Prediction of subcellular localization using sequence-biased recurrent networks

Motivation: Targeting peptides direct nascent proteins to their specific subcellular compartment. Knowledge of targeting signals enables informed drug design and reliable annotation of gene products. However, due to the low similarity of such sequences and the dynamical nature of the sorting process, the computational prediction of subcellular localization of proteins is challenging. Results: We contrast the use of feed forward models as employed by the popular TargetP/SignalP predictors with a sequence-biased recurrent network model. The models are evaluated in terms of performance at the residue level and at the sequence level, and demonstrate that recurrent networks improve the overall prediction performance. Compared to the original results reported for TargetP, an ensemble of the tested models increases the accuracy by 6 and 5% on non-plant and plant data, respectively.

Genorne sequence of the thermostable Newcastle disease virus (strain I-2) reveals a possible phenotypic locus

The complete genome sequence of the Australian 1-2 heat-tolerant Newcastle disease virus (NDV) vaccine (master seed stocks) was determined and compared to the sequence of the parent virus from which it had been derived after exposure of the parent stock at 56 degrees C for 30 min. Nucleotide changes were observed at a number of positions with synonymous mutations being greater than those observed for non-synonymous mutations. Sequence data for the HN gene of a parental culture of V4 and two heat-tolerant variants of V4 were obtained. These were compared with the data for the 1-2 viruses and with published sequences for parental V4 and for a number of ND vaccine strains. Sequence analyses did not reveal the ARG 303 deletion in the HN protein, previously claimed to be responsible for the thermostable phenotype. No consistent changes were detected that would indicate involvement of the HN protein in heat resistance. The majority of alterations were observed in the L protein of the virus and it is proposed that these alterations were responsible for the heat-tolerant phenotype of the 1-2 NDV vaccine. (c) 2005 Elsevier B.V. All rights reserved.

Participation and transparency in food law

La governance del settore alimentare si fonda su una struttura multilivello, ove poteri locali, nazionali, sovranazionali e globali interagiscono. In tale assetto, ogni regolatore è chiamato a proteggere interessi diversi tra loro, tra cui l'ambiente, la salute umana, il benessere animale e la libera concorrenza. La regolazione del settore alimentare, inoltre, impone la considerazione di aspetti etici e culturali, dotati di una forte matrice territoriale. In questo sistema, i valori che entrano in gioco non sono egualmente rappresentati, ma quelli considerati "minori" sono sovente sovrastati dalle esigenze di protezione di un unico interesse: la libera concorrenza su scala globale. Ne deriva che la regolazione del settore alimentare necessita di un nuovo equilibrio. Questo può richiedere sia l'adozione di nuove regole - soprattutto a livello sovranazionale - sia un'interpretazione maggiormente inclusiva dei principi e delle regole già esistenti da parte delle Corti. Tuttavia, risulta maggiormente urgente e di immediata efficacia permettere ai soggetti interessati, siano essi privati o pubblici, di partecipare alla formulazione delle politiche e delle decisioni inerenti il settore alimentare. La partecipazione procedurale è in grado di soddisfare esigenze differenti e talvolta opposte, pertanto essa è regolata dal legislatore a seconda dello scopo finale prefissato. Principalmente, essa è vista come una applicazione diretta dei principi di democrazia e trasparenza; tuttavia, il suo reale impatto sul risultato finale delle decisioni pubbliche può scostarsi considerevolemente da tale paradigma. Lo scopo di tale lavoro è analizzare i diversi modelli partecipativi implementati nei vari livelli di governo, al fine di determinarne il reale impatto sui soggetti interessati e sul bilanciamento degli interessi in gioco. La conclusione dimostra un certo livello di perplessità per ciò che riguarda l'assetto di tali garanzie nella regolazione del settore alimentare, dove lo sviluppo del concetto di democrazia partecipativa e di bilancio tra gli interessi rilevanti è ancora acerbo.

Leisure at work in Britain, West Germany, France and Japan : a cross-cultural comparative study

The aim of this thesis was to investigate the impact of changing values and attitudes toward work and the workplace in Britain, West Germany, France and Japan. A cross-national approach was adopted in order to gain a better understanding of differences and similarities in behaviour and to identify aspects specific to each society. Although the relationship between work and leisure has been thoroughly examined and there is a growing body of literature on changes in the values associated with these two phenomena, little research has been carried out into leisure at work. Studies of work time have tended to consider it as a homogeneous block, whereas recent research suggests that more attention should be devoted to unravelling the multiple uses of time at the workplace. The present study sought to review and analyse this new approach to the study of work time, and special attention is devoted to an examination of definitions of leisure, recreation, free time and work within the context of the workplace. The cross-cultural comparative approach gave rise to several problems due to the number of countries involved and the unusual combination of factors being investigated. The main difficulties were differences in the amount and quality of literature available, the non-comparability of existing data, definitions of concepts and socio-linguistic terms, and problems over access to organizations for fieldwork. Much of the literature generalizes about patterns of behaviour and few authors isolate factors specific to particular societies. In this thesis new empirical work is therefore used to ascertain the extent to which generalizations can be made from the literature and characteristics peculiar to each of the four countries identified. White-collar employees in large, broadly comparable companies were studied using identical questionnaires in the appropriate language. Respondents selected were men and women, aged between 20-65 years and either managers or non-managers. Patterns of leisure at work were found to be broadly similar in the national contexts, but with the Japanese and the West Germans experiencing the least leisure at work, and the British and the French perceiving the most. The general trend seems to be toward convergence of attitudes regarding leisure at work in the four countries. Explanations for variations in practice were sought within the wider societal contexts of each country.

Stock market efficiency before and after a financial liberalisation reform:do breaks in volatility dynamics matter?

This article focuses on the deviations from normality of stock returns before and after a financial liberalisation reform, and shows the extent to which inference based on statistical measures of stock market efficiency can be affected by not controlling for breaks. Drawing from recent advances in the econometrics of structural change, it compares the distribution of the returns of five East Asian emerging markets when breaks in the mean and variance are either (i) imposed using certain official liberalisation dates or (ii) detected non-parametrically using a data-driven procedure. The results suggest that measuring deviations from normality of stock returns with no provision for potentially existing breaks incorporates substantial bias. This is likely to severely affect any inference based on the corresponding descriptive or test statistics.

A framework for performance evaluation of employment offices:a case of Tunisia

This paper proposes a new framework for evaluating the performance of employment offices based on non-parametric technique of data envelopment analysis. This framework is explained using the assessment of technical efficiency of 82 employment offices in Tunisia which are under the direction of the National Agency for Employment and Independent Work. We further investigated the exogenous factors that may explain part of the variation in efficiency scores using a bootstrapping approach in period January 2006 to December 2008. Given the specialisation of employment offices, we used the proposed approach for the efficiency evaluation of graduate employment offices and multi-services employment offices, separately.

FP6-ist INFRAWEBS European Research Project

Project Focus: The main INFRAWEBS project focus and objective is the development of an application-oriented software toolset for creating, maintaining and executing WSMO-based Semantic Web Services (SWS) within their whole life cycle. This next generation of tools and systems will enable software and service providers to build open and extensible development platforms for web service applications. These services will run on open standards and specifications, such as BPEL4WS, WSMO, WSMX, WSML, SPARQL, RDF, etc. In particular, they will be compliant with WSMO (Web Services Modelling Ontology), a W3C initiative in Semantic Web services.

A knowledge driven approach towards the validation of externally acquired traceability datasets in supply chain business processes

The sharing of near real-time traceability knowledge in supply chains plays a central role in coordinating business operations and is a key driver for their success. However before traceability datasets received from external partners can be integrated with datasets generated internally within an organisation, they need to be validated against information recorded for the physical goods received as well as against bespoke rules defined to ensure uniformity, consistency and completeness within the supply chain. In this paper, we present a knowledge driven framework for the runtime validation of critical constraints on incoming traceability datasets encapuslated as EPCIS event-based linked pedigrees. Our constraints are defined using SPARQL queries and SPIN rules. We present a novel validation architecture based on the integration of Apache Storm framework for real time, distributed computation with popular Semantic Web/Linked data libraries and exemplify our methodology on an abstraction of the pharmaceutical supply chain.

Modelling and linking transformations in EPCIS governing supply chain business processes

Supply chains comprise of complex processes spanning across multiple trading partners. The various operations involved generate large number of events that need to be integrated in order to enable internal and external traceability. Further, provenance of artifacts and agents involved in the supply chain operations is now a key traceability requirement. In this paper we propose a Semantic web/Linked data powered framework for the event based representation and analysis of supply chain activities governed by the EPCIS specification. We specifically show how a new EPCIS event type called "Transformation Event" can be semantically annotated using EEM - The EPCIS Event Model to generate linked data, that can be exploited for internal event based traceability in supply chains involving transformation of products. For integrating provenance with traceability, we propose a mapping from EEM to PROV-O. We exemplify our approach on an abstraction of the production processes that are part of the wine supply chain.

Estimation of average annual daily traffic (AADT) using geographically weighted regression (GWR) method and geographic information system (GIS)

Annual average daily traffic (AADT) is important information for many transportation planning, design, operation, and maintenance activities, as well as for the allocation of highway funds. Many studies have attempted AADT estimation using factor approach, regression analysis, time series, and artificial neural networks. However, these methods are unable to account for spatially variable influence of independent variables on the dependent variable even though it is well known that to many transportation problems, including AADT estimation, spatial context is important. ^ In this study, applications of geographically weighted regression (GWR) methods to estimating AADT were investigated. The GWR based methods considered the influence of correlations among the variables over space and the spatially non-stationarity of the variables. A GWR model allows different relationships between the dependent and independent variables to exist at different points in space. In other words, model parameters vary from location to location and the locally linear regression parameters at a point are affected more by observations near that point than observations further away. ^ The study area was Broward County, Florida. Broward County lies on the Atlantic coast between Palm Beach and Miami-Dade counties. In this study, a total of 67 variables were considered as potential AADT predictors, and six variables (lanes, speed, regional accessibility, direct access, density of roadway length, and density of seasonal household) were selected to develop the models. ^ To investigate the predictive powers of various AADT predictors over the space, the statistics including local r-square, local parameter estimates, and local errors were examined and mapped. The local variations in relationships among parameters were investigated, measured, and mapped to assess the usefulness of GWR methods. ^ The results indicated that the GWR models were able to better explain the variation in the data and to predict AADT with smaller errors than the ordinary linear regression models for the same dataset. Additionally, GWR was able to model the spatial non-stationarity in the data, i.e., the spatially varying relationship between AADT and predictors, which cannot be modeled in ordinary linear regression. ^

The effect of cross -age tutoring routines on the tutor's perception of self as reader

Perception of self as a non-reader has been identified as one of the factors why poor readers disengage from the reading process (Strang, 1967; Rosow, 1992), thus impeding progress. Perception and informational processes influence judgments of personal efficacy (Bandura, 1997). The student's sense of reading efficacy that influence effort expenditure and ultimately achievement, is often overlooked (Athey, 1985; Pajares, 1996). Academic routines within educational programs are implemented without adequate information on whether routines promote or impede efficacy growth. Cross-age tutoring, a process known to improve participants' academic achievement, motivation, and provide opportunities for authentic reading practice, has been successfully incorporated into reading instruction designs (Allen, 1976; Cohen, Kulik & Kulik, 1982; Labbo & Teale, 1990; Riessman, 1993). This study investigated the impact teacher-designed routines within a cross-age tutoring model, have on the tutor's sense of reading self-efficacy. ^ The Reader Self-Perception Scale (Henk & Melnick, 1992) was administered, pre- and post-treatment, to 118 fifth grade students. Preceding the initial survey administration intact classes were randomly assigned to 1 of 3 commonly utilized cross-age tutoring routines or designated as the non-treatment population. The data derived from the Reader Self-Perception Scale was analyzed using an analysis of covariance (ANCOVA). Results indicated that participation as a cross-age tutor does not significantly increase the tutor's perception of self as reader in 1 or more of the 4 modes of information influencing self-efficacy as compared to the non-treatment group. ^ The results of this study suggests that although a weekly tutoring session that delivers educationally credible routines impacts achievement and motivation, efficacy effect was not evident. Possible explanation and recommendations for future studies are proposed. ^

Flexible pavement layer moduli determination : an adaptive artificial neural network approach

The estimation of pavement layer moduli through the use of an artificial neural network is a new concept which provides a less strenuous strategy for backcalculation procedures. Artificial Neural Networks are biologically inspired models of the human nervous system. They are specifically designed to carry out a mapping characteristic. This study demonstrates how an artificial neural network uses non-destructive pavement test data in determining flexible pavement layer moduli. The input parameters include plate loadings, corresponding sensor deflections, temperature of pavement surface, pavement layer thicknesses and independently deduced pavement layer moduli.

Ethnicity and reaccumulation : an ecological analysis

This study looks at the process of reaccumulation of resources in Miami following Hurricane Andrew. Emphasis is on differences between four major ethnic groups: Anglos, African- Americans, Cubans and non-Cuban Hispanics. Secondary data is used to analyze measures of housing recovery on a census block group level. Results indicate that, while there are ethnic consequences on a block groups level, support for enclave hypotheses are equivocal.

Fabrication of a New Multifunctional Interface Between La,Sr manganite and C60

In questo lavoro abbiamo sperimentato due modi diversi per ottenere un monolayer di C60 su La,Sr manganite (LSMO): desorbendo C60 da un campione di 5nm cresciuto su un substrato di LSMO e crescendo, sempre su LSMO, sei campioni di C60 a diversi spessori nominali. Il campione desorbito è stato analizzato mediante misure STS ed STM, mentre i campione cresciuti a diversi spessori sono stati misurati mediante non-cntact AFM. Ciò che è emerso in entrambi i casi è che le molecole di C60 non interagiscono con il substrato di LSMO. Nel primo caso infatti si è visto che è stato desorbito quasi tutto il C60 presente sul campione; la superficie della manganite risulta solo parzialmente ricoperta da molecole di C60. Nel secondo caso invece si nota che il C60 cresce formando isole che arrivano a ricoprire la superficie di LSMO solo per film dallo spessore nominale superiore a 30nm.

Sperimentazione costruttiva e tecnologica di un padiglione temporaneo

La tesi ha come oggetto di studio la progettazione e realizzazione in autocostruzione del padiglione temporaneo dal nome Modulo Eco in Piazzale della Pace a Parma. Per “autocostruzione” si intende il processo in cui il committente di un immobile partecipa attivamente alla fase realizzativa dello stesso. È un percorso molto impegnativo, che richiede una forte motivazione ma allo stesso tempo molto appagante. Ad oggi in Italia non esiste una normativa nazionale che codifichi le modalità e le regole dell’edificare in autocostruzione. La partecipazione attiva nel processo realizzativo di personale non addetto ai lavori aumenta automaticamente i rischi legati all’inesperienza e alla mancanza di formazione in materia. L’attenzione quindi alla sicurezza e soprattutto all’iniziale formazione dei nuovi operai in cantiere permette di ridurre notevolmente tali pericoli. Il progetto è stato ideato dall’associazione culturale Manifattura Urbana in collaborazione con il Comune di Parma. Posizionato in Piazzale della Pace, in pieno centro, questo spazio ospiterà l’ufficio Sportello Energia del Comune stesso. È infatti interesse dell’amministrazione dare un’importanza significativa alle tematiche energetiche, non lasciando tutte le relative riflessioni solamente a tecnici ma rivolgendosi invece direttamente ai cittadini, per informarli e sensibilizzarli. È stato quindi deciso di progettare e realizzare un padiglione temporaneo, facilmente costruibile (con l’aiuto di studenti, volontari e interessati), con un minimo impatto ambientale e allo stesso tempo ad alta efficienza energetica, non solo rispettante ma superante tutti gli standard di bassi consumi energetici previsti dalla normativa per le nuove costruzioni. Il progetto è totalmente autofinanziato dalle aziende fornitrici partner, che sponsorizzano in forma gratuita il materiale da costruzione e formano direttamente in cantiere i volontari per imparare a gestirlo, in cambio di visibilità all’interno del progetto.