation process, they are specifically addressed in this paper, and in particular the issue of models a priori parameterisation. We thus implemented and tested a standard procedure to parameterize the soil components of a modified version of the CERES models. The procedure converts routinely-available soil properties into functional characteristics by means of pedo-transfer functions. The resulting predictions of soil water and nitrogen dynamics, as well as crop biomass, nitrogen content and leaf area index were compared to observations from trials conducted in five locations across Europe (southern Italy, northern Spain, northern France and northern Germany). In three cases, the model’s performance was judged acceptable when compared to experimental errors on the measurements, based on a test of the model’s root mean squared error (RMSE). Significant deviations between observations and model outputs were however noted in all sites, and could be ascribed to various model routines. In decreasing importance, these were: water balance, the turnover of soil organic matter, and crop N uptake. A better match to field observations could therefore be achieved by visually adjusting related parameters, such as field-capacity water content or the size of soil microbial biomass. As a result, model predictions fell within the measurement errors in all sites for most variables, and the model’s RMSE was within the range of published values for similar tests. We conclude that the proposed a priori method yields acceptable simulations with only a 50% probability, a figure which may be greatly increased through a posteriori calibration. Modellers should thus exercise caution when extrapolating their models to a large sample of pedo-climatic conditions for which they have only limited information.