Analysis of sensitivity with respect to a compositional parameter : A comment on 'Local sensitivity analysis for compositional data with application to soil texture in hydrologic modelling' by L. Loosvelt and co-authors

A comment about the article “Local sensitivity analysis for compositional data with application to soil texture in hydrologic modelling” writen by L. Loosvelt and co-authors. The present comment is centered in three specific points. The first one is related to the fact that the authors avoid the use of ilr-coordinates. The second one refers to some generalization of sensitivity analysis when input parameters are compositional. The third tries to show that the role of the Dirichlet distribution in the sensitivity analysis is irrelevant

Modelling variation of needle density of Scots pine at high latitudes

[Abstract]

Individual differences in control of language interference in late bilinguals are mainly related to general executive abilities

Background: Recent research based on comparisons between bilinguals and monolinguals postulates that bilingualism enhances cognitive control functions, because the parallel activation of languages necessitates control of interference. In a novel approach we investigated two groups of bilinguals, distinguished by their susceptibility to cross-language interference, asking whether bilinguals with strong language control abilities ('non-switchers") have an advantage in executive functions (inhibition of irrelevant information, problem solving, planning efficiency, generative fluency and self-monitoring) compared to those bilinguals showing weaker language control abilities ('switchers"). Methods: 29 late bilinguals (21 women) were evaluated using various cognitive control neuropsychological tests [e.g., Tower of Hanoi, Ruff Figural Fluency Task, Divided Attention, Go/noGo] tapping executive functions as well as four subtests of the Wechsler Adult Intelligence Scale. The analysis involved t-tests (two independent samples). Non-switchers (n = 16) were distinguished from switchers (n = 13) by their performance observed in a bilingual picture-naming task. Results: The non-switcher group demonstrated a better performance on the Tower of Hanoi and Ruff Figural Fluency task, faster reaction time in a Go/noGo and Divided Attention task, and produced significantly fewer errors in the Tower of Hanoi, Go/noGo, and Divided Attention tasks when compared to the switchers. Non-switchers performed significantly better on two verbal subtests of the Wechsler Adult Intelligence Scale (Information and Similarity), but not on the Performance subtests (Picture Completion, Block Design). Conclusions: The present results suggest that bilinguals with stronger language control have indeed a cognitive advantage in the administered tests involving executive functions, in particular inhibition, self-monitoring, problem solving, and generative fluency, and in two of the intelligence tests. What remains unclear is the direction of the relationship between executive functions and language control abilities.

Modelling the effect of temperature on height increment of Scots pine at high latitudes

Abstract

Modelling of crowded polymers elucidate effects of double-strand breaks in topological domains of bacterial chromosomes.

Using numerical simulations of pairs of long polymeric chains confined in microscopic cylinders, we investigate consequences of double-strand DNA breaks occurring in independent topological domains, such as these constituting bacterial chromosomes. Our simulations show a transition between segregated and mixed state upon linearization of one of the modelled topological domains. Our results explain how chromosomal organization into topological domains can fulfil two opposite conditions: (i) effectively repulse various loops from each other thus promoting chromosome separation and (ii) permit local DNA intermingling when one or more loops are broken and need to be repaired in a process that requires homology search between broken ends and their homologous sequences in closely positioned sister chromatid.

Apertium Advanced Web Interface : A first step towards interactivity and language tools convergence

This documents sums up a projectaimed at building a new web interfaceto the Apertium machine translationplatform, including pre-editing andpost-editing environments. It containsa description of the accomplished workon this project, as well as an overviewof possible evolutions.

Linear prediction application for modelling the relationships between a large number of stand characteristics of Norway spruce stands

Abstract

An Italian to Catalan RBMT system reusing data from existing language pairs

This paper presents an Italian to CatalanRBMT system automatically built bycombining the linguistic data of theexisting pairs Spanish-Catalan andSpanish-Italian. A lightweight manualpostprocessing is carried out in order tofix inconsistencies in the automaticallyderived dictionaries and to add very frequentwords that are missing accordingto a corpus analysis. The system isevaluated on the KDE4 corpus and outperformsGoogle Translate by approximatelyten absolute points in terms ofboth TER and GTM.

Individual-based modelling and simulation: towards a better understanding of growth dynamics from small inocula

Postprint (published version)

Hybrid model of a double-fed induction machine and back-to-back converter

This report details the port interconnection of two subsystems: a power electronics subsystem (a back-to-back AC/AC converter (B2B), coupled to a phase of the power grid), and an electromechanical subsystem (a doubly-fed induction machine (DFIM), coupled mechanically to a flywheel and electrically to the power grid and to a local varying load). Both subsystems have been essentially described in previous reports (deliverables D 0.5 and D 4.3.1), although some previously unpublished details are presented here. The B2B is a variable structure system (VSS), due to the presence of control-actuated switches: however from a modelling and simulation, as well as a control-design, point of view, it is sensible to consider modulated transformers (MTF in the bond-graph language) instead of the pairs of complementary switches. The port-Hamiltonian models of both subsystems are presents and coupled through a power-preserving interconnection, and the Hamiltonian description of the whole system is obtained; detailed bond-graphs of all the subsystems and the complete system are provided.

Quantitative modelling of transcription factor binding sites

Abstract One of the most important issues in molecular biology is to understand regulatory mechanisms that control gene expression. Gene expression is often regulated by proteins, called transcription factors which bind to short (5 to 20 base pairs),degenerate segments of DNA. Experimental efforts towards understanding the sequence specificity of transcription factors is laborious and expensive, but can be substantially accelerated with the use of computational predictions. This thesis describes the use of algorithms and resources for transcriptionfactor binding site analysis in addressing quantitative modelling, where probabilitic models are built to represent binding properties of a transcription factor and can be used to find new functional binding sites in genomes. Initially, an open-access database(HTPSELEX) was created, holding high quality binding sequences for two eukaryotic families of transcription factors namely CTF/NF1 and LEFT/TCF. The binding sequences were elucidated using a recently described experimental procedure called HTP-SELEX, that allows generation of large number (> 1000) of binding sites using mass sequencing technology. For each HTP-SELEX experiments we also provide accurate primary experimental information about the protein material used, details of the wet lab protocol, an archive of sequencing trace files, and assembled clone sequences of binding sequences. The database also offers reasonably large SELEX libraries obtained with conventional low-throughput protocols.The database is available at http://wwwisrec.isb-sib.ch/htpselex/ and and ftp://ftp.isrec.isb-sib.ch/pub/databases/htpselex. The Expectation-Maximisation(EM) algorithm is one the frequently used methods to estimate probabilistic models to represent the sequence specificity of transcription factors. We present computer simulations in order to estimate the precision of EM estimated models as a function of data set parameters(like length of initial sequences, number of initial sequences, percentage of nonbinding sequences). We observed a remarkable robustness of the EM algorithm with regard to length of training sequences and the degree of contamination. The HTPSELEX database and the benchmarked results of the EM algorithm formed part of the foundation for the subsequent project, where a statistical framework called hidden Markov model has been developed to represent sequence specificity of the transcription factors CTF/NF1 and LEF1/TCF using the HTP-SELEX experiment data. The hidden Markov model framework is capable of both predicting and classifying CTF/NF1 and LEF1/TCF binding sites. A covariance analysis of the binding sites revealed non-independent base preferences at different nucleotide positions, providing insight into the binding mechanism. We next tested the LEF1/TCF model by computing binding scores for a set of LEF1/TCF binding sequences for which relative affinities were determined experimentally using non-linear regression. The predicted and experimentally determined binding affinities were in good correlation.

Hemispheric language asymmetry in first episode psychosis and schizotypy : the role of cannabis consumption and cognitive disorganization

Cannabis use has been related to an elevated psychosis risk and attenuated cognitive functioning. Cannabis-related cognitive impairments are also observed in populations along the psychosis dimension. We here investigated whether a potential behavioural marker of the psychosis dimension (attenuated functional hemispheric asymmetry) is even further attenuated in individuals using cannabis (CU) versus those not using cannabis (nCU). We tested 29 patients with first episode psychosis (FEP; 11 CU) and 90 healthy controls (38 CU) on lateralized lexical decisions assessing left hemisphere language dominance. In patients, psychotic symptoms were assessed (PANSS). In controls, self-reported schizotypy was assessed (O-LIFE questionnaire). Results indicated that nCU FEP patients had a relative reduced hemispheric asymmetry, as did controls with increasing cognitive disorganisation scores, in particular when belonging to the group of nCU controls. Positive, disorganised and negative PANSS scores in patients and negative and positive schizotypy in controls were unrelated to hemispheric asymmetry. These findings suggest that cannabis use balances rather than exacerbates uncommon hemispheric laterality patterns. Moreover, in healthy populations, the potential stabilisation of typical hemispheric asymmetry in CU might be most relevant to individuals with elevated cognitive disorganisation. We discuss the potential beneficial and harmful effects of cannabis use along the psychosis dimension together with propositions for future studies that should account for the mediating role of additional substances (e.g. nicotine), cannabis composition (e.g. cannabidiol content), and individual differences (e.g. physical health, or absence of significant polysubstance use).

Semantiikan hyödyntäminen dokumenttienhallinnassa

Työn tavoitteena on etsiä asiakasyritykselle sähköteknisen dokumentoinnin hallintaan sopiva järjestelmäratkaisu vertailemalla insinööritoimistojen käyttämien suunnittelujärjestelmien ja yleisten dokumenttien hallintajärjestelmien soveltuvuutta asiakasympäristöön. Työssä tutkitaan sopivien metatietojen kuvaustapojen käyttökelpoisuutta sähköteknisen dokumentoinnin hallintaan esimerkkiprojektien avulla. Työn sisältö koostuu neljästä pääkohdasta. Ensimmäisessä jaksossa tarkastellaan dokumentin ominaisuuksia ja elinkaarta luonnista aktiivikäyttöön, arkistointiin ja hävitykseen. Samassa yhteydessä kerrotaan dokumenttienhallinnan perustehtävistä. Toisessa jaksossa käsitellään dokumenttien kuvailun tavoitteita, kuvailusuosituksia ja -standardeja sekä luonnollisen kielen käyttöä sisällönkuvailussa. Tarkastelukohteina suosituksista ovat W3C:n julkaisemat suositukset, Dublin Core, JHS 143 ja SFS-EN 82045. Kolmannessa jaksossa tarkastellaan teollisuuden dokumentoinnin ominaispiirteitä ja käyttötarkoitusta. Teollisuudessa on monia erilaisia järjestelmäympäristöjä tehtaan sisällä ja työssä kuvataan dokumenttienhallinnan integrointitarpeita muihin järjestelmiin. Viimeisessä jaksossa kuvaillaan erilaisia dokumentoinnin hallintaympäristöjä alkaen järeimmästä päästä tuotetiedon hallintajärjestelmistä siirtyen pienempiinsuunnittelujärjestelmiin ja lopuksi yleisiin dokumenttien hallintajärjestelmiin. Tässä osassa on myös luettelo ohjelmistotoimittajista. Työn tuloksena on laadittu valituista dokumenttityypeistä metatietokuvaukset kahden eri kuvaustavan (JHS 143 ja SFS-EN 82045) avulla ja on todettu molemmat kuvaustavat käyttökelpoisiksi sähköteknisen dokumentoinnin käsittelyyn.Nämä kuvaukset palvelevat asiakasta dokumenttienhallintaprojektin määrittelytyössä. Asiakkaalle on tehty myös vertailu sopivista järjestelmävaihtoehdoista hankintaa varten.

Use of anisotropic modelling in electrical impedance tomography: description of method and preliminary assessment of utility in imaging brain function in the adult human head.

Electrical Impedance Tomography (EIT) is an imaging method which enables a volume conductivity map of a subject to be produced from multiple impedance measurements. It has the potential to become a portable non-invasive imaging technique of particular use in imaging brain function. Accurate numerical forward models may be used to improve image reconstruction but, until now, have employed an assumption of isotropic tissue conductivity. This may be expected to introduce inaccuracy, as body tissues, especially those such as white matter and the skull in head imaging, are highly anisotropic. The purpose of this study was, for the first time, to develop a method for incorporating anisotropy in a forward numerical model for EIT of the head and assess the resulting improvement in image quality in the case of linear reconstruction of one example of the human head. A realistic Finite Element Model (FEM) of an adult human head with segments for the scalp, skull, CSF, and brain was produced from a structural MRI. Anisotropy of the brain was estimated from a diffusion tensor-MRI of the same subject and anisotropy of the skull was approximated from the structural information. A method for incorporation of anisotropy in the forward model and its use in image reconstruction was produced. The improvement in reconstructed image quality was assessed in computer simulation by producing forward data, and then linear reconstruction using a sensitivity matrix approach. The mean boundary data difference between anisotropic and isotropic forward models for a reference conductivity was 50%. Use of the correct anisotropic FEM in image reconstruction, as opposed to an isotropic one, corrected an error of 24 mm in imaging a 10% conductivity decrease located in the hippocampus, improved localisation for conductivity changes deep in the brain and due to epilepsy by 4-17 mm, and, overall, led to a substantial improvement on image quality. This suggests that incorporation of anisotropy in numerical models used for image reconstruction is likely to improve EIT image quality.