Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters

Background: The arrangement of regulatory motifs in gene promoters, or promoterarchitecture, is the result of mutation and selection processes that have operated over manymillions of years. In mammals, tissue-specific transcriptional regulation is related to the presence ofspecific protein-interacting DNA motifs in gene promoters. However, little is known about therelative location and spacing of these motifs. To fill this gap, we have performed a systematic searchfor motifs that show significant bias at specific promoter locations in a large collection ofhousekeeping and tissue-specific genes.Results: We observe that promoters driving housekeeping gene expression are enriched inparticular motifs with strong positional bias, such as YY1, which are of little relevance in promotersdriving tissue-specific expression. We also identify a large number of motifs that show positionalbias in genes expressed in a highly tissue-specific manner. They include well-known tissue-specificmotifs, such as HNF1 and HNF4 motifs in liver, kidney and small intestine, or RFX motifs in testis,as well as many potentially novel regulatory motifs. Based on this analysis, we provide predictionsfor 559 tissue-specific motifs in mouse gene promoters.Conclusion: The study shows that motif positional bias is an important feature of mammalianproximal promoters and that it affects both general and tissue-specific motifs. Motif positionalconstraints define very distinct promoter architectures depending on breadth of expression andtype of tissue.

Standards for Single Span Prefabricated Bridges, Phase I - Concept Development, TR-663, 2014

In coordination with a Technical Advisory Committee (TAC) consisting of County Engineers and Iowa DOT representatives, the Iowa DOT has proposed to develop a set of standards for a single span prefabricated bridge system for use on the local road system. The purpose of the bridge system is to improve bridge construction, accelerate project delivery, improve worker safety, be cost effective, reduce impacts to the travelling public by reducing traffic disruptions and the duration of detours, and allow local forces to construct the bridges. HDR Inc. was selected by the Iowa DOT to perform the initial concept screening of the bridge system. This Final Report summarizes the initial conceptual effort to investigate potential systems, make recommendations for a preferred system and propose initial details to be tested in the laboratory in Phase 2 of the project. The prefabricated bridge components were to be based on the following preliminary criteria set forth by the TAC. The criteria were to be verified and/ or modified as part of the conceptual development. - 24’ and 30’ roadway widths - Skews of 0o, 15o, and 30o - Span lengths of 30’ – 70’ in 10’ increments using precast concrete beams - Voided box beams could be considered - Limit precast element weight to 45,000 pounds for movement and placement of beams - Beams could be joined transversely with threaded rods - Abutment concepts may included precast as well as an option for cast-in-place abutments with pile foundations In addition to the above criteria, there was an interest to use a single-width prefabricated bridge component to simplify fabrication as well as a desire to utilize non-prestressed concrete systems where possible to allow for precasting of the beam modules by local forces or local precast plants. The SL-1 modular steel bridge rail was identified for use with this single span prefabricated bridge system.

Machine learning for spatial environmental data. Theory, applications and software

The book presents the state of the art in machine learning algorithms (artificial neural networks of different architectures, support vector machines, etc.) as applied to the classification and mapping of spatially distributed environmental data. Basic geostatistical algorithms are presented as well. New trends in machine learning and their application to spatial data are given, and real case studies based on environmental and pollution data are carried out. The book provides a CD-ROM with the Machine Learning Office software, including sample sets of data, that will allow both students and researchers to put the concepts rapidly to practice.

Estequiometria i metabolòmica d'Alopecurus pratensis i Holcus lanatus en condicions de sequera

La variabilitat de l’estequiometria elemental dels organismes a causa de l’ontogènia i dels canvis en les condicions ambientals està relacionada amb la variabilitat metabolòmica. Això és degut a que els elements operen majoritàriament com a parts de compostos moleculars. Així doncs, la hipòtesi realitzada per Rivas-Ubach et al., (2012), la qual postula que els estudis estequiomètrics i metabolòmics d’un conjunt d’espècies vegetals exposades a condicions ambientals diferents han de mostrar la flexibilitat que posseeix un organisme a l’hora de modular la seva estequiometria i el seu metaboloma per tal de mantenir la forma òptima sota condicions variants, esdevé la base que sustenta l’experiment EVENT II. A partir de l’estudi de les relacions estequiomètriques, -principalment C:N:P- i del metabolisme d’Alopecurus pratensis i Holcus lanatus en situacions simulades de sequera, s’han obtingut resultats que evidencien una clara diferenciació a nivell d’espècie, de part de la planta i de tractament. El metabolisme i l’estequiometria diferencial que presenten ambdues gramínies dóna suport a la hipòtesi del nínxol biogeoquímic. A nivell de parts de la planta, s’observa un clar augment de la relació C:nutrients a la part aèria, mentre que a les arrels, aquesta relació disminueix. La part aèria doncs, necessita més C per invertir en funcions estructurals, mentre que l’elevada concentració de nutrients i metabòlits a les arrels donen indicis de la presència de mecanismes osmòtics per a facilitar l’entrada d’aigua, i de creixement, per a la recerca de noves fonts d’aigua, observant-se una disminució de la relació part aèria:arrels. Un altre factor que demostra aquest creixement radicular són les baixes relacions N:P trobades, fet que dóna suport a la hipòtesi de la velocitat de creixement.

quantiNemo: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation.

quantiNemo is an individual-based, genetically explicit stochastic simulation program. It was developed to investigate the effects of selection, mutation, recombination and drift on quantitative traits with varying architectures in structured populations connected by migration and located in a heterogeneous habitat. quantiNemo is highly flexible at various levels: population, selection, trait(s) architecture, genetic map for QTL and/or markers, environment, demography, mating system, etc. quantiNemo is coded in C++ using an object-oriented approach and runs on any computer platform. Availability: Executables for several platforms, user's manual, and source code are freely available under the GNU General Public License at http://www2.unil.ch/popgen/softwares/quantinemo.

Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses.

Correlates of immune-mediated protection to most viral and cancer vaccines are still unknown. This impedes the development of novel vaccines to incurable diseases such as HIV and cancer. In this study, we have used functional genomics and polychromatic flow cytometry to define the signature of the immune response to the yellow fever (YF) vaccine 17D (YF17D) in a cohort of 40 volunteers followed for up to 1 yr after vaccination. We show that immunization with YF17D leads to an integrated immune response that includes several effector arms of innate immunity, including complement, the inflammasome, and interferons, as well as adaptive immunity as shown by an early T cell response followed by a brisk and variable B cell response. Development of these responses is preceded, as demonstrated in three independent vaccination trials and in a novel in vitro system of primary immune responses (modular immune in vitro construct [MIMIC] system), by the coordinated up-regulation of transcripts for specific transcription factors, including STAT1, IRF7, and ETS2, which are upstream of the different effector arms of the immune response. These results clearly show that the immune response to a strong vaccine is preceded by coordinated induction of master transcription factors that lead to the development of a broad, polyfunctional, and persistent immune response that integrates all effector cells of the immune system.

La Docència de l'avaluació psicològica des d'una perspectiva integradora i professionalitzadora

Es presenta un projecte de millora de la qualitat docent, iniciat durant el curs acadèmic 2009-2010, en el qual es desenvolupà un treball conjunt amb les assignatures de Psicodiagnòstic, Psicologia Clínica Infantil i Neuropsicologia per tal de dissenyar un mòdul adreçat als alumnes de tercer de Grau en Psicologia, posant en comú les aportacions més recents en l’àmbit de l’avaluació i el diagnòstic psicològic, amb la finalitat d’afavorir la formació clínica dels estudiants. La finalitat d’aquest projecte era l’elaboració d’una proposta de Pla Docent del mòdul d’Avaluació i Diagnòstic Psicològic II, integrant els resultats de la metodologia plantejada en els seminaris i en coherència amb el plantejament del mateix mòdul, que s’imparteix, prèviament, durant el primer quadrimestre, tot intentant establir connexions entre les tres matèries. L’objectiu final és oferir als estudiants un plantejament modular integrador que els permeti assolir les competències previstes en el pla d’estudis de l’Espai Europeu d’Educació Superior. Entre les propostes per a aquest mòdul es presenta el treball d’un cas interdisciplinari des de les franges de petit grup, com també un plantejament de les matèries de forma conjunta i coordinada. En aquest projecte també s’ha volgut tenir en compte la valoració dels mateixos estudiants, que han estat partícips del procés.

Neural networks complemented with genetic algorithms and fuzzy systems for predicting nitrogenous effluent variables in wastewater treatment plants

This work focuses on the prediction of the two main nitrogenous variables that describe the water quality at the effluent of a Wastewater Treatment Plant. We have developed two kind of Neural Networks architectures based on considering only one output or, in the other hand, the usual five effluent variables that define the water quality: suspended solids, biochemical organic matter, chemical organic matter, total nitrogen and total Kjedhal nitrogen. Two learning techniques based on a classical adaptative gradient and a Kalman filter have been implemented. In order to try to improve generalization and performance we have selected variables by means genetic algorithms and fuzzy systems. The training, testing and validation sets show that the final networks are able to learn enough well the simulated available data specially for the total nitrogen

Projecte MQD per al disseny dels mòduls de Fonaments dels esports en el grau de CAFE (FPCEE-URL)

Les exigències estructurals i metodològiques nascudes de la implementació de l’Espai Europeu d’Educació Superior arran de la Declaració de Bolonya han comportat replantejaments profunds dels plans d’estudi universitaris i, sobretot, de la comprensió dels processos d’aprenentatge i avaluació dels alumnes basats en les competències. La necessitat del professorat de replantejar el seu compromís pedagògic d’acord a les noves directrius i la oportunitat de reflexionar de manera creativa i original en base a un programa de millora de la qualitat universitària han confluït en el present Projecte de Mòdul de Fonaments dels Esports. Aquesta proposta modular ajunta el rigor per potenciar les noves directrius pedagògiques universitàries i la satisfacció d’haver dedicat un temps a la reflexió col·lectiva que pugui servir de guia o exemple als diferents mòduls d’esports que el Grau en Ciències de l’Activitat Física i l’Esport proposa. Així, en base als eixos de lògica epistemològica, disseny i temporalització curricular i, finalment l’avaluació competencial, es desenvoluparan les principals aportacions metodològiques del projecte sense que al final, amb la perspectiva dels cursos ja passats, es puguin discutir els seus encerts i les seves possibilitats de millora. La qualitat en l’ensenyament dels esports n’ha estat el referent.