Modeling sequencing errors by combining Hidden Markov models.

Among the largest resources for biological sequence data is the large amount of expressed sequence tags (ESTs) available in public and proprietary databases. ESTs provide information on transcripts but for technical reasons they often contain sequencing errors. Therefore, when analyzing EST sequences computationally, such errors must be taken into account. Earlier attempts to model error prone coding regions have shown good performance in detecting and predicting these while correcting sequencing errors using codon usage frequencies. In the research presented here, we improve the detection of translation start and stop sites by integrating a more complex mRNA model with codon usage bias based error correction into one hidden Markov model (HMM), thus generalizing this error correction approach to more complex HMMs. We show that our method maintains the performance in detecting coding sequences.

Avaluació de set materials representatius del programa didàctic aplicat a les Escoles Bressol Municipals de Mataró dins del projecte de formació del professorat 2006/07

ii. Desprès de finalitzar el primer any d’aplicació del projecte “La música a les Escoles Bressol Municipals de Mataró”, s’inicia la present recerca, en la que participen tots els grups que formen part del projecte, amb l’objectiu de valorar-ho i veure’n la continuïtat. Es detecta que els materials emprats en la proposta didàctica són l’element que ha esdevingut més exitós fins al moment. Definint-ne una mostra de set materials, es procedeix a determinar l’ús que les educadores els atorguen en relació a la proposta didàctica i a avaluar-los

Modeling of in-situ crystallization processes in the Permian mafic layered intrusion of Mont Collon (Dent Blanche nappe, western Alps)

The Mont Collon mafic complex is one of the best preserved examples of the Early Permian magmatism in the Central Alps, related to the intra-continental collapse of the Variscan belt. It mostly consists (> 95 vol.%) of ol+hy-nonnative plagioclase-wehrlites, olivine- and cpx-gabbros with cumulitic structures, crosscut by acid dikes. Pegmatitic gabbros, troctolites and anorthosites outcrop locally. A well-preserved cumulative, sequence is exposed in the Dents de Bertol area (center of intrusion). PT-calculations indicate that this layered magma chamber emplaced at mid-crustal levels at about 0.5 GPa and 1100 degrees C. The Mont Collon cumulitic rocks record little magmatic differentiation, as illustrated by the restricted range of clinopyroxene mg-number (Mg#(cpx)=83-89). Whole-rock incompatible trace-element contents (e.g. Nb, Zr, Ba) vary largely and without correlation with major-element composition. These features are characteristic of an in-situ crystallization process with variable amounts of interstitial liquid L trapped between the cumulus mineral phases. LA-ICPMS measurements show that trace-element distribution in the latter is homogeneous, pointing to subsolidus re-equilibration between crystals and interstitial melts. A quantitative modeling based on Langmuir's in-situ crystallization equation successfully duplicated the REE concentrations in cumulitic minerals of all rock facies of the intrusion. The calculated amounts of interstitial liquid L vary between 0 and 35% for degrees of differentiation F of 0 to 20%, relative to the least evolved facies of the intrusion. L values are well correlated with the modal proportions of interstitial amphibole and whole-rock incompatible trace-element concentrations (e.g. Zr, Nb) of the tested samples. However, the in-situ crystallization model reaches its limitations with rock containing high modal content of REE-bearing minerals (i.e. zircon), such as pegmatitic gabbros. Dikes of anorthositic composition, locally crosscutting the layered lithologies, evidence that the Mont Collon rocks evolved in open system with mixing of intercumulus liquids of different origins and possibly contrasting compositions. The proposed model is not able to resolve these complex open systems, but migrating liquids could be partly responsible for the observed dispersion of points in some correlation diagrams. Absence of significant differentiation with recurrent lithologies in the cumulitic pile of Dents de Bertol points to an efficiently convective magma chamber, with possible periodic replenishment, (c) 2005 Elsevier B.V. All rights reserved.

Modeling resting-state functional networks when the cortex falls asleep: local and global changes.

The transition from wakefulness to sleep represents the most conspicuous change in behavior and the level of consciousness occurring in the healthy brain. It is accompanied by similarly conspicuous changes in neural dynamics, traditionally exemplified by the change from "desynchronized" electroencephalogram activity in wake to globally synchronized slow wave activity of early sleep. However, unit and local field recordings indicate that the transition is more gradual than it might appear: On one hand, local slow waves already appear during wake; on the other hand, slow sleep waves are only rarely global. Studies with functional magnetic resonance imaging also reveal changes in resting-state functional connectivity (FC) between wake and slow wave sleep. However, it remains unclear how resting-state networks may change during this transition period. Here, we employ large-scale modeling of the human cortico-cortical anatomical connectivity to evaluate changes in resting-state FC when the model "falls asleep" due to the progressive decrease in arousal-promoting neuromodulation. When cholinergic neuromodulation is parametrically decreased, local slow waves appear, while the overall organization of resting-state networks does not change. Furthermore, we show that these local slow waves are structured macroscopically in networks that resemble the resting-state networks. In contrast, when the neuromodulator decrease further to very low levels, slow waves become global and resting-state networks merge into a single undifferentiated, broadly synchronized network.

Isotermes d'adsorpció d'alquilfenols en sediments i altres materials

Projecte de recerca elaborat a partir d’una estada al Center of Applied Geosciences de la Eberhard Karls Universität entre abril i octubre del 2007. Durant l'estada es va adquirir la tècnica per a la realització d'isotermes d'adsorció aplicant-la posteriorment a l'estudi de dos compostos del grup dels alquilfenols (nonilfenol i octilfenol). Aquestes isotermes es van realitzar en diversos sediments provinents de la conca hidrogràfica del riu Ebre i en altres dos materials (lignit i torba), tots ells amb diferent contingut de carboni orgànic total (que varia entre 0,4% per a un dels sediments i 47,8% per a la torba), per a estudiar la influència d'aquest paràmetre en els comportament del nonilfenol pel que fa a l'adsorció. Per altra banda es va afegir l’octilfenol a l’estudi, tant per separat com en combinació amb el nonilfenol, i es va extendre la isoterma per al nonilfenol a concentracions més baixes, properes a les concentracions que es poden trobar d’aquest compost al medi. Aquestes últimes isotermes es van realitzar utilitzant en tots els casos un dels sediments del riu Ebre, amb un contingut de carboni orgànic del 5,8 %, per a poder comparar els resultats sense la influència d’aquest paràmetre. Totes les mostres es van analitzar utilitzant un cromatogràf de gasos acoblat a un espectròmetre de masses.

3-Regime symmetric STAR modeling and exchange rate reversion

The breakdown of the Bretton Woods system and the adoption of generalized oating exchange rates ushered in a new era of exchange rate volatility and uncer- tainty. This increased volatility lead economists to search for economic models able to describe observed exchange rate behavior. In the present paper we propose more general STAR transition functions which encompass both threshold nonlinearity and asymmetric e¤ects. Our framework allows for a gradual adjustment from one regime to another, and considers threshold e¤ects by encompassing other existing models, such as TAR models. We apply our methodology to three di¤erent exchange rate data-sets, one for developing countries, and o¢ cial nominal exchange rates, the sec- ond emerging market economies using black market exchange rates and the third for OECD economies.

Preparació de materials monolítics quirals contenint derivats de poli-4R-hidroxi-L-prolina per a la separació de molècules enantiomèriques per cromatografia líquida

Projecte de recerca elaborat a partir d’una estada a la Universitat de California a Berkeley, Estats Units, entre març i juny de 2007. La cromatografia líquida emprant fases estacionàries quirals ha estat una de les tècniques més desenvolupades per a la separació d’enantiòmers. A més de presentar una elevada enantioselectivitat, és desitjable que els materials utilitzats amb aquesta finalitat permetin separacions altament cost-efectives. Una alternativa a l’us de mètodes més convencionals, en què el selector quiral està ancorat sobre gel de sílice particulada, és la utilització de materials monolítics, que es caracteritzen per ser d’una sola peça i altament porosos. L’elevada porositat d’aquests materials, una de les característiques que els fan més útils, permet treballar amb un flux de fase mòbil molt superior al permès amb les matrius convencionals. Aquest fet permet disminucions considerables dels temps d’anàlisi amb pressions de columna molt inferiors als límits establerts per garantir la seva durabilitat. D’altra banda, l’enantioselectivitat i la resolució vers als diferents analits es manté constant. El projecte, de quatre mesos de durada, s’ha centrat en la preparació de materials monolítics quirals de naturalesa orgànica o inorgànica contenint com a selectors quirals derivats de poli-hidroxi-prolina. Aquest materials s’han aplicat com a fases estacionàries quirals en cromatografia líquida en format estàndard i capil•lar. Els resultats cromatogràfics (selectivitat i eficiència) s’han comparat amb els obtinguts amb columnes de matriu particulada preparades prèviament.

Technical Appendix-3-Regime asymmetric STAR modeling and exchange rate reversion

The breakdown of the Bretton Woods system and the adoption of generalized oating exchange rates ushered in a new era of exchange rate volatility and uncer- tainty. This increased volatility lead economists to search for economic models able to describe observed exchange rate behavior. The present is a technical Appendix to Cerrato et al. (2009) and presents detailed simulations of the proposed methodology and additional empirical results.

Body mass index, cigarette smoking, and alcohol consumption and cancers of the oral cavity, pharynx, and larynx: modeling odds ratios in pooled case-control data.

Odds ratios for head and neck cancer increase with greater cigarette and alcohol use and lower body mass index (BMI; weight (kg)/height(2) (m(2))). Using data from the International Head and Neck Cancer Epidemiology Consortium, the authors conducted a formal analysis of BMI as a modifier of smoking- and alcohol-related effects. Analysis of never and current smokers included 6,333 cases, while analysis of never drinkers and consumers of < or =10 drinks/day included 8,452 cases. There were 8,000 or more controls, depending on the analysis. Odds ratios for all sites increased with lower BMI, greater smoking, and greater drinking. In polytomous regression, odds ratios for BMI (P = 0.65), smoking (P = 0.52), and drinking (P = 0.73) were homogeneous for oral cavity and pharyngeal cancers. Odds ratios for BMI and drinking were greater for oral cavity/pharyngeal cancer (P < 0.01), while smoking odds ratios were greater for laryngeal cancer (P < 0.01). Lower BMI enhanced smoking- and drinking-related odds ratios for oral cavity/pharyngeal cancer (P < 0.01), while BMI did not modify smoking and drinking odds ratios for laryngeal cancer. The increased odds ratios for all sites with low BMI may suggest related carcinogenic mechanisms; however, BMI modification of smoking and drinking odds ratios for cancer of the oral cavity/pharynx but not larynx cancer suggests additional factors specific to oral cavity/pharynx cancer.

Modeling U.S. Inflation Dynamics: A Bayesian Nonparametric Approach

This paper uses an infinite hidden Markov model (IIHMM) to analyze U.S. inflation dynamics with a particular focus on the persistence of inflation. The IHMM is a Bayesian nonparametric approach to modeling structural breaks. It allows for an unknown number of breakpoints and is a flexible and attractive alternative to existing methods. We found a clear structural break during the recent financial crisis. Prior to that, inflation persistence was high and fairly constant.

Ciutadania i drets humans (Disseny de cursos i materials docents per a la educació no universitària)

El projecte Ciutadania i Drets humans és un projecte d’innovació pedagògica dirigit a crear els materials necessaris per a l’ensenyament dels drets humans a l’educació secundària, utilitzant les noves tecnologies. Els continguts del projecte (primer any) són: Dignitat i justícia, Llibertat i seguretat, Igualtat i violència de gènere i Llibertat d’expressió. El mètode per a l’ensenyament parteix de la dinàmica d’estudi de cas. Amb aquesta finalitat els alumnes realitzaran a l’aula, exercicis de representació i anàlisis de diversos casos tractats per tribunals internacionals, nacionals i autonòmics així com instàncies de defensa dels ciutadans. Els alumnes poden desenvolupar habilitats cognitives tals com l’argumentació oral i escrita, la reflexió, el debat, la crítica i la presa de consciència de la diversitat de perspectives. A nivell de contingut tindran els coneixements bàsics dels sistemes de protecció dels drets, tals com el Tribunal Europeu de Drets Humans, el Síndic de Greuges i altres òrgans de garantia. El material elaborat consta d’una web per als alumnes com a eina de suport als continguts treballats a l’aula i una web per al professorat de secundària amb continguts, mètodes i casos, en forma de temes i unitats didàctiques.

Fusion of Multi-Atlas Segmentations with Spatial Distribution Modeling

In recent years, multi-atlas fusion methods have gainedsignificant attention in medical image segmentation. Inthis paper, we propose a general Markov Random Field(MRF) based framework that can perform edge-preservingsmoothing of the labels at the time of fusing the labelsitself. More specifically, we formulate the label fusionproblem with MRF-based neighborhood priors, as an energyminimization problem containing a unary data term and apairwise smoothness term. We present how the existingfusion methods like majority voting, global weightedvoting and local weighted voting methods can be reframedto profit from the proposed framework, for generatingmore accurate segmentations as well as more contiguoussegmentations by getting rid of holes and islands. Theproposed framework is evaluated for segmenting lymphnodes in 3D head and neck CT images. A comparison ofvarious fusion algorithms is also presented.