Good genes and good luck: Ammonoid diversity and the end-Permian mass extinction

The end-Permian mass extinction removed more than 80% of marine genera. Ammonoid cephalopods were among the organisms most affected by this crisis. The analysis of a global diversity data set of ammonoid genera covering about 106 million years centered on the Permian-Triassic boundary (PTB) shows that Triassic ammonoids actually reached levels of diversity higher than in the Permian less than 2 million years after the PTB. The data favor a hierarchical rather than logistic model of diversification coupled with a niche incumbency hypothesis. This explosive and nondelayed diversification contrasts with the slow and delayed character of the Triassic biotic recovery as currently illustrated for other, mainly benthic groups such as bivalves and gastropods.

Safety and Mobility Impacts of Winter Weather --Phase 3, SPR RB01-012, 2014

Highway agencies spend millions of dollars to ensure safe and efficient winter travel. However, the effectiveness of winter-weather maintenance practices on safety and mobility are somewhat difficult to quantify. Safety and Mobility Impacts of Winter Weather - Phase 1 investigated opportunities for improving traffic safety on state-maintained roads in Iowa during winter-weather conditions. In Phase 2, three Iowa Department of Transportation (DOT) high-priority sites were evaluated and realistic maintenance and operations mitigation strategies were also identified. In this project, site prioritization techniques for identifying roadway segments with the potential for safety improvements related to winter-weather crashes, were developed through traditional naïve statistical methods by using raw crash data for seven winter seasons and previously developed metrics. Additionally, crash frequency models were developed using integrated crash data for four winter seasons, with the objective of identifying factors that affect crash frequency during winter seasons and screening roadway segments using the empirical Bayes technique. Based on these prioritization techniques, 11 sites were identified and analyzed in conjunction with input from Iowa DOT district maintenance managers and snowplow operators and the Iowa DOT Road Weather Information System (RWIS) coordinator.

Reconeixement de punts clau en imatges mitjançant l'algorisme Random Ferns

Treball final de carrera basat en el reconeixement de punts clau en imatges mitjançant l'algorisme Random Ferns.

A Note on Interviewer Performance Measures in centralised CATI Surveys

Interviewer performance with respect to convincing sample members to participate in surveys is an important dimension of survey quality. However, unlike in CAPI surveys where each sample case 'belongs' to one interviewer, there are hardly any good measures of interview performance for centralised CATI surveys, where even single contacts are assigned to interviewers at random. If more than one interviewer works one sample case, it is not clear how to attribute success or failure to the interviewers involved. In this article, we propose two correlated methods to measure interviewer contact performance in centralised CATI surveys. Their modelling must take complex multilevel clustering effects, which need not be hierarchical, into account. Results are consistent with findings from CAPI data modelling, and we find that when comparing effects with a direct ('naive') measure of interviewer contact results, interviewer random effects are largely underestimated using the naive measure.

Multiscale assessment of plant diversity in wooded pastures of the Jura mountains

Résumé La diminution de la biodiversité, à toutes les échelles spatiales et sur l'ensemble de la planète, compte parmi les problèmes les plus préoccupants de notre époque. En terme de conservation, il est aujourd'hui primordial de mieux comprendre les mécanismes qui créent et maintiennent la biodiversité dans les écosystèmes naturels ou anthropiques. La présente étude a pour principal objectif d'améliorer notre compréhension des patrons de biodiversité végétale et des mécanismes sous jacents, dans un écosystème complexe, riche en espèces et à forte valeur patrimoniale, les pâturages boisés jurassiens. Structure et échelle spatiales sont progressivement reconnues comme des dimensions incontournables dans l'étude des patrons de biodiversité. De plus, ces deux éléments jouent un rôle central dans plusieurs théories écologiques. Toutefois, peu d'hypothèses issues de simulations ou d'études théoriques concernant le lien entre structure spatiale du paysage et biodiversité ont été testées de façon empirique. De même, l'influence des différentes composantes de l'échelle spatiale sur les patrons de biodiversité est méconnue. Cette étude vise donc à tester quelques-unes de ces hypothèses et à explorer les patrons spatiaux de biodiversité dans un contexte multi-échelle, pour différentes mesures de biodiversité (richesse et composition en espèces) à l'aide de données de terrain. Ces données ont été collectées selon un plan d'échantillonnage hiérarchique. Dans un premier temps, nous avons testé l'hypothèse élémentaire selon laquelle la richesse spécifique (le nombre d'espèces sur une surface donnée) est liée à l'hétérogénéité environnementale quelque soit l'échelle. Nous avons décomposé l'hétérogénéité environnementale en deux parties, la variabilité des conditions environnementales et sa configuration spatiale. Nous avons montré que, en général, la richesse spécifique augmentait avec l'hétérogénéité de l'environnement : elle augmentait avec le nombre de types d'habitats et diminuait avec l'agrégation spatiale de ces habitats. Ces effets ont été observés à toutes les échelles mais leur nature variait en fonction de l'échelle, suggérant une modification des mécanismes. Dans un deuxième temps, la structure spatiale de la composition en espèces a été décomposée en relation avec 20 variables environnementales et 11 traits d'espèces. Nous avons utilisé la technique de partition de la variation et un descripteur spatial, récemment développé, donnant accès à une large gamme d'échelles spatiales. Nos résultats ont montré que la structure spatiale de la composition en espèces végétales était principalement liée à la topographie, aux échelles les plus grossières, et à la disponibilité en lumière, aux échelles les plus fines. La fraction non-environnementale de la variation spatiale de la composition spécifique avait une relation complexe avec plusieurs traits d'espèces suggérant un lien avec des processus biologiques tels que la dispersion, dépendant de l'échelle spatiale. Dans un dernier temps, nous avons testé, à plusieurs échelles spatiales, les relations entre trois composantes de la biodiversité : la richesse spécifique totale d'un échantillon (diversité gamma), la richesse spécifique moyenne (diversité alpha), mesurée sur des sous-échantillons, et les différences de composition spécifique entre les sous-échantillons (diversité beta). Les relations deux à deux entre les diversités alpha, beta et gamma ne suivaient pas les relations attendues, tout du moins à certaines échelles spatiales. Plusieurs de ces relations étaient fortement dépendantes de l'échelle. Nos résultats ont mis en évidence l'importance du rapport d'échelle (rapport entre la taille de l'échantillon et du sous-échantillon) lors de l'étude des patrons spatiaux de biodiversité. Ainsi, cette étude offre un nouvel aperçu des patrons spatiaux de biodiversité végétale et des mécanismes potentiels permettant la coexistence des espèces. Nos résultats suggèrent que les patrons de biodiversité ne peuvent être expliqués par une seule théorie, mais plutôt par une combinaison de théories. Ils ont également mis en évidence le rôle essentiel joué par la structure spatiale dans la détermination de la biodiversité, quelque soit le composant de la biodiversité considéré. Enfin, cette étude souligne l'importance de prendre en compte plusieurs échelles spatiales et différents constituants de l'échelle spatiale pour toute étude relative à la diversité spécifique. Abstract The world-wide loss of biodiversity at all scales has become a matter of urgent concern, and improving our understanding of local drivers of biodiversity in natural and anthropogenic ecosystems is now crucial for conservation. The main objective of this study was to further our comprehension of the driving forces controlling biodiversity patterns in a complex and diverse ecosystem of high conservation value, wooded pastures. Spatial pattern and scale are central to several ecological theories, and it is increasingly recognized that they must be taken -into consideration when studying biodiversity patterns. However, few hypotheses developed from simulations or theoretical studies have been tested using field data, and the evolution of biodiversity patterns with different scale components remains largely unknown. We test several such hypotheses and explore spatial patterns of biodiversity in a multi-scale context and using different measures of biodiversity (species richness and composition), with field data. Data were collected using a hierarchical sampling design. We first tested the simple hypothesis that species richness, the number of species in a given area, is related to environmental heterogeneity at all scales. We decomposed environmental heterogeneity into two parts: the variability of environmental conditions and its spatial configuration. We showed that species richness generally increased with environmental heterogeneity: species richness increased with increasing number of habitat types and with decreasing spatial aggregation of those habitats. Effects occurred at all scales but the nature of the effect changed with scale, suggesting a change in underlying mechanisms. We then decomposed the spatial structure of species composition in relation to environmental variables and species traits using variation partitioning and a recently developed spatial descriptor, allowing us to capture a wide range of spatial scales. We showed that the spatial structure of plant species composition was related to topography at the coarsest scales and insolation at finer scales. The non-environmental fraction of the spatial variation in species composition had a complex relationship with several species traits, suggesting a scale-dependent link to biological processes, particularly dispersal. Finally, we tested, at different spatial scales, the relationships between different components of biodiversity: total sample species richness (gamma diversity), mean species .richness (alpha diversity), measured in nested subsamples, and differences in species composition between subsamples (beta diversity). The pairwise relationships between alpha, beta and gamma diversity did not follow the expected patterns, at least at certain scales. Our result indicated a strong scale-dependency of several relationships, and highlighted the importance of the scale ratio when studying biodiversity patterns. Thus, our results bring new insights on the spatial patterns of biodiversity and the possible mechanisms allowing species coexistence. They suggest that biodiversity patterns cannot be explained by any single theory proposed in the literature, but a combination of theories is sufficient. Spatial structure plays a crucial role for all components of biodiversity. Results emphasize the importance of considering multiple spatial scales and multiple scale components when studying species diversity.

Optimal CD8 T cell responsiveness is controlled within a defined TCR affinity window

Protective immune responses relyon TCR-mediated recognition of antigenspresented by MHC molecules. Tcells directed against tumor antigensare thought to express TCRs of loweraffinity/avidity than pathogen-specificT lymphocytes. An attractivestrategy to improve anti-tumor T cellresponses is to adoptively transferCD8+ T cells engineered with TCRsof optimized affinity. However, themechanisms that control optimal Tcell activation and responsiveness remainpoorly defined. We aim at characterizingTCR-pMHC binding parametersand downstream signalingevents that regulate T cell functionalityby using an in silico designedpanel of tumor antigen-specific TCRsof incremental affinity for pMHC(Kd100 M- 15 nM).We found that optimalT cell responses (cytokine secretionand target cell killing) occurredwithin a well-defined window ofTCR-pMHC binding affinity (5 M-1 M), while drastic functional declinewas detected in T cells expressingvery low and very high TCRaffinities,which was not caused by any increasein apoptosis. Whole-genomemicroarray analysis revealed that Tcells with optimal TCR affinitieshighly up-regulated transcription ofgenes typical of T cell activation (i.e.IFN-, NF-B and TNFR), while reducedexpression was detected in Tcells of very low or very high TCR affinity.Strikingly, hierarchical clusteringshowed that the latter two variantsclustered together with the un-stimulatedcontrol Tcells.Yet, despite commonclustering, several genes seemedto be differentially expressed, suggestingthat the mechanisms involvedin this "unresponsiveness state" maydiffer between those two variants. Finally,calcium influx assays also demonstratedattenuated responses in Tcells of very high TCR affinity. Ourresults indicate that optimal T cellfunction is tightly controlled within adefinedTCRaffinity window throughvery proximal TCR-mediated mechanisms,possibly at the TCR-pMHCbinding interface. Uncovering themechanisms regulating optimal/maximalT cell function is essential to understandand promote therapeutic designlike adoptive T cell therapy.

Sense of coherence and job characteristics in predicting burnout in a South African sample

Orientation: Research that considers the effects of individual characteristics and job characteristics jointly in burnout is necessary, especially when one considers the possibility of curvilinear relationships between job characteristics and burnout. Research purpose: This study examines the contribution of sense of coherence (SOC) and job characteristics to predicting burnout by considering direct and moderating effects. Motivation for this study: Understanding the relationships of individual and job characteristics with burnout is necessary for preventing burnout. It also informs the design of interventions. Research design, approach and method: The participants were 632 working adults (57% female) in South Africa. The measures included the Job Content Questionnaire, the Sense of Coherence Questionnaire and the Maslach Burnout Inventory. The authors analysed the data using hierarchical multiple regression with the enter method. Main findings: Job characteristics and SOC show the expected direct effects on burnout. SOC has a direct negative effect on burnout. Job demands and supervisor social support show nonlinear relationships with burnout. SOC moderates the effect of demands on burnout and has a protective function so that the demands-burnout relationship differs for those with high and low SOC. Practical/managerial implications: The types of effects, the shape of the stressor-strain relationship and the different contributions of individual and job characteristics have implications for designing interventions. Contribution/value add: SOC functions differently when combined with demands, control and support. These different effects suggest that it is not merely the presence or absence of a job characteristic that is important for well-being outcomes but how people respond to its presence or absence.

Active deformation fields: dense deformation field estimation for atlas-based segmentation using the active contour framework.

This paper presents a new and original variational framework for atlas-based segmentation. The proposed framework integrates both the active contour framework, and the dense deformation fields of optical flow framework. This framework is quite general and encompasses many of the state-of-the-art atlas-based segmentation methods. It also allows to perform the registration of atlas and target images based on only selected structures of interest. The versatility and potentiality of the proposed framework are demonstrated by presenting three diverse applications: In the first application, we show how the proposed framework can be used to simulate the growth of inconsistent structures like a tumor in an atlas. In the second application, we estimate the position of nonvisible brain structures based on the surrounding structures and validate the results by comparing with other methods. In the final application, we present the segmentation of lymph nodes in the Head and Neck CT images, and demonstrate how multiple registration forces can be used in this framework in an hierarchical manner.

Global invasion history of the fire ant Solenopsis invicta.

The fire ant Solenopsis invicta is a significant pest that was inadvertently introduced into the southern United States almost a century ago and more recently into California and other regions of the world. An assessment of genetic variation at a diverse set of molecular markers in 2144 fire ant colonies from 75 geographic sites worldwide revealed that at least nine separate introductions of S. invicta have occurred into newly invaded areas and that the main southern U.S. population is probably the source of all but one of these introductions. The sole exception involves a putative serial invasion from the southern United States to California to Taiwan. These results illustrate in stark fashion a severe negative consequence of an increasingly massive and interconnected global trade and travel system.

Comparação bayesiana de modelos de previsão de diferenças esperadas nas progênies no melhoramento genético de gado Nelore

O objetivo deste trabalho foi realizar uma análise bayesiana de modelos auto-regressivos de ordem p, AR(p), para dados em painel referentes às diferenças esperadas nas progênies (DEP) de touros da raça Nelore publicados de 2000 a 2006. Neste trabalho, adotou-se o modelo AR(2), indicado pela análise prévia da função de autocorrelação parcial. As comparações entre as prioris, realizadas por meio do Fator de Bayes e do Pseudo-Fator de Bayes, indicaram superioridade da priori independente t-Student multivariada - Gama inversa em relação à priori hierárquica Normal multivariada - Gama inversa e a priori de Jeffreys. Os resultados indicam a importância de se dividir os animais em grupos homogêneos de acordo com a acurácia. Constatou-se também que, em média, a eficiência de previsão dos valores de DEP para um ano futuro foi próxima de 80%.

Alps, genes, and chromosomes: their role in the formation of species in the Sorex araneus group (Mammalia, Insectivora), as inferred from two hybrid zones.

During the Pleistocene glaciations, the Alps were an efficient barrier to gene flow between isolated populations, often leading to allopatric speciation. Afterwards, the Alps strongly influenced the post-glacial recolonization of Europe and represent a major suture zone between differentiated populations. Two hybrid zones in the Swiss and French Alps between genetically and chromosomally well-differentiated species-the Valais shrew, Sorex antinorii, and the common shrew, S. araneus-were studied karyotypically and by analyzing the distribution of seven microsatellite loci. In the center of the Haslital hybrid zone the two species coexist over a distance of 900 m. Hybrid karyotypes, among them the most complex known in Sorex, are rare. F-statistics based on microsatellite data revealed a strong heterozygote deficit only in the center of the zone, due to the sympatric distribution of the two species with little hybridization between them. Structuring within the species (both F(IS) and F(ST)) was low. An hierarchical analysis showed a high level of interspecific differentiation. Results were compared with those previously reported in another hybrid zone located at Les Houches in the French Alps. Genetic structuring within and between species was comparable in both hybrid zones, although chromosomal incompatibilities are more important in Haslital, where a linkage block of the race-specific chromosomes should additionally impede gene flow. Evidence for a more restricted gene flow in Haslital comes from the genetically intermediate hybrid karyotypes, whereas in Les Houches, hybrid karyotypes are genetically identical to individuals of the pure karyotypic races. Genic and chromosomal introgression was observed in Les Houches, but not in Haslital. The possible influence of a river, separating the two species at Les Houches, on gene flow is discussed.

Where and how family members spend time at home? A quantitative analysis of the observational tracking on the everyday lives of Italian families

This paper examines a dataset that derives from an observational tracking, in order to analyze where and how middle-class working families spend time at home. We use an ethnographic approach to study the everyday lives of Italian dual-income middle-class families, with the aim to analyze quantitatively the use of home spaces and the types of activities of family members on weekday afternoons and evenings. The different analyses (multiple correspondence analysis, agglomerative hierarchical cluster, discriminant analysis) show how particular spaces and activities in these spaces are dominated by certain family members. We suggest a combination of qualitative and quantitative methodologies as useful tools to explore in detail the everyday lives of families, and to understand how family members use the domestic spaces. In particular, we consider relevant the use of quantitative analyses to examine ethnographic data, especially in connection with the methodological reflexivity among researchers

Deciphering the global organization of clustering in real complex networks

We uncover the global organization of clustering in real complex networks. To this end, we ask whether triangles in real networks organize as in maximally random graphs with given degree and clustering distributions, or as in maximally ordered graph models where triangles are forced into modules. The answer comes by way of exploring m-core landscapes, where the m-core is defined, akin to the k-core, as the maximal subgraph with edges participating in at least m triangles. This property defines a set of nested subgraphs that, contrarily to k-cores, is able to distinguish between hierarchical and modular architectures. We find that the clustering organization in real networks is neither completely random nor ordered although, surprisingly, it is more random than modular. This supports the idea that the structure of real networks may in fact be the outcome of self-organized processes based on local optimization rules, in contrast to global optimization principles.

Confirmatory factor analysis of an integrated model of psycopathology assessed with MMPI-2-RF and the MCMI-III

We presented an integrated hierarchical model of psychopathology that more accurately captures empirical patterns of comorbidity between clinical syndromes and personality disorders.In order to verify the structural validity of the model proposed, this study aimed to analyze the convergence between the Restructured Clinical (RC) scales and Personality scales (PSY-5) of the MMPI-2-RF and the Clinical Syndrome and Personality Disorder scales of the MCMI-III.The MMPI-2-RF and MCMI-III were administered to a clinical sample of 377 outpatients (167 men and 210 women).The structural hypothesiswas assessed by using a Confirmatory Factor Analytic design with four common superordinate factors. An independent-cluster-basis solution was proposed based on maximum likelihood estimation and the application of several fit indices.The fit of the proposed model can be considered as good and more so if we take into account its complexity.

Wave-height hazard analysis in Eastern Coast of Spain : Bayesian approach using generalized Pareto distribution

Standard practice of wave-height hazard analysis often pays little attention to the uncertainty of assessed return periods and occurrence probabilities. This fact favors the opinion that, when large events happen, the hazard assessment should change accordingly. However, uncertainty of the hazard estimates is normally able to hide the effect of those large events. This is illustrated using data from the Mediterranean coast of Spain, where the last years have been extremely disastrous. Thus, it is possible to compare the hazard assessment based on data previous to those years with the analysis including them. With our approach, no significant change is detected when the statistical uncertainty is taken into account. The hazard analysis is carried out with a standard model. Time-occurrence of events is assumed Poisson distributed. The wave-height of each event is modelled as a random variable which upper tail follows a Generalized Pareto Distribution (GPD). Moreover, wave-heights are assumed independent from event to event and also independent of their occurrence in time. A threshold for excesses is assessed empirically. The other three parameters (Poisson rate, shape and scale parameters of GPD) are jointly estimated using Bayes' theorem. Prior distribution accounts for physical features of ocean waves in the Mediterranean sea and experience with these phenomena. Posterior distribution of the parameters allows to obtain posterior distributions of other derived parameters like occurrence probabilities and return periods. Predictives are also available. Computations are carried out using the program BGPE v2.0