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  • Many ecological questions require information on species' optimal conditions or critical limits along environmental gradients. These attributes can be compared to answer questions on niche partitioning, species coexistence and niche conservatism. However, these comparisons are unconvincing when existing methods do not quantify the uncertainty in the attributes or rely on assumptions about the shape of species' responses to the environmental gradient. The aim of this study was to develop a model to quantify the uncertainty in the attributes of species response curves and allow them to be tested for substantive differences without making assumptions about the shape of the responses. We developed a model that used Bayesian penalised splines to produce and compare response curves for any two given species. These splines allow the data to determine the shape of the response curves rather than making a priori assumptions. The models were implemented using the R2OpenBUGS package for R, which uses Markov Chain Monte Carlo simulation to repetitively fit alternative response curves to the data. As each iteration produces a different curve that varies in optima, niche breadth and limits, the model estimates the uncertainty in each of these attributes and the probability that the two curves are different. The models were tested using two datasets of mosses from Antarctica. Both datasets had a high degree of scatter, which is typical of ecological research. This noise resulted in considerable uncertainty in the optima and limits of species response curves, but substantive differences were found. Schistidium antarctici was found to inhabit wetter habitats than Ceratodon purpureus, and Polytrichastrum alpinum had a lower optimal temperature for photosynthesis than Chorisodontium aciphyllum under high light conditions. Our study highlights the importance of considering uncertainty in physiological optima and other attributes of species response curves. We found that apparent differences in optima of 7.5°C were not necessarily substantive when dealing with noisy ecological data, and it is necessary to consider the uncertainty in attributes when comparing the curves for different species. The model introduced here could increase the robustness of research on niche partitioning, species coexistence and niche conservatism.
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  • Experimental capabilities of molecular spectroscopy and its applications nowadays require a sub-percent or even sub-per mille accuracy of the representation of the shapes of molecular transitions. This implies the necessity of using more advanced line-shape models which are characterized by many more parameters than a simple Voigt profile. It is a great challenge for modern molecular spectral databases to store and maintain the extended set of line-shape parameters as well as their temperature dependences. It is even more challenging to reliably retrieve these parameters from experimental spectra over a large range of pressures and temperatures. In this paper we address this problem starting from the case of the H2 molecule for which the non-Voigt line-shape effects are exceptionally pronounced. For this purpose we reanalyzed the experimental data reported in the literature. In particular, we performed detailed line-shape analysis of high-quality spectra obtained with cavity-enhanced techniques. We also report the first high-quality cavity-enhanced measurement of the H2 fundamental vibrational mode. We develop a correction to the Hartmann–Tran profile (HTP) which adjusts the HTP to the particular model of the velocity-changing collisions. This allows the measured spectra to be better represented over a wide range of pressures. The problem of storing the HTP parameters in the HITRAN database together with their temperature dependences is also discussed.
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  • The atomistic pathways of deformation twinning can be computed ab initio, and quantified by two variables: strain which describes shape change of a periodic supercell, and shuffling which describes non-affine displacements of the internal degrees of freedom. The minimum energy path involves juxta-position of both. But if one can obtain the same saddle point by continuously increasing the strain and relaxing the internal degrees of freedom by steepest descent, we call the path strain-controlled, and vice versa. Surprisingly, we find the {101¯2}〈101¯1¯〉 twinning of Mg is shuffling-controlled at the smallest lengthscale of the irreducible lattice correspondence pattern, that is, the reaction coordinate at the level of 4 atoms is dominated by non-affine displacements, instead of strain. Shuffling-controlled deformation twinning is expected to have different temperature and strain-rate sensitivities from strain-controlled deformation twinning due to relatively weaker strength of long-range elastic interactions, in particular at the twin nucleation stage. As the twin grows large enough, however, elastic interactions and displacive character of the transformation should always turn dominant.
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  • How to calibrate the parameters of car-following models based on observed traffic data is a vital problem in traffic simulation. Usually, the core of calibration is cast into an optimization problem, in which the decision variables are car-following model parameters and the objective function usually characterizes the difference between empirical vehicle movements and their simulated correspondences. Since the objective function is usually nonlinear and non-convex, various greedy or stochastic algorithms had been proposed during the last two decades. However, the performance of these algorithms remains to be further examined. In this paper, we revisit this important problem with a special focus on the geometric feature of the objective function. First, we prove that, from a global perspective, most existing objective functions are Lipschitz continuous. Second, we show that, from a local perspective, many of these objective functions are relatively flat around the global optimal solution. Based on these two features, we propose a new global optimization algorithm that integrates global direct search and local gradient search to find the optimal solution in an efficient manner. We compare this new algorithm with several existing algorithms, including Nelder–Mead (NM) algorithm, sequential quadratic programming (SQP) algorithm, genetic algorithm (GA), and simultaneous perturbation stochastic approximation (SPSA) algorithm, on NGSIM trajectory datasets. Results demonstrate that the proposed algorithm has a fast convergence speed and a high probability of finding the global optimal solution. Moreover, it has only two major configuration parameters that can be easily determined in practice.
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  • Pachycephalosaurs, a group of ornithischian dinosaurs with distinctive cranial ornamentation and skull domes, underwent dramatic changes in cranial morphology during ontogeny. This has caused debate about whether some specimens belong to juveniles or adults, which impacts studies of pachycephalosaur phylogeny and evolution. One such debate concerns a small skull roof specimen from the Campanian (Upper Cretaceous) of New Mexico, NMMNH P-33898, which was originally described as an indeterminate juvenile but later regarded as a mature adult and erected as the holotype of a new small-bodied species, Stegoceras novomexicanum. We restudied NMMNH P-33898 using computed tomography scanning, morphometric and phylogenetic analyses, and comparisons to growth series of other pachycephalosaurs (Stegoceras validum, Pachycephalosaurus wyomingensis). We conclude that two purported paratype specimens of Stegoceras novomexicanum cannot be referred to the same taxon as the holotype, that the holotype and controversial paratypes all belong to immature specimens and not aberrant small-bodied adults, but that current evidence cannot clearly determine whether NMMNH P-33898 is a juvenile belonging to its own diagnostic species (S. novomexicanum) or is a juvenile of Stegoceras validum, Sphaerotholus goodwini, or another known taxon. We review the pachycephalosaur record of New Mexico and demonstrate that pachycephalosaurs were important components of dinosaur faunas in the southern part of Western North America during the ∼15 million years before the end-Cretaceous extinction, just as they were in roughly contemporaneous northern localities.
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  • High resolution (0.011cm–1) room temperature (295K) Fourier transform absorption spectra (FTS) of acetylene have been analyzed in the 8280–8700cm−1 range dominated by the ν1+ν2+ν3 band at 8512cm−1. Line positions and intensities were retrieved from FTS spectra recorded at 3.84 and 56.6hPa. As a result, a list of 1001 lines was constructed with intensities ranging between about 2×10−26 and 10−22cm/molecule. Comparison with accurate predictions provided by a global effective operator model led to the assignment of 629 12C2H2 lines. In addition, 114 lines of the 13C12CH2 isotopologue were assigned using information available in the literature. The 12C2H2 lines belong to thirteen bands, nine of which being newly reported. The 13C12CH2 lines belong to three bands, the intensities of which being reported for the first time. Spectroscopic parameters of the 12C2H2 upper vibrational levels were derived from band-by-band analyses of the line positions (typical rms are on the order of 0.002cm−1). Three of the analyzed bands were found to be affected by rovibrational perturbations, which are discussed in the frame of a global effective Hamiltonian. The obtained line parameters are compared with those of the two bands included in the HITRAN 2012 database.
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  • Current taxonomic treatments of New Zealand and temperate Australian members of the gastropod subfamily Cantharidinae imply that species on either side of the Tasman Sea are closely related and, in some cases, congeneric. Such a close relationship, however, entails a relatively recent divergence of Australian and New Zealand lineages, which seems inconsistent with what is known about cantharidine larval development in general. In order to address these issues, mitochondrial and nuclear DNA sequences were used to ascertain how cantharidine genera became established over the wide geographical range of temperate Australia and New Zealand, including their subantarctic islands. Our robust and dated phylogenies (based on 16S, COI, 12S and 28S sequences) revealed that Australian and New Zealand species fall into endemic clades that have been separated for, at most, 35million years. This divergence date postdates a vicariant split by around 50million years and we suggest that, once again, long-distance trans-Tasman dispersal has played a pivotal role in molluscan evolution in this part of the world. Our results also show that the current classification requires revision. We recognize three genera (Cantharidus [comprising 2 subgenera: Cantharidus s.str. and Pseudomargarella n. subgen.], Micrelenchus [comprising 2 subgenera: Micrelenchus s.str. and Mawhero] and Roseaplagis n. gen.) for New Zealand cantharidine species. In our dated BEAST tree, these genera form a clade with the endemic Australian Prothalotia and South African Oxystele. Other temperate Australian cantharidines in our study fall into previously recognized genera (Phasianotrochus, Thalotia, Calthalotia), which are all quite distinct from Cantharidus in spite of some authors considering various of them to be possible synonyms. Finally, we remove the Australian genus Cantharidella from the Cantharidinae to the subfamily Trochinae and erect a new genus, Cratidentium n. gen., also in the Trochinae, to accommodate several Australian species previously considered to belong to Cantharidella.
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  • Using density functional theory (DFT) and Monte Carlo (MC) simulations, we studied the surface segregation phenomena of Au atoms in the extended and nanoparticle surfaces of Cu–Au alloys. Our MC simulations predicted significant Au enrichment in the outermost layer of (111) and (100) extended surfaces, and Au enrichment in the two outermost layers of (110) extended surfaces. The equilibrium Cu–Au nanoparticles were predicted to develop into an Au-enriched shell structure, where Au atoms preferably segregate to the (100) facets while Cu atoms are mainly located on the (111) facet of the nanoparticles. Our simulation predictions agree with experimental measurements.
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  • Structure-reactivity relationships of Amadori rearrangement products compared to their related ketoses were derived from multiple NMR spectroscopic techniques. Besides structure elucidation of six Amadori rearrangement products derived from d-glucose and d-galactose with l-alanine, l-phenylalanine and l-proline, especially quantitative 13C selective saturation transfer NMR spectroscopy was applied to deduce information on isomeric systems. It could be shown exemplarily that the Amadori compound N-(1-deoxy-d-fructos-1-yl)-l-proline exhibits much higher isomerisation rates than d-fructose, which can be explained by C-1 substituent mediated intramolecular catalysis. In combination with a reduced carbonyl activity of Amadori compounds compared to their related ketoses which results in an increased acyclic keto isomer concentration, the results on isomerisation dynamics lead to a highly significant increased reactivity of Amadori compounds. This can be clearly seen, comparing approximated carbohydrate milieu stability time constants (ACuSTiC) which is 1 s for N-(1-deoxy-d-fructos-1-yl)-l-proline and 10 s for d-fructose at pD 4.20 ± 0.05 at 350 K. In addition, first NMR spectroscopic data are provided, which prove that α-pyranose of (amino acid substituted) d-fructose adopts both, 2C5 and 5C2 conformation.
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  • Due to the growth in demand for shallow geothermal energy, the development of an integrated management system to organize the exploitation of this resource is mandatory to protect both groundwater and the users’ rights. This paper proposes a methodology to establish a market of shallow geothermal energy use rights which will represent an advance in the management of this resource. The new concept developed to define the basic unit of management is the thermal plot. It is related to the shallow geothermal potential of a registered plot of land. This methodology is based on a GIS framework (ArcGIS, ESRI) and is composed of a geospatial database (Personal Geodatabase, ESRI) to store the main information required to manage the SGE systems, such as groundwater velocity, thermal conductivity or thermal heat capacity, and a set of GIS tools used to define, implement and control this use rights market. The exchanged heat rate and thermal disturbance are calculated on the basis of analytical solutions of heat transport equation in porous media. Thermal impacts derived from the exploitation of this resource can also be registered geographically, by taking into account the groundwater flow direction and adjusting the thermal impact to the available plot. A synthetic application of this methodology is presented for the Metropolitan Area of Barcelona, Spain.
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