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Infection with helminthic parasites, including the soil-transmitted helminth Trichuris trichiura (human whipworm), has been shown to modulate host immune responses and, consequently, to have an impact on the development and manifestation of chronic human inflammatory diseases. De novo derivation of helminth proteomes from sequencing of transcriptomes will provide valuable data to aid identification of parasite proteins that could be evaluated as potential immunotherapeutic molecules in near future. Herein, we characterized the transcriptome of the adult stage of the human whipworm T. trichiura, using next-generation sequencing technology and a de novo assembly strategy. Nearly 17.6 million high-quality clean reads were assembled into 6414 contiguous sequences, with an N50 of 1606bp. In total, 5673 protein-encoding sequences were confidentially identified in the T. trichiura adult worm transcriptome; of these, 1013 sequences represent potential newly discovered proteins for the species, most of which presenting orthologs already annotated in the related species T. suis. A number of transcripts representing probable novel non-coding transcripts for the species T. trichiura were also identified. Among the most abundant transcripts, we found sequences that code for proteins involved in lipid transport, such as vitellogenins, and several chitin-binding proteins. Through a cross-species expression analysis of gene orthologs shared by T. trichiura and the closely related parasites T. suis and T. muris it was possible to find twenty-six protein-encoding genes that are consistently highly expressed in the adult stages of the three helminth species. Additionally, twenty transcripts could be identified that code for proteins previously detected by mass spectrometry analysis of protein fractions of the whipworm somatic extract that present immunomodulatory activities. Five of these transcripts were amongst the most highly expressed protein-encoding sequences in the T. trichiura adult worm. Besides, orthologs of proteins demonstrated to have potent immunomodulatory properties in related parasitic helminths were also predicted from the T. trichiura de novo assembled transcriptome.
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Magnesium aluminium hydroxycarbonate hydrotalcites (denoted as MgAl–CO3-HTs) with different Mg/Al molar ratios (4, 3 and 2) were synthesised by the co-precipitation method under low supersaturation conditions, and then treated with sodium dodecylsulfate (SDS) and sodium dodecylbenzenesulfonate (SDBS) surfactants to produce the nanocomposites — organo-hydrotalcites; dodecylsulfate-hydrotalcites(DS-HTs) and dodecylbenzenesulfonate-hydrotalcites (DBS-HTs) through calcination-reconstruction method. Powder X-ray diffraction (PXRD) and infrared spectroscopy analysis of intercalated samples showed that dodecylsulfate and dodecylbenzenesulfonate guests were successfully intercalated into the parent hydrotalcites, with the PXRD revealing that the species could assume varying configurations within the interlayer gallery regions of this clay based materials, displaying monolayer and bilayer orientations.
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Tree stumps left after clear-cutting have replaced naturally formed logs as the most common type of coarse woody debris in managed boreal forests. It is therefore necessary to understand stump importance for the biodiversity of wood-inhabiting organisms, including fungi, and determine their role in hosting species of conservation interest. We analyzed wood from 485 Norway spruce (Picea abies) stumps from 41 clear-cuts at seven localities along a latitudinal gradient from northern to southern Sweden using 454-sequencing. We also collated data about the known ecology of the 86 identified macro-basidiomycetes. In total, 1355 fungal operational taxonomic units were detected, of which 19% were identified down to genus or species level. The most widespread fungi were generalists, such as Leptodontidium elatius, Resinicium bicolor, Fomitopsis pinicola, and Coniophora puteana. Five species of conservation interest were detected, but were not abundant (Kneiffiella curvispora, Metulodontia nivea, Perenniporia subacida, Postia placenta, and Climacocystis borealis). Fungal community composition changed with stump age and along the latitudinal gradient.
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The Central Andean Plateau (15°–27°S) is a high plateau in excess of 3km elevation, associated with thickened crust along the western edge of the South America plate, in the convergent margin between the subducting Nazca plate and the Brazilian craton. We have calculated receiver functions using seismic data from a recent portable deployment of broadband seismometers in the Bolivian orocline (12°–21°S) region and combined them with waveforms from 38 other stations in the region to investigate crustal thickness and crust and mantle structures. Results from the receiver functions provide a more detailed map of crustal thickness than previously existed, and highlight mid-crustal features that match well with prior studies. The active volcanic arc and Altiplano have thick crust with Moho depths increasing from the central Altiplano (65km) to the northern Altiplano (75km). The Eastern Cordillera shows large along strike variations in crustal thickness. Along a densely sampled SW–NE profile through the Bolivian orocline there is a small region of thin crust beneath the high peaks of the Cordillera Real where the average elevations are near 4km, and the Moho depth varies from 55 to 60km, implying the crust is undercompensated by ~5km. In comparison, a broader region of high elevations in the Eastern Cordillera to the southeast near ~20°S has a deeper Moho at ~65–70km and appears close to isostatic equilibrium at the Moho. Assuming the modern-day pattern of high precipitation on the flanks of the Andean plateau existed since the late Miocene, we suggest that climate induced exhumation can explain some of the variations in present day crustal structure across the Bolivian orocline. We also suggest that south of the orocline at ~20°S, the thicker and isostatically compensated crust is due to the absence of erosional exhumation and the occurrence of lithospheric delamination.
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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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