Thermotectonic History of the Kluane Ranges and Evolution of the Eastern Denali Fault Zone in Southwestern Yukon, Canada

Exhumation and landscape evolution along strike‐slip fault systems reflect tectonic processes that accommodate and partition deformation in orogenic settings. We present 17 new apatite (U‐Th)/He (He), zircon He, apatite fission‐track (FT), and zircon FT dates from the eastern Denali fault zone (EDFZ) that bounds the Kluane Ranges in Yukon, Canada. The dates elucidate patterns of deformation along the EDFZ. Mean apatite He, apatite FT, zircon He, and zircon FT sample dates range within ~26–4, ~110–12, ~94–28, and ~137–83 Ma, respectively. A new zircon U‐Pb date of 113.9 ± 1.7 Ma (2σ) complements existing geochronology and aids in interpretation of low‐temperature thermochronometry data patterns. Samples ≤2 km southwest of the EDFZ trace yield the youngest thermochronometry dates. Multimethod thermochronometry, zircon He date‐effective U patterns, and thermal history modeling reveal rapid cooling ~95–75 Ma, slow cooling ~75–30 Ma, and renewed rapid cooling ~30 Ma to present. The magnitude of net surface uplift constrained by published paleobotanical data, exhumation, and total surface uplift from ~30 Ma to present are ~1, ~2–6, and ~1–7 km, respectively. Exhumation is highest closest to the EDFZ trace but substantially lower than reported for the central Denali fault zone. We infer exhumation and elevation changes associated with ~95–75 Ma terrane accretion and EDFZ activity, relief degradation from ~75–30 Ma, and ~30 Ma to present exhumation and surface uplift as a response to flat‐slab subduction and transpressional deformation. Integrated results reveal new constraints on landscape evolution within the Kluane Ranges directly tied to the EDFZ during the last ~100 Myr

A dynamic Bayesian Markov model for health economic evaluations of interventions against infectious diseases

Health economic evaluations of interventions against infectious diseases are commonly based on the predictions of compartmental models such as ordinary differential equation (ODE) systems and Markov models. In contrast to standard Markov models which are static, ODE systems are dynamic by definition and therefore able to account for the effects of herd immunity. This is crucial in pathogens which are transmissible between humans to prevent incorrect model outcomes. The computational effort of fully probabilistic ODE systems is considerably high. Thus, most ODE-based models in the literature are deterministic; they do not account for parameter uncertainty and probabilistic sensitivity analysis cannot be conducted straightforwardly. Yet, it is an essential part of health economic evaluations to investigate the impact of parameter uncertainty on decision making. We present an innovative approach of a dynamic Markov model with Bayesian inference. We extend a static Markov model by directly incorporating the force of infection of the pathogen into the health state allocation algorithm, accounting for the effects of herd immunity. As a consequence, the output of our fully probabilistic Bayesian Markov model is based on dynamic interactions between individuals, and at the same time eligible to conduct probabilistic sensitivity analysis straightforwardly. We introduce a case study of a fictional chronic sexually transmitted infection. By means of this constructed example, we show that our methodology produces results which are comparable to a Bayesian ODE system, yet at lower cost of implementation and computation. In contrast to probabilistic methodology, deterministic models tend to underestimate disease prevalence and thus the benefits of vaccination

The GNAT library for local and remote gene mention normalization

Summary: Identifying mentions of named entities, such as genes or diseases, and normalizing them to database identifiers have become an important step in many text and data mining pipelines. Despite this need, very few entity normalization systems are publicly available as source code or web services for biomedical text mining. Here we present the Gnat Java library for text retrieval, named entity recognition, and normalization of gene and protein mentions in biomedical text. The library can be used as a component to be integrated with other text-mining systems, as a framework to add user-specific extensions, and as an efficient stand-alone application for the identification of gene and protein names for data analysis. On the BioCreative III test data, the current version of Gnat achieves a Tap-20 score of 0.1987

Social Studies Preservice Teachers’ Citizenship Knowledge and Perceptions of the U.S. Naturalization Test

Teacher educators from six states invited their social studies methodology students to complete an abbreviated version of the U.S. Citizenship and Immigration Services (USCIS) Naturalization Test. The preservice teachers were also asked to share their conceptions of citizenship and evaluate the naturalization test. The findings from this study indicated that although this sample of preservice teachers had limited conceptions of citizenship, most were able to get a satisfactory score on the test. The authors discuss the implications of these results and suggest ways to broaden citizenship education in teacher preparation programs

Evidence for a correlation between the sizes of quiescent galaxies and local environment to z ~ 2

We present evidence for a strong relationship between galaxy size and environment for the quiescent population in the redshift range 1 < z < 2. Environments were measured using projected galaxy overdensities on a scale of 400 kpc, as determined from ~ 96,000 K-band selected galaxies from the UKIDSS Ultra Deep Survey (UDS). Sizes were determined from ground-based K-band imaging, calibrated using space-based CANDELS HST observations in the centre of the UDS field, with photometric redshifts and stellar masses derived from 11-band photometric fitting. From the resulting size-mass relation, we confirm that quiescent galaxies at a given stellar mass were typically ~ 50 % smaller at z ~ 1.4 compared to the present day. At a given epoch, however, we find that passive galaxies in denser environments are on average significantly larger at a given stellar mass. The most massive quiescent galaxies (M_stellar > 2 x 10^11 M_sun) at z > 1 are typically 50 % larger in the highest density environments compared to those in the lowest density environments. Using Monte Carlo simulations, we reject the null hypothesis that the size-mass relation is independent of environment at a significance > 4.8 sigma for the redshift range 1 < z < 2. In contrast, the evidence for a relationship between size and environment is much weaker for star-forming galaxies.Comment: Accepted for publication in MNRAS. 16 pages, 11 figures, 6 table

Cluster Performance reconsidered: Structure, Linkages and Paths in the German Biotechnology Industry, 1996-2003

This paper addresses the evolution of biotechnology clusters in Germany between 1996 and 2003, paying particular attention to their respective composition in terms of venture capital, basic science institutions and biotechnology firms. Drawing upon the significance of co-location of "money and ideas", the literature stressing the importance of a cluster's openness and external linkages, and the path dependency debate, the paper aims to analyse how certain cluster characteristics correspond with its overall performance. After identifying different cluster types, we investigate their internal and external interconnectivity in comparative manner and draw on changes in cluster composition. Our results indicate that the structure, i.e. to which group the cluster belongs, and the openness towards external knowledge flows deliver merely unsystematic indications with regard to a cluster's overall success. Its ability to change composition towards a more balanced ratio of science and capital over time, on the other hand, turns out as a key explanatory factor. Hence, the dynamic perspective proves effective illuminating cluster growth and performance, where our explorative findings provide a promising avenue for further evolutionary research

Supernova rates from the SUDARE VST-Omegacam search II. Rates in a galaxy sample

This is the second paper of a series in which we present measurements of the Supernova (SN) rates from the SUDARE survey. In this paper, we study the trend of the SN rates with the intrinsic colours, the star formation activity and the mass of the parent galaxies. We have considered a sample of about 130000 galaxies and a SN sample of about 50 events. We found that the SN Ia rate per unit mass is higher by a factor of six in the star-forming galaxies with respect to the passive galaxies. The SN Ia rate per unit mass is also higher in the less massive galaxies that are also younger. These results suggest a distribution of the delay times (DTD) less populated at long delay times than at short delays. The CC SN rate per unit mass is proportional to both the sSFR and the galaxy mass. The trends of the Type Ia and CC SN rates as a function of the sSFR and the galaxy mass that we observed from SUDARE data are in agreement with literature results at different redshifts. The expected number of SNe Ia is in agreement with the observed one for all four DTD models considered both in passive and star-forming galaxies so we can not discriminate between different progenitor scenarios. The expected number of CC SNe is higher than the observed one, suggesting a higher limit for the minimum progenitor mass. We also compare the expected and observed trends of the SN Ia rate with the intrinsic U - J colour of the parent galaxy, assumed as a tracer of the age distribution. While the slope of the relation between the SN Ia rate and the U - J color in star-forming galaxies can be reproduced well by all four DTD models considered, only the steepest of them is able to account for the rates and colour in star-forming and passive galaxies with the same value of the SN Ia production efficiency.Comment: A& A accepte

Translational web robots for pathogen genome analysis

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pubmed2ensembl: A Resource for Mining the Biological Literature on Genes

The last two decades have witnessed a dramatic acceleration in the production of genomic sequence information and publication of biomedical articles. Despite the fact that genome sequence data and publications are two of the most heavily relied-upon sources of information for many biologists, very little effort has been made to systematically integrate data from genomic sequences directly with the biological literature. For a limited number of model organisms dedicated teams manually curate publications about genes; however for species with no such dedicated staff many thousands of articles are never mapped to genes or genomic regions.To overcome the lack of integration between genomic data and biological literature, we have developed pubmed2ensembl (http://www.pubmed2ensembl.org), an extension to the BioMart system that links over 2,000,000 articles in PubMed to nearly 150,000 genes in Ensembl from 50 species. We use several sources of curated (e.g., Entrez Gene) and automatically generated (e.g., gene names extracted through text-mining on MEDLINE records) sources of gene-publication links, allowing users to filter and combine different data sources to suit their individual needs for information extraction and biological discovery. In addition to extending the Ensembl BioMart database to include published information on genes, we also implemented a scripting language for automated BioMart construction and a novel BioMart interface that allows text-based queries to be performed against PubMed and PubMed Central documents in conjunction with constraints on genomic features. Finally, we illustrate the potential of pubmed2ensembl through typical use cases that involve integrated queries across the biomedical literature and genomic data.By allowing biologists to find the relevant literature on specific genomic regions or sets of functionally related genes more easily, pubmed2ensembl offers a much-needed genome informatics inspired solution to accessing the ever-increasing biomedical literature