The UniProt-GO Annotation database in 2011.

The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360,000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set.

A theoretical and practical study on linear reforms of dual taxes

[cat] En aquest treball extenem les reformes lineals introduïdes per Pfähler (1984) al cas d’impostos duals. Estudiem l’efecte relatiu que els retalls lineals duals d’un impost dual tenen sobre la distribució de la desigualtat -es pot fer un estudi simètric per al cas d’augments d’impostos-. Tambe introduïm mesures del grau de progressivitat d’impostos duals i mostrem que estan connectades amb el criteri de dominació de Lorenz. Addicionalment, estudiem l’elasticitat de la càrrega fiscal de cadascuna de les reformes proposades. Finalment, gràcies a un model de microsimulació i una gran base de dades que conté informació sobre l’IRPF espanyol de l’any 2004, 1) comparem l’efecte que diferents reformes tindrien sobre l’impost dual espanyol i 2) estudiem quina redistribució de la riquesa va suposar la reforma dual de l’IRPF (Llei ’35/2006’) respecte l’anterior impost.

The determinants of social spending in Spain (1880-1960): Is Lindert right?

[spa] El principal objetivo de este artículo se centra en analizar los orígenes del Estado de Bienestar en España a partir del marco teórico elaborado por Peter Lindert. Con este fin, se ofrece un análisis econométrico de los factores que determinaron la evolución del gasto social público en este país entre 1880 y 1960. Utilizando nueva evidencia cuantitativa, se construyó un panel de datos por quinquenios con el porcentaje de gasto social respecto al PIB desagregado en tres partidas: sanidad, seguridad social y beneficencia. El análisis permite insertar el caso español en el debate internacional y los resultados revelan interesantes singularidades de este país.

Breaking the panels: an application to the GDP per capita

This paper proposes a test statistic for the null hypothesis of panel stationarity that allows for the presence of multiple structural breaks. Two different speci¿cations are considered depending on the structural breaks affecting the individual effects and/or the time trend. The model is ¿exible enough to allow the number of breaks and their position to differ across individuals. The test is shown to have an exact limit distribution with a good ¿nite sample performance. Its application to a typical panel data set of real per capita GDP gives support to the trend stationarity of these series

Sibling competition and the risk of falling out of the nest

In birds, sibling competition encompasses several activities, one of which is jostling for position, that is, competing for the location in the nest where parents predictably deliver food items. We hypothesized that nestlings that compete by jostling for position may fall out of the nest either accidentally or because siblings push each other to reduce brood size. This hypothesis predicts that in a competitive environment needy nestlings trade-off the benefit of being fed against the cost of falling out of the nest. As a first attempt to evaluate this hypothesis, we experimentally manipulated the number of young per brood in the colonial Alpine swift, Apus melba. Nestlings fell out of their colony more frequently when reared in enlarged than in reduced broods. Because brood size manipulation affects not only the number of young per nest but also their body condition, we analysed an extended data set to disentangle these two factors. This analysis showed that, independently of brood size, nestlings in poor condition and those reared in broods where sibling differed markedly in weight were more likely to disappear from the colony. Nestling disappearance also occurred predominantly in nests close to the colony entrances. Although nestling swifts can wander in the colony and become adopted in neighbouring nests, we found no evidence that wandering per se increased the risk of falling out of the colony. Our study therefore highlights a novel cost of scramble competition.

Impacts on the deep-sea ecosystem by a severe coastal storm

Major coastal storms, associated with strong winds, high waves and intensified currents, and occasionally with heavy rains and flash floods, are mostly known because of the serious damage they can cause along the shoreline and the threats they pose to navigation. However, there is a profound lack of knowledge on the deep-sea impacts of severe coastal storms. Concurrent measurements of key parameters along the coast and in the deep-sea are extremely rare. Here we present a unique data set showing how one of the most extreme coastal storms of the last decades lashing the Western Mediterranean Sea rapidly impacted the deep-sea ecosystem. The storm peaked the 26th of December 2008 leading to the remobilization of a shallow-water reservoir of marine organic carbon associated with fine particles and resulting in its redistribution across the deep basin. The storm also initiated the movement of large amounts of coarse shelf sediment, which abraded and buried benthic communities. Our findings demonstrate, first, that severe coastal storms are highly efficient in transporting organic carbon from shallow water to deep water, thus contributing to its sequestration and, second, that natural, intermittent atmospheric drivers sensitive to global climate change have the potential to tremendously impact the largest and least known ecosystem on Earth, the deep-sea ecosystem.

Pedotransfer functions to estimate proctor test parameters under different tillage systems

The Proctor test is time-consuming and requires sampling of several kilograms of soil. Proctor test parameters were predicted in Mollisols, Entisols and Vertisols of the Pampean region of Argentina under different management systems. They were estimated from a minimum number of readily available soil properties (soil texture, total organic C) and management (training data set; n = 73). The results were used to generate a soil compaction susceptibility model, which was subsequently validated using a second group of independent data (test data set; n = 24). Soil maximum bulk density was estimated as follows: Maximum bulk density (Mg m-3) = 1.4756 - 0.00599 total organic C (g kg-1) + 0.0000275 sand (g kg-1) + 0.0539 management. Management was equal to 0 for uncropped and untilled soils and 1 for conventionally tilled soils. The established models predicted the Proctor test parameters reasonably well, based on readily available soil properties. Tillage systems induced changes in the maximum bulk density regardless of total organic matter content or soil texture. The lower maximum apparent bulk density values under no-tillage require a revision of the relative compaction thresholds for different no-tillage crops.

Pavement Markings and Safety Final Report, November 2010

Previous research on pavement markings from a safety perspective tackled various issues such as pavement marking retroreflectivity variability, relationship between pavement marking retroreflectivity and driver visibility, or pavement marking improvements and safety. A recent research interest in this area has been to find a correlation between retroreflectivity and crashes, but a significant statistical relationship has not yet been found. This study investigates such a possible statistical relationship by analyzing five years of pavement marking retroreflectivity data collected by the Iowa Department of Transportation (DOT) on all state primary roads and corresponding crash and traffic data. This study developed a spatial-temporal database using measured retroreflectivity data to account for the deterioration of pavement markings over time along with statewide crash data to attempt to quantify a relationship between crash occurrence probability and pavement marking retroreflectivity. First, logistic regression analyses were done for the whole data set to find a statistical relationship between crash occurrence probability and identified variables, which are road type, line type, retroreflectivity, and traffic (vehicle miles traveled). The analysis looked into subsets of the data set such as road type, retroreflectivity measurement source, high crash routes, retroreflectivity range, and line types. Retroreflectivity was found to have a significant effect in crash occurrence probability for four data subsets—interstate, white edge line, yellow edge line, and yellow center line data. For white edge line and yellow center line data, crash occurrence probability was found to increase by decreasing values of retroreflectivity.

Roadway Lighting and Safety: Phase II – Monitoring Quality, Durability and Efficiency, November 2011

This Phase II project follows a previous project titled Strategies to Address Nighttime Crashes at Rural, Unsignalized Intersections. Based on the results of the previous study, the Iowa Highway Research Board (IHRB) indicated interest in pursuing further research to address the quality of lighting, rather than just the presence of light, with respect to safety. The research team supplemented the literature review from the previous study, specifically addressing lighting level in terms of measurement, the relationship between light levels and safety, and lamp durability and efficiency. The Center for Transportation Research and Education (CTRE) teamed with a national research leader in roadway lighting, Virginia Tech Transportation Institute (VTTI) to collect the data. An integral instrument to the data collection efforts was the creation of the Roadway Monitoring System (RMS). The RMS allowed the research team to collect lighting data and approach information for each rural intersection identified in the previous phase. After data cleanup, the final data set contained illuminance data for 101 lighted intersections (of 137 lighted intersections in the first study). Data analysis included a robust statistical analysis based on Bayesian techniques. Average illuminance, average glare, and average uniformity ratio values were used to classify quality of lighting at the intersections.

Preisach modeling of hysteresis for a pseudoelastic Cu-Zn-Al single crystal

Stress-strain trajectories associated with pseudoelastic behavior of a Cu¿19.4 Zn¿13.1 Al (at.%) single crystal at room temperature have been determined experimentally. For a constant cross-head speed the trajectories and the associated hysteresis behavior are perfectly reproducible; the trajectories exhibit memory properties, dependent only on the values of return points, where transformation direction is reverted. An adapted version of the Preisach model for hysteresis has been implemented to predict the observed trajectories, using a set of experimental first¿order reversal curves as input data. Explicit formulas have been derived giving all trajectories in terms of this data set, with no adjustable parameters. Comparison between experimental and calculated trajectories shows a much better agreement for descending than for ascending paths, an indication of a dissymmetry between the dissipation mechanisms operative in forward and reverse directions of martensitic transformation.

Genetic and karyotypic structure in the shrews of the Sorex araneus group: are they independent?

The species of the common shrew (Sorex araneus) group are morphologically very similar but exhibit high levels of karyotypic variation. Here we used genetic variation at 10 microsatellite markers in a data set of 212 individuals mostly sampled in the western Alps and composed of five karyotypic taxa (Sorex coronatus, Sorex antinorii and the S. araneus chromosome races Cordon, Bretolet and Vaud) to investigate the concordance between genetic and karyotypic structure. Bayesian analysis confirmed the taxonomic status of the three sampled species since individuals consistently grouped according to their taxonomical status. However, introgression can still be detected between S. antinorii and the race Cordon of S. araneus. This observation is consistent with the expected low karyotypic complexity of hybrids between these two taxa. Geographically based cryptic substructure was discovered within S. antinorii, a pattern consistent with the different postglaciation recolonization routes of this species. Additionally, we detected two genetic groups within S. araneus notwithstanding the presence of three chromosome races. This pattern can be explained by the probable hybrid status of the Bretolet race but also suggests a relatively low impact of chromosomal differences on genetic structure compared to historical factors. Finally, we propose that the current data set (available at http://www.unil.ch/dee/page7010_en.html#1) could be used as a reference by those wanting to identify Sorex individuals sampled in the western Alps.

A fast 3D approach for coronary MRA.

Two-dimensional (2D)-breath-hold coronary magnetic resonance angiography (MRA) has been shown to be a fast and reliable method to depict the proximal coronary arteries. Recent developments, however, allow for free-breathing navigator gated and navigator corrected three-dimensional (3D) coronary MRA. These 3D approaches have potential for improved signal-to-noise ratio (SNR) and allow for the acquisition of adjacent thin slices without the misregistration problems known from 2D approaches. Still, a major impediment of a 3D acquisition is the increased scan time. The purpose of this study was the implementation of a free-breathing navigator gated and corrected ultra-fast 3D coronary MRA technique, which allows for scan times of less than 5 minutes. Twelve healthy adult subjects were examined in the supine position using a navigator gated and corrected ECG triggered ultra-fast 3D interleaved gradient echo planar imaging sequence (TFE-EPI). A 3D slab, consisting of 20 slices with a reconstructed slice thickness of 1.5 mm, was acquired with free-breathing. The diastolic TFE-EPI acquisition block was preceded by a T2prep pre-pulse, a diaphragmatic navigator pulse, and a fat suppression pre-pulse. With a TR of 19 ms and an effective TE of 5.4 ms, the duration of the data acquisition window duration was 38 ms. The in-plane spatial resolution was 1.0-1.3 mm*1.5-1.9 mm. In all cases, the entire left main (LM) and extensive portions of the left anterior descending (LAD) and right coronary artery (RCA) could be visualized with an average scan time for the entire 3D-volume data set of 2:57 +/- 0:51 minutes. Average contiguous vessel length visualized was 53 +/- 11 mm (range: 42 to 75 mm) for the LAD and 84 +/- 14 mm (range: 62 to 112 mm) for the RCA. Contrast-to-noise between coronary blood and myocardium was 5.0 +/- 2.3 for the LM/LAD and 8.0 +/- 2.9 for the RCA, resulting in an excellent suppression of myocardium. We present a new approach for free-breathing 3D coronary MRA, which allows for scan times superior to corresponding 2D coronary MRA approaches, and which takes advantage of the enhanced SNR of 3D acquisitions and the post-processing benefits of thin adjacent slices. The robust image quality and the short average scanning time suggest that this approach may be useful for screening the major coronary arteries or identification of anomalous coronary arteries. J. Magn. Reson. Imaging 1999;10:821-825.

Patient-perceived health-related quality of life during recovery after total hip arthroplasty – a 6-month follow-up study

Potilaiden käsitys terveyteen liittyvästä elämänlaadusta lonkan tekonivelleikkauksen jälkeisenä toipumisaikana – kuuden kuukauden seurantatutkimus Tässä kaksivaiheisessa seurantatutkimuksessa tarkasteltiin potilaiden käsitystä terveyteen liittyvästä elämänlaadusta lonkan tekonivelleikkauksen jälkeisenä toipumisaikana. Tutkimuksen ensimmäisessä vaiheessa tarkoituksena oli sekä kuvailla potilaiden kokemuksia potilaana olosta, saamastaan hoidosta ja terveyspalveluorganisaatiosta että analysoida aikaisempien tutkimusten perusteella leikkauksen tuloksia potilaan kannalta. Toisessa vaiheessa tarkoituksena oli arvioida potilaiden kokemaa elämänlaatua leikkauksen jälkeen, ja sitä vaikuttivatko primaaritulokset (fyysinen toimintakyky, kipu, ahdistus) tai taloudelliset seuraukset (potilaiden itsensämaksamat kustannukset, palvelujen käyttö) terveyteen liittyvään elämänlaatuun. Tutkimuksen tavoitteena oli löytää mahdolliset kriittiset ajankohdat tai tekijät, jotka saattavat hidastaa toipumista ja siten huonontaa potilaiden elämänlaatua. Tätä tietoa voidaan käyttää hoitotyössä kun suunnitellaan sopivaa hoitoa ja tukea toipumisajalle. Tutkimuksen ensimmäisessä vaiheessa primaarileikkaukseen tulevat potilaat (n = 17) kuvailivat teemahaastatteluissa kokemuksiaan kahdesti leikkauksen jälkeen. Haastatteluaineisto analysoitiin induktiivisella sisällönanalyysilla. Lisäksi 17 tutkimusartikkelista analysoitiin deduktiivisella sisällönanalyysilla leikkauksen tuloksia potilaalle, tuloksiin vaikuttavia tekijöitä ja käytetyt tutkimusmetodit. Toisessa vaiheessa primaari- tai revisioleikkaukseen tulevat potilaat (n = 100) arvioivat leikkauksen tuloksia kuuden kuukauden ajan leikkauksen jälkeen: terveyteen liittyvää elämänlaatua, primaarituloksia ja taloudellisia seurauksia. Aineisto kerättiin erilaisilla mittareilla: Sickness Impact Profile, Finnish Version, Stait-Trait Anxiety Inventory, ja Numeric Rating Scale. Lisäksi käytettiin tätä tutkimusta varten tehtyjä kyselylomakkeita: Fyysinen toimintakyky-mittari, Palvelujen käyttö-mittari ja Kustannusmittari. Tutkimuksen toiseen vaiheen tulokset analysoitiin tilastollisilla menetelmillä. Potilaiden terveyteen liittyvä elämänlaatu parani ja kipu lievittyi leikkauksen jälkeen ja fyysinen toimintakyky lisääntyi toipumisaikana. Positiivisista muutoksista huolimatta potilaat kokivat ahdistusta samassa määrin kuin ennen leikkaustakin. Palvelujen käyttö vaihteli toipumisajan kuluessa ja potilaiden maksamissa kustannuksissa oli suuria vaihteluita. Fyysisen toimintakyvyn lisääntyminen ja kivun lieveneminen paransivat terveyteen liittyvää elämänlaatua. Sen sijaan huonompi elämänlaatu toipumisaikana oli yhteydessä suurempaan palvelujen käyttöön, kun taas kustannuksilla ei ollut yhteyttä elämänlaatuun. Potilaiden ominaispiirteet tulisi ottaa enemmän huomioon suunniteltaessa sopivaa leikkauksenjälkeistä hoitoa ja tukea. Potilaat tarvitsevat yksilöllisiä ohjeita, sillä monet taustatekijät (esim. ikä, sukupuoli, preoperatiivinen kipu, siviilisääty, ja leikkaustyyppi) vaikuttavat toipumiseen.

Evaluation of statistical and geostatistical models of digital soil properties mapping in tropical mountain regions

Soil properties have an enormous impact on economic and environmental aspects of agricultural production. Quantitative relationships between soil properties and the factors that influence their variability are the basis of digital soil mapping. The predictive models of soil properties evaluated in this work are statistical (multiple linear regression-MLR) and geostatistical (ordinary kriging and co-kriging). The study was conducted in the municipality of Bom Jardim, RJ, using a soil database with 208 sampling points. Predictive models were evaluated for sand, silt and clay fractions, pH in water and organic carbon at six depths according to the specifications of the consortium of digital soil mapping at the global level (GlobalSoilMap). Continuous covariates and categorical predictors were used and their contributions to the model assessed. Only the environmental covariates elevation, aspect, stream power index (SPI), soil wetness index (SWI), normalized difference vegetation index (NDVI), and b3/b2 band ratio were significantly correlated with soil properties. The predictive models had a mean coefficient of determination of 0.21. Best results were obtained with the geostatistical predictive models, where the highest coefficient of determination 0.43 was associated with sand properties between 60 to 100 cm deep. The use of a sparse data set of soil properties for digital mapping can explain only part of the spatial variation of these properties. The results may be related to the sampling density and the quantity and quality of the environmental covariates and predictive models used.

Comparing the artificial neural network with parcial least squares for prediction of soil organic carbon and pH at different moisture content levels using visible and near-infrared spectroscopy

Visible and near infrared (vis-NIR) spectroscopy is widely used to detect soil properties. The objective of this study is to evaluate the combined effect of moisture content (MC) and the modeling algorithm on prediction of soil organic carbon (SOC) and pH. Partial least squares (PLS) and the Artificial neural network (ANN) for modeling of SOC and pH at different MC levels were compared in terms of efficiency in prediction of regression. A total of 270 soil samples were used. Before spectral measurement, dry soil samples were weighed to determine the amount of water to be added by weight to achieve the specified gravimetric MC levels of 5, 10, 15, 20, and 25 %. A fiber-optic vis-NIR spectrophotometer (350-2500 nm) was used to measure spectra of soil samples in the diffuse reflectance mode. Spectra preprocessing and PLS regression were carried using Unscrambler® software. Statistica® software was used for ANN modeling. The best prediction result for SOC was obtained using the ANN (RMSEP = 0.82 % and RPD = 4.23) for soil samples with 25 % MC. The best prediction results for pH were obtained with PLS for dry soil samples (RMSEP = 0.65 % and RPD = 1.68) and soil samples with 10 % MC (RMSEP = 0.61 % and RPD = 1.71). Whereas the ANN showed better performance for SOC prediction at all MC levels, PLS showed better predictive accuracy of pH at all MC levels except for 25 % MC. Therefore, based on the data set used in the current study, the ANN is recommended for the analyses of SOC at all MC levels, whereas PLS is recommended for the analysis of pH at MC levels below 20 %.