1,274 research outputs found

    TLS2trees: A scalable tree segmentation pipeline for TLS data

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    1. Above-ground biomass (AGB) is an important metric used to quantify the mass of carbon stored in terrestrial ecosystems. For forests, this is routinely estimated at the plot scale (typically 1 ha) using inventory measurements and allometry. In recent years, terrestrial laser scanning (TLS) has appeared as a disruptive technology that can generate a more accurate assessment of tree and plot scale AGB; however, operationalising TLS methods has had to overcome a number of challenges. One such challenge is the segmentation of individual trees from plot level point clouds that are required to estimate woody volume, this is often done manually (e.g. with interactive point cloud editing software) and can be very time consuming. / 2. Here we present TLS2trees, an automated processing pipeline and set of Python command line tools that aims to redress this processing bottleneck. TLS2trees consists of existing and new methods and is specifically designed to be horizontally scalable. The processing pipeline is demonstrated on 7.5 ha of TLS data captured across 10 plots of seven forest types; from open savanna to dense tropical rainforest. / 3. A total of 10,557 trees are segmented with TLS2trees: these are compared to 1281 manually segmented trees. Results indicate that TLS2trees performs well, particularly for larger trees (i.e. the cohort of largest trees that comprise 50% of total plot volume), where plot-wise tree volume bias is ±0.4 m3 and %RMSE is 60%. Segmentation performance decreases for smaller trees, for example where DBH ≤10 cm; a number of reasons are suggested including performance of semantic segmentation step. / 4. The volume and scale of TLS data captured in forest plots is increasing. It is suggested that to fully utilise this data for activities such as monitoring, reporting and verification or as reference data for satellite missions an automated processing pipeline, such as TLS2trees, is required. To facilitate improvements to TLS2trees, as well as modification for other laser scanning modes (e.g. mobile and UAV laser scanning), TLS2trees is a free and open-source software

    Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor.

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    BACKGROUND: The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed. RESULTS: Focusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species' genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n=80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes. CONCLUSIONS: Results suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g., in ostrich and budgerigar lineages). Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor.The authors would like to thank Alain Vignal and Thomas Faraut of INRA Toulouse (France) for access to the duck chromosome assembly data. This research was funded in part by PL-Grid Infrastructure (DML), Biotechnology and Biological Sciences Research Council BB/K008161 (DML, DKG), BB/K008226/1 (DML), BB/J010170/1 (DML, MF) and a knowledge transfer partnership award (DKG and Cytocell Ltd). The authors are grateful to Malcolm Ferguson-Smith’s lab (Cambridge, UK) for producing the flow-sorted chicken microchromosome paints. We also thank Cytocell Ltd (Cambridge, UK) for technical support in FISH technologies.This article was originally published in BMC Genomics 2014, 15:1060 doi:10.1186/1471-2164-15-106

    Two warm, low-density sub-Jovian planets orbiting bright stars in K2 campaigns 13 and 14

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    We report the discovery of two planets transiting the bright stars HD 89345 (EPIC 248777106, V=9.376V=9.376, K=7.721K=7.721) in K2 Campaign 14 and HD 286123 (EPIC 247098361, V=9.822V=9.822, K=8.434K=8.434) in K2 Campaign 13. Both stars are G-type stars, one of which is at or near the end of its main sequence lifetime, and the other that is just over halfway through its main sequence lifetime. HD 89345 hosts a warm sub-Saturn (0.66 RJR_J, 0.11 MJM_J, Teq=1100T_\mathrm{eq}=1100 K) in an 11.81-day orbit. The planet is similar in size to WASP-107b, which falls in the transition region between ice giants and gas giants. HD 286123 hosts a Jupiter-sized, low-mass planet (1.06 RJR_J, 0.39 MJM_J, Teq=1000T_\mathrm{eq}=1000 K) in an 11.17-day, mildly eccentric orbit, with e=0.255±0.035e=0.255\pm0.035. Given that they orbit relatively evolved main-sequence stars and have orbital periods longer than 10 days, these planets are interesting candidates for studies of gas planet evolution, migration, and (potentially) re-inflation. Both planets have spent their entire lifetimes near the proposed stellar irradiation threshold at which giant planets become inflated, and neither shows any sign of radius inflation. They probe the regime where inflation begins to become noticeable and are valuable in constraining planet inflation models. In addition, the brightness of the host stars, combined with large atmospheric scale heights of the planets, makes these two systems favorable targets for transit spectroscopy to study their atmospheres and perhaps provide insight into the physical mechanisms that lead to inflated hot Jupiters.Comment: 16 pages, 12 figures; accepted for publication in A

    TESS delivers its first Earth-sized planet and a warm sub-Neptune

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    The future of exoplanet science is bright, as TESS once again demonstrates with the discovery of its longest-period confirmed planet to date. We hereby present HD 21749b (TOI 186.01), a sub-Neptune in a 36-day orbit around a bright (V = 8.1) nearby (16 pc) K4.5 dwarf. TESS measures HD21749b to be 2.610.16+0.17^{+0.17}_{-0.16} RR_{\oplus}, and combined archival and follow-up precision radial velocity data put the mass of the planet at 22.71.9+2.222.7^{+2.2}_{-1.9} MM_{\oplus}. HD 21749b contributes to the TESS Level 1 Science Requirement of providing 50 transiting planets smaller than 4 RR_{\oplus} with measured masses. Furthermore, we report the discovery of HD 21749c (TOI 186.02), the first Earth-sized (Rp=0.8920.058+0.064RR_p = 0.892^{+0.064}_{-0.058} R_{\oplus}) planet from TESS. The HD21749 system is a prime target for comparative studies of planetary composition and architecture in multi-planet systems.Comment: Published in ApJ Letters; 5 figures, 1 tabl

    Physical Parameters of the Multiplanet Systems HD 106315 and GJ 9827

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    HD 106315 and GJ 9827 are two bright, nearby stars that host multiple super-Earths and sub-Neptunes discovered by K2 that are well suited for atmospheric characterization. We refined the planets' ephemerides through Spitzer transits, enabling accurate transit prediction required for future atmospheric characterization through transmission spectroscopy. Through a multiyear high-cadence observing campaign with Keck/High Resolution Echelle Spectrometer and Magellan/Planet Finder Spectrograph, we improved the planets' mass measurements in anticipation of Hubble Space Telescope transmission spectroscopy. For GJ 9827, we modeled activity-induced radial velocity signals with a Gaussian process informed by the Calcium II H&K lines in order to more accurately model the effect of stellar noise on our data. We measured planet masses of M_b = 4.87 ± 0.37 M_⊕, M_c = 1.92 ± 0.49 M_⊕, and M_d = 3.42 ± 0.62 M_⊕. For HD 106315, we found that such activity radial velocity decorrelation was not effective due to the reduced presence of spots and speculate that this may extend to other hot stars as well (T_(eff) > 6200 K). We measured planet masses of M_b = 10.5 ± 3.1 M_⊕ and M_c = 12.0 ± 3.8 M_⊕. We investigated all of the planets' compositions through comparison of their masses and radii to a range of interior models. GJ 9827 b and GJ 9827 c are both consistent with a 50/50 rock-iron composition, GJ 9827 d and HD 106315 b both require additional volatiles and are consistent with moderate amounts of water or hydrogen/helium, and HD 106315 c is consistent with a ~10% hydrogen/helium envelope surrounding an Earth-like rock and iron core

    Physical Parameters of the Multiplanet Systems HD 106315 and GJ 9827

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    HD 106315 and GJ 9827 are two bright, nearby stars that host multiple super-Earths and sub-Neptunes discovered by K2 that are well suited for atmospheric characterization. We refined the planets' ephemerides through Spitzer transits, enabling accurate transit prediction required for future atmospheric characterization through transmission spectroscopy. Through a multiyear high-cadence observing campaign with Keck/High Resolution Echelle Spectrometer and Magellan/Planet Finder Spectrograph, we improved the planets' mass measurements in anticipation of Hubble Space Telescope transmission spectroscopy. For GJ 9827, we modeled activity-induced radial velocity signals with a Gaussian process informed by the Calcium II H&K lines in order to more accurately model the effect of stellar noise on our data. We measured planet masses of M_b = 4.87 ± 0.37 M_⊕, M_c = 1.92 ± 0.49 M_⊕, and M_d = 3.42 ± 0.62 M_⊕. For HD 106315, we found that such activity radial velocity decorrelation was not effective due to the reduced presence of spots and speculate that this may extend to other hot stars as well (T_(eff) > 6200 K). We measured planet masses of M_b = 10.5 ± 3.1 M_⊕ and M_c = 12.0 ± 3.8 M_⊕. We investigated all of the planets' compositions through comparison of their masses and radii to a range of interior models. GJ 9827 b and GJ 9827 c are both consistent with a 50/50 rock-iron composition, GJ 9827 d and HD 106315 b both require additional volatiles and are consistent with moderate amounts of water or hydrogen/helium, and HD 106315 c is consistent with a ~10% hydrogen/helium envelope surrounding an Earth-like rock and iron core

    High-Power Test of Two Prototype X-band Accelerating Structures Based on SwissFEL Fabrication Technology

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    This article presents the design, construction, and high-power test of two XX-band radio frequency (RF) accelerating structures built as part of a collaboration between CERN and the Paul Scherrer Institute (PSI) for the compact linear collider (CLIC) study. The structures are a modified 'tuning-free' variant of an existing CERN design and were assembled using Swiss free electron laser (SwissFEL) production methods. The purpose of the study is two-fold. The first objective is to validate the RF properties and high-power performance of the tuning-free, vacuum brazed PSI technology. The second objective is to study the structures' high-gradient behavior to provide insight into the breakdown and conditioning phenomena as they apply to high-field devices in general. Low-power RF measurements showed that the structure field profiles were close to the design values, and both structures were conditioned to accelerating gradients in excess of 100 MV/m in CERN's high-gradient test facility. Measurements performed during the second structure test suggest that the breakdown rate (BDR) scales strongly with the accelerating gradient, with the best fit being a power law relation with an exponent of 31.14. In both cases, the test results indicate that stable, high-gradient operation is possible with tuning-free, vacuum brazed structures of this kind

    <i>TESS</i> Spots a Compact System of Super-Earths around the Naked-eye Star HR 858

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    Transiting Exoplanet Survey Satellite (TESS) observations have revealed a compact multiplanet system around the sixth-magnitude star HR 858 (TIC 178155732, TOI 396), located 32 pc away. Three planets, each about twice the size of Earth, transit this slightly evolved, late F-type star, which is also a member of a visual binary. Two of the planets may be in mean motion resonance. We analyze the TESS observations, using novel methods to model and remove instrumental systematic errors, and combine these data with follow-up observations taken from a suite of ground-based telescopes to characterize the planetary system. The HR 858 planets are enticing targets for precise radial velocity observations, secondary eclipse spectroscopy, and measurements of the Rossiter–McLaughlin effect
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