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  • American Association for the Advancement of Science
  • American Institute of Physics (AIP)
  • Blackwell Publishing Ltd
  • Institute of Physics
  • Oxford University Press
  • 2020-2024  (826)
  • 1990-1994
  • 1960-1964
  • 2021  (826)
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  • 1
    Publication Date: 2023-10-26
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2021. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved.
    Description: Relative location of microearthquakes that occurred at Mt Pollino (Italy) from 2011 to 2013 have been analyzed with the aim of a detailed imaging of the geometry of active faults. We identified 27 clusters composed of a number of earthquakes from 9 to 33, with local magnitude in the range 0.6–2.7. The relative location shows that the distribution of hypocentres in each cluster is characterized by extension from few tens of meters to at most 350 m. For each cluster the hypocentre distribution was fitted by a plane to infer the fault orientation, and results were compared with the fault plane solutions corresponding to the focal mechanism of earthquakes of the same cluster. The comparison shows a good agreement in most of the cases. The relative location analysis, generally applied to earthquakes with similar waveform, has been improved to permit also the relative location of earthquakes characterized by not similar signals. To achieve this purpose a modified procedure that overcome the condition of very similar waveforms has been applied to estimate the time delay between first pulses of the master events. The relative location of master events of all clusters shows a precise imaging of the relative position of all analysed sources and allows also to follow with high accuracy the evolution in time of the seismic swarm within the selected periods. The hypocentre position of master events and the nearly parallel fitting planes of any clusters suggest that most of the analyzed earthquakes were produced by different patches of the same fault. The final results depict a main fault plane characterized by NW–SE strike, dip of about 35–45° and depth between 4.5 and 6.5 km b.s.l. Focal mechanisms, used also to evaluate the local stress field, are mostly of normal type with few strike slip solutions for the shallowest events. This result is in good agreement with the local tectonic stress regime that is characterized by predominant NE–SW transtension, as inferred from structural, seismological and geophysical data.
    Description: Published
    Description: 637–648
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: Persistence, memory, correlations, clustering, Spatial analysis, Crustal imaging, Earthquake source observations, Seismicity and tectonics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 2
    Publication Date: 2023-10-31
    Description: Since the Mesozoic, central and eastern European tectonics have been dominated by the closure of the Tethyan Ocean as the African and European plates collided. In the Miocene, the edge of the East European Craton and Moesian Platform were reworked in collision during the Carpathian orogeny and lithospheric extension formed the Pannonian Basin. To investigate the mantle deformation signatures associated with this complex collisional-extensional system, we carry out SKS splitting analysis at 123 broad-band seismic stations in the region. We compare our measurements with estimates of lithospheric thickness and recent seismic tomography models to test for correlation with mantle heterogeneities. Reviewing splitting delay times in light of xenolith measurements of anisotropy yields estimates of anisotropic layer thickness. Fast polarization directions are mostly NW–SE oriented across the seismically slow West Carpathians and Pannonian Basin and are independent of geological boundaries, absolute plate motion direction or an expected palaeo-slab roll-back path. Instead, they are systematically orthogonal to maximum stress directions, implying that the indenting Adria Plate, the leading deformational force in Central Europe, reset the upper-mantle mineral fabric in the past 5 Ma beneath the Pannonian Basin, overprinting the anisotropic signature of earlier tectonic events. Towards the east, fast polarization directions are perpendicular to steep gradients of lithospheric thickness and align along the edges of fast seismic anomalies beneath the Precambrian-aged Moesian Platform in the South Carpathians and the East European Craton, supporting the idea that craton roots exert a strong influence on the surrounding mantle flow. Within the Moesian Platform, SKS measurements become more variable with Fresnel zone arguments indicating a shallow fossil lithospheric source of anisotropy likely caused by older tectonic deformation frozen in the Precambrian. In the Southeast Carpathian corner, in the Vrancea Seismic Zone, a lithospheric fragment that sinks into the mantle is sandwiched between two slow anomalies, but smaller SKS delay times reveal weaker anisotropy occurs mainly to the NW side, consistent with asymmetric upwelling adjacent to a slab, slower mantle velocities and recent volcanism.
    Description: Published
    Description: 2105–2118
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: Seismic anisotropy ; geodynamics ; Seismic anisotropy and geodynamics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
    Publication Date: 2023-11-21
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2021. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved.
    Description: On 24 August 2016 at 01:36 UTC a ML6.0 earthquake struck several villages in central Italy, among which Accumoli, Amatrice and Arquata del Tronto. The earthquake was recorded by about 350 seismic stations, causing 299 fatalities and damage with macroseismic intensities up to 11. The maximum acceleration was observed at Amatrice station (AMT) reaching 916 cm s–2 on E–W component, with epicentral distance of 15 km and Joyner and Boore distance to the fault surface (RJB) of less than a kilometre. Motivated by the high levels of observed ground motion and damage, we generate broad-band seismograms for engineering purposes by adopting a hybrid method. To infer the low frequency seismograms, we considered the kinematic slip model by Tinti et al . The high frequency seismograms were produced using a stochastic finite-fault model approach based on dynamic corner-frequency. Broadband synthetic time-series were therefore obtained by merging the low and high frequency seismograms. Simulated hybrid ground motions were compared both with the observed ground motions and the ground-motion prediction equations (GMPEs), to explore their performance and to retrieve the region-specific parameters endorsed for the simulations. In the near-fault area we observed that hybrid simulations have a higher capability to detect near source effects and to reproduce the source complexity than the use of GMPEs. Indeed, the general good consistency found between synthetic and observed ground motion (both in the time and frequency domain), suggests that the use of regional-specific source scaling and attenuation parameters together with the source complexity in hybrid simulations improves ground motion estimations. To include the site effect in stochastic simulations at selected stations, we tested the use of amplification curves derived from HVRSs (horizontal-to-vertical response spectra) and from HVSRs (horizontal-to-vertical spectral ratios) rather than the use of generic curves according to NTC18 Italian seismic design code. We generally found a further reduction of residuals between observed and simulated both in terms of time histories and spectra.
    Description: Published
    Description: 1753–1779
    Description: 6T. Studi di pericolosità sismica e da maremoto
    Description: JCR Journal
    Keywords: 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
    Publication Date: 2023-11-16
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2020. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved
    Description: This study describes a deep convolutional neural network (CNN) based technique for the prediction of intensity measurements (IMs) of ground shaking. The input data to the CNN model consists of multistation 3C broadband and accelerometric waveforms recorded during the 2016 Central Italy earthquake sequence for M $\ge$ 3.0. We find that the CNN is capable of predicting accurately the IMs at stations far from the epicenter and that have not yet recorded the maximum ground shaking when using a 10 s window starting at the earthquake origin time. The CNN IM predictions do not require previous knowledge of the earthquake source (location and magnitude). Comparison between the CNN model predictions and the predictions obtained with Bindi et al. (2011) GMPE (which require location and magnitude) has shown that the CNN model features similar error variance but smaller bias. Although the technique is not strictly designed for earthquake early warning, we found that it can provide useful estimates of ground motions within 15-20 sec after earthquake origin time depending on various setup elements (e.g., times for data transmission, computation, latencies). The technique has been tested on raw data without any initial data pre-selection in order to closely replicate real-time data streaming. When noise examples were included with the earthquake data, the CNN was found to be stable predicting accurately the ground shaking intensity corresponding to the noise amplitude.
    Description: Published
    Description: 1379–1389
    Description: 8T. Sismologia in tempo reale
    Description: JCR Journal
    Keywords: Physics - Geophysics; Physics - Geophysics ; 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 5
    Publication Date: 2023-11-16
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2020. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved.
    Description: In volcanoes, topography, shallow heterogeneity and even shallow morphology can substan- tially modify seismic coda signals. Coda waves are an essential tool to monitor eruption dynamics and model volcanic structures jointly and independently from velocity anomalies: it is thus fundamental to test their spatial sensitivity to seismic path effects. Here, we apply the Multiple Lapse Time Window Analysis (MLTWA) to measure the relative importance of scattering attenuation vs absorption at Mount St Helens volcano before its 2004 erup- tion. The results show the characteristic dominance of scattering attenuation in volcanoes at lower frequencies (3–6 Hz), while absorption is the primary attenuation mechanism at 12 and 18 Hz. Scattering attenuation is similar but seismic absorption is one order of magnitude lower than at open-conduit volcanoes, like Etna and Kilauea, a typical behaviour of a (rela- tively) cool magmatic plumbing system. Still, the seismic albedo (measuring the ratio between seismic energy emitted and received from the area) is anomalously high (0.95) at 3 Hz. A radiative-transfer forward model of far- and near-field envelopes confirms this is due to strong near-receiver scattering enhancing anomalous phases in the intermediate and late coda across the 1980 debris avalanche and central crater. Only above this frequency and in the far-field diffusion onsets at late lapse times. The scattering and absorption parameters derived from MLTWA are used as inputs to construct 2-D frequency-dependent bulk sensitivity kernels for the S-wave coda in the multiple-scattering (using the Energy Transport Equations—ETE) and diffusive (AD, independent of MLTWA results) regimes. At 12 Hz, high coda-attenuation anomalies characterize the eastern side of the volcano using both kernels, in spatial correla- tion with low-velocity anomalies from literature. At 3 Hz, the anomalous albedo, the forward modelling, and the results of the tomographic imaging confirm that shallow heterogeneity beneath the extended 1980 debris-avalanche and crater enhance anomalous intermediate and late coda phases, mapping shallow geological contrasts. We remark the effect this may have on coda-dependent source inversion and tomography, currently used across the world to image and monitor volcanoes. At Mount St Helens, higher frequencies and deep borehole data are necessary to reconstruct deep volcanic structures with coda waves.
    Description: Scottish Alliance for Geosciences Environment and Society and the Kleinman Grant for Volcano Research
    Description: Published
    Description: 169-188
    Description: 1T. Struttura della Terra
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: 3IT. Calcolo scientifico
    Description: JCR Journal
    Keywords: NorthAmerica ; Wave scattering and diffraction. ; Codawaves ; Seismicattenuation ; Seismic tomography ; Volcano seismology ; 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
    Publication Date: 2023-11-14
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2020. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved.
    Description: To evaluate the site response using both empirical approaches (e.g. standard spectral ratio, ground motion models (GMMs), generalized inversion techniques, etc.) and numerical 1-D/2-D analyses, the definition of the reference motion, that is the ground motion recorded at stations unaffected by site-effects due to topographic, stratigraphic or basin effects, is needed. The main objective of this work is to define a robust strategy to identify the seismic stations that can be considered as reference rock sites, using six proxies for the site response: three proxies are related to the analysis of geophysical and seismological data (the repeatable site term from the residual analysis, the resonance frequencies from horizontal-to-vertical spectral ratios on noise or earthquake signals, the average shear wave velocity in the first 30 m); the remaining ones concern geomorphological and installation features (outcropping rocks or stiff soils, flat topography and absence of interaction with structures). We introduce a weighting scheme to take into account the availability and the quality of the site information, as well as the fulfillment of the criterion associated to each proxy. We also introduce a hierarchical index, to take into account the relevance of the proposed proxies in the description of the site effects, and an acceptance threshold for reference rock sites identification. The procedure is applied on a very large data set, composed by accelerometric and velocimetric waveforms, recorded in Central Italy in the period 2008–2018. This data set is composed by more than 30 000 waveforms relative to 450 earthquakes in the magnitude range 3.2–6.5 and recorded by more than 450 stations. A total of 36 out of 133 candidate stations are identified as reference sites: the majority of them are installed on rock with flat topography, but this condition is not sufficient to guarantee the absence of amplifications, especially at high frequencies. Seismological analyses are necessary to exclude stations affected by resonances. We test the impact of using these sites by calibrating a GMMs. The results show that for reference rock sites the median predictions are reduced down to about 45 per cent at short periods in comparison to the generic rock motions.
    Description: Published
    Description: 2053–2067
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 7
    Publication Date: 2023-11-14
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2020. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved.
    Description: We compile a data set of Rayleigh-wave phase velocities between pairs of stations, based on teleseismic events located on the same great circle as the two stations. We validate our observations against dispersion estimates based on ambient-noise cross correlations at the same station pairs. Discrepancies between the results of the two methods can in principle be explained by deviations in the wave propagation path between earthquake and receivers, due to lateral heterogeneity in the Earth’s structure, but the latter effect has, so far, not been precisely quantified nor corrected for. We implement an algorithm to measure the arrival angle of earthquake-generated surface waves and correct the dispersion measurements accordingly. Application to a data set from the Central-Western Mediterranean shows that the arrival-angle correction almost entirely accounts for the discrepancy in question, decreasing significantly the velocity bias for a wide range of periods.
    Description: Published
    Description: 1838–1844
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 8
    Publication Date: 2023-11-16
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2021. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2021. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved.
    Description: Three dimensional attenuation images of Mt Etna volcano obtained by the analysis of Q-coda from local volcano-tectonic earthquakes are presented in this work. Seismic sources are confined inside the Etna structure with a maximum focal depth of 35 km below the sea level. The space distribution of the attenuation values was calculated by using 3-D weighting functions derived by the sensitivity kernels of Pacheco & Snieders and approximated by a polynomial interpolation, represented in the maps by using a backprojection method. Data were analyzed in four bands with central frequency placed at 1.5, 3, 6 and 12 Hz, respectively. We observed a frequency dependence of Q-coda with values that range from 55 at 1.5 Hz to 218 at 12 Hz. Q-coda space distribution in the Etna area shows almost uniformity in the average attenuation in the first 35 km below the surface. The images were derived with a resolution of 5 km. We observe as one of our main conclusions that Q-coda attenuation space anomalies are correlated with the areas of highest structural heterogeneities and are distributed along the well-known tectonic structures which characterize the crust in Mt Etna region. Previous and numerous velocity and attenuation images describing the structure of Mt Etna support our main conclusion: high Q-coda volumes almost coincide with the zones marked by high velocity and relative low total attenuation for direct waves.
    Description: Published
    Description: 544–558
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 9
    Publication Date: 2023-11-29
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2020. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved.
    Description: On 24 January 2020 an Mw 6.8 earthquake occurred at 20:55 local time (17:55 UTC) in eastern Turkey, close to the town of Sivrice in the Elazığ province, causing widespread considerable seismic damage in buildings. In this study, we analyse the main features of the rupture process and the seismic ground shaking during the Elazığ earthquake. We first use Interferometric Synthetic Aperture Radar (InSAR) interferograms (Sentinel-1 satellites) to constrain the fault geometry and the coseismic slip distribution of the causative fault segment. Then, we utilize this information to analyse the ground motion characteristics of the main shock in terms of peak ground acceleration (PGA), peak ground velocity (PGV) and spectral accelerations. The absence of seismic registrations in near-field for this earthquake imposes major constraints on the computation of seismic ground motion estimations in the study area. To do this, we have used a stochastic finite-fault simulation method to generate high-frequency ground motions synthetics for the Mw 6.8 Elazığ 2020 earthquake. Finally, we evaluate the potential state of stress of the unruptured portions of the causative fault segment as well as of adjacent segments, using the Coulomb stress failure function variations. Modelling of geodetic data shows that the 2020 Elazığ earthquake ruptured two major slip patches (for a total length of about 40 km) located along the Pütürge segment of the well-known left-lateral strike-slip East Anatolian Fault Zone (EAFZ), with up to 2.3 m of slip and an estimated geodetic moment of 1.70 × 1019 Nm (equivalent to a Mw 6.8). The position of the hypocentre supports the evidence of marked WSW rupture directivity during the main shock. In terms of ground motion characteristics, we observe that the high-frequency stochastic ground motion simulations have a good capability to reproduce the source complexity and capture the ground motion attenuation decay as a function of distance, up to the 200 km. We also demonstrate that the design spectra corresponding to 475 yr return period, provided by the new Turkish building code is not exceeded by the simulated seismograms in the epicentral area where there are no strong motion stations and no recordings available. Finally, based on the Coulomb stress distribution computation, we find that the Elazığ main shock increased the stress level of the westernmost part of the Pütürge fault and of the adjacent Palu segment and as a result of an off-fault lobe.
    Description: Published
    Description: 1054–1068
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 10
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    Oxford University Press
    In:  EPIC3Conservation Physiology, Oxford University Press, 9(1), ISSN: 2051-1434
    Publication Date: 2024-01-01
    Description: We studied the ontogeny of osmoregulation of the Asian shore crab Hemigrapsus sanguineus at an invaded area in the North Sea. H. sanguineus is native to Japan and China but has successfully invaded the Atlantic coast of North America and Europe. In the invaded areas, H. sanguineus is becoming a keystone species as driver of community structure and the adults compete with the shore crab Carcinus maenas. Strong osmoregulatory abilities may confer the potential to use and invade coastal areas already earlier in the life cycle. We reared larvae and first juveniles at 24°C in seawater from hatching to intermoult of each developmental stage (zoea I-V, megalopa, crab I). We exposed each stage to a range of salinities (0–39 ppt) for 24 h, and then we quantified haemolymph osmolality, using nano-osmometry. In addition, we quantified osmolality in field-collected adults after acclimation to the test salinities for 6 days. Larvae of H. sanguineus were able to hyper-osmoregulate at low salinities (15 and 20 ppt) over the complete larval development, although the capacity was reduced at the zoeal stage V; at higher salinities (25–39 ppt), all larval stages were osmoconformers. The capacity to slightly hypo-regulate at high salinity appeared in the first juvenile. Adults were able to hyper-osmoregulate at low salinities and hypo-regulate at concentrated seawater (39 ppt). H. sanguineus showed a strong capacity to osmoregulate as compared to its native competitor C. maenas, which only hyper-regulates at the first and last larval stages and does not hypo-regulate at the juvenile-adult stages. The capacity of H. sanguineus to osmoregulate over most of the life cycle should underpin the potential to invade empty niches in the coastal zone (characterized by low salinity and high temperatures). Osmoregulation abilities over the whole life cycle also constitute a strong competitive advantage over C. maenas.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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  • 11
    Publication Date: 2024-02-07
    Description: Full waveform inversion (FWI) is a data-fitting technique capable of generating high-resolution velocity models with a resolution down to half the seismic wavelength. FWI is applied typically to densely sampled seismic data. In this study, we applied FWI to 3D wide-angle seismic data acquired using sparsely spaced ocean bottom seismometers (OBSs) from the Deep Galicia Margin west of Iberia. Our dataset samples the S-reflector, a low-angle detachment present in this area. Here we highlight differences between 2D, 2.5D and 3D-FWI performances using a real sparsely spaced dataset. We performed 3D FWI in the time domain and compared the results with 2D and 2.5D FWI results from a profile through the 3D model. When overlaid on multichannel seismic images, the 3D FWI results constrain better the complex faulting within the pre- and syn-rift sediments and crystalline crust compared to the 2D result. Furthermore, we estimate variable serpentinisation of the upper mantle below the S-reflector along the profile using 3D FWI, reaching a maximum of 45 per cent. Differences in the data residuals of the 2D, 2.5D and 3D inversions suggest that 2D inversion can be prone to overfitting when using a sparse dataset. To validate our results, we performed tests to recover the anomalies introduced by the inversions in the final models using synthetic datasets. Based on our comparison of the velocity models, we conclude that the use of 3D data can partially mitigate the problem of receiver sparsity in FWI.
    Type: Article , PeerReviewed
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  • 12
    Publication Date: 2024-02-07
    Description: Probing seismic anisotropy of the lithosphere provides valuable clues on the fabric of rocks. We present a 3-D probabilistic model of shear wave velocity and radial anisotropy of the crust and uppermost mantle of Europe, focusing on the mountain belts of the Alps and Apennines. The model is built from Love and Rayleigh dispersion curves in the period range 5–149 s. Data are extracted from seismic ambient noise recorded at 1521 broad-band stations, including the AlpArray network. The dispersion curves are first combined in a linearized least squares inversion to obtain 2-D maps of group velocity at each period. Love and Rayleigh maps are then jointly inverted at depth for shear wave velocity and radial anisotropy using a Bayesian Monte Carlo scheme that accounts for the trade-off between radial anisotropy and horizontal layering. The isotropic part of our model is consistent with previous studies. However, our anisotropy maps differ from previous large scale studies that suggested the presence of significant radial anisotropy everywhere in the European crust and shallow upper mantle. We observe instead that radial anisotropy is mostly localized beneath the Apennines while most of the remaining European crust and shallow upper mantle is isotropic. We attribute this difference to trade-offs between radial anisotropy and thin (hectometric) layering in previous studies based on least-squares inversions and long period data (〉30 s). In contrast, our approach involves a massive data set of short period measurements and a Bayesian inversion that accounts for thin layering. The positive radial anisotropy (VSH 〉 VSV) observed in the lower crust of the Apennines cannot result from thin layering. We rather attribute it to ductile horizontal flow in response to the recent and present-day extension in the region.
    Type: Article , PeerReviewed
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  • 13
    Publication Date: 2024-02-07
    Description: Seismic full waveform inversion (FWI) is a powerful method for estimating quantitative subsurface physical parameters from seismic data. As the full waveform inversion is a non-linear problem, the linearized approach updates model iteratively from an initial model, which can get trapped in local minima. In the presence of a high velocity contrast, such as at Moho, the reflection coefficient and recorded waveforms from wide-aperture seismic acquisition are extremely non-linear around critical angles. The problem at the Moho is further complicated by the interference of lower crustal (Pg) and upper mantle (Pn) turning ray arrivals with the critically reflected Moho arrivals (PmP). In order to determine velocity structure near Moho, a non-linear method should be used. We propose to solve this strong non-linear FWI problem at Moho using a trans-dimensional Markov chain Monte Carlo (MCMC) method, where the earth model between lower crust and upper mantle is idealy parameterized with a 1-D assumption using a variable number of velocity interfaces. Different from common MCMC methods that require determining the number of unknown as a fixed prior before inversion, trans-dimensional MCMC allows the flexibility for an automatic estimation of both the model complexity (e.g. the number of velocity interfaces) and the velocity-depth structure from the data. We first test the algorithm on synthetic data using four representative Moho models and then apply to an ocean bottom seismometer (OBS) data from the Mid-Atlantic Ocean. A 2-D finite-difference solution of an acoustic wave equation is used for data simulation at each iteration of MCMC search, for taking into account the lateral heterogeneities in the upper crust, which is constrained from travel time tomography and is kept unchanged during inversion; the 1-D model parameterization near Moho enables an efficient search of the trans-dimensional model space. Inversion results indicate that, with very little prior and the wide-aperture seismograms, the trans-dimensional FWI method is able to infer the posterior distribution of both the number of velocity interfaces and the velocity-depth model for a strong nonlinear problem, making the inversion a complete data-driven process. The distribution of interface matches the velocity discontinuities. We find that the Moho in the study area is a transition zone of 0.7 km, or a sharp boundary with velocities from around 7 km/s in the lower crust to 8 km/s of the upper mantle; both provide nearly identical waveform match for the field data. The ambiguity comes from the resolution limit of the band-limited seismic data and limited offset range for PmP arrivals.
    Type: Article , PeerReviewed
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  • 14
    Publication Date: 2024-02-07
    Description: To constrain seismic anisotropy under and around the Alps in Europe, we study SKS shear wave splitting from the region densely covered by the AlpArray seismic network. We apply a technique based on measuring the splitting intensity, constraining well both the fast orientation and the splitting delay. Four years of teleseismic earthquake data were processed, from 723 temporary and permanent broad-band stations of the AlpArray deployment including ocean-bottom seismometers, providing a spatial coverage that is unprecedented. The technique is applied automatically (without human intervention), and it thus provides a reproducible image of anisotropic structure in and around the Alpine region. As in earlier studies, we observe a coherent rotation of fast axes in the western part of the Alpine chain, and a region of homogeneous fast orientation in the Central Alps. The spatial variation of splitting delay times is particularly interesting though. On one hand, there is a clear positive correlation with Alpine topography, suggesting that part of the seismic anisotropy (deformation) is caused by the Alpine orogeny. On the other hand, anisotropic strength around the mountain chain shows a distinct contrast between the Western and Eastern Alps. This difference is best explained by the more active mantle flow around the Western Alps. The new observational constraints, especially the splitting delay, provide new information on Alpine geodynamics.
    Type: Article , PeerReviewed
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  • 15
    Publication Date: 2021-10-26
    Description: Eccentric millisecond pulsars (eMSPs) with white dwarf companions exhibit orbital eccentricities orders of magnitude larger than predicted by turbulent convection in the white dwarfs’ red giant progenitors. The orbital periods of eMSPs cluster around P = 20–30 d, remarkably close to the red giant convective eddy turnover time teddy. We propose that the anomalously large eccentricities are resonantly driven by convective flows somehow made coherent when the turnover time matches the tidally locked red giant’s spin period, which is also the tidal forcing period. Numerical simulations of rotating red giants and magnetic field studies of stars show some evidence for especially ordered flow patterns when the convective Rossby number P/teddy is of order unity. We show that resonant convection boosts eccentricities by a factor of (tnuc/P)1/2 ≈ 3 × 103 over the random-walk values that characterize conventional MSPs, in good agreement with observations (tnuc is the giant’s nuclear burning time-scale). We also show how variations in the eddy turnover time arising from red giant metallicity variations can reproduce the observed effective width of the resonance, ΔP/P ≈ 0.4.
    Print ISSN: 1745-3925
    Electronic ISSN: 1745-3933
    Topics: Physics
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  • 16
    Publication Date: 2021-10-28
    Description: The long-term evolutionary impacts of whole genome duplication (WGD) are strongly influenced by the ensuing rediploidization process. Following autopolyploidization, rediploidization involves a transition from tetraploid to diploid meiotic pairing, allowing duplicated genes (ohnologues) to diverge genetically and functionally. Our understanding of autopolyploid rediploidization has been informed by a WGD event ancestral to salmonid fishes, where large genomic regions are characterized by temporally delayed rediploidization, allowing lineage-specific ohnologue sequence divergence in the major salmonid clades. Here, we investigate the long-term outcomes of autopolyploid rediploidization at genome-wide resolution, exploiting a recent ‘explosion’ of salmonid genome assemblies, including a new genome sequence for the huchen (Hucho hucho). We developed a genome alignment approach to capture duplicated regions across multiple species, allowing us to create 121,864 phylogenetic trees describing genome-wide ohnologue divergence across salmonid evolution. Using molecular clock analysis, we show that 61% of the ancestral salmonid genome experienced an initial ‘wave’ of rediploidization in the late Cretaceous (85-106 Mya). This was followed by a period of relative genomic stasis lasting 17-39 My, where much of the genome remained tetraploid. A second rediploidization wave began in the early Eocene and proceeded alongside species diversification, generating predictable patterns of lineage-specific ohnologue divergence, scaling in complexity with the number of speciation events. Using gene set enrichment, gene expression, and codon-based selection analyses, we provide insights into potential functional outcomes of delayed rediploidization. This study enhances our understanding of delayed autopolyploid rediploidization and has broad implications for future studies of WGD events.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
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  • 17
    Publication Date: 2021-10-28
    Description: To assess the number of life-bearing worlds in astrophysical environments, it is necessary to take the intertwined processes of abiogenesis (birth), extinction (death), and transfer of life (migration) into account. We construct a mathematical model that incorporates this trio of mechanisms and accordingly derive the probability distribution function and other statistical properties (e.g. mean) for the number of worlds with biospheres. We show that a given astrophysical setting may become eventually saturated with life if the rate of successful transfers of organisms is higher than the extinction rate of biospheres. Based on the available data, we suggest that this criterion might be fulfilled for star-forming clusters (and perhaps the Galactic bulge under optimal circumstances), thereby indicating that such regions could constitute promising abodes for hosting and detecting life.
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  • 18
    Publication Date: 2021-10-28
    Description: We present a search for disturbed, candidate ram pressure stripping galaxies across more than 50 spectroscopically selected SDSS groups and clusters. Forty-eight ram pressure candidates are visually identified in these systems using high quality UNIONS imaging from the Canada-France Hawaii Telescope, covering ∼6200 deg2 and ∼2800 deg2 in the u- and r-bands respectively. Ram pressure candidates are found in groups and clusters spanning a wide range in halo mass and include ∼30 ram pressure candidates in the group regime (Mh 〈 1014). The observed frequency of ram pressure candidates shows substantial scatter with group/cluster mass, but on average is larger in clusters (Mh ≥ 1014 M⊙) than groups (Mh 〈 1014 M⊙) by a factor of ∼2. We find that ram pressure candidates are most commonly low-mass galaxies and have enhanced star formation rates relative to star-forming field galaxies. The enhancement in star formation is largely independent of galaxy mass and strongest for galaxies in clusters. As a result of the large survey footprint and excellent image quality from UNIONS, we are able to identify disturbed galaxies, potentially affected by ram pressure stripping, across a wide range of host environment.
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  • 19
    Publication Date: 2021-10-28
    Description: We present a comprehensive study of three large long-duration flares detected on an active M-dwarf binary EQ Peg using the Soft X-Ray Telescope of the AstroSat observatory. The peak X-ray luminosities of the flares in the 0.3–7 keV band are found to be within ∼5–10 ×  1030 $ m {erg}~ m {s}^{-1}$. The e-folding rise- and decay-times of the flares are derived to be in the range of 3.4–11 and 1.6–24 ks, respectively. Spectral analysis indicates the presence of three temperature corona with the first two plasma temperatures remain constant during all the flares and the post-flare observation at ∼3 and ∼9 MK. The flare temperature peaked at 26, 16, and 17 MK, which are 2, 1.3, and 1.4 times more than the minimum value, respectively. The peak emission measures are found to be 3.9–7.1 ×  1053 cm−3, whereas the abundances peaked at 0.16–0.26 times the solar abundances. Using quasi-static loop modelling, we derive loop-lengths for all the flares as 2.5±0.5 ×  1011, 2.0 ± 0.5 ×  1011, and 2.5 ± 0.9 ×  1011 cm, respectively. The density of the flaring plasma is estimated to be 4.2 ± 0.8 ×  1010, 3.0 ± 0.7 ×  1010, 2.2 ± 0.8 ×  1010 cm−3 for flares F1, F2, and F3, respectively. Whereas the magnetic field for all three flares is estimated to be
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  • 20
    Publication Date: 2021-10-28
    Description: Summary We have studied the active and recent tectonics of New Guinea, using earthquake source modelling, analysis of gravity anomalies, seismic reflection profiles, and thermal and mechanical models. Our aim is to investigate the behaviour and evolution of a young continental deformation belt, and to explore the effects of lateral variations in foreland rheology on the deformation. We find that along-strike gradients in the lithosphere thickness of the southern foreland have resulted in correlated changes in seismogenic thickness, likely due to the effects on the temperature structure of the crust. The resulting variation in the strength of the foreland means that in the east, the foreland is broken through on thrust faults, whereas in the west it is relatively intact. The lack of correlation between the elevation of the mountain belt and the seismogenic thickness of the foreland is likely to be due to the time taken to thicken the crust in the mountains following changes in the rheology of the underthrusting foreland, as the thinned passive margin of northern Australia is consumed. The along-strike variation in whether the force exerted between the mountains and the lowlands is able to break the foreland crust enables us to estimate the effective coefficient of friction on foreland faults to be in the range of 0.01-0.28. We use force-balance calculations to show that the recent tectonic re-organisation in western New Guinea is likely to be due to the development of increasing curvature in the Banda Arc, and that the impingement of continental material on the subduction zone may explain the unusually low force it exerts on western New Guinea.
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  • 21
    Publication Date: 2021-10-29
    Description: Almost twenty years after its initial release, the Eukaryotic Linear Motif (ELM) resource remains an invaluable source of information for the study of motif-mediated protein-protein interactions. ELM provides a comprehensive, regularly updated and well-organised repository of manually curated, experimentally validated short linear motifs (SLiMs). An increasing number of SLiM-mediated interactions are discovered each year and keeping the resource up-to-date continues to be a great challenge. In the current update, 30 novel motif classes have been added and five existing classes have undergone major revisions. The update includes 411 new motif instances mostly focused on cell-cycle regulation, control of the actin cytoskeleton, membrane remodelling and vesicle trafficking pathways, liquid-liquid phase separation and integrin signalling. Many of the newly annotated motif-mediated interactions are targets of pathogenic motif mimicry by viral, bacterial or eukaryotic pathogens, providing invaluable insights into the molecular mechanisms underlying infectious diseases. The current ELM release includes 317 motif classes incorporating 3934 individual motif instances manually curated from 3867 scientific publications. ELM is available at: http://elm.eu.org.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
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  • 22
    Publication Date: 2021-10-28
    Description: Summary On 2020 December 29, the Mw 6.4 Petrinja earthquake hit the Kupa Valley region and set a record for the largest earthquake in northwestern (NW) Croatia. The coseismic surface displacements are well obtained on three pairs of interferometric synthetic aperture radar (InSAR) images from Sentinel-1 satellites. The interferograms exhibit coseismic ground deformation with a maximum line-of-sight (LOS) displacement of 0.4 m. Based on the coseismic deformation field, we investigate both the fault geometry and the coseismic slip distribution. The results show a dextral event with a peak slip of 3.50 m at a depth of 3.47 km. The shallow depth and unusually large coseismic slip correspond to obvious ground deformation and serious damage in the epicentral zone. The 2020 earthquake highlights an unmapped, steeply dipping strike-slip fault, which possibly enabled a potential ‘curve cut-off’ process on the bending segment of the Pokupsko fault in the context of ∼N-S compression in NW Croatia. The large coseismic slip and high stress drop associated with the Mw 6.4 Petrinja earthquake are likely products of the geometrically complex fault zones and immature seismotectonic environment in NW Croatia.
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  • 23
    Publication Date: 2021-10-28
    Description: Pathogenic variants that disrupt human mitochondrial protein synthesis are associated with a clinically heterogenous group of diseases. Despite an impairment in oxidative phosphorylation being a common phenotype, the underlying molecular pathogenesis is more complex than simply a bioenergetic deficiency. Currently, we have limited mechanistic understanding on the scope by which a primary defect in mitochondrial protein synthesis contributes to organelle dysfunction. Since the proteins encoded in the mitochondrial genome are hydrophobic and need co-translational insertion into a lipid bilayer, responsive quality control mechanisms are required to resolve aberrations that arise with the synthesis of truncated and misfolded proteins. Here, we show that defects in the OXA1L-mediated insertion of MT-ATP6 nascent chains into the mitochondrial inner membrane are rapidly resolved by the AFG3L2 protease complex. Using pathogenic MT-ATP6 variants, we then reveal discrete steps in this quality control mechanism and the differential functional consequences to mitochondrial gene expression. The inherent ability of a given cell type to recognize and resolve impairments in mitochondrial protein synthesis may in part contribute at the molecular level to the wide clinical spectrum of these disorders.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 24
    Publication Date: 2021-10-30
    Description: Motivation Coiled-coil is composed of two or more helices that are wound around each other. It widely exists in proteins and has been discovered to play a variety of critical roles in biology processes. Generally, there are three types of structural features in coiled-coil: coiled-coil domain (CCD), oligomeric state, and register. However, most of the existing computational tools only focus on one of them. Results Here, we describe a new deep learning model, CoCoPRED, which is based on convolutional layers, bidirectional long short-term memory, and attention mechanism. It has three networks, i.e., CCD network, oligomeric state network, and register network, corresponding to the three types of structural features in coiled-coil. This means CoCoPRED has the ability of fulfilling comprehensive prediction for coiled-coil proteins. Through the 5-fold cross-validation experiment, we demonstrate that CoCoPRED can achieve better performance than the state-of-the-art models on both CCD prediction and oligomeric state prediction. Further analysis suggests the CCD prediction may be a performance indicator of the oligomeric state prediction in CoCoPRED. The attention heads in CoCoPRED indicate that registers a, b, and e are more crucial for the oligomeric state prediction. Availability CoCoPRED is available at http://www.csbio.sjtu.edu.cn/bioinf/CoCoPRED. Supplementary information Supplementary data are available at Bioinformatics online.
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  • 25
    Publication Date: 2021-10-28
    Description: Studies of planetary systems of stars in star-forming regions and young clusters open a window on the formative stages of planetary evolution. We obtained high-cadence high-resolution infrared spectroscopy of the solar-mass Taurus association-member V1298 Tau during a transit of its 10R⊕-size ‘b’ planet. We measured the systemic radial velocity and find that the kinematics of V1298 Tau suggest an affiliation with a ≳6 Myr-old subgroup. A comparison of V1298 Tau and the nearby, co-moving star 2M0405 with stellar evolution models suggests an age of ∼10-25 Myr. We measured the projected spin-orbit angle of ‘b’ as $lambda =15_{-16}^{+15}$ and $lambda = 2_{-4}^{+12}$ degrees using the apparent RV shift and change in line profile, respectively, induced by the transient occultation of the rotating star by the planet. These values indicate a prograde orbit like that of the interior ‘c’ planet of V1298 Tau and point to a co-planar multi-planet system that formed within a disk. We also measured variation in the strength of the 1083 nm triplet of neutral orthohelium as a probe of any extended/escaping atmosphere around ‘b’. We detect a steady decrease in absorption over the transit which appears to arise from the star or its planetary system. While this variation could be ascribed to ‘b’ or possibly to the immediately preceding transit of ‘d’, we cannot rule out that this is due to rapid variation in the stellar disk-integrated flux in the triplet. The amplitude of variation (∼0.04 nm) is consistent with moderate estimates of atmospheric escape driven by XUV radiation from the central star.
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  • 26
    Publication Date: 2021-10-28
    Description: We present light curve analyses of two newly identified detached eclipsing binaries, HD 96609 and HD 303734, in the region of the richly populated open cluster NGC 3532. HD 96609 is composed of two main sequence stars (B9-A0V + A2V) with masses and radii of M1 = 2.66 ± 0.02M⊙, M2 = 1.84 ± 0.01M⊙, R1 = 2.740 ± 0.006R⊙, R2 = 1.697 ± 0.005R⊙. The positions of the components on log M − log R plane suggests log(age/yr) 8.55, corresponding 350 ± 40 Myr of age, which agrees with the 300 ± 100 Myr age of NGC 3532 estimated in previous studies. We find the distance of HD 96609 as 460 ± 17 pc, which is consistent with the $484^{+35}_{-30}$ pc distance of NGC 3532, estimated from GAIA parallaxes. HD 303734 is an interesting totally eclipsing binary with a quite shallow secondary eclipse. Using photometric properties of the system in conjunction with theoretical calibrations, we estimate that HD 303734 consists of A6V + K3V components. HD 96609 and HD 303734 are the second and third eclipsing binaries discovered in the region of NGC 3532, after the first one, GV Car.
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  • 27
    Publication Date: 2021-10-28
    Description: We propose a novel approach to obtain the growth rate of cosmic structures, f(z), from the evolution of the cosmic homogeneity scale, RH(z). Our methodology needs two ingredients in a specific functional form: RH(z) data and the matter two-point correlation function today, i.e., ξ(r, z = 0). We use a Gaussian Process approach to reconstruct the function RH. In the absence of suitable observational information of the matter correlation function in the local Universe, z ≃ 0, we assume a fiducial cosmology to obtain ξ(r, z = 0). For this reason, our final result turns out to be a consistency test of the cosmological model assumed. Our results show a good agreement between: (i) the growth rate $f^{R_{ext{H}}}(z)$ obtained through our approach, (ii) the fΛCDM(z) expected in the fiducial model, and (iii) the best-fit f(z) from data compiled in the literature. Moreover, using this data compilation, we perform a Gaussian Process to reconstruct the growth rate function fdata(z) and compare it with the function $f^{R_{ext{H}}}(z)$ finding a concordance of
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  • 28
    Publication Date: 2021-08-01
    Print ISSN: 0036-0279
    Electronic ISSN: 1468-4829
    Topics: Mathematics
    Published by Institute of Physics
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  • 29
    Publication Date: 2021-10-30
    Description: Motivation Adverse Outcome Pathways (AOPs) are a conceptual framework developed to support the use of alternative toxicology approaches in the risk assessment. AOPs are structured linear organizations of existing knowledge illustrating causal pathways from the initial molecular perturbation triggered by various stressors, through key events (KEs) at different levels of biology, to the ultimate health or ecotoxicological adverse outcome. Results Artificial intelligence can be used to systematically explore available toxicological data that can be parsed in the scientific literature. Recently a tool called AOP-helpFinder was developed to identify associations between stressors and KEs supporting thus documentation of AOPs. To facilitate the utilization of this advanced bioinformatics tool by the scientific and the regulatory community, a webserver was created. The proposed AOP-helpFinder webserver uses better performing version of the tool which reduces the need for manual curation of the obtained results. As an example, the server was successfully applied to explore relationships of a set of endocrine disruptors with metabolic-related events. The AOP-helpFinder webserver assists in a rapid evaluation of existing knowledge stored in the PubMed database, a global resource of scientific information, to build AOPs and Adverse Outcome Networks (AONs) supporting the chemical risk assessment. Availability and implementation AOP-helpFinder is available at http://aop-helpfinder.u-paris-sciences.fr/index.php
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  • 30
    Publication Date: 2021-08-01
    Print ISSN: 0036-0279
    Electronic ISSN: 1468-4829
    Topics: Mathematics
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  • 31
    Publication Date: 2021-10-30
    Description: Motivation Differential network inference is a fundamental and challenging problem to reveal gene interactions and regulation relationships under different conditions. Many algorithms have been developed for this problem; however, they do not consider the differences between the importance of genes, which may not fit the real-world situation. Different genes have different mutation probabilities, and the vital genes associated with basic life activities have less fault tolerance to mutation. Equally treating all genes may bias the results of differential network inference. Thus, it is necessary to consider the importance of genes in the models of differential network inference. Results Based on the Gaussian graphical model with adaptive gene importance regularization, we develop a novel importance-penalized joint graphical Lasso method, IPJGL, for differential network inference. The presented method is validated by the simulation experiments as well as the real datasets. Furthermore, to precisely evaluate the results of differential network inference, we propose a new metric named APC2 for the differential levels of gene pairs. We apply IPJGL to analyze the TCGA colorectal and breast cancer datasets and find some candidate cancer genes with significant survival analysis results, including SOST for colorectal cancer and RBBP8 for breast cancer. We also conduct further analysis based on the interactions in the Reactome database and confirm the utility of our method. Availability R source code of importance-penalized joint graphical lasso is freely available at https://github.com/Wu-Lab/IPJGL. Supplementary information Supplementary materials are available at Bioinformatics online.
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  • 32
    Publication Date: 2021-10-28
    Description: Evolutionary radiation is a widely recognized mode of species diversification, but its underlying mechanisms have not been unambiguously resolved for species-rich cosmopolitan plant genera. In particular, it remains largely unknown how biological and environmental factors have jointly driven its occurrence in specific regions. Here we use Rhododendron, the largest genus of woody plants in the Northern Hemisphere, to investigate how geographic and climatic factors, as well as functional traits, worked together to trigger plant evolutionary radiations and shape the global patterns of species richness based on a solid species phylogeny. Using 3437 orthologous nuclear genes, we reconstructed the first highly supported and dated backbone phylogeny of Rhododendron comprising 200 species that represent all subgenera, sections, and nearly all multi-species subsections, and found that most extant species originated by evolutionary radiations when the genus migrated southwards from circumboreal areas to tropical/subtropical mountains, showing rapid increases of both net diversification rate and evolutionary rate of environmental factors in the Miocene. We also found that the geographically uneven diversification of Rhododendron led to a much higher diversity in Asia than in other continents, which was mainly driven by two environmental variables, i.e., elevation range and annual precipitation, and were further strengthened by the adaptation of leaf functional traits. Our study provides a good example of integrating phylogenomic and ecological analyses in deciphering the mechanisms of plant evolutionary radiations, and sheds new light on how the intensification of the Asian monsoon has driven evolutionary radiations in large plant genera of the Himalaya-Hengduan Mountains.
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  • 33
    Publication Date: 2021-10-28
    Description: Motivation The adoption of current single-cell DNA methylation sequencing protocols is hindered by incomplete coverage, outlining the need for effective imputation techniques. The task of imputing single-cell (methylation) data requires models to build an understanding of underlying biological processes. Results We adapt the transformer neural network architecture to operate on methylation matrices through combining axial attention with sliding window self-attention. The obtained CpG Transformer displays state-of-the-art performances on a wide range of scBS-seq and scRRBS-seq datasets. Furthermore, we demonstrate the interpretability of CpG Transformer and illustrate its rapid transfer learning properties, allowing practitioners to train models on new datasets with a limited computational and time budget. Availability and Implementation CpG Transformer is freely available at https://github.com/gdewael/cpg-transformer. Supplementary information Supplementary data are available at Bioinformatics online.
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  • 34
  • 35
    Publication Date: 2021-10-01
    Description: Here, the corrosion weight-loss method, surface analysis technology, and electrochemical test methods were used to study the corrosion behavior and electrochemical characteristics of experimental samples of Q345R steel in a sterile solution (pH 2.0) and a solution containing T. ferrooxidans. The growth cycle of T. ferrooxidans was determined to be approximately 8 days. The corrosion weight-loss method showed that the corrosion rate of Q345R carbon steel coupons decreased with time in the T. ferrooxidans system and the sterile system; the corrosion rate was approximately two times higher in the T. ferrooxidans system than in the sterile system. The corrosion morphology results showed that the presence of T. ferrooxidans promotes the corrosion of Q345R steel and increases the local corrosion of the matrix material. The electrochemical test results showed that after 5 days of corrosion, the polarization resistance of the T. ferrooxidans system was approximately 50% of that of the sterile system, and the corrosion current density of the T. ferrooxidans system was approximately twice as high as that of the sterile system. Therefore, T. ferrooxidans can accelerate the corrosion of Q345R steel two-fold.
    Electronic ISSN: 2053-1591
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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  • 36
    Publication Date: 2021-10-29
    Description: High mass proto-stars create Ultra-Compact H ii regions (UCHII) at the stage of evolution when most of the accretion is finished but the star is still heavily embedded in molecular material. The morphologies of UCHII regions reflect the interactions of stellar winds, stellar motions, and density structure in the molecular cloud; they are complex and it has been very difficult to interpret them. We here present data obtained with TEXES on the NASA IRTF of the [Nei,ii] emission line in the proto-cluster of young OB stars in W33 Main. The data cube has a spatial resolution of ∼1.4 arcsec and true velocity resolution ∼5 km s-1; with Aλ ∼ 0.02AV it is relatively unaffected by extinction. We have run 3D hydrodynamic and line profile simulations, using PLUTO and RADMC-3D, of the gas structures created by multiple windy stars moving relative to each other through the ambient cloud. By iterative comparison of the data cube and the simulations, we arrive at models that reproduce the different morphology and kinematic structure of each UCHII region in W33 Main. The results indicate that each sub-source probably holds multiple exciting stars, permitting an improved view of the stellar population, and finds the stellar trajectories, which may determine the dynamical development of the proto-cluster.
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  • 37
    Publication Date: 2021-10-29
    Description: Bayesian evidence ratios are widely used to quantify the statistical consistency between different experiments. However, since the evidence ratio is prior dependent, the precise translation between its value and the degree of concordance/discordance requires additional information. The most commonly adopted metric, the Jeffreys scale, can falsely suggest agreement between datasets when priors are chosen to be sufficiently wide. This work examines evidence ratios in a DES-Y1 simulated analysis, focusing on the internal consistency between weak lensing and galaxy clustering. We study two scenarios using simulated data in controlled experiments. First, we calibrate the expected evidence ratio distribution given noise realizations around the best fit DES-Y1 ΛCDM cosmology. Second, we show the behavior of evidence ratios for noiseless fiducial data vectors simulated using a modified gravity model, which generates internal tension in the LCDM analysis. We find that the evidence ratio of noise realizations generated at all confidence levels was biased towards agreement and show, with a modified gravity model, that the choice of prior could conceal the discrepancies between weak lensing and galaxy clustering induced by prior effects in unlike cosmological models, concluding that the evidence ratio in a DES-Y1 study is, indeed, biased towards agreement. Boundary effects can also influence conclusions about the inconsistency induced by modified gravity, even in a noiseless data vector simulation.
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  • 38
    Publication Date: 2021-10-01
    Electronic ISSN: 1742-5468
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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  • 39
    Publication Date: 2021-10-29
    Description: Detailed spectropolarimetric studies may hold the key to probing the explosion mechanisms and the progenitor scenarios of Type Ia supernovae (SNe Ia). We present multi-epoch spectropolarimetry and imaging polarimetry of SN 2019ein, an SN Ia showing high expansion velocities at early phases. The spectropolarimetry sequence spans from ∼−11 to +10 days relative to peak brightness in the B-band. We find that the level of the continuum polarization of SN 2019ein, after subtracting estimated interstellar polarization, is in the range 0.0–0.3%, typical for SNe Ia. The polarization position angle remains roughly constant before and after the SN light-curve peak, implying that the inner regions share the same axisymmetry as the outer layers. We observe high polarization ($sim 1\%$) across both the Si ii λ6355 and Ca ii near-infrared triplet features. These two lines also display complex polarization modulations. The spectropolarimetric properties of SN 2019ein rule out a significant departure from spherical symmetry of the ejecta for up to a month after the explosion. These observations disfavour merger-induced and double-detonation models for SN 2019ein. The imaging polarimetry shows weak evidence for a modest increase in polarization after ∼20 days since the B-band maximum. If this rise is real and is observed in other SNe Ia at similar phases, we may have seen, for the first time, an aspherical interior similar to what has been previously observed for SNe IIP. Future polarization observations of SNe Ia extending to post-peak epochs will help to examine the inner structure of the explosion.
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  • 40
    Publication Date: 2021-10-29
    Description: Summary We deployed a seismic network near the source region of the 2017 Mw 6.5 Jiuzhaigou earthquake to monitor aftershock activity and to investigate the local fault structure. An aftershock deployment of Array of small Arrays (AsA) and a Geometric Mean Envelop (GME) algorithm are adopted to enhance detection performance. We also adopt a set of association, relocation, and matched-filter techniques to obtain a detailed regional catalog. 16,742 events are detected and relocated, including 1,279 aftershocks following the Mw 4.8 aftershock. We develop a joint inversion algorithm utilizing locations of event clusters and focal mechanisms to determine the geometry of planar faults. Six segments were finally determined, in which three segments are related to the Huya fault reflecting a change in fault dip direction near the mainshock hypocenter, while the other segments reflect branches showing orthogonal and conjugate geometries with the Huya fault. Aftershocks were active on branching faults between the Huya and Minjiang faults indicating that the mainshock may have ruptured both major faults. We also resolve a fault portion with ‘weak strength’ near the mainshock hypocenter, which is characterized by limited co-seismic slips, concentrated afterslip, low aftershock activities, high b-value, and high sensitivity to stress changes. These phenomena can be explained by fault frictional properties at conditional stable sliding status, which may be related to the localized high pore-fluid pressure produced by the fluid intrusion.
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  • 41
    Publication Date: 2021-10-29
    Description: We study gravitational lensing of gravitational waves from compact object binaries as a probe of compact dark matter (DM) objects such as primordial black holes. Assuming a point mass lens, we perform parameter estimation of lensed gravitational wave signals from compact object binaries to determine the detectability of the lens with ground based laser interferometers. Then, considering binary populations that LIGO-Virgo has been probing, we derive a constraint on the abundance of compact DM from non-observation of lensed events. We find that the LIGO-Virgo observations imply that compact objects heavier than Ml = 200 M⊙ can not constitute all DM and less than $40{{ m per cent}}$ of DM can be in compact objects heavier than Ml = 400 M⊙. We also show that the DM fraction in compact objects can be probed by LIGO in its final sensitivity for Ml 〉 40 M⊙ reaching $2{{ m per cent}}$ of the DM abundance at Ml 〉 200 M⊙, and by ET for Ml 〉 1 M⊙ reaching DM fraction as low as 7 × 10−5 at Ml 〉 40 M⊙.
    Print ISSN: 0035-8711
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  • 42
  • 43
    Publication Date: 2021-10-01
    Description: Electropolishing (EP) is a reliable post-processing method of the drilled metals for achieving a high-quality surface finish with an appropriate material removal rate. This process has many applications due to its advantages such as improving the surface quality by removing the surface peaks on a micro-scale. The aim of most attempts on this process is setting up the optimum parameters to obtain maximum Material Removal Rate (MRR) with minimum surface roughness. In the present wo k, electropolishing of AISI 4340 low alloy steel immersed in eco-friendly NaCl solution has been studied numerically and experimentally. So, primarily a simulation model was developed for the EP process on cylinder parts in COMSOL Multiphysics which was validated with experimental approaches. The results revealed that the numerical model would be convenient for EP. The experiments were performed using Response Surface Methodology (RSM) to evaluate the effect of input variables on the responses. The effects of input variables electrolyte temperature, current intensity, and primary gap were investigated on the outputs MRR and surface roughness at five levels. Based on the results, the electrolyte temperature and current intensity were more effective parameters on the outputs. Results of ANOVA and regression analysis approach revealed that by increasing the current and electrolyte temperature, the MRR increases correspondingly and surface roughness declines and the primary gap has a reverse effect on the MRR. Finally, by performing a multi-objective optimization using Derringer’s desirability approach, the EP of AISI 4340 with an eco-friendly NaCl solution was optimized.
    Electronic ISSN: 2053-1591
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Published by Institute of Physics
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  • 44
    Publication Date: 2021-10-01
    Description: Sn63Pb37/SAC305 mixed solder joint is inevitably in the electronic device requiring high reliability, such as health care, aerospace etc. However, the usage history of mixed solder joint is relatively short and as such their interfacial behaviour and reliability in service has not been completely figure out. Herein, the evolution of microstructures in fully mixed Sn63Pb37/SAC305 BGA solder joints during high-temperature storage were systematically studied. After reflow soldering process, the Pb-rich phases uniformly distributed in the fully mixed joint. During the thermal aging test, the size of Pb-rich phases gradually coarsened. The intermetallic compound (IMC) layers thickness at the two-side interface (upper interface: between the pad on substrate and solder; lower interface: between the pad on PCB and solder) were also increased. Moreover, the growth kinetics models of two-side IMC layer were successfully established according to the Arrhenius equation. IMC layer grows faster at higher temperature, because of higher diffusion coefficient. With the increasing of aging time, the fracture position partially moved from the interface between Ni layer and IMC layer into IMC internal. These results may provide support for the reliable applications of mixed Sn63Pb37/SAC305 solder joints.
    Electronic ISSN: 2053-1591
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Published by Institute of Physics
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  • 45
    Publication Date: 2021-08-15
    Description: Genetic variation and phenotypic plasticity are both important to adaptive evolution. However, how they act together on particular traits remains poorly understood. Here, we integrated phenotypic, genomic, and transcriptomic data from two allopatric but closely related congeneric oyster species, Crassostrea angulata from southern/warm environments and Crassostrea gigas from northern/cold environments, to investigate the roles of genetic divergence and plasticity in thermal adaptation. Reciprocal transplantation experiments showed that both species had higher fitness in their native habitats than in nonnative environments, indicating strong adaptive divergence. The southern species evolved higher transcriptional plasticity, and the plasticity was adaptive, suggesting that increased plasticity is important for thermal adaptation to warm climates. Genome-wide comparisons between the two species revealed that genes under selection tended to respond to environmental changes and showed higher sequence divergence in noncoding regions. All genes under selection and related to energy metabolism exhibited habitat-specific expression with genes involved in ATP production and lipid catabolism highly expressed in warm/southern habitats, and genes involved in ATP consumption and lipid synthesis were highly expressed in cold/northern habitats. The gene for acyl-CoA desaturase, a key enzyme for lipid synthesis, showed strong selective sweep in the upstream noncoding region and lower transcription in the southern species. These results were further supported by the lower free fatty acid (FFA) but higher ATP content in southern species and habitat, pointing to significance of ATP/FFA trade-off. Our findings provide evidence that noncoding variation and transcriptional plasticity play important roles in shaping energy metabolism for thermal adaptation in oysters.
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  • 46
    Publication Date: 2021-07-30
    Description: Domestication and breeding have reshaped the genomic architecture of chicken, but the retention and loss of genomic elements during these evolutionary processes remain unclear. We present the first chicken pan-genome constructed using 664 individuals, which identified an additional approximately 66.5-Mb sequences that are absent from the reference genome (GRCg6a). The constructed pan-genome encoded 20,491 predicated protein-coding genes, of which higher expression levels are observed in conserved genes relative to dispensable genes. Presence/absence variation (PAV) analyses demonstrated that gene PAV in chicken was shaped by selection, genetic drift, and hybridization. PAV-based genome-wide association studies identified numerous candidate mutations related to growth, carcass composition, meat quality, or physiological traits. Among them, a deletion in the promoter region of IGF2BP1 affecting chicken body size is reported, which is supported by functional studies and extra samples. This is the first time to report the causal variant of chicken body size quantitative trait locus located at chromosome 27 which was repeatedly reported. Therefore, the chicken pan-genome is a useful resource for biological discovery and breeding. It improves our understanding of chicken genome diversity and provides materials to unveil the evolution history of chicken domestication.
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  • 47
    Publication Date: 2021-07-01
    Description: Aspect sentiment classification is an important research topic in natural language processing and computational linguistics, assisting in automatically review analysis and emotional tendency judgement. Different from extant methods that focus on text sequence representations, this paper presents a network framework to learn representation from concurrence-words relation graph (LRCWG), so as to improve the Macro-F1 and accuracy. The LRCWG first employs the multi-head attention mechanism to capture the sentiment representation from the sentences which can learn the importance of text sequence representation. And then, it leverages the priori sentiment dictionary information to construct the concurrence relations of sentiment words with Graph Convolution Network (GCN). This assists in that the learnt context representation can keep both the semantics integrity and the features of sentiment concurrence-words relations. The designed algorithm is experimentally evaluated with all the five benchmark datasets and demonstrated that the proposed aspect sentiment classification can significantly improve the prediction performance of learning task.
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  • 48
    Publication Date: 2021-07-28
    Description: Penelope-like elements (PLEs) are an enigmatic clade of retrotransposons whose reverse transcriptases (RTs) share a most recent common ancestor with telomerase RTs. The single ORF of canonical endonuclease (EN)+ PLEs encodes RT and a C-terminal GIY–YIG EN that enables intrachromosomal integration, whereas EN− PLEs lack EN and are generally restricted to chromosome termini. EN+ PLEs have only been found in animals, except for one case of horizontal transfer to conifers, whereas EN− PLEs occur in several kingdoms. Here, we report a new, deep-branching PLE clade with a permuted domain order, whereby an N-terminal GIY–YIG EN is linked to a C-terminal RT by a short domain with a characteristic CxC motif. These N-terminal EN+ PLEs share a structural organization, including pseudo-LTRs and complex tandem/inverted insertions, with canonical EN+ PLEs from Penelope/Poseidon, Neptune, and Nematis clades, and show insertion bias for microsatellites, but lack canonical hammerhead ribozyme motifs. However, their phylogenetic distribution is much broader. The Naiads, found in numerous invertebrate phyla, can reach tens of thousands of copies per genome. In spiders and clams, Naiads independently evolved to encode selenoproteins containing multiple selenocysteines. Chlamys, which lack the CCHH motif universal to PLE ENs, occur in green algae, spike mosses (targeting ribosomal DNA), and slime molds. Unlike canonical PLEs, RTs of N-terminal EN+ PLEs contain the insertion-in-fingers domain (IFD), strengthening the link between PLEs and telomerases. Additionally, we describe Hydra, a novel metazoan C-terminal EN+ clade. Overall, we conclude that PLE diversity, taxonomic distribution, and abundance are comparable with non-LTR and LTR-retrotransposons.
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  • 49
    Publication Date: 2021-07-28
    Description: In mammals, the placenta mediates maternal–fetal nutrient and waste exchange and acts in an immunomodulatory way to facilitate maternal–fetal tolerance. The placenta is highly diverse across mammalian species, yet the molecular mechanisms that distinguish the placenta of human from other mammals are not fully understood. Using an interspecies transcriptomic comparison of human, macaque, and mouse late-gestation placentae, we identified hundreds of genes with lineage-specific expression—including dozens that are placentally enriched and potentially related to pregnancy. We further annotated the enhancers for different human tissues using epigenomic data and demonstrate that the placenta and chorion are unique in that their enhancers display the least conservation. We identified numerous lineage-specific human placental enhancers and found they highly overlap with specific families of endogenous retroviruses (ERVs), including MER21A, MER41A/B, and MER39B that were previously linked to immune response and placental function. Among these ERV families, we further demonstrate that MER41A/B insertions create dozens of lineage-specific serum response factor-binding loci in human, including one adjacent to FBN2, a placenta-specific gene with increased expression in humans that produces the peptide hormone placensin to stimulate glucose secretion and trophoblast invasion. Overall, our results demonstrate the prevalence of lineage-specific placental enhancers which are frequently associated with ERV insertions and likely facilitate the lineage-specific evolution of the mammalian placenta.
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  • 50
    Publication Date: 2021-07-28
    Description: True sea snakes (Hydrophiini) are among the last and most successful clades of vertebrates that show secondary marine adaptation, exhibiting diverse phenotypic traits and lethal venom systems. To better understand their evolution, we generated the first chromosome-level genomes of two representative Hydrophiini snakes, Hydrophis cyanocinctus and H. curtus. Through comparative genomics we identified a great expansion of the underwater olfaction-related V2R gene family, consisting of more than 1,000 copies in both snakes. A series of chromosome rearrangements and genomic structural variations were recognized, including large inversions longer than 30 megabase (Mb) on sex chromosomes which potentially affect key functional genes associated with differentiated phenotypes between the two species. By integrating multiomics we found a significant loss of the major weapon for elapid predation, three-finger toxin genes, which displayed a dosage effect in H. curtus. These genetic changes may imply mechanisms that drove the divergent evolution of adaptive traits including prey preferences between the two closely related snakes. Our reference-quality sea snake genomes also enrich the repositories for addressing important issues on the evolution of marine tetrapods, and provide a resource for discovering marine-derived biological products.
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  • 51
    Publication Date: 2021-07-29
    Description: The recent and exclusively in humans and a few other higher primates expressed APOL1 (apolipoprotein L1) gene is linked to African human trypanosomiasis (also known as African sleeping sickness) as well as to different forms of kidney diseases. Whereas APOL1’s role as a trypanolytic factor is well established, pathobiological mechanisms explaining its cytotoxicity in renal cells remain unclear. In this study, we compared the APOL family members using a combination of evolutionary studies and cell biological experiments to detect unique features causal for APOL1 nephrotoxic effects. We investigated available primate and mouse genome and transcriptome data to apply comparative phylogenetic and maximum likelihood selection analyses. We suggest that the APOL gene family evolved early in vertebrates and initial splitting occurred in ancestral mammals. Diversification and differentiation of functional domains continued in primates, including developing the two members APOL1 and APOL2. Their close relationship could be diagnosed by sequence similarity and a shared ancestral insertion of an AluY transposable element. Live-cell imaging analyses showed that both expressed proteins show a strong preference to localize at the endoplasmic reticulum (ER). However, glycosylation and secretion assays revealed that—unlike APOL2—APOL1 membrane insertion or association occurs in different orientations at the ER, with the disease-associated mutants facing either the luminal (cis) or cytoplasmic (trans) side of the ER. The various pools of APOL1 at the ER offer a novel perspective in explaining the broad spectrum of its observed toxic effects.
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  • 52
    Publication Date: 2021-07-29
    Description: Sexually dimorphic development is responsible for some of the most remarkable phenotypic variation found in nature. Alternative splicing of the transcription factor gene doublesex (dsx) is a highly conserved developmental switch controlling the expression of sex-specific pathways. Here, we leverage sex-specific differences in butterfly wing color pattern to characterize the genetic basis of sexually dimorphic development. We use RNA-seq, immunolocalization, and motif binding site analysis to test specific predictions about the role of dsx in the development of structurally based ultraviolet (UV) wing patterns in Zerene cesonia (Southern Dogface). Unexpectedly, we discover a novel duplication of dsx that shows a sex-specific burst of expression associated with the sexually dimorphic UV coloration. The derived copy consists of a single exon that encodes a DNA binding but no protein-binding domain and has experienced rapid amino-acid divergence. We propose the novel dsx paralog may suppress UV scale differentiation in females, which is supported by an excess of Dsx-binding sites at cytoskeletal and chitin-related genes with sex-biased expression. These findings illustrate the molecular flexibility of the dsx gene in mediating the differentiation of secondary sexual characteristics.
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  • 53
    Publication Date: 2021-08-28
    Description: The fishery for Northern Atlantic cod (Gadus morhua) off Newfoundland and Labrador, Eastern Canada, presents the most spectacular case of an exploited stock crashed in a few decades by an industrial bottom trawl fishery under a seemingly sophisticated management regime after half a millennium of sustainable fishing. The fishery, which had generated annual catches of 100000 to 200000 tonnes from the beginning of the 16th century to the 1950s,  peaked in 1968 at 810000 tonnes, followed by a devastating collapse and closure 24 years later. Since then, stock recovery may have been hindered by premature openings, with vessels targeting the remains of the cod population. Previous research paid little attention towards using multicentury time series to inform sustainable catches and recovery plans. Here, we show that a simple stock assessment model can be used to model the cod population trajectory for the entire period from 1508 to 2019 for which catch estimates are available. The model suggests that if fishing effort and mortality had been stabilized in the 1980s,  precautionary annual yields of about 200000 tonnes could have been sustained. Our analysis demonstrates the value of incorporating prior knowledge to counteract shifting baseline effects on reference points and contemporary perceptions of historical stock status.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
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  • 54
    Publication Date: 2021-08-13
    Description: Since 1996, the European Union has required that fishery products of 35 fish species or groups of species, including crustaceans and cephalopods, be graded before being landed on the basis of commercial size-categories. A multi-stage sampling scheme to estimate catch-at-length and catch-at-age compositions of total annual landings has been conducted in Portuguese waters since 2009. All species and their size-categories are sampled concurrently from random trips within representatively selected site-days annually. In an effort to improve cost-efficiency of the biological catch sampling of commercial landings in Portugal, a size- category sampling scheme was tested during 2017, taking advantage of the stratification of horse mackerel landings, induced by the mandatory grading of landings by size-category. The total number of site-days (primary sampling units), fish boxes sampled, and specimens of horse mackerel sampled for length and age across strata during the pilot study were 30%, 57%, and 12% of the sampling carried out under the standard concurrent scheme, respectively. The assignment of horse mackerel length to the six commercial size-categories was highly consistent across site-days. Our study shows that the concurrent sampling, where trips are subsampled within site-days, could miss some size-categories by chance, resulting in poor estimates of catch-at-length especially for small fish present at the market during a site-day. The size-category sampling scheme ensured subsamples of fish from all size-categories within a site-day, and achieved data on catch-at-age that are fit-for purpose at 24% of the total cost for the standard concurrent sampling. The effect of sampling designs and sample sizes on horse mackerel stock assessment outputs showed that the onshore biological sampling to estimate catch-at-age compositions for stock assessment is optimized with the size-category sampling scheme. Pilot field experiments should be carried out for selected species that evidence consistent size grading among commercial categories.
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  • 55
    Publication Date: 2021-06-15
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 56
    Publication Date: 2021-06-30
    Description: The mechanisms by which transposable elements (TEs) can be horizontally transferred between animals are unknown, but viruses are possible candidate vectors. Here, we surveyed the presence of host-derived TEs in viral genomes in 35 deep sequencing data sets produced from 11 host–virus systems, encompassing nine arthropod host species (five lepidopterans, two dipterans, and two crustaceans) and six different double-stranded (ds) DNA viruses (four baculoviruses and two iridoviruses). We found evidence of viral-borne TEs in 14 data sets, with frequencies of viral genomes carrying a TE ranging from 0.01% to 26.33% for baculoviruses and from 0.45% to 7.36% for iridoviruses. The analysis of viral populations separated by a single replication cycle revealed that viral-borne TEs originating from an initial host species can be retrieved after viral replication in another host species, sometimes at higher frequencies. Furthermore, we detected a strong increase in the number of integrations in a viral population for a TE absent from the hosts’ genomes, indicating that this TE has undergone intense transposition within the viral population. Finally, we provide evidence that many TEs found integrated in viral genomes (15/41) have been horizontally transferred in insects. Altogether, our results indicate that multiple large dsDNA viruses have the capacity to shuttle TEs in insects and they underline the potential of viruses to act as vectors of horizontal transfer of TEs. Furthermore, the finding that TEs can transpose between viral genomes of a viral species sets viruses as possible new niches in which TEs can persist and evolve.
    Print ISSN: 0737-4038
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  • 57
    Publication Date: 2021-06-30
    Description: In higher plants, whole-genome duplication (WGD) is thought to facilitate the evolution of C4 photosynthesis from C3 photosynthesis. To understand this issue, we used new and existing leaf-development transcriptomes to construct two coding sequence databases for C4Gynandropsis gynandra and C3Tarenaya hassleriana, which shared a WGD before their divergence. We compared duplicated genes in the two species and found that the WGD contributed to four aspects of the evolution of C4 photosynthesis in G. gynandra. First, G. gynandra has retained the duplicates of ALAAT (alanine aminotransferase) and GOGAT (glutamine oxoglutarate aminotransferase) for nitrogen recycling to establish a photorespiratory CO2 pump in bundle sheath (BS) cells for increasing photosynthesis efficiency, suggesting that G. gynandra experienced a C3–C4 intermediate stage during the C4 evolution. Second, G. gynandra has retained almost all known vein-development-related paralogous genes derived from the WGD event, likely contributing to the high vein complexity of G. gynandra. Third, the WGD facilitated the evolution of C4 enzyme genes and their recruitment into the C4 pathway. Fourth, several genes encoding photosystem I proteins were derived from the WGD and are upregulated in G. gynandra, likely enabling the NADH dehydrogenase-like complex to produce extra ATPs for the C4 CO2 concentration mechanism. Thus, the WGD apparently played an enabler role in the evolution of C4 photosynthesis in G. gynandra. Importantly, an ALAAT duplicate became highly expressed in BS cells in G. gynandra, facilitating nitrogen recycling and transition to the C4 cycle. This study revealed how WDG may facilitate C4 photosynthesis evolution.
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  • 58
    Publication Date: 2021-06-02
    Description: We report the discovery of large amounts of previously undetected cold neutral atomic hydrogen (H i) around the core triplet galaxies in the nearby NGC 7232 galaxy group with MeerKAT. With a physical resolution of ∼1 kpc, we detect a complex web of low-surface-brightness H i emission down to a 4σ column density level of ∼1 × 1019 cm−2 (over 44  km s−1). The newly discovered H i streams extend over ∼20 arcmin corresponding to 140 kpc in projection. This is approximately three times the H i extent of the galaxy triplet (52 kpc). The H i debris has an H i mass of ∼6.6 × 109 M⊙, more than 50 per cent of the total H i mass of the triplet. Within the galaxy triplet, NGC 7233 and NGC 7232 have lost a significant amount of H i while NGC 7232B appears to have an excess of H i. The H i deficiency in NGC 7232 and NGC 7233 indicates that galaxy–galaxy interaction in the group concentrates on this galaxy pair while the other disc galaxies have visited them over time. In comparison to the AMIGA sample of isolated galaxies, we find that with regards to its total H i mass the NGC 7232/3 galaxy triplet is not H i-deficient. Despite the many interactions associated to the triplet galaxies, no H i seems to have been lost from the group (yet).
    Print ISSN: 0035-8711
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  • 59
    Publication Date: 2021-06-04
    Description: Clustering is a widely used technique in data mining applications and various pattern recognition applications, in which data objects are divided into groups. K-means algorithm is one of the most classical clustering algorithms. In this algorithm, the initial clustering centers are randomly selected, this results in unstable clustering results. To solve this problem, an optimized algorithm to select the initial centers is proposed. In the proposed algorithm, dispersion degree is defined, which is based on entropy. In the algorithm, all the objects are firstly grouped into a big cluster, and the object that has the maximum dispersion degree and the object that has the minimum dispersion degree are selected as the initial clustering centers from the initial big cluster. And then other objects in the biggest cluster are partitioned to the initial clusters to which the objects are nearest. The partition process will be repeated until the cluster number is equal to the specified value k. Finally, the partitioned k clusters and their cluster centers are applied to k-means algorithm as initial clusters and centers. Several experiments are conducted on real data sets to evaluate the proposed algorithm. The proposed algorithm is compared with traditional k-means algorithm and max-min distance clustering algorithm, and experimental results show that the improved k-means algorithm is stable in selecting initial clustering, because it can select unique initial clustering centers. The optimized algorithm’s effectiveness and feasibility are also verified by experiments, and the algorithm can reduce the times of iterations and has more stable clustering results and higher accuracy.
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  • 60
    Publication Date: 2021-05-18
    Description: Pathogens and associated outbreaks of infectious disease exert selective pressure on human populations, and any changes in allele frequencies that result may be especially evident for genes involved in immunity. In this regard, the 1346-1353 Yersinia pestis-caused Black Death pandemic, with continued plague outbreaks spanning several hundred years, is one of the most devastating recorded in human history. To investigate the potential impact of Y. pestis on human immunity genes, we extracted DNA from 36 plague victims buried in a mass grave in Ellwangen, Germany in the 16th century. We targeted 488 immune-related genes, including HLA, using a novel in-solution hybridization capture approach. In comparison with 50 modern native inhabitants of Ellwangen, we find differences in allele frequencies for variants of the innate immunity proteins Ficolin-2 and NLRP14 at sites involved in determining specificity. We also observed that HLA-DRB1*13 is more than twice as frequent in the modern population, whereas HLA-B alleles encoding an isoleucine at position 80 (I-80+), HLA C*06:02 and HLA-DPB1 alleles encoding histidine at position 9 are half as frequent in the modern population. Simulations show that natural selection has likely driven these allele frequency changes. Thus, our data suggest that allele frequencies of HLA genes involved in innate and adaptive immunity responsible for extracellular and intracellular responses to pathogenic bacteria, such as Y. pestis, could have been affected by the historical epidemics that occurred in Europe.
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  • 61
    Publication Date: 2021-05-14
    Description: Advances in phylogenomics contribute toward resolving long-standing evolutionary questions. Notwithstanding, genetic diversity contained within more than a billion biological specimens deposited in natural history museums remains recalcitrant to analysis owing to challenges posed by its intrinsically degraded nature. Yet that tantalizing resource could be critical in overcoming taxon sampling constraints hindering our ability to address major evolutionary questions. We addressed this impediment by developing phyloHyRAD, a new bioinformatic pipeline enabling locus recovery at a broad evolutionary scale from HyRAD-X exome capture of museum specimens of low DNA integrity using a benchtop RAD-derived exome-complexity-reduction probe set developed from high DNA integrity specimens. Our new pipeline can also successfully align raw RNAseq transcriptomic and ultraconserved element reads with the RAD-derived probe catalog. Using this method, we generated a robust timetree for Carabinae beetles, the lack of which had precluded study of macroevolutionary trends pertaining to their biogeography and wing-morphology evolution. We successfully recovered up to 2,945 loci with a mean of 1,788 loci across the exome of specimens of varying age. Coverage was not significantly linked to specimen age, demonstrating the wide exploitability of museum specimens. We also recovered fragmentary mitogenomes compatible with Sanger-sequenced mtDNA. Our phylogenomic timetree revealed a Lower Cretaceous origin for crown group Carabinae, with the extinct Aplothorax Waterhouse, 1841 nested within the genus Calosoma Weber, 1801 demonstrating the junior synonymy of Aplothorax syn. nov., resulting in the new combination Calosomaburchellii (Waterhouse, 1841) comb. nov. This study compellingly illustrates that HyRAD-X and phyloHyRAD efficiently provide genomic-level data sets informative at deep evolutionary scales.
    Electronic ISSN: 1759-6653
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  • 62
    Publication Date: 2021-04-30
    Description: Laplacian support vector machine (LapSVM) is an extremely popular classification method and relies on a small number of labels and a Laplacian regularization to complete the training of the support vector machine (SVM). However, the training of SVM model and Laplacian matrix construction are usually two independent process. Therefore, In this paper, we propose a new adaptive LapSVM method to realize semi-supervised learning with a primal solution. Specifically, the hinge loss of unlabelled data is considered to maximize the distance between unlabelled samples from different classes and the process of dealing with labelled data are similar to other LapSVM methods. Besides, the proposed method embeds the Laplacian matrix acquisition into the SVM training process to improve the effectiveness of Laplacian matrix and the accuracy of new SVM model. Moreover, a novel optimization algorithm considering primal solver is proposed to our adaptive LapSVM model. Experimental results showed that our method outperformed all comparison methods in terms of different evaluation metrics on both real datasets and synthetic datasets.
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  • 63
    Publication Date: 2021-05-14
    Description: Spectral clustering is widely applied in real applications, as it utilizes a graph matrix to consider the similarity relationship of subjects. The quality of graph structure is usually important to the robustness of the clustering task. However, existing spectral clustering methods consider either the local structure or the global structure, which can not provide comprehensive information for clustering tasks. Moreover, previous clustering methods only consider the simple similarity relationship, which may not output the optimal clustering performance. To solve these problems, we propose a novel clustering method considering both the local structure and the global structure for conducting nonlinear clustering. Specifically, our proposed method simultaneously considers (i) preserving the local structure and the global structure of subjects to provide comprehensive information for clustering tasks, (ii) exploring the nonlinear similarity relationship to capture the complex and inherent correlation of subjects and (iii) embedding dimensionality reduction techniques and a low-rank constraint in the framework of adaptive graph learning to reduce clustering biases. These constraints are considered in a unified optimization framework to result in one-step clustering. Experimental results on real data sets demonstrate that our method achieved competitive clustering performance in comparison with state-of-the-art clustering methods.
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  • 64
    Publication Date: 2021-03-02
    Description: Summary We describe improvements to BAli-Phy, a Markov chain Monte Carlo (MCMC) program that jointly estimates phylogeny, alignment and other parameters from unaligned sequence data. Version 3 is substantially faster for large trees, and implements covarion models, additional codon models and other new models. It implements ancestral state reconstruction, allows prior selection for all model parameters, and can also analyze multiple genes simultaneously. Availability and implementation Software is available for download at http://www.bali-phy.org. C++ source code is freely available on Github under the GPL2 License. Supplementary information Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 65
    Publication Date: 2021-01-21
    Description: Thermoacidophilic archaea belonging to the order Sulfolobales thrive in extreme biotopes, such as sulfuric hot springs and ore deposits. These microorganisms have been model systems for understanding life in extreme environments, as well as for probing the evolution of both molecular genetic processes and central metabolic pathways. Thermoacidophiles, such as the Sulfolobales, use typical microbial responses to persist in hot acid (e.g. motility, stress response, biofilm formation), albeit with some unusual twists. They also exhibit unique physiological features, including iron and sulfur chemolithoautotrophy, that differentiate them from much of the microbial world. Although first discovered 〉50 years ago, it was not until recently that genome sequence data and facile genetic tools have been developed for species in the Sulfolobales. These advances have not only opened up ways to further probe novel features of these microbes but also paved the way for their potential biotechnological applications. Discussed here are the nuances of the thermoacidophilic lifestyle of the Sulfolobales, including their evolutionary placement, cell biology, survival strategies, genetic tools, metabolic processes and physiological attributes together with how these characteristics make thermoacidophiles ideal platforms for specialized industrial processes.
    Print ISSN: 0168-6445
    Electronic ISSN: 1574-6976
    Topics: Biology
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  • 66
    Publication Date: 2021-08-01
    Print ISSN: 1063-7869
    Electronic ISSN: 1468-4780
    Topics: Physics
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  • 67
    Publication Date: 2021-10-29
    Print ISSN: 1054-660X
    Electronic ISSN: 1555-6611
    Topics: Physics
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  • 68
    Publication Date: 2021-10-29
    Description: Summary Stoneley modes are a special subset of normal modes whose energy is confined along the core-mantle boundary. As such, they offer a unique glimpse into Earth structure at the base of the mantle. They are often observed through coupling with mantle modes due to rotation, ellipticity and lateral heterogeneity, though they can be detected without such coupling. In this study, we explore the relative sensitivities of seismic spectra of two low-frequency Stoneley modes to several factors, taking as reference the fully coupled computation up to 3 mHz in model S20RTS. The factors considered are (i) theoretical, by exploring the extent to which various coupling approximations can accurately reproduce reference spectra; and (ii) model-based, by exploring how various Earth parameters such as core-mantle boundary topography, attenuation, and S-wave and P-wave structures, and the seismic source solution may influence the spectra. We find that mode-pair coupling is insufficiently accurate, but coupling modes within a range of ±0.1 mHz produces acceptable spectra, compared to full coupling. This has important implications for splitting function measurements, which are computed under the assumption of isolated modes or at best, mode-pair or group coupling. We find that uncertainties in the P-wave velocity mantle model dominate compared to other model parameters. In addition, we also test several hypothetical models of mantle density structure against real data. These tests indicate that, with the low-frequency Stoneley mode spectral data considered here, it is difficult to make any firm statement on whether the large-low-shear-velocity-provinces are denser or lighter than their surroundings. We conclude that better constraints on long wavelength elastic mantle structure, particularly P-wave velocity, need to be obtained, before making further statements on deep mantle density heterogeneity. In particular, a dense anomaly confined to a thin layer at the base of the mantle (less than ∼100-200 km) may not be resolvable using the two Stoneley modes tested here, while the ability of higher frequency Stoneley modes to resolve it requires further investigations.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
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  • 69
    Publication Date: 2021-10-27
    Description: Using the recent GAIA eDR3 catalogue we construct a sample of solar neighbourhood isolated wide binaries satisfying a series of strict signal-to-noise data cuts, exclusion of random association criteria and detailed colour-magnitude diagram selections, to minimize the presence of any kinematic contaminating effects having been discussed in the literature to date. Our final high-purity sample consists of 423 binary pairs within 130 pc of the sun and in all cases high-quality GAIA single-stellar fits for both components of each binary (final average RUWE values of 0.99), both also restricted to the cleanest region of the main sequence. We find kinematics fully consistent with Newtonian expectations for separations, s, below 0.009 pc, with relative velocities scaling with ΔV∝s−1/2 and a total binary mass, Mb, velocity scaling consistent with $Delta V propto M_{b}^{1/2}$. For the separation region of s 〉 0.009 pc we obtain significantly different results, with a separation independent ΔV ≈ 0.5 km/s and a $Delta V propto M_{b}^{0.24 pm 0.21}$. This situation is reminiscent of the low acceleration galactic baryonic Tully-Fisher phenomenology, and indeed, the change from the two regimes we find closely corresponds to the a ≲ a0 transition. These results are at odds not only with Newtonian expectations, but also with MOND predictions, where the presence of an external field effect implies only small deviations from Newtonian dynamics are expected for Solar Neighbourhood wide binaries.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
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  • 70
    Publication Date: 2021-10-29
    Description: Understanding the spatial distribution of metals within galaxies allows us to study the processes of chemical enrichment and mixing in the interstellar medium (ISM). In this work, we map the two-dimensional distribution of metals using a Gaussian Process Regression (GPR) for 19 star-forming galaxies observed with the Very Large Telescope/Multi Unit Spectroscopic Explorer (VLT–MUSE) as part of the PHANGS–MUSE survey. We find that 12 of our 19 galaxies show significant two-dimensional metallicity variation. Those without significant variations typically have fewer metallicity measurements, indicating this is due to the dearth of H ii regions in these galaxies, rather than a lack of higher-order variation. After subtracting a linear radial gradient, we see no enrichment in the spiral arms versus the disc. We measure the 50 per cent correlation scale from the two-point correlation function of these radially-subtracted maps, finding it to typically be an order of magnitude smaller than the fitted GPR kernel scale length. We study the dependence of the two-point correlation scale length with a number of global galaxy properties. We find no relationship between the 50 per cent correlation scale and the overall gas turbulence, in tension with existing theoretical models. We also find more actively star forming galaxies, and earlier type galaxies have a larger 50 per cent correlation scale. The size and stellar mass surface density do not appear to correlate with the 50 per cent correlation scale, indicating that perhaps the evolutionary state of the galaxy and its current star formation activity is the strongest indicator of the homogeneity of the metal distribution.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
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  • 71
    Publication Date: 2021-10-01
    Description: Mo/alumina cermet-based selective coatings are of great interest for concentrated solar-thermal power systems, in particular, parabolic trough collectors. We report on the sputter deposition of high-performance multilayer Mo/alumina cermet coatings on stainless steel with a solar absorptance of 94% and a thermal emittance of 8% (at 400 °C), and excellent thermal stability. The selective coatings were deposited in a 0.95 m3 sputtering chamber in order to correlate the deposition parameters, such as presence of residual gases, deposition power, and sputtering method (DC or RF), with the coating composition and the resulting optical properties. X-ray photoelectron spectroscopy, x-ray diffraction, and Raman spectroscopy have been applied to quantitatively describe the effect of residual oxygen on the distribution of oxidation states of Mo in the metallic infrared reflector layer, the high and low metallic volume fraction cermet layers, as well as the composition of the alumina top layer. The results provide strategies to obtain optimal selective coatings under conditions where residual oxygen cannot be avoided, which are essential for a successful transition from a laboratory to pre-industrial scale of vacuum deposition systems.
    Electronic ISSN: 2053-1591
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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  • 72
    Publication Date: 2021-10-27
    Description: Butterfly hysteresis behaviors show more complicated characteristics than single-loop hysteresis behaviors, which include two crossed single loops in opposite orientation. Most available hysteresis models used for describing the single-loop hysteresis behavior fail to predict the butterfly hysteresis. Therefore, it is a great challenge to build a hysteresis model to describe the butterfly hysteresis behavior. To this end, butterfly hysteresis operators including the butterfly play operator, the butterfly Krasnosel’skii–Pokrovskii kernel, and the butterfly asymmetric shift operator, are proposed to describe butterfly hysteresis effects. To further improve the modeling accuracy, a butterfly hysteresis structure containing the butterfly hysteresis operator and the neural networks for weight prediction and unmodeled dynamics is developed. The validation of the proposed structure is carried out on a dielectric elastomer-actuated system.
    Print ISSN: 0964-1726
    Electronic ISSN: 1361-665X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 73
    Publication Date: 2021-10-01
    Description: Performance of MOF-derived micrometer porous Fe2O3 as the oxidizer in Zr-fuelled thermite is compared with commercial nano-sized Fe2O3 by characterizing thermal and combustion behavior of Fe2O3/Zr mixture via differential scanning calorimetry, optical emission measurement as well as composition and morphology analysis on condensed combustion products. Results show that thermal behaviors of Fe2O3/Zr with a slow heating rate have little difference regardless of the kind of Fe2O3. However, MOF-derived micrometer porous Fe2O3 show an obvious superiority in enhancing combustion of Fe2O3/Zr heated by a high rate. Combustion reactions of Fe2O3/Zr under high heating rates are probably rate-controlled by condensed reaction. The better performance of MOF-derived Fe2O3 is attributed to its larger contact area with Zr particle in that micrometer porous Fe2O3 particles are easily broken into primitive nano-sized particles, which effectively avoid the agglomeration of oxidizer. The MOF-derived Fe2O3 particles obtained at calcination temperature of 550 °C enable the best combustion performance of Fe2O3/Zr thermite. This should be because the crystallinity and porous structure of 550 °C-Fe2O3 are more favorable for the mass transfer process during high-rate combustion.
    Electronic ISSN: 2053-1591
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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  • 74
    Publication Date: 2021-10-29
    Description: The generation of a large cold plasma jet while maintaining the reproducibility and homogeneity of the discharge is one of the major challenges encountered by the plasma community to efficiently apply this technology in the industry. Here, we report on the discharge in a recently developed device called the plasma candle (PC), wherein a stable plasma jet with a diameter of 20 mm can be generated at atmospheric pressure and temperature. Unlike the discharge morphology previously reported for conventional plasma jet devices, the unique configuration of PC device resulted in distinctive discharge patterns. Homogenous discharge was generated in the electrode gap and followed by a swirling discharge toward the tube nozzle. Fast photography and electrical measurements revealed that filament propagation and its morphology form the visually observable swirl discharge. Detailed analysis indicated that residual helium metastable species (Hem) and their penning ionization play an essential role in the discharge mode and its transition, which was verified by changing the feeding gas and the frequency of the applied voltage. For instance, it is found that only filamentary discharge was observed along the entire tube at frequencies less than 3 kHz, at which the time between consecutive discharges was long enough for Hem decay. Consequently, the homogenous discharge pattern was recovered by increasing the pre-ionization levels by adding a trace of impurities (N2, O2 or H2O) to the feeding gas. However, the level of these impurities must be carefully adjusted to achieve a homogenous discharge without negatively affecting the jet properties. A trivial change in the gas impurity, in the range of adsorption and desorption of water from the gas tubing, is sufficient to cause a noticeable change and instability in the discharge mode. This finding is critical to predicting the production of reactive species and plasma-surface interaction for different applications.
    Print ISSN: 0022-3727
    Electronic ISSN: 1361-6463
    Topics: Physics
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  • 75
    Publication Date: 2021-11-01
    Electronic ISSN: 1367-2630
    Topics: Physics
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  • 76
    Publication Date: 2021-11-01
    Electronic ISSN: 1367-2630
    Topics: Physics
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  • 77
    Publication Date: 2021-10-29
    Print ISSN: 0031-8949
    Electronic ISSN: 1402-4896
    Topics: Physics
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  • 78
    Publication Date: 2021-10-20
    Description: Summary Whole genome assembly (WGA) of bacterial genomes with short reads is a quite common task as DNA sequencing has become cheaper with the advances of its technology. The process of assembling a genome has no absolute golden standard and it requires to perform a sequence of steps each of which can involve combinations of many different tools. However, the quality of the final assembly is always strongly related to the quality of the input data. With this in mind we built WGA-LP, a package that connects state-of-the-art programs for microbial analysis and novel scripts to check and improve the quality of both samples and resulting assemblies. WGA-LP, with its conservative decontamination approach, has shown to be capable of creating high quality assemblies even in the case of contaminated reads. Availability and implementation WGA-LP is available on GitHub (https://github.com/redsnic/WGA-LP) and Docker Hub (https://hub.docker.com/r/redsnic/wgalp). The web app for node visualization is hosted by shinyapps.io (https://redsnic.shinyapps.io/ContigCoverageVisualizer/). Supplementary information Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 79
    Publication Date: 2021-10-29
    Print ISSN: 0031-8949
    Electronic ISSN: 1402-4896
    Topics: Physics
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  • 80
    Publication Date: 2021-10-20
    Description: An exomoon on a non-perfectly circular orbit experiences tidal heating that is capable to significantly contribute to the thermal brightness of the moon. Here we argue that the thermal heat is unevenly distributed on the moon’s surface, the emission of the tidal heat is limited to a few hotspots on the surface. A well-known example is the tidally heated Io. Due to their significantly increased temperature, the hotspots enhance the energy emission in thermal wavelengths. We made simulations using Monte Carlo method to examine this contribution, and to predict about the possible detectability of such a spotted exomoon. We found that in the case of large, Earth-sized companions to Jupiters around red dwarf stars exhibit a thermal flux that enables the direct detection of the moon, due to its photometric signal that can exceed ≈100 ppm in the most favourable configurations.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
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  • 81
    Publication Date: 2021-10-27
    Description: Grain boundary (GB) segregation can substantially affect the performance of materials by greatly changing the chemical compositions of GB. It is well known that GB segregation is essentially attributed to the structural differences between the bulk of grain and GB. Nevertheless, we still lack a clear understanding about the correlation between nanoscale intergranular structures and solute segregation. In this work, by using the phase-field crystal model, we performed atomic scale simulations to investigate the segregation of Li atoms to symmetric ⟨110⟩ tilt GBs in binary Al–Li alloys. It was found that the amount of segregated solute increases proportionally to GB misorientation angle in the case of low-angle tilt GBs, and converges at high-angle tilt GBs, except some special GBs with coincidence-site lattice. This is analogous to the dependences of GB energy and density on the misorientation angle. The correlations among GB structure, misfit strain around GBs and solute segregation are quantified at atomic scale. In low-angle tilt GBs, Li atoms are segregated to the compress zone around the core of intergranular dislocations to release the misfit strain energy. In the general high-angle tilt GBs, since the GB structure and misfit strain energy is uniform, the segregated atoms distribute homogeneously along GB. Particularly, the regular arrangement of structural units in some low Σ GBs lead to very low misfit strain energy, and accordingly to a periodically distributed and very low amount of solute segregation.
    Print ISSN: 0965-0393
    Electronic ISSN: 1361-651X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 82
    Publication Date: 2021-10-29
    Description: Nephrops (Nephrops norvegicus) is an economically valuable target species in the North Sea. Although individual Nephrops populations are scattered, the crustacean is managed regionally by the European Union (EU). The spatial competition for fisheries in the North Sea is growing especially due to expanding offshore wind farms (OWF) and newly implemented marine protected areas (MPA). Moreover, the Brexit affects the availability of EU fishing quotas and adds to the overall uncertainty EU fishers face. We compare landings and catches to scientifically advised quantities and perform an overlap analysis of fishing grounds with current and future OWFs and MPAs. Furthermore, we explore the German Nephrops fleet using high-resolution spatial fishing effort and catch data. Our results confirm earlier studies showing that Nephrops stocks have been fished above scientific advice. Present OWFs and MPAs marginally overlap with Nephrops fishing grounds, whereas German fishing grounds are covered up to 45% in future scenarios. Co-use strategies with OWFs could mitigate the loss of fishing opportunities. Decreased cod quotas due to Brexit and worse stock conditions, lowers Germany's capability to swap Nephrops quotas with the UK. We support the call for a new management strategy of individual Nephrops populations and the promotion of selective fishing gears.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
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  • 83
    Publication Date: 2021-10-01
    Electronic ISSN: 2515-7639
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 84
    Publication Date: 2021-10-30
    Description: Assessment of zooplankton abundance, distribution, community composition, and temporal variability is critical to understanding the effects of climate variability and change on lower trophic level production and availability for consumption by larger consumers. Zooplankton sampling is performed across the Canadian continental shelf system by Fisheries and Oceans Canada's Atlantic Zone Monitoring Programme (AZMP). Sampling includes semi-monthly to monthly collection of zooplankton using vertical net tows (VNTs) deployed from near-bottom to surface at stations on the central Scotian Shelf (Stn 2, 150 m depth) and Newfoundland Shelf (Stn 27, 175 m depth), and by Continuous Plankton Recorders (CPRs) in the near-surface layers along routes over the Scotian and Newfoundland shelves (0–10 m depth). Here, we compare abundance metrics for 11 copepod taxa collected using both gear types in both regions between 1999 and 2015. Seasonal cycles of VNT and CPR abundance were similar for near-surface residents. VNT: CPR abundance ratios varied year-round for vertical migrants, as ontogenetic migrants shifted their vertical distribution, and as diel migrants changed their migratory behaviour. For some taxa, differences in annual average VNT: CPR abundance ratios between regions suggest differences in vertical distribution, while for others differences in inter-annual variability for VNT and CPR abundances suggest differences in the dynamics of the near- and sub-surface components of the populations.
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  • 85
    Publication Date: 2021-11-02
    Description: In this paper, an integrated microprism matrix for light coupling and optical sensing systems is presented. The matrix was fabricated by use of controlled negative pressure glass thermal reflow process by the use of monocrystalline mold. The single glass microprism had height of 250 µm or 350 µm with base width respectively 350 µm or 500 µm. The matrix was formed by 10 × 10 microprisms with distance between the microprisms from 150 µm to 400 µm. It corresponded to total area of the matrixes from 28 mm2 to 74 mm2. The controlled coupling of the beam into a substrate was obtained through determination of optimal geometric dimensions of microprisms and configuration of a measurement setup. Optimal position of the fluorescence induction light source in relation to the matrixes (0.5 cm to 4.5 cm distance, 30° angle of incidence) and microfluidic channel (4 mm) were determined. The fluorimetric tests (with excitation by 470 nm laser diode in all the experiments) carried out using fluorescein solution, microbeads and porcine oocyte indicated the possibility of using a microprism matrix for fluorimetric image-based 500 nm long-pass detection in lab-on-a-chip platforms.
    Print ISSN: 0960-1317
    Electronic ISSN: 1361-6439
    Topics: Electrical Engineering, Measurement and Control Technology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 86
    Publication Date: 2021-10-01
    Description: In order to meet the requirements of future national defense for high temperature electromagnetic (EM) absorbing performance, a series of FexCo30Ni60−xSi5Al5 (x = 30, 35, 40, 45) high-entropy alloys (HEAs) powders was prepared and their Curie temperatures (TC) were measured by a self-made Wheatstone bridge. According to the results, varying the Fe/Ni ratio affected the crystal structure, Curie temperature, oxidation resistance, and electromagnetic absorbing properties of the above compounds. Since Fe has a BCC structure and is thus easier to form the solid solutions with Si and Al, the crystal structure of the alloy has changed from FCC toward BCC with increasing Fe dopant content. In turn, the Curie temperature (TC) decreased from 473.68 °C to 358.07 °C, being lower than their initial oxidation temperature (〉800 °C). The reflection losses (RL) of powders at room temperature and high temperatures (≤500 °C) were calculated as well. It was found that the flake powders after ball milling gained a larger aspect ratio, resulting in the better absorption effect, which was due to high toughness and low strength characteristics of the initial FCC structure. Furthermore, the permittivity and permeability of alloys upon heating reached impedance matching at a certain temperature, thus achieving the greater RLmax value. Finally, the high-temperature EM absorption characteristics of HEAs were shown to merit a thorough study.
    Electronic ISSN: 2053-1591
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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  • 87
    Publication Date: 2021-11-01
    Description: Neutron radiation induces point defects and affects the diffusivity of atoms and the kinetics of precipitation. The phase-field simulation reveals the influence of migration energy of vacancy on the radiation-enhanced precipitation in Fe–Cu alloy. The study shows that radiation-enhanced diffusion (RED) also depends on the diffusivity of vacancy-associated migration energy and not only on the dose rate; the low migration energy of vacancy results in accelerated precipitation and a higher volume fraction of Cu precipitates. Interestingly, decreasing migration energy from 1.0 eV to 0.9 eV results in a 30% increase in the precipitates’ volume fraction. Also, the combination of the lowest dose rate 5.0 × 10−3 dpa s−1 and highest migration energy 1.0 eV delays the precipitation. The study also examines the influence of migration energy of vacancy on the radius of Cu precipitates. The lowest migration energy, 0.9 eV, increases the radius up to one-third. Finally, the work presents the drawbacks of the analytical digital image processing technique in the quantitative comparison with the script.
    Print ISSN: 0965-0393
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  • 88
    Publication Date: 2021-10-29
    Description: Kilovoltage cone-beam computed tomography (CBCT)-based image-guided radiation therapy (IGRT) is used for daily delivery of radiation therapy, especially for stereotactic body radiation therapy (SBRT), which imposes particularly high demands for setup accuracy. The clinical applications of CBCTs are constrained, however, by poor soft tissue contrast, image artifacts, and instability of Hounsfield unit (HU) values. Here, we propose a new deep learning-based method to generate synthetic CTs (sCT) from thoracic CBCTs. A deep-learning model which integrates histogram matching (HM) into a cycle-consistent adversarial network (Cycle-GAN) framework, called HM-Cycle-GAN, was trained to learn mapping between thoracic CBCTs and paired planning CTs. Perceptual supervision was adopted to minimize blurring of tissue interfaces. An informative maximizing loss was calculated by feeding CBCT into the HM-Cycle-GAN to evaluate the image histogram matching between the planning CTs and the sCTs. The proposed algorithm was evaluated using data from 20 SBRT patients who each received 5 fractions and therefore 5 thoracic CBCTs. To reduce the effect of anatomy mismatch, original CBCT images were pre-processed via deformable image registrations with the planning CT before being used in model training and result assessment. We used planning CTs as ground truth for the derived sCTs from the correspondent co-registered CBCTs. The mean absolute error (MAE), peak signal-to-noise ratio (PSNR), and normalized cross-correlation (NCC) indices were adapted as evaluation metrics of the proposed algorithm. Assessments were done using Cycle-GAN as the benchmark. The average MAE, PSNR, and NCC of the sCTs generated by our method were 66.2 HU, 30.3 dB, and 0.95, respectively, over all CBCT fractions. Superior image quality and reduced noise and artifact severity were seen using the proposed method compared to the results from the standard Cycle-GAN method. Our method could therefore improve the accuracy of IGRT and corrected CBCTs could help improve online adaptive RT by offering better contouring accuracy and dose calculation.
    Electronic ISSN: 2057-1976
    Topics: Biology , Medicine , Physics , Technology
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  • 89
    Publication Date: 2021-10-30
    Print ISSN: 1754-9957
    Electronic ISSN: 1754-9965
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Law , Economics
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  • 90
    Publication Date: 2021-11-01
    Electronic ISSN: 2058-8585
    Topics: Electrical Engineering, Measurement and Control Technology
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  • 91
    Publication Date: 2021-10-29
    Description: Purpose. To investigate indirect radiation-induced changes in airways as precursors to atelectasis post radiation therapy (RT). Methods. Three Wisconsin Miniature Swine (WMS TM ) underwent a research course of 60 Gy in 5 fractions delivered to a targeted airway/vessel in the inferior left lung. The right lung received a max point dose
    Electronic ISSN: 2057-1976
    Topics: Biology , Medicine , Physics , Technology
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  • 92
    Publication Date: 2021-10-28
    Description: Mg alloys are highly expected for the wide application in the next-generation industry, while significant improvement of the plasticity of polycrystalline Mg alloys is crucial. For this purpose, it is essential to get insights into the atomic configurations, energetics, and mechanical responses of Mg grain boundaries (GBs). In this study, we investigated the overall features of atomic configurations and energies of [ 1 1 ¯ 00 ] and [ 1 2 ¯ 10 ] symmetric tilt GBs in hcp Mg by density-functional theory. We systematically constructed atomic models of coincidence-site lattice GBs by the arrangement of structural units in the full range of rotation angles. We observed that special GBs show clear cusps in both the GB-energy and excess-volume curves against the rotation angle. The reason of the stability/instability of each GB configuration was analyzed by ab initio local energy and local stress based on Bader partitioning. The features of local energies and stresses in Mg GBs are quite different from those in other materials with covalent or partial-covalent bonding nature. We observed substantial variations of local energies, local stresses and Bader charges of GB atoms, and charge inhomogeneity in a GB region, reflecting the structural disorder. Stable GBs are characterized by modest ranges of such variations and by moderate charge homogeneity. These results could be utilized in general to understand the interface stability and deformation mechanism of Mg and other simple metals.
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  • 93
    Publication Date: 2021-10-30
    Description: Mitigating bycatch of non-target fish species is a common objective in fisheries management that may be supported by the gathering of data from fishery observer programs and quantitative analysis of bycatch risk factors. We build three GLM models based on Chinese tuna longline fishery observer data in terms of analysis of total bycatch rate (TB rate), total bycatch ratio (TB ratio), and species-specific bycatch rate, respectively. The positive log-linear models assumed a Gaussian observation error model and a linear combination of categorical independent variables, including area, year, month, depth, and bycatch species. Results show that distributions of TB rate and TB ratio followed different trends and a latitudinal decrease was observed from both the northern and southern hemisphere of the equator. Comprehensively, the Pacific is a better place to fish compared to the Indian and Atlantic Oceans in terms of relatively lower TB rate and TB ratio. Fishing in open oceans can somehow avoid a high TB ratio than fishing in coastal waters. As a result, we recommend area 2SW, 2SE, 2 NW, 14SW, 14SE, and 14 NW as appropriate fishing ground for Albacore (Thunnus alalunga) while area 11N,  11S, 18SW, and 18SE to be appropriate fishing ground for fishing bigeye tuna (Thunnus obesus). Setting fishing gears deeper than 500 m would also help to get a low TB rate and TB ratio.
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  • 94
    Publication Date: 2021-10-28
    Description: The European Variation Archive (EVA; https://www.ebi.ac.uk/eva/) is a resource for sharing all types of genetic variation data (SNPs, indels, and structural variants) for all species. The EVA was created in 2014 to provide FAIR access to genetic variation data and has since grown to be a primary resource for genomic variants hosting 〉3 billion records. The EVA and dbSNP have established a compatible global system to assign unique identifiers to all submitted genetic variants. The EVA is active within the Global Alliance of Genomics and Health (GA4GH), maintaining, contributing and implementing standards such as VCF, Refget and Variant Representation Specification (VRS). In this article, we describe the submission and permanent accessioning services along with the different ways the data can be retrieved by the scientific community.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 95
    Publication Date: 2021-10-28
    Description: The DMASS sample is a photometric sample from the DES Year 1 data set designed to replicate the properties of the CMASS sample from BOSS, in support of a joint analysis of DES and BOSS beyond the small overlapping area. In this paper, we present the measurement of galaxy-galaxy lensing using the DMASS sample as gravitational lenses in the DES Y1 imaging data. We test a number of potential systematics that can bias the galaxy-galaxy lensing signal, including those from shear estimation, photometric redshifts, and observing conditions. After careful systematic tests, we obtain a highly significant detection of the galaxy-galaxy lensing signal, with total S/N = 25.7. With the measured signal, we assess the feasibility of using DMASS as gravitational lenses equivalent to CMASS, by estimating the galaxy-matter cross-correlation coefficient rcc. By jointly fitting the galaxy-galaxy lensing measurement with the galaxy clustering measurement from CMASS, we obtain $r_{ m cc}=1.09^{+0.12}_{-0.11}$ for the scale cut of 4h−1 Mpc and $r_{ m cc}=1.06^{+0.13}_{-0.12}$ for 12h−1 Mpc in fixed cosmology. By adding the angular galaxy clustering of DMASS, we obtain rcc = 1.06 ± 0.10 for the scale cut of 4h−1 Mpc and rcc = 1.03 ± 0.11 for 12h−1 Mpc. The resulting values of rcc indicate that the lensing signal of DMASS is statistically consistent with the one that would have been measured if CMASS had populated the DES region within the given statistical uncertainty. The measurement of galaxy-galaxy lensing presented in this paper will serve as part of the data vector for the forthcoming cosmology analysis in preparation.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 96
    Publication Date: 2021-10-29
    Description: Although many studies have been done and advanced progress has been made in understanding partial discharge (PD) behavior in the void, this is not the case firinception of PD, especially its stochastic nature. The statistical behaviors of PD inception voltage (PDIV) and inception time delay (PDTD) inside the void were investigated in this study through repeated tests to observe the stochastic nature of PD inception. The results show that the PDIV and PDTD of the void are highly dispersed and obey Weibull and exponential distributions, respectively. The significant dispersion of PDIV can be attributed to the statistical time delay of PD inception. The lengthy inception delay is attributable to a lack of free electrons. The exponential distribution of PDTD indicates that free-electron generation is completely random; further, the stochastic nature of void PD inception is determined by the supply of free electrons. The test method (voltage rise rate, test time, and test time interval), void parameters (size, material, and surface condition), and background radiation determine PD inception by affecting the volume ionization or surface-emission process providing free electrons. Enhanced background ionization or significant increase in test voltage and test time allow for the effective detection of void defects during PD tests. This work contributes to an empirical understanding of the physical process of PD inception in voids and improving existing PD testing technologies.
    Print ISSN: 0022-3727
    Electronic ISSN: 1361-6463
    Topics: Physics
    Published by Institute of Physics
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  • 97
    Publication Date: 2021-10-29
    Print ISSN: 0143-0807
    Electronic ISSN: 1361-6404
    Topics: Physics
    Published by Institute of Physics
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  • 98
    Publication Date: 2021-10-29
    Print ISSN: 0143-0807
    Electronic ISSN: 1361-6404
    Topics: Physics
    Published by Institute of Physics
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  • 99
    Publication Date: 2021-10-30
    Description: Eukaryotic genome and methylome encode DNA fragments’ propensity to form nucleosome particles. Although the mechanical properties of DNA possibly orchestrate such encoding, the definite link between ‘omics’ and DNA energetics has remained elusive. Here, we bridge the divide by examining the sequence-dependent energetics of highly bent DNA. Molecular dynamics simulations of 42 intact DNA minicircles reveal that each DNA minicircle undergoes inside-out conformational transitions with the most likely configuration uniquely prescribed by the nucleotide sequence and methylation of DNA. The minicircles’ local geometry consists of straight segments connected by sharp bends compressing the DNA’s inward-facing major groove. Such an uneven distribution of the bending stress favors minimum free energy configurations that avoid stiff base pair sequences at inward-facing major grooves. Analysis of the minicircles’ inside-out free energy landscapes yields a discrete worm-like chain model of bent DNA energetics that accurately account for its nucleotide sequence and methylation. Experimentally measuring the dependence of the DNA looping time on the DNA sequence validates the model. When applied to a nucleosome-like DNA configuration, the model quantitatively reproduces yeast and human genomes’ nucleosome occupancy. Further analyses of the genome-wide chromatin structure data suggest that DNA bending energetics is a fundamental determinant of genome architecture.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 100
    Publication Date: 2021-10-29
    Description: There is a widely observed phenomenon in the microwave absorption field that an absorber always exhibits good oblique incidence absorption capacity if it has high performance at normal incidence. However, if a certain angle is exceeded, this kind of effective absorptive capacity will no longer be maintained. Besides, an absorber performs differently for incident transverse electric (TE) and transverse magnetic (TM) waves: for the TE case, the absorber can no longer obtain effective absorption; for the TM case, another efficient absorption region was observed at higher frequencies even when the incident angle exceeded 80°. These phenomena are widely found in the literature, which demonstrates that they are caused by physical laws rather than material properties. To demonstrate the underlying reason, in this study, the common spherical carbonyl iron-polyurethane composite absorbers were fabricated as a typical example. Their absorbing performance was investigated via both simulation and experiment. All the phenomena mentioned above were observed, studied in detail by employing the multiple reflection model, and explained quantitatively. Further, along with establishing the underlying mechanism of electromagnetic wave transmission in the absorber, two formulas were deduced to predict: (a) the maximum incident angle for efficient absorption of the TE polarized wave; and (b) the required absorber thickness for obtaining efficient absorption for a large incident angle of the TM polarized wave.
    Print ISSN: 0022-3727
    Electronic ISSN: 1361-6463
    Topics: Physics
    Published by Institute of Physics
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