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Severe plastic deformation has made it possible to alter the grain size of metal surface to nanoscale. With refined nanograins, the grain boundary effect on diffusion and phase transformation cannot be neglected. Consequently, the widely used conventional 1D nitriding model is not applicable. In this study, a 2D model considering grain boundary diffusion has been developed to investigate nanocrystalline nitriding. As a multi-physical process, both phase transition and diffusion are modeled. Cellular automata method was used to integrate the two models, and more importantly to deal with the moving 2D interface induced by grain boundaries. The phase transition model and diffusion model were validated with experimental data and the Maxwell–Garnett effective diffusion model, respectively. After validation, nitriding of nanocrystalline iron at low temperature (300°C) was simulated and compared with nitriding of coarse-grained (μm level) iron. In addition, the growth kinetic, composition and spatial distribution of the nitride layer in nanocrystalline nitriding, with different temperatures, surface nitrogen concentrations and different grain sizes, were studied. It has been found that these parameters could significantly affect the growth rate as well as the composition of the nitrided layers. The results also demonstrated that the presence of nanoscale grain can not only decrease nitriding temperature and nitriding duration making low temperature nitriding possible, but also increase the volume fraction of ∊ and γ′ phases in the nitride layer and therefore a better nitriding quality.
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The kinetics of permeation across epithelial and endothelial cell sheets and across cell membranes is determinant for the pharmacokinetics of a drug. In vitro transport experiments with cultured cells or artificial barriers have tremendously improved the predictability of the in vivo behaviour of tested compounds. This article focuses on the parameters and calculation methods that are used to describe permeation quantitatively, with a focus on in vitro experiments and the prediction of intestinal absorption and blood–brain barrier passage. It shows under which in vitro experimental conditions standard calculations are adequate and under which conditions equations should be adapted to the experimental details. The impact of volume differences between donor and receiver compartments, pH gradients, addition of albumin, accumulation in the barrier and unidirectional transport by an efflux transporter on the results is shown in simulations. The article should make researchers aware of experimental factors that affect the outcome of a permeation experiment and how to account for this during data analysis. Finally, strategies to predict the in vivo behaviour of a compound based on the in vitro data are discussed. The goal of the article is to support researchers in choosing experimental conditions and calculation methods that deliver appropriate and reproducible results in permeation studies in vitro.
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Wind-blown dunes are a record of the climatic history in Titan’s equatorial region. Through modeling of the climatic conditions associated with Titan’s historical orbital configurations (arising from apsidal precessions of Saturn’s orbit), we present evidence that the orientations of the dunes are influenced by orbital forcing. Analysis of 3 Titan general circulation models (GCMs) in conjunction with a sediment transport model provides the first direct intercomparison of results from different Titan GCMs. We report variability in the dune orientations predicted for different orbital epochs of up to 70°. Although the response of the GCMs to orbital forcing varies, the orbital influence on the dune orientations is found to be significant across all models. Furthermore, there is near agreement among the two models run with surface topography, with 3 out of the 5 dune fields matching observation for the most recent orbital cycle. Through comparison with observations by Cassini, we find situations in which the observed dune orientations are in best agreement with those modeled for previous orbital configurations or combinations thereof, representing a larger portion of the cycle. We conclude that orbital forcing could be an important factor in governing the present-day dune orientations observed on Titan and should be considered when modeling dune evolution.
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Random domino tilings of the Aztec diamond shape exhibit interesting features and some of the statistical properties seen in random matrix theory. As a statistical mechanical model it can be thought of as a dimer model or as a certain random surface. We consider the Aztec diamond with a two-periodic weighting which exhibits all three possible phases that occur in these types of models, often referred to as solid, liquid and gas. To analyze this model, we use entries of the inverse Kasteleyn matrix which give the probability of any configuration of dominoes. A formula for these entries, for this particular model, was derived by Chhita and Young (2014). In this paper, we find a major simplification of this formula expressing entries of the inverse Kasteleyn matrix by double contour integrals which makes it possible to investigate their asymptotics. In a part of the Aztec diamond, where the asymptotic analysis is simpler, we use this formula to show that the entries of the inverse Kasteleyn matrix converge to the known entries of the full-plane inverse Kasteleyn matrices for the different phases. We also study the detailed asymptotics of the inverse Kasteleyn matrix at both the ‘liquid–solid’ and ‘liquid–gas’ boundaries, and find the extended Airy kernel in the next order asymptotics. Finally we provide a potential candidate for a combinatorial description of the liquid–gas boundary.
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Chloroplast sequence data are widely used to infer phylogenies of plants and algae. With the increasing availability of complete chloroplast genome sequences, the opportunity arises to resolve ancient divergences that were heretofore problematic. On the flip side, properly analyzing large multi-gene data sets can be a major challenge, as these data may be riddled with systematic biases and conflicting signals. Our study contributes new data from nine complete and four fragmentary chloroplast genome sequences across the green algal order Sphaeropleales. Our phylogenetic analyses of a 56-gene data set show that analyzing these data on a nucleotide level yields a well-supported phylogeny – yet one that is quite different from a corresponding amino acid analysis. We offer some possible explanations for this conflict through a range of analyses of modified data sets. In addition, we characterize the newly sequenced genomes in terms of their structure and content, thereby further contributing to the knowledge of chloroplast genome evolution.
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Nutrient and pesticide pollution are widespread agricultural stressors. Fungicides may affect freshwater fungi, which play an important role in litter decomposition (LD), whereas moderate nutrient enrichment can stimulate LD. We examined potential interaction effects of nutrients and fungicides on decomposer communities and LD in a 14-day two-factorial (fungicide and nutrient treatments) mesocosm experiment. Fungicide exposure was limited to 4days to simulate episodic contamination. Only the microbial community responded significantly to the experimental factors, though non-significant increases >20% were found for invertebrate decomposer weight gain and LD under high-nutrient conditions. Fungal community structure responded more strongly to fungicides than sporulation. Sporulation responded strongest to nutrients. Bacterial community structure was affected by both factors, although only nutrients influenced bacterial density. Our results suggest effects from fungicides at field-relevant levels on the microbial community. Whether these changes propagate to invertebrate communities and LD remains unclear and should be analysed under longer and recurrent fungicide exposure.
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Pogostemon (Lamiaceae; Lamioideae) sensu lato is a large genus consisting of about 80 species with a disjunct African/Asian distribution. The infrageneric taxonomy of the genus has historically been troublesome due to morphological variability and putative convergent evolution within the genus. Notably, some species of Pogostemon are obligately aquatic, perhaps the only Lamiaceae taxa which exhibit this trait. Phylogenetic analyses using the nuclear ribosomal internal transcribed spacer (ITS) and five plastid regions (matK, rbcL, rps16, trnH-psbA, trnL-F), confirmed the monophyly of Pogostemon and its sister relationship with the genus Anisomeles. Pogostemon was resolved into two major clades, and none of the three morphologically defined subgenera of Pogostemon were supported as monophyletic. Inflorescence type (spikes with more than two lateral branches vs. a single terminal spike, or rarely with two lateral branches) is phylogenetically informative and consistent with the two main clades we recovered. Accordingly, a new infrageneric classification of Pogostemon consisting of two subgenera is proposed. Molecular dating and biogeographic diversification analyses suggest that Pogostemon split from its sister genus in southern and southeast Asia in the early Miocene. The early strengthening of the Asia monsoon system that was triggered by the uplifting of the Qinghai–Tibetan Plateau may have played an important role in the subsequent diversification of the genus. In addition, our results suggest that transoceanic long-distance dispersal of Pogostemon from Asia to Africa occurred at least twice, once in the late Miocene and again during the late-Miocene/early-Pliocene.
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African bovids are a famous example of a taxonomic group in which the correlated evolution of body size, feeding mode, gregariousness, and social organization in relation to the preferred habitat type has been investigated. A continuum has been described ranging from small-bodied, sedentary, solitary or socially monogamous, forest- or bush-dwelling, browsing species that seek shelter from predation in dense vegetation, to large-bodied, migratory, highly gregarious, grazing taxa inhabiting open savannahs and relying on flight or group-defense behaviors when facing predators. Here, we examined a geographically widespread clade within the Bovidae (the genus Gazella) that shows minimal interspecific variation in body size and asked if we could still uncover correlated changes of key ecological and behavioral traits during repeated transitions from open-land to mountain-dwelling. Our study used a multi-locus phylogeny (based on sequence variation of Cytb and six nuclear intron markers) of all extant members of the genus Gazella to infer evolutionary patterns of key ecological and behavioral traits and to estimate ancestral character states using Bayesian inference. At the base of the Gazella-phylogeny, open plains were inferred as the most likely habitat type, and three independent transitions toward mountain-dwelling were uncovered. Those shifts coincided with shifts from migratory to sedentary lifestyles. Character estimation for group size was largely congruent with movement patterns in that species forming large groups tended to be migratory, while small group size was correlated with a sedentary lifestyle. Evolutionary patterns of two other conspicuous traits (twinning ability vs. exclusive singleton births and hornless vs. horned females) did not follow this trend in the Gazella-phylogeny. Furthermore, we inferred the genus Gazella to have emerged in the Late Miocene to Pliocene (10–3Mya), and estimating ancestral ranges based on a Dispersal–Extinction–Cladogenesis model found the Middle East to be the most likely origin of the genus.
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In this paper, we introduce a new procedure for the estimation in the nonlinear functional regression model where the explanatory variable takes values in an abstract function space and the residual process is autocorrelated. Moreover, we consider the case where the response variable takes its values in Rd. The procedure consists in a pre-whitening transformation of the dependent variable based on the estimated autocorrelation. We establish both consistency and asymptotic normality of the regression function estimate. For kernel methods encountered in the literature, the correlation structure is commonly ignored (the so-called “working independence estimator”); we show here that there is a strong benefit in taking into account the autocorrelation in the error process. We also find that the improvement in efficiency can be large in our functional setting, up to 25% in the presence of high autocorrelation levels. We observe that the additional step of iterating the fitting process actually deteriorates the estimation. We illustrate the skills of the methods on simulations as well as on application on ozone levels over the US.
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The pleurocarpous mosses (i.e., Hypnanae) are a species-rich group of land plants comprising about 6,000 species that share the development of female sex organs on short lateral branches, a derived trait within mosses. Many of the families within Hypnales, the largest order of pleurocarpous mosses, trace their origin to a rapid radiation less than 100 million years ago, just after the rise of the angiosperms. As a result, the phylogenetic resolution among families of Hypnales, necessary to test evolutionary hypotheses, has proven difficult using one or few loci. We present the first phylogenetic inference from high-throughput sequence data (transcriptome sequences) for pleurocarpous mosses. To test hypotheses of gene family evolution, we built a species tree of 21 pleurocarpous and six acrocarpous mosses using over one million sites from 659 orthologous genes. We used the species tree to investigate the genomic consequences of the shift to pleurocarpy and to identify whether patterns common to other plant radiations (gene family expansion, whole genome duplication, or changes in the molecular signatures of selection) could be observed. We found that roughly six percent of all gene families have expanded in the pleurocarpous mosses, relative to acrocarpous mosses. These gene families are enriched for several gene ontology (GO) terms, including interaction with other organisms. The increase in copy number coincident with the radiation of Hypnales suggests that a process such as whole genome duplication or a burst of small-scale duplications occurred during the diversification. In over 500 gene families we found evidence of a reduction in purifying selection. These gene families are enriched for several terms in the GO hierarchy related to “tRNA metabolic process.” Our results reveal candidate genes and pathways that may be associated with the transition to pleurocarpy, illustrating the utility of phylotranscriptomics for the study of molecular evolution in non-model species.
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