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  • Articles  (551)
  • Oxford University Press  (421)
  • American Institute of Physics  (69)
  • Taylor & Francis  (56)
  • American Association for the Advancement of Science (AAAS)
  • American Chemical Society (ACS)
  • American Geophysical Union (AGU)
  • American Institute of Physics (AIP)
  • 2020-2024  (551)
  • 2021  (551)
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  • 1
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    American Geophysical Union (AGU)
    In:  EPIC3Journal of Advances in Modeling Earth Systems, American Geophysical Union (AGU), 13(10), ISSN: 1942-2466
    Publication Date: 2023-06-21
    Description: We propose to make the damping time scale, which governs the decay of pseudo-elastic waves in the Elastic Viscous Plastic (EVP) sea-ice solvers, independent of the external time step and large enough to warrant numerical stability for a moderate number of internal time steps. A necessary condition is that the forcing on sea ice varies slowly on the damping time scale, in which case an EVP solution may still approach a Viscous Plastic one, but on a time scale longer than a single external time step. In this case, the EVP method becomes very close to the recently proposed modified EVP (mEVP) method in terms of stability and simulated behavior. In a simple test case dealing with sea ice breaking under the forcing of a moving cyclone, the EVP method with an enlarged damping time scale can simulate linear kinematic features which are very similar to those from the traditional EVP implementation, although a much smaller number of internal time steps is used. There is more difference in sea-ice thickness and linear kinematic features simulated in a realistic Arctic configuration between using the traditional and our suggested choices of EVP damping time scales, but it is minor considering model uncertainties associated with choices of many other parameters in sea-ice models.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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  • 2
    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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  • 3
    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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  • 4
    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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  • 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: 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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  • 6
    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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  • 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: 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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  • 8
    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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  • 9
    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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  • 10
    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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  • 11
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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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  • 12
    Publication Date: 2024-03-14
    Description: The presence of clouds in the Arctic regulates the surface energy budget (SEB) over the sea-ice surface and the ice-free ocean. Following several previous field campaigns, the cloud-radiation relationship, including cloud vertical structure and phase, has been elucidated; however, modeling of this relationship has matured slowly. In recognition of the recent decline in the Arctic sea-ice extent, representation of the cloud system in numerical models should consider the effects of areas covered by sea ice and ice-free areas. Using an in situ stationary meteorological observation data set obtained over the ice-free Arctic Ocean by the Japanese Research Vessel Mirai (September 2014), coordinated evaluation of six regional climate models (RCMs) with nine model runs was performed by focusing on clouds and the SEB. The most remarkable findings were as follows: (1) reduced occurrence of unstable stratification with low-level cloud water in all models in comparison to the observations, (2) significant differences in cloud water representations between single- and double-moment cloud schemes, (3) extensive differences in partitioning of hydrometeors including solid/liquid precipitation, and (4) pronounced lower-tropospheric air temperature biases. These issues are considered as the main sources of SEB uncertainty over ice-free areas of the Arctic Ocean. The results from a coupled RCM imply that the SEB is constrained by both the atmosphere and the ocean (and sea ice) with considerable feedback. Coordinated improvement of both stand-alone atmospheric and coupled RCMs would promote a more comprehensive and improved understanding of the Arctic air-ice-sea coupled system.
    Repository Name: EPIC Alfred Wegener Institut
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  • 13
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    American Geophysical Union (AGU)
    In:  EPIC3Journal of Geophysical Research Earth Surface, American Geophysical Union (AGU), 126(12), ISSN: 2169-9003
    Publication Date: 2024-03-14
    Description: Bedforms of Thwaites Glacier, West Antarctica both record and affect ice flow, as shown by geophysical data and simple models. Thwaites Glacier flows across the tectonic fabric of the West Antarctic rift system with its bedrock highs and sedimentary basins. Swath radar and seismic surveys of the glacier bed have revealed soft-sediment flutes 100 m or more high extending 15 km or more across basins downglacier from bedrock highs. Flutes end at prominent hard-bedded moats on stoss sides of the next topographic highs. We use simple models to show that ice flow against topography increases pressure between ice and till upglacier along the bed over a distance that scales with the topography. In this basal zone of high pressure, ice-contact water would be excluded, thus increasing basal drag by increasing ice-till coupling and till flux, removing till to allow bedrock erosion that creates moats. Till carried across highlands would then be deposited in lee-side positions forming bedforms that prograde downglacier over time, and that remain soft on top through feedbacks that match till-deformational fluxes from well upglacier of the topography. The bedforms of the part of Thwaites surveyed here are prominent because ice flow has persisted over a long time on this geological setting, not because ice flow is anomalous. Bedform development likely has caused evolution of ice flow over time as till and lubricating water were redistributed, moats were eroded and bedforms grew.
    Repository Name: EPIC Alfred Wegener Institut
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  • 14
    Publication Date: 2024-04-22
    Description: Large stocks of soil organic carbon (SOC) have accumulated in the northern hemisphere permafrost region, but their current mounts and future fate remain uncertain. By analyzing an unprecedented dataset combining 〉2,700 soil profiles with environmental variables in a geospatial framework, we generated spatially explicit estimates of permafrost-region SOC stocks, quantified spatial heterogeneity, and identified key environmental predictors. We estimated 1014−175+194 Pg C are stored in the top 3 m of permafrost region soils. The greatest uncertainties occurred in circumpolar toe-slope positions and in flat areas of the Tibetan region. We found that soil wetness index and elevation are the dominant topographic controllers and surface air temperature (circumpolar region) and precipitation (Tibetan region) are significant climatic controllers of SOC stocks. Our results provide the first high-resolution geospatial assessment of permafrost region SOC stocks and their relationships with environmental factors, which are crucial for modeling the response of permafrost affected soils to changing climate.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev , info:eu-repo/semantics/article
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  • 15
    Publication Date: 2024-01-18
    Description: The North Atlantic Basin is a major sink for atmospheric carbon dioxide (CO2) due in part to the extensive plankton blooms which form there supported by nutrients supplied by the three-dimensional ocean circulation. Hence, changes in ocean circulation and/or stratification may influence primary production and biological carbon export. In this study, we assess this possibility by evaluating inorganic nutrient budgets for 2004 and 2010 in the North Atlantic based on observations from the transatlantic A05-24.5°N and the Greenland-Portugal OVIDE hydrographic sections, to which we applied a box inverse model to solve the circulation and estimate the across-section nutrient transports. Full water column nutrient budgets were split into upper and lower meridional overturning circulation (MOC) limbs. According to our results, anomalous circulation in early 2010, linked to extreme negative NAO conditions, led to an enhanced northward advection of more nutrient-rich waters by the upper overturning limb, which resulted in a significant nitrate and phosphate convergence north of 24.5°N. Combined with heaving of the isopycnals, this anomalous circulation event in 2010 favored an enhancement of the nutrient consumption (5.7 ± 4.1 kmol-P s−1) and associated biological CO2 uptake (0.25 ± 0.18 Pg-C yr−1, upper-bound estimate), which represents a 50% of the mean annual sea–air CO2 flux in the region. Our results also suggest a transient state of deep silicate divergence in both years. Both results are indicative of a MOC-driven modulation of the biological carbon uptake (by the upper MOC limb) and nutrient inventories (by the lower MOC limb) in the North Atlantic.
    Repository Name: EPIC Alfred Wegener Institut
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  • 16
    Publication Date: 2021-10-27
    Description: The origin of the eclogites that reside in cratonic mantle roots has long been debated. In the classic Roberts Victor kimberlite locality in South Africa, the strongly contrasting textural and geochemical features of two types of eclogites have led to different genetic models. We studied a new suite of 63 eclogite xenoliths from the former Roberts Victor Mine. In addition to major- and trace-element compositions for all new samples, we determined 18O/16O for garnet from 34 eclogites. Based on geochemical and textural characteristics we identify a large suite of Type I eclogites (n = 53) consistent with previous interpretations that these rocks originate from metamorphosed basaltic-picritic lavas or gabbroic cumulates from oceanic crust, crystallised from melts of depleted MORB mantle. We identify a smaller set of Type II eclogites (n = 10) based on geochemical and textural similarity to eclogites in published literature. We infer their range to very low δ18O values combined with their varied, often very low Zr/Hf ratios and LREE-depleted nature to indicate a protolith origin via low-pressure clinopyroxene-bearing oceanic cumulates formed from melts that were more depleted in incompatible elements than N-MORB. These compositions are indicative of derivation from a residual mantle source that experienced preferential extraction of incompatible elements and fractionation of Zr-Hf during previous melting.
    Print ISSN: 0022-3530
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  • 17
    Publication Date: 2021-10-27
    Description: We present results from a new cosmological hydrodynamics simulation campaign of protocluster (PC) regions, FOREVER22: FORmation and EVolution of galaxies in Extremely-overdense Regions motivated by SSA22. The simulations cover a wide range of cosmological scales using three different zoom set-ups in a parent volume of $(714.2~ m cMpc)^{3}$: PCR (Proto-Cluster Region; V = (28.6 cMpc)3, SPH particle mass, mSPH = 4.1 × 106 M⊙ and final redshift, zend = 2.0), BCG (Brightest proto-Cluster Galaxy; V ∼ (10 cMpc)3, mSPH = 5.0 × 105 M⊙ and zend = 4.0 ), and First ( V ∼ (3 cMpc)3, mSPH = 7.9 × 103 M⊙ and zend = 9.5) runs, that allow to focus on different aspects of galaxy formation. In the PCR runs, we follow 10 PCs, each harbouring 1–4 SMBHs with ${ m M_{ m BH}}ge 10^{9}~{ m M_{odot }}$. One of the PC cores shows a spatially close arrangement of seven starburst galaxies with ${ m SFR} gtrsim 100~{ m { m M_{odot }}~{ m yr^{-1}}}$ each, that are dust-obscured and would appear as submillimeter galaxies with flux ≳ 1  mJy at $1.1~ m mm$ in observations. The BCG runs show that the total SFRs of haloes hosting BCGs are affected by AGN feedback, but exceed $1000~{ m { m M_{odot }}~{ m yr^{-1}}}$ at z ≲ 6. The First runs resolve mini-haloes hosting population (Pop) III stars and we show that, in PC regions, the dominant stellar population changes from Pop III to Pop II at z ≳ 20, and the first galaxies with ${ m SFR} gtrsim 18~{ m { m M_{odot }}~{ m yr^{-1}}}$ form at z ∼ 10. These can be prime targets for future observations with the James Webb Space Telescope. Our simulations successfully reproduce the global star formation activities in observed PCs and suggest that PCs can kickstart cosmic reionization.
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  • 18
    Publication Date: 2021-10-27
    Description: Using hydrodynamical N-body simulations, we show that the observed structure and kinematics of the extremely metal-poor, dwarf irregular galaxy DDO 68 is compatible with a merger event with at least two smaller satellite galaxies. We were able to obtain a self-consistent model that simultaneously reproduces several of its observed features, including: the very asymmetric and disturbed shape of the stellar component, the overall ${ m H, small {I}}$ distribution and its velocity field, the arc-like stellar structure to the west, the low-surface brightness stellar stream to the north. The model implies the interaction of the main progenitor of DDO 68 with two systems with dynamical masses 7 × 108 M⊙ and almost 108 M⊙ – 1/20 and 1/150 times the dynamical mass of DDO 68, respectively. We show that the merger between DDO 68 and the most massive of its satellites offers a route to explain the large offset of DDO 68 from the mass-metallicity relation. Assuming that the interacting galaxies have metallicities prior to the merger compatible with those of galaxies with similar stellar masses, we provide quantitative evidence that gas mixing alone does not suffice at diluting the gas of the two components; according to our simulations, the ${ m H, small {II}}$ regions observed along the Cometary Tail trace the low metallicity of the accreted satellite rather than that of DDO 68’s main body. In this case, the mass corresponding to the low metallicity is that of the secondary body and DDO 68 becomes consistent with the mass-metallicity relation.
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  • 19
    Publication Date: 2021-10-27
    Description: We study differential rotation in late-stage shell convection in a 3D hydrodynamic simulation of a rapidly rotating 16 M⊙ helium star with a particular focus on the convective oxygen shell. We find that the oxygen shell develops a quasi-stationary pattern of differential rotation that is neither described by uniform angular velocity as assumed in current stellar evolution models of supernova progenitors, nor by uniform specific angular momentum. Instead, the oxygen shell develops a positive angular velocity gradient with faster rotation at the equator than at the pole by tens of percent. We show that the angular momentum transport inside the convection zone is not adequately captured by a diffusive mixing-length flux proportional to the angular velocity or angular momentum gradient. Zonal flow averages reveal stable large-scale meridional flow and an entropy deficit near the equator that mirrors the patterns in the angular velocity. The structure of the flow is reminiscent of simulations of stellar surface convection zones and the differential rotation of the Sun, suggesting that similar effects are involved; future simulations will need to address in more detail how the interplay of buoyancy, inertial forces, and turbulent stresses shapes differential rotation during late-stage convection in massive stars. If convective regions develop positive angular velocity gradients, angular momentum could be shuffled out of the core region more efficiently, potentially making the formation of millisecond magnetars more difficult. Our findings have implications for neutron star birth spin periods and supernova explosion scenarios that involve rapid core rotation.
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  • 20
    Publication Date: 2021-10-27
    Description: We present a multi-wavelength investigation of the H ii region G347.600+00.211, located at a distance of 7.9 kpc. We analyse the gas and dust properties aiming to disentangle the origin of the region as well as its role in the formation of new stars. G347.600+00.211 is very conspicuous at 1420 MHz and infrared wavelengths, showing an incomplete shell-like structure with two distinct zones of very intense emission. The infrared bubble S8 is part of the shell structure. The spatial distribution of the molecular gas shows the presence of six clouds located around the ionized region and showing a good morphological correlation with the 8 μm emission. Cold dust is coincident with the dense gas shown in the CO measurements. As for the origin of the region, we found that the massive cluster [DBS2003]179 and two Wolf–Rayet (WR) stars are located at the same distance than the ionized gas. Based on a stellar density analysis, we inferred that one of the WR stars, 1181-81L, is also a probable member of the cluster. Both the cluster and the WR stars are not only within the ring–like structure, but are also located near the two spots of very heightened emission, suggesting they may be responsible for this bright emission. Finally, as expanding H ii regions are hypothesised to trigger star formation, we used different infrared point source catalogues to search for young stellar object candidates (cYSOs). A total of 33 cYSOs and 4 CH ii regions were identified projected on to the photo–dissociation regions and molecular clouds.
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  • 21
    Publication Date: 2021-10-27
    Description: Neutron stars in low mass X-ray binaries are hypothesised to emit continuous gravitational waves that may be detectable by ground-based observatories. The torque balance model predicts that a higher accretion rate produces larger-amplitude gravitational waves, hence low mass X-ray binaries with high X-ray flux are promising targets for gravitational wave searches. The detection of X-ray pulsations would identify the spin frequency of these neutron stars, and thereby improve the sensitivity of continuous gravitational-wave searches by reducing the volume of the search parameter space. We perform a semi-coherent search for pulsations in the two low mass X-ray binaries Scorpius X-1 and Cygnus X-2 using X-ray data from the Rossi X-ray Timing Explorer Proportional Counter Array. We find no clear evidence for pulsations, and obtain upper limits (at 90 per cent confidence) on the fractional pulse amplitude, with the most stringent being 0.034 per cent for Scorpius X-1 and 0.23 per cent for Cygnus X-2. These upper limits improve upon those in previous work by factors of ∼8.2 and ∼1.6 respectively.
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  • 22
    Publication Date: 2021-10-27
    Description: We develop a sophisticated model of FRB observations, accounting for the intrinsic cosmological gas distribution and host galaxy contributions, and give the most detailed account yet of observational biases due to burst width, dispersion measure, and the exact telescope beamshape. Our results offer a significant increase in both accuracy and precision beyond those previously obtained. Using results from ASKAP and Parkes, we present our best-fit FRB population parameters in a companion paper. Here, we consider in detail the expected and fitted distributions in redshift, dispersion measure, and signal-to-noise. We estimate that the unlocalised ASKAP FRBs arise from z 〈 0.5, with between a third and a half within z 〈 0.1. Our predicted source-counts (‘logN–logS’) distribution confirms previous indications of a steepening index near the Parkes detection threshold of 1 Jy ms. We find no evidence for a minimum FRB energy, and rule out Emin 〉 1039.0 erg at 90 per cent C.L. Importantly, we find that above a certain DM, observational biases cause the Macquart (DM–z) relation to become inverted, implying that the highest-DM events detected in the unlocalised Parkes and ASKAP samples are unlikely to be the most distant. More localized FRBs will be required to quantitatively estimate this effect, though its cause is a well-understood observational bias. Works assuming a 1–1 DM–z relation may therefore derive erroneous results. Our analysis of errors suggests that limiting factors in our analysis are understanding of FRB spectral behaviour, sensitivity response of search experiments, and the treatment of the repeating population and luminosity function.
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  • 23
    Publication Date: 2021-10-28
    Description: Structural variants have a considerable impact on human genomic diversity. However, their evolutionary history remains mostly unexplored. Here, we developed a new method to identify potentially adaptive structural variants based on a similarity-based analysis that incorporates genotype frequency data from 26 populations simultaneously. Using this method, we analyzed 57,629 structural variants and identified 576 structural variants that show unusual population differentiation. Of these putatively adaptive structural variants, we further showed that 24 variants are multiallelic and overlap with coding sequences, and 20 variants are significantly associated with GWAS traits. Closer inspection of the haplotypic variation associated with these putatively adaptive and functional structural variants reveals deviations from neutral expectations due to (i) population differentiation of rapidly evolving multi-allelic variants, (ii) incomplete sweeps, and (iii) recent population-specific negative selection. Overall, our study provides new methodological insights, documents hundreds of putatively adaptive variants, and introduces evolutionary models that may better explain the complex evolution of structural variants.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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  • 24
    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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  • 25
    Publication Date: 2021-10-28
    Description: The regeneration-associated gene (RAG) expression program is activated in injured peripheral neurons after axotomy and enables long-distance axon re-growth. Over 1000 genes are regulated, and many transcription factors are upregulated or activated as part of this response. However, a detailed picture of how RAG expression is regulated is lacking. In particular the transcriptional targets and specific functions of the various transcription factors are unclear. Jun was the first regeneration-associated transcription factor identified and the first shown to be functionally important. Here we fully define the role of Jun in the RAG expression program in regenerating facial motor neurons. At 1, 4, and 14 days after axotomy, Jun upregulates 11%, 23% and 44% of the RAG program, respectively. Jun functions relevant to regeneration include cytoskeleton production, metabolic functions and cell activation, and the down-regulation of neurotransmission machinery. In silico analysis of promoter regions of Jun targets identifies stronger over-representation of AP1-like sites than CRE-like sites, although CRE sites were also over-represented in regions flanking AP1 sites. Strikingly, in motor neurons lacking Jun, an alternative SRF-dependent gene expression program is initiated after axotomy. The promoters of these newly expressed genes exhibit over-representation of CRE sites in regions near to SRF target sites. This alternative gene expression program includes plasticity-associated transcription factors, and leads to an aberrant early increase in synapse density on motor neurons. Jun thus has the important function in the early phase after axotomy of pushing the injured neuron away from a plasticity response and towards a regenerative phenotype.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 26
    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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  • 27
    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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  • 28
    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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  • 29
    Publication Date: 2021-10-28
    Description: The demographics of dark matter substructure depend sensitively on the nature of dark matter. Optimally leveraging this probe requires accurate theoretical predictions regarding the abundance of subhaloes. These predictions are hampered by artificial disruption in numerical simulations, by large halo-to-halo variance, and by the fact that the results depend on the baryonic physics of galaxy formation. In particular, numerical simulations have shown that the formation of a central disc can drastically reduce the abundance of substructure compared to a dark matter-only simulation, which has been attributed to enhanced destruction of substructure due to disc shocking. We examine the impact of discs on substructure using the semi-analytical subhalo model SatGen, which accurately models the tidal evolution of substructure free of the numerical disruption that still hampers N-body simulations. Using a sample of 10,000 merger trees of Milky Way-like haloes, we study the demographics of subhaloes that are evolved under a range of composite halo–disc potentials with unprecedented statistical power. We find that the overall subhalo abundance is relatively insensitive to properties of the disc aside from its total mass. For a disc that contains 5% of Mvir, the mean subhalo abundance within rvir is suppressed by ${lesssim }10\%$ relative to the no-disc case, a difference that is dwarfed by halo-to-halo variance. For the same disc mass, the abundance of subhaloes within 50 kpc is reduced by ${sim }30\%$. We argue that the disc mainly drives excess mass loss for subhaloes with small pericentric radii and that the impact of disc shocking is negligible.
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  • 30
    Publication Date: 2021-10-28
    Description: The role of uric acid during primate evolution has remained elusive ever since it was discovered over 100 years ago that humans have unusually high levels of the small molecule in our serum. It has been difficult to generate a neutral or adaptive explanation in part because the uricase enzyme evolved to become a pseudogene in apes thus masking typical signals of sequence evolution. Adding to the difficulty is a lack of clarity on the functional role of uric acid in apes. One popular hypothesis proposes that uric acid is a potent antioxidant that increased in concentration to compensate for the lack of vitamin C synthesis in primate species ∼65 million years ago (Mya). Here, we have expanded on our previous work with resurrected ancient uricase proteins to better resolve the reshaping of uricase enzymatic activity prior to ape evolution. Our results suggest that the pivotal death-knell to uricase activity occurred between 20-30 Mya despite small sequential modifications to its catalytic efficiency for the tens of millions of years since primates lost their ability to synthesize vitamin C, and thus the two appear uncorrelated. We also use this opportunity to demonstrate how molecular evolution can contribute to biomedicine by presenting ancient uricases to human immune cells that assay for innate reactivity against foreign antigens. A highly stable and highly catalytic ancient uricase is shown to elicit a lower immune response in more human haplotypes than other uricases currently in therapeutic development.
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  • 31
    Publication Date: 2021-10-30
    Description: Background Almost half of aromatase inhibitor (AI)-treated breast cancer patients experience AI-associated musculoskeletal symptoms (AIMSS); 20-30% discontinue treatment because of severe symptoms. We hypothesized that we could identify predictors of pain reduction in AIMSS intervention trials by combining data from previously conducted trials. Methods We pooled patient-level data from 3 randomized trials testing interventions (omega-3 fatty acids, acupuncture, and duloxetine) for AIMSS that had similar eligibility criteria and the same patient-reported outcome measures. Only patients with baseline Brief Pain Inventory (BPI) average pain score of ≥ 4 of 10 were included. The primary outcome examined was 2-point reduction in average pain from baseline to week 12. Variable cut-point selection and logistic regression were used. Risk models were built by summing the number of factors statistically significantly associated with pain reduction. Analyses were stratified by study and adjusted for treatment arm. Results For the 583 analyzed patients, the four factors statistically significantly associated with pain reduction were FACT Functional Well-Being 〉24 and Physical Well-Being 〉14 (higher scores reflect better function), and WOMAC
    Electronic ISSN: 2515-5091
    Topics: Chemistry and Pharmacology , Medicine
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  • 32
    Publication Date: 2021-10-28
    Description: A simple model for star formation based on supernova (SN) feedback and gravitational heating via the collapse of perturbations in gravitationally unstable disks reproduces the Schmidt-Kennicutt relation between the star formation rate (SFR) per unit area, ΣSFR, and the gas surface density, Σg, remarkably well. The gas velocity dispersion, σg, is derived self-consistently in conjunction with ΣSFR and is found to match the observations. Gravitational instability triggers ‘gravito-turbulence’ at the scale of the least stable perturbation mode, boosting σg at $Sigma _{g}gtrsim , Sigma _{g}^extrm {thr}=50, { m M}_odot , { m pc}^{-2}$, and contributing to the pressure needed to carry the disk weight vertically. ΣSFR is reduced to the observed level at $Sigma _{g}gtrsim , Sigma _{g}^extrm {thr}$, whereas at lower surface densities, SN feedback is the prevailing energy source. Our proposed star formation recipes require efficiencies of order 1 per cent, and the Toomre parameter, Q, for the joint gaseous and stellar disk is predicted to be close to the critical value for marginal stability for $Sigma _{g}lesssim , Sigma _{g}^extrm {thr}$, spreading to lower values and larger gas velocity dispersion at higher Σg.
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  • 33
    Publication Date: 2021-10-29
    Description: Polycyclic Aromatic Hydrocarbons (PAHs) are carbon-based molecules resulting from the union of aromatic rings and related species, which are likely responsible for strong infrared emission features. In this work, using a sample of 50 Seyfert galaxies (DL 〈 100 Mpc) we compare the circumnuclear (inner kpc) PAH emission of AGN to that of a control sample of star-forming galaxies (22 luminous infrared galaxies and 30 H ii galaxies), and investigate the differences between central and extended PAH emission. Using Spitzer/InfraRed Spectrograph spectral data of Seyfert and star-forming galaxies and newly developed PAH diagnostic model grids, derived from theoretical spectra, we compare the predicted and observed PAH ratios. We find that star-forming galaxies and AGN-dominated systems are located in different regions of the PAH diagnostic diagrams. This suggests that not only are the size and charge of the PAH molecules different, but also the nature and hardness of the radiation field that excite them. We find tentative evidence that PAH ratios in AGN-dominated systems are consistent with emission from larger PAH molecules (Nc 〉 300–400) as well as neutral species. By subtracting the spectrum of the central source from the total, we compare the PAH emission in the central versus extended region of a small sample of AGN. In contrast to the findings for the central regions of AGN-dominated systems, the PAH ratios measured in the extended regions of both type 1 and type 2 Seyfert galaxies can be explained assuming similar PAH molecular size distribution and ionized fractions of molecules to those seen in central regions of star-forming galaxies (100 〈 Nc 〈 300).
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  • 34
    Publication Date: 2021-10-28
    Description: Motivation With the advancement of sequencing technologies, genomic data sets are constantly being expanded by high volumes of different data types. One recently introduced data type in genomic science is genomic signals, which are usually short-read coverage measurements over the genome. To understand and evaluate the results of such studies, one needs to understand and analyze the characteristics of the input data. Results SigTools is an R-based genomic signals visualization package developed with two objectives: 1) to facilitate genomic signals exploration in order to uncover insights for later model training, refinement, and development by including distribution and autocorrelation plots. 2) to enable genomic signals interpretation by including correlation, and aggregation plots. In addition, our corresponding web application, SigTools-Shiny, extends the accessibility scope of these modules to people who are more comfortable working with graphical user interfaces instead of command-line tools. Availability SigTools source code, installation guide, and manual is freely available on http://github.com/shohre73.
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  • 35
    Publication Date: 2021-10-28
    Print ISSN: 1363-2469
    Electronic ISSN: 1559-808X
    Topics: Architecture, Civil Engineering, Surveying , Geosciences
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  • 36
    Publication Date: 2021-10-01
    Print ISSN: 1070-6631
    Electronic ISSN: 1089-7666
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  • 37
    Publication Date: 2021-10-01
    Print ISSN: 1070-6631
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  • 38
    Publication Date: 2021-10-28
    Print ISSN: 1363-2469
    Electronic ISSN: 1559-808X
    Topics: Architecture, Civil Engineering, Surveying , Geosciences
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  • 39
    Publication Date: 2021-10-29
    Print ISSN: 1748-6025
    Electronic ISSN: 1748-6033
    Topics: Geosciences
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  • 40
    Publication Date: 2021-10-30
    Description: The Enthalpy Based Thermal Evolution of Loops (EBTEL) approximate model for static and dynamic coronal loops is developed to include the effect of a loop cross-sectional area which increases from the base of the transition region (TR) to the corona. The TR is defined as the part of a loop between the top of the chromosphere and the location where thermal conduction changes from an energy loss to an energy gain. There are significant differences from constant area loops due to the manner in which the reduced volume of the TR responds to conductive and enthalpy fluxes from the corona. For static loops with modest area variation the standard picture of loop energy balance is retained, with the corona and TR being primarily a balance between heating and conductive losses in the corona, and downward conduction and radiation to space in the TR. As the area at the loop apex increases, the TR becomes thicker and the density in TR and corona larger. For large apex areas, the coronal energy balance changes to one primarily between heating and radiation, with conduction playing an increasingly unimportant role, and the TR thickness becoming a significant fraction of the loop length. Approximate scaling laws are derived that give agreement with full numerical solutions for the density, but not the temperature. For non-uniform areas, dynamic loops have a higher peak temperature and are denser in the radiative cooling phase by of order 50% than the constant area case for the examples considered. They also show a final rapid cooling and draining once the temperature approaches 1 MK. Although the magnitude of the emission measure will be enhanced in the radiative phase, there is little change in the important observational diagnostic of its temperature dependence.
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  • 41
    Publication Date: 2021-10-01
    Electronic ISSN: 2158-3226
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  • 42
  • 43
    Publication Date: 2021-10-29
    Description: Neutron star models with maximum mass close to 2 M⊙ reach high central densities, which may activate nucleonic and hyperon direct Urca neutrino emission. To alleviate the tension between fast theoretical cooling rates and thermal luminosity observations of moderately magnetized, isolated thermally-emitting stars (with Lγ ≳ 1031 erg s−1 at t ≳ 105.3 yr), some internal heating source is required. The power supplied by the internal heater is estimated for both a phenomenological source in the inner crust and Joule heating due to magnetic field decay, assuming different superfluidity models and compositions of the outer stellar envelope. It is found that a thermal power of W(t) ≈ 1034 erg s−1 allows neutron star models to match observations of moderately magnetized, isolated stars with ages t ≳ 105.3 yr. The requisite W(t) can be supplied by Joule heating due to crust-confined initial magnetic configurations with (i) mixed poloidal-toroidal fields, with surface strength Bdip = 1013 G at the pole of the dipolar poloidal component and ∼90 per cent of the magnetic energy stored in the toroidal component; and (ii) poloidal-only configurations with Bdip = 1014 G.
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  • 44
    Publication Date: 2021-10-25
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
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  • 45
    Publication Date: 2021-07-19
    Print ISSN: 0309-8265
    Electronic ISSN: 1466-1845
    Topics: Geography
    Published by Taylor & Francis
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  • 46
    Publication Date: 2021-10-29
    Description: Summary The numerical simulation of seismic wave propagation in realistic heterogeneous media, as sedimentary basins, is a key element of seismic hazard estimation. Many numerical methods in two dimensions are based on unstructured triangular meshes and explicit time schemes. However, the presence of thin layers and tangential stratigraphic contacts in sedimentary basins entails poorly shaped mesh elements: some triangle heights are extremely small compared to the edge lengths, which requires small time steps in the simulations and thus leads to prohibitive computation times. We compare manual and automatic geological model simplification techniques to modify problematic areas of the domain, so as to improve the quality of the triangulated mesh. We modify the shape and the connectivity between rock units in the basin, with the objective to reduce the computation time without significantly changing the physical response of the geological medium. These simplification techniques are applied in an investigation of site effects in the lower Var valley, a densely urbanized area located near the city of Nice (South-East of France). Numerical simulations of plane wave propagation in a heterogeneous 2D profile are carried out with a discontinuous Galerkin finite element method. Five simplified meshes are generated and the impacts of the simplifications are analyzed in comparison to the reference model. We compare the time solutions and the transfer functions obtained on the surface of the basin. The results show that the simplification procedures, in particular automatic modifications of the model, yield a significant performance gain, with a ratio higher than 55, while having a negligible impact on the ground motion response.
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  • 47
    Publication Date: 2021-10-30
    Description: In this work, we use the constrained Gaussian realization technique to study the early growth of supermassive black holes (SMBHs) in cosmological hydrodynamic simulations, exploring its relationship with features of the initial density peaks on large scales, ∼ 1 h−1Mpc. Our constrained simulations of volume (20 h−1Mpc)3 successfully reconstruct the large-scale structure as well as the black hole growth for the hosts of the rare 109 M⊙ SMBHs found in the BlueTides simulation at z ∼ 7. We run a set of simulations with constrained initial conditions by imposing a $5 sigma _0( m R_G)$ peak on the scale of $ m R_G = 1$ h−1Mpc varying different peak features, such as the shape and compactness as well as the tidal field surrounding the peak. We find that initial density peaks with high compactness and low tidal field induce the most rapid BH growth at early epochs. This is because compact density peaks with a more spherical large scale matter distribution lead to the formation of the highest gas inflows (mostly radial) in the centers of halos which boost the early BH accretion. Moreover, such initially compact density peaks in low tidal field regions also lead to a more compact BH host galaxy morphology. Our findings can help explain the tight correlation between BH growth and host galaxy compactness seen in observations.
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  • 48
    Publication Date: 2021-10-30
    Description: We conducted a drift-scan observation campaign using the 305-m Arecibo telescope in January and March 2020 when the observatory was temporarily closed during the intense earthquakes and the initial outbreak of the COVID-19 pandemic, respectively. The primary objective of the survey was to search for fast radio transients, including Fast Radio Bursts (FRBs) and Rotating Radio Transients (RRATs). We used the 7-beam ALFA receiver to observe different sections of the sky within the declination region ∼(10–20) deg on 23 nights and collected 160 hours of data in total. We searched our data for single-pulse transients, of covering up to a maximum dispersion measure of 11 000 pc cm−3 at which the dispersion delay across the entire bandwidth is equal to the 13 s transit length of our observations. The analysis produced more than 18 million candidates. Machine learning techniques sorted the radio frequency interference and possibly astrophysical candidates, allowing us to visually inspect and confirm the candidate transients. We found no evidence for new astrophysical transients in our data. We also searched for emission from repeated transient signals, but found no evidence for such sources. We detected single pulses from two known pulsars in our observations and their measured flux densities are consistent with the expected values. Based on our observations and sensitivity, we estimated the upper limit for the FRB rate to be
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  • 49
    Publication Date: 2021-10-27
    Description: Background To observe a long-term prognosis in late-onset multiple acyl-coenzyme-A dehydrogenation deficiency(MADD) patients and to determine whether riboflavin should be administrated in the long-term and high-dosage manner. Methods We studied the clinical, pathological and genetic features of 110 patients with late-onset MADD in a single neuromuscular center. The plasma riboflavin levels and a long-term follow-up were performed. Results Fluctuating proximal muscle weakness, exercise intolerance and dramatic responsiveness to riboflavin treatment were essential clinical features for all 110 MADD patients. Among them, we identified 106 cases with ETFDH variants, 1 case with FLAD1 variants and 3 cases without causal variants. On muscle pathology, fibers with cracks, atypical ragged red fibers(aRRFs) and diffuse decrease of SDH activity were the distinctive features of these MADD patients. The plasma riboflavin levels before treatment were significantly decreased in these patients as compared to healthy controls. Among 48 MADD patients with a follow-up of 6.1 years on average, 31 patients were free of muscle weakness recurrence, while 17 patients had episodes of slight muscle weakness upon riboflavin withdrawal, but recovered after retaking a small-dose of riboflavin for a short-term. Multivariate Cox regression analysis showed vegetarian diet and masseter weakness were independent risk factors for muscle weakness recurrence. Conclusion Fibers with cracks, aRRFs and diffuse decreased SDH activity distinguish MADD from other genotypes of lipid storage myopathy. For late-onset MADD, increased fatty acid oxidation and reduced riboflavin levels can induce episodes of muscle symptoms, which can be treated by short-term and small-dose of riboflavin therapy.
    Print ISSN: 0964-6906
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  • 50
    Publication Date: 2021-10-27
    Description: Introduction In the era of personalized medicine with more and more patient specific targeted therapies being used, we need reliable, dynamic, faster, and sensitive biomarkers both to track the causes of disease and to develop and evolve therapies during the course of treatment. Metabolomics recently has shown substantial evidence to support its emerging role in disease diagnosis and prognosis. Aside from biomarkers and development of therapies, it is also an important goal to understand the involvement of mitochondrial DNA mtDNA in metabolic regulation, aging, and disease development. Somatic mutations of the mitochondrial genome are also heavily implicated in age-related disease and aging. The general hypothesis is that an alteration in the concentration of metabolite profiles (possibly conveyed by lifestyle and environmental factors) influences the increase of mutation rate in the mtDNA, and thereby contributes to a range of pathophysiological alterations observed in complex diseases. Methods We performed an inverted mitochondrial genome wide association analysis between mitochondrial nucleotide variants (mtSNVs) and concentration of metabolites. We used 151 metabolites and the whole sequenced mitochondrial genome from 2718 individuals to identify genetic variants associated with metabolite profiles. Because of the high coverage, next generation sequencing-based analysis of the mitochondrial genome allows for an accurate detection of mitochondrial heteroplasmy and for identification of variants associated with the metabolome. Results The strongest association was found for mt715G 〉 A located in the MT-12SrRNA with the metabolite ratio C2/C10:1 (p-value = 6.82*10−09, β = 0.909). The second most significant mtSNV was found for mt3714A 〉 G located in the MT-ND1 with the metabolite ratio PC ae C42:5/PC ae C44:5 (p-value = 1.02*10−08, β = 3.631). A large number of significant metabolite ratios were observed involving PC aa C36:6 and the variant mt10689G 〉 A, located in the MT-ND4L gene. Conclusion These results show an important interconnection between mitochondria and metabolite concentrations. Considering that some of the significant metabolites found in this study have been previously related to complex diseases such as neurological disorders and metabolic conditions, these associations found here might play a crucial role for further investigations of such complex diseases. Understanding the mechanisms that control human health and disease, in particular the role of genetic predispositions and their interaction with environmental factors is a prerequisite for the development of safe and efficient therapies for complex disorders.
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  • 51
    Publication Date: 2021-10-19
    Description: Motivation Reverse engineering of gene regulatory networks (GRNs) has long been an attractive research topic in system biology. Computational prediction of gene regulatory interactions has remained a challenging problem due to the complexity of gene expression and scarce information resources. The high-throughput spatial gene expression data, like in situ hybridization images that exhibit temporal and spatial expression patterns, has provided abundant and reliable information for the inference of GRNs. However, computational tools for analyzing the spatial gene expression data are highly underdeveloped. Results In this study, we develop a new method for identifying gene regulatory interactions from gene expression images, called ConGRI. The method is featured by a contrastive learning scheme and deep Siamese convolutional neural network architecture, which automatically learns high-level feature embeddings for the expression images and then feeds the embeddings to an artificial neural network to determine whether or not the interaction exists. We apply the method to a Drosophila embryogenesis dataset and identify GRNs of eye development and mesoderm development. Experimental results show that ConGRI outperforms previous traditional and deep learning methods by a large margin, which achieves accuracies of 76.7% and 68.7% for the GRNs of early eye development and mesoderm development, respectively. It also reveals some master regulators for Drosophila eye development. Availabilityand implementation https://github.com/lugimzheng/ConGRI. Supplementary information Supplementary data are available at Bioinformatics online.
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  • 52
    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.
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  • 53
    Publication Date: 2021-10-27
    Description: Parametric modeling of galaxy cluster density profiles from weak lensing observations leads to a mass bias, whose detailed understanding is critical in deriving accurate mass-observable relations for constraining cosmological models. Drawing from existing methods, we develop a robust framework for calculating this mass bias in one-parameter fits to simulations of dark matter haloes. We show that our approach has the advantage of being independent of the absolute noise level, so that only the number of haloes in a given simulation and the representativeness of the simulated haloes for real clusters limit the accuracy of the bias estimation. While we model the bias as a lognormal distribution and the haloes with a Navarro-Frenk-White profile, our method can be generalized to any bias distribution and parametric model of the radial mass distribution. We find that the lognormal assumption is not strictly valid in the presence of miscentring of haloes. We investigate the use of cluster centers derived from weak lensing in the context of mass bias, and tentatively find that such centroids can yield sensible mass estimates if the convergence peak has a signal-to-noise ratio approximately greater than four. In this context we also find that the standard approach to estimating the positional uncertainty of weak lensing mass peaks using bootstrapping severely underestimates the true positional uncertainty for peaks with low signal-to-noise ratios. Though we determine the mass and redshift dependence of the bias distribution for a few experimental setups, our focus remains providing a general approach to computing such distributions.
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  • 54
    Publication Date: 2021-10-27
    Description: 3C 84 (NGC 1275) is the radio source at the center of the Perseus Cluster and exhibits a bright radio jet. We observed the source with the Global Millimeter VLBI Array (GMVA) between 2008 and 2015, with a typical angular resolution of ∼50 μas. The observations revealed a consistent double nuclear structure separated by ∼770 gravitational radii assuming a Black Hole mass of 3.2 × 108 M⊙. The region is likely too broad and bright to be the true jet base anchored in the accretion disk or Black Hole ergosphere. A cone and parabola were fit to the stacked (time averaged) image of the nuclear region. The data did not strongly prefer either fit, but combined with a jet/counter-jet ratio analysis, an upper limit on the viewing angle to the inner jet region of ≤35○ was found. This provides evidence for a variation of the viewing angle along the jet (and therefore a bent jet) within ∼0.5 parsec of the jet launching region. In the case of a conical jet, the apex is located ∼2400 gravitational radii upstream of the bright nuclear region and up to ∼600 gravitational radii upstream in the parabolic case. We found a possible correlation between the brightness temperature and relative position angle of the double nuclear components, which may indicate rotation within the jet.
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  • 55
    Publication Date: 2021-10-30
    Description: Canonical non-homologous end-joining (cNHEJ) is the prominent mammalian DNA double-strand breaks (DSBs) repair pathway operative throughout the cell cycle. Phosphorylation of Ku70 at ser27-ser33 (pKu70) is induced by DNA DSBs and has been shown to regulate cNHEJ activity, but the underlying mechanism remained unknown. Here, we established that following DNA damage induction, Ku70 moves from nucleoli to the sites of damage, and once linked to DNA, it is phosphorylated. Notably, the novel emanating functions of pKu70 are evidenced through the recruitment of RNA Pol II and concomitant formation of phospho-53BP1 foci. Phosphorylation is also a prerequisite for the dynamic release of Ku70 from the repair complex through neddylation-dependent ubiquitylation. Although the non-phosphorylable ala-Ku70 form does not compromise the formation of the NHEJ core complex per se, cells expressing this form displayed constitutive and stress-inducible chromosomal instability. Consistently, upon targeted induction of DSBs by the I-SceI meganuclease into an intrachromosomal reporter substrate, cells expressing pKu70, rather than ala-Ku70, are protected against the joining of distal DNA ends. Collectively, our results underpin the essential role of pKu70 in the orchestration of DNA repair execution in living cells and substantiated the way it paves the maintenance of genome stability.
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    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 56
    Publication Date: 2021-10-27
    Description: Summary We present a technique for lithofacies classification of well-log data using an active semi-supervised algorithm. This method considers both the input of domain experts and the distribution characteristics of well-log properties. It aims to obtain lithofacies that are more geologically meaningful and seismically interpretable than the conventional clustering methods. We impose guidance from experts (e.g., geologist, petrophysicist and seismic interpreter) as pairwise constraints. The acquired constraints were incorporated into facies classification in two ways: modification of the objective function and optimization of the classification subspace. An iterative expectation-maximization (EM) algorithm was used to minimize the objective function. We applied the method to a set of well logs from the Glitne field, North Sea, where six lithofacies had been defined initially. Classification results illustrated that facies predicted with the semi-supervised approach achieved good matches with true labels. Comparisons among different methods (semi-supervised method, quadratic determinant analysis and expectation-maximization with Gaussian mixture model algorithm) also demonstrated that the proposed method significantly outperformed the others. We also tested a scenario with five facies, where we combined silty shale and shale into one group due to significant overlap in the elastic domain. Results demonstrated that the semi-supervised approach produced facies that were more consistent with expert intention, and they were more geologically interpretable. The techniques and results illustrated here could be performed in different types of reservoir facies classification, and the facies classified using semi-supervised algorithm honors the input of the users and data characteristics.
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  • 57
    Publication Date: 2021-10-27
    Description: We present the MaNGA PyMorph photometric Value Added Catalogue (MPP-VAC-DR17) and the MaNGA Deep Learning Morphological VAC (MDLM-VAC-DR17) for the final data release of the MaNGA survey, which is part of the SDSS Data Release 17 (DR17). The MPP-VAC-DR17 provides photometric parameters from Sérsic and Sérsic+Exponential fits to the 2D surface brightness profiles of the MaNGA DR17 galaxy sample in the g, r, and i bands (e.g. total fluxes, half light radii, bulge-disk fractions, ellipticities, position angles, etc.). The MDLM-VAC-DR17 provides Deep Learning-based morphological classifications for the same galaxies. The MDLM-VAC-DR17 includes a number of morphological properties: e.g. a T-Type, a finer separation between elliptical and S0, as well as the identification of edge-on and barred galaxies. While the MPP-VAC-DR17 simply extends the MaNGA PyMorph photometric VAC published in the SDSS Data Release 15 (MPP-VAC-DR15) to now include galaxies which were added to make the final DR17, the MDLM-VAC-DR17 implements some changes and improvements compared to the previous release (MDLM-VAC-DR15): namely, the low-end of the T-Types are better recovered in this new version. The catalogue also includes a separation between Early- or Late-type (ETG, LTG), which classifies the two populations in a complementary way to the T-Type, especially at the intermediate types (-1 〈 T-Type 〈 2), where the T-Type values show a large scatter. In addition, k −fold based uncertainties on the classifications are also provided. To ensure robustness and reliability, we have also visually inspected all the images. We describe the content of the catalogues and show some interesting ways in which they can be combined.
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  • 58
    Publication Date: 2021-10-27
    Description: We describe the Dark Energy Survey (DES) Deep Fields, a set of images and associated multi-wavelength catalogue (ugrizJHKs) built from Dark Energy Camera (DECam) and Visible and Infrared Survey Telescope for Astronomy (VISTA) data. The DES Deep Fields comprise 11 fields (10 DES supernova fields plus COSMOS), with a total area of ∼30 square degrees in ugriz bands and reaching a maximum i-band depth of 26.75 (AB, 10σ, 2″). We present a catalogue for the DES 3-year cosmology analysis of those four fields with full 8-band coverage, totalling 5.88 sq. deg. after masking. Numbering 2.8million objects (1.6million post masking), our catalogue is drawn from images coadded to consistent depths of r = 25.7, i = 25, z = 24.3 mag. We use a new model-fitting code, built upon established methods, to deblend sources and ensure consistent colours across the u-band to Ks-band wavelength range. We further detail the tight control we maintain over the point-spread function modelling required for the model fitting, astrometry and consistency of photometry between the four fields. The catalogue allows us to perform a careful star-galaxy separation and produces excellent photometric redshift performance (NMAD = 0.023 at i 〈 23). The Deep-Fields catalogue will be made available as part of the cosmology data products release, following the completion of the DES 3-year weak lensing and galaxy clustering cosmology work.
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  • 59
    Publication Date: 2021-10-27
    Description: Galactic black hole X-ray binaries (BHXBs) provide excellent laboratories to study accretion, as their relatively quick evolution allows us to monitor large changes in the in-flowing and/or out-flowing material over human timescales. However, the details of how the inflow-outflow coupling evolves during a BHXB outburst remain an area of active debate. In this work we attempt to probe the physical changes underlying the system evolution, by performing a systematic analysis of the multi-wavelength data of three BHXB sources: XTE J1752-223, MAXI J1659-152, and XTE J1650-500, during hard and hard-intermediate states. Using the power spectral hue which characterises the X-ray variability properties, we identify several clusters of BHXB epochs and perform the joint multi-wavelength spectral modelling to test their commonality with a physical jet model. Under the assumption that the corona is related to the base of the jet, we find that the power spectral hue traces the variation of the coronal radius (from ∼10Rg − ∼ 40Rg) in multiple BHXBs at hard and hard-intermediate states, and that the data are consistent with moderately truncated accretion discs (
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  • 60
    Publication Date: 2021-10-27
    Description: We have previously described two flow cytometry-based in vitro genotoxicity tests: micronucleus (MN) scoring (MicroFlow ®) and a multiplexed DNA damage response biomarker assay (MultiFlow ®). Here, we describe a strategy for combining the assays in order to efficiently supplement MN analyses with a panel of biomarkers that comment on cytotoxicity (i.e., relative nuclei count, relative increased nuclei count, cleaved PARP-positive chromatin, and ethidium monoazide-positive chromatin) and genotoxic mode of action (i.e., γH2AX, phospho-histone H3, p53 activation, and polyploidy). For these experiments, human TK6 cells were exposed to each of 32 well-studied reference chemicals in 96-well plates for 24 continuous hr. The test chemicals were evaluated over a range of concentrations in the presence and absence of a rat liver S9-based metabolic activation system. MultiFlow assay data were acquired at 4 and 24 hr, and MN were scored at 24 hr. Testing 32 chemicals in two metabolic activation arms translated into 64 a priori calls: 42 genotoxicants and 22 non-genotoxicants. The MN assay showed high sensitivity and moderate specificity (90% and 68%, respectively). When a genotoxic call required significant MN and MultiFlow responses, specificity increased to 95% without adversely affecting sensitivity. The dose response data were analyzed with PROAST Benchmark Dose (BMD) software in order to calculate potency metrics for each endpoint, and ToxPi software was used to synthesize the resulting lower and upper bound 90% confidence intervals into visual profiles. The BMD/ToxPi combination was found to represent a powerful strategy for synthesizing multiple BMD confidence intervals, as the software output provided MoA information as well as insights into genotoxic potency.
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  • 61
    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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  • 62
    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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  • 63
    Publication Date: 2021-10-30
    Description: Summary Constitutive theory for viscoelasticity has broad application to solid mantle or ice deformations driven by tides, surface mass variations, and post-seismic flow. Geophysical models using higher order viscoelasticity can better accommodate geodetic observations than lower-order theory, typically provided by tensor versions of Maxwell, 4-parameter Burgers or standard linear (Zener) rheology. We derive, for the first time, a mathematical description of a compressible version of the extended Burgers material (EBM) model paradigm which has a distribution function of relaxation spectra. The latter model is often used for parameterizing high temperature background transient responses in the rock physics and mechanics laboratory setting and have demonstrated application to low frequency seismic wave attenuation. A new generalization of this practical anelastic model is presented and applied to the glacial isostatic adjustment momentum equations, thus providing useful guidance for generating initial-value boundary problem-solving software for quite general coding strategies. The solutions for the vertical motion response to a suddenly imposed surface load reveal a short-term transience of substantial amplitude.
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  • 64
    Publication Date: 2021-10-29
    Description: Quantifying the flux of cosmic rays reaching exoplanets around M dwarfs is essential to understand their possible effects on exoplanet habitability. Here, we investigate the propagation of Galactic cosmic rays as they travel through the stellar winds (astrospheres) of five nearby M dwarfs, namely: GJ 15A, GJ 273, GJ 338B, GJ 411 and GJ 887. Our selected stars each have 1 or 2 detected exoplanets and they all have wind mass-loss rates constrained by Lyman-α observations. Our simulations use a combined 1D magnetohydrodynamic (MHD) Alfvén-wave-driven stellar wind model and 1D cosmic ray transport model. We find that GJ 411 and GJ 887 have Galactic cosmic rays fluxes comparable with Earth’s at their habitable zones. On the other hand, GJ 15A, GJ 273 and GJ 338B receive a lower Galactic cosmic ray flux in their habitable zones. All exoplanets in our sample, with exception of GJ 15A c and GJ 411 c, have a significantly lower flux of Galactic cosmic rays than values observed at the Earth because they orbit closer-in. The fluxes found here can be further used for chemical modelling of planetary atmospheres. Finally, we calculate the radiation dose at the surface of the habitable-zone planet GJ 273 b, assuming it has an Earth-like atmosphere. This planet receives up to 209 times less 15 MeV energy cosmic ray fluxes than values observed at Earth. However, for high-energy cosmic rays (∼ GeV), the difference in flux is only 2.3 times smaller, which contributes to GJ 273 b receiving a significant surface radiation dose of 0.13 mSv/yr (40 per cent of the annual dose on Earth’s surface).
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  • 65
    Publication Date: 2021-10-01
    Electronic ISSN: 2158-3226
    Topics: Physics
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  • 66
    Publication Date: 2021-10-28
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
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  • 67
    Publication Date: 2021-10-25
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
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  • 68
    Publication Date: 2021-10-28
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
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  • 69
    Publication Date: 2021-10-29
    Description: High cadence, high quality observations of active galactic nuclei (AGN) clearly show continuum variations with lags, relative to the shortest observed variable UV continuum, that increase with wavelength (‘lag spectra’). These have been attributed to the irradiation and heating of the central accretion disk by the central X-ray emitting corona. An alternative explanation, connecting the observed lag-spectra to line and continuum emission from gas in the broad line region (BLR), has also been proposed. In this paper I show the clear spectral signature of the time-dependent diffuse gas emission in the lag-spectrum of 6 AGN. I also show a new lag-luminosity relationship for 9 objects which is a scaled down version of the well known τ(Hβ)-L5100 relationship in AGN. The shape of the lag-spectrum, and its normalization, are entirely consistent with diffuse emission from radiation pressure supported clouds in a BLR with a covering factor of about 0.2. While some contributions to the continuum lag from the irradiated disk cannot be excluded, there is no need for this explanation.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 70
    Publication Date: 2021-10-01
    Electronic ISSN: 2158-3226
    Topics: Physics
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  • 71
    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.
    Print ISSN: 0035-8711
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  • 72
    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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  • 73
    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.
    Print ISSN: 0035-8711
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  • 74
    Publication Date: 2021-10-30
    Description: We present VIVACE, the VIrac VAriable Classification Ensemble, a catalogue of variable stars extracted from an automated classification pipeline for the Vista Variables in the Vía Láctea (VVV) infrared survey of the Galactic bar/bulge and southern disc. Our procedure utilises a two-stage hierarchical classifier to first isolate likely variable sources using simple variability summary statistics and training sets of non-variable sources from the Gaia early third data release, and then classify candidate variables using more detailed light curve statistics and training labels primarily from OGLE and VSX. The methodology is applied to point-spread-function photometry for ∼490 million light curves from the VIRAC v2 astrometric and photometric catalogue resulting in a catalogue of ∼1.4 million likely variable stars, of which ∼39, 000 are high-confidence (classification probability 〉0.9) RR Lyrae ab stars, ∼8000 RR Lyrae c/d stars, ∼187, 000 detached/semi-detached eclipsing binaries, ∼18, 000 contact eclipsing binaries, ∼1400 classical Cepheid variables and ∼2200 Type II Cepheid variables. Comparison with OGLE-4 suggests a completeness of around 90  per cent for RRab and ≲ 60 per cent for RRc/d, and a misclassification rate for known RR Lyrae stars of around 1 per cent for the high confidence sample. We close with two science demonstrations of our new VIVACE catalogue: first, a brief investigation of the spatial and kinematic properties of the RR Lyrae stars within the disc/bulge, demonstrating the spatial elongation of bar-bulge RR Lyrae stars is in the same sense as the more metal-rich red giant population whilst having a slower rotation rate of ∼40 km s−1kpc−1; and secondly, an investigation of the Gaia EDR3 parallax zeropoint using contact eclipsing binaries across the Galactic disc plane and bulge.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
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  • 75
    Publication Date: 2021-10-30
    Description: Magnetars, the likely sources of Fast Radio Bursts (FRBs), produce both steady highly relativistic magnetized winds, and occasional ejection events. We demonstrate that the requirement of conservation of the magnetic flux dominates the overall dynamics of magnetic explosions. This is missed in conventional hydrodynamic models of the ejections as expanding shell with parametrically added magnetic field, as well as one-dimensional models of magnetic disturbances. Magnetic explosions from magnetars come into force balance with the pre-flare wind close to the light cylinder. They are then advected quietly with the wind, or propagate as electromagnetic disturbances. No powerful shock waves are generated in the wind.
    Print ISSN: 0035-8711
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  • 76
    Publication Date: 2021-10-01
    Print ISSN: 1070-6631
    Electronic ISSN: 1089-7666
    Topics: Physics
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  • 77
    Publication Date: 2021-10-29
    Description: To reduce and analyse astronomical images, astronomers can rely on a wide range of libraries providing low-level implementations of legacy algorithms. However, combining these routines into robust and functional pipelines requires a major effort which often ends up in instrument-specific and poorly maintainable tools, yielding products that suffer from a low-level of reproducibility and portability. In this context, we present prose, a Python framework to build modular and maintainable image processing pipelines. Built for astronomy, it is instrument-agnostic and allows the construction of pipelines using a wide range of building blocks, pre-implemented or user-defined. With this architecture, our package provides basic tools to deal with common tasks such as automatic reduction and photometric extraction. To demonstrate its potential, we use its default photometric pipeline to process 26 TESS candidates follow-up observations and compare their products to the ones obtained with AstroImageJ, the reference software for such endeavors. We show that prose produces light curves with lower white and red noise while requiring less user interactions and offering richer functionalities for reporting.
    Print ISSN: 0035-8711
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  • 78
    Publication Date: 2021-10-01
    Print ISSN: 1070-6631
    Electronic ISSN: 1089-7666
    Topics: Physics
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  • 79
    Publication Date: 2021-10-29
    Description: Light and water availability are likely to vary over the lifespan of closed-canopy forest trees with understory trees experiencing greater limitations to growth by light and canopy trees greater limitation due to drought. As drought and shade have opposing effects on isotope discrimination (Δ13C), paired measurement of ring width and Δ13C can potentially be used to differentiate between water and light limitations on tree growth. We tested this approach for Cedrela trees from three tropical forests in Bolivia and Mexico that differ in rainfall and canopy structure. Using lifetime ring width and Δ13C data for trees of up to and over 200 years old, we assessed how controls on tree growth changed from understory to the canopy. Growth and Δ13C are mostly anti-correlated in the understory but this anti-correlation disappeared or weakened when trees reached the canopy, especially at the wettest site. This indicates that understory growth variation is controlled by photosynthetic carbon assimilation (A) due to variation in light levels. Once trees reached the canopy, inter-annual variation in growth and Δ13C at one of the dry sites showed positive correlations, indicating inter-annual variation in growth is driven by variation in water stress affecting stomatal conductance (gs). Paired analysis of ring widths and carbon isotopes provides significant insight to discerning between environmental factors controlling growth over trees’ life; strong light limitations for understory trees in closed-canopy moist forests switched to drought stress for (sub)canopy trees in dry forests. We show that combined isotope and ring width measurements can significantly improve our insights in tree functioning and be used to disentangle limitations due to shade from those due to drought.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 80
    Publication Date: 2021-10-29
    Description: Whilst the underlying assumption of the Friedman-Lemaître-Robertson-Walker (FLRW) cosmological model is that matter is homogeneously distributed throughout the universe, gravitational influences over the life of the universe have resulted in mass clustered on a range of scales. Hence we expect that, in our inhomogeneous universe, the view of an observer will be influenced by the location and local environment. Here we analyse the one-point probability distribution functions and angular power spectra of weak-lensing (WL) convergence and magnification numerically to investigate the influence of our local environment on WL statistics in relativistic N-body simulations. To achieve this, we numerically solve the null geodesic equations which describe the propagation of light bundles backwards in time from today, and develop a ray-tracing algorithm, and from these calculate various WL properties. Our findings demonstrate how cosmological observations of large-scale structure through WL can be impacted by the locality of the observer. We also calculate the constraints on the cosmological parameters as a function of redshift from the theoretical and numerical study of the angular power spectrum of WL convergence. This study concludes the minimal redshift for the constraint on the parameter Ωm (H0) is z ∼ 0.2 (z ∼ 0.6) beyond which the local environment’s effect is negligible and the data from WL surveys are more meaningful above that redshift. The outcomes of this study will have direct consequences for future surveys, where percent-level-precision is necessary.
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  • 81
    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
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  • 82
    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.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
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  • 83
    Publication Date: 2021-11-07
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
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  • 84
    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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  • 85
    Publication Date: 2021-11-07
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
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  • 86
    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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  • 87
    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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  • 88
  • 89
    Publication Date: 2021-10-30
    Description: Motivation Alignment-free (AF) distance/similarity functions are a key tool for sequence analysis. Experimental studies on real datasets abound and, to some extent, there are also studies regarding their control of false positive rate (Type I error). However, assessment of their power, i.e., their ability to identify true similarity, has been limited to some members of the D2 family. The corresponding experimental studies have concentrated on short sequences, a scenario no longer adequate for current applications, where sequence lengths may vary considerably. Such a State of the Art is methodologically problematic, since information regarding a key feature such as power is either missing or limited. Results By concentrating on a representative set of word-frequency based AF functions, we perform the first coherent and uniform evaluation of the power, involving also Type I error for completeness. Two Alternative models of important genomic features (CIS Regulatory Modules and Horizontal Gene Transfer), a wide range of sequence lengths from a few thousand to millions, and different values of k have been used. As a result, we provide a characterization of those AF functions that is novel and informative. Indeed, we identify weak and strong points of each function considered, which may be used as a guide to choose one for analysis tasks. Remarkably, of the fifteen functions that we have considered, only four stand out, with small differences between small and short sequence length scenarios. Finally, in order to encourage the use of our methodology for validation of future AF functions, the Big Data platform supporting it is public. Availability The software is available at: https://github.com/pipp8/power_statistics 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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  • 90
    Publication Date: 2021-10-28
    Description: The divide-and-conquer strategy is commonly used for protein structure determination, but its applications to high-resolution structure determination of RNAs have been limited. Here, we introduce an integrative approach based on the divide-and-conquer strategy that was undertaken to determine the solution structure of an RNA model system, the Neurospora VS ribozyme. NMR and SAXS studies were conducted on a minimal trans VS ribozyme as well as several isolated subdomains. A multi-step procedure was used for structure determination that first involved pairing refined NMR structures with SAXS data to obtain structural subensembles of the various subdomains. These subdomain structures were then assembled to build a large set of structural models of the ribozyme, which was subsequently filtered using SAXS data. The resulting NMR-SAXS structural ensemble shares several similarities with the reported crystal structures of the VS ribozyme. However, a local structural difference is observed that affects the global fold by shifting the relative orientation of the two three-way junctions. Thus, this finding highlights a global conformational change associated with substrate binding in the VS ribozyme that is likely critical for its enzymatic activity. Structural studies of other large RNAs should benefit from similar integrative approaches that allow conformational sampling of assembled fragments.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 91
    Publication Date: 2021-10-27
    Print ISSN: 1469-3062
    Electronic ISSN: 1752-7457
    Topics: Geosciences , Political Science
    Published by Taylor & Francis
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  • 92
    Publication Date: 2021-10-28
    Description: Summary Distributed Acoustic Sensing (DAS) networks promise to revolutionize observational seismology by providing cost-effective, highly dense spatial sampling of the seismic wavefield, especially by utilizing pre-deployed telecomm fiber in urban settings for which dense seismic network deployments are difficult to construct. However, each DAS channel is sensitive only to one projection of the horizontal strain tensor and therefore gives an incomplete picture of the horizontal seismic wavefield, limiting our ability to make a holistic analysis of instrument response. This analysis has therefore been largely restricted to pointwise comparisons where a fortuitious coincidence of reference three-component seismometers and co-located DAS cable allows. We evaluate DAS instrument response by comparing DAS measurements from the PoroTomo experiment with strain-rate wavefield reconstructed from the nodal seismic array deployed in the same experiment, allowing us to treat the entire DAS array in a systematic fashion irrespective of cable geometry relative to the location of nodes. We found that, while the phase differences are in general small, the amplitude differences between predicted and observed DAS strain-rates average a factor of 2 across the array and correlate with near-surface geology, suggesting that careful assessment of DAS deployments is essential for applications that require reliable assessments of amplitude. We further discuss strategies for empirical gain corrections and optimal placement of point sensor deployments to generate the best combined sensitivity with an already deployed DAS cable, from a wavefield reconstruction perspective.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
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  • 93
    Publication Date: 2021-10-28
    Description: Birds in the clade Palaeognathae, excluding Tinamiformes, have morphologically conserved karyotypes and less differentiated ZW sex chromosomes compared with those of other birds. In particular, the sex chromosomes of the ostrich and emu have exceptionally large recombining pseudoautosomal regions (PARs), while non-PARs are classified into two strata according to the date of their origins: stratum 0 (S0) and stratum 1 (S1). However, the construction and analysis of the genome sequences in these regions in the clade Palaeognathae can be challenging because assembling the S1 region is difficult owing to low sequence diversity between gametologs (Z-linked and W-linked sequences). We addressed this issue by applying the Platanus-allee assembler and successfully constructed the haplotype-resolved (phased) assembly for female emu, cassowary, and ostrich using only sequence read data derived from the Illumina platform. Comparative genomic and phylogenetic analyses based on assembled Z-linked and W-linked sequences confirmed that the S1 region of emu and cassowary formed in their common ancestor. Moreover, the interspersed repetitive sequence landscapes in the S1 regions of female emu showed an expansion of younger repetitive elements in the W-linked S1 region, suggesting an interruption in homologous recombination in the S1 region. These results provide novel insights into the trajectory of sex chromosome evolution in the clade Palaeognathae and suggest that the Illumina-based phased assembly method is an effective approach for elucidating the evolutionary process underlying the transition from homomorphic to differentiated sex chromosomes.
    Electronic ISSN: 1759-6653
    Topics: Biology
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  • 94
    Publication Date: 2021-10-28
    Description: The metallicity of a star affects its evolution in a variety of ways, changing stellar radii, luminosities, lifetimes, and remnant properties. In this work, we use the population synthesis code binary_c to study how metallicity affects novae in the context of binary stellar evolution. We compute a 16-point grid of metallicities ranging from Z = 10−4 to 0.03, presenting distributions of nova white dwarf masses, accretion rates, delay-times, and initial system properties at the two extremes of our 16-point metallicity grid. We find a clear anti-correlation between metallicity and the number of novae produced, with the number of novae at Z = 0.03 roughly half that at Z = 10−4. The white dwarf mass distribution has a strong systematic variation with metallicity, while the shape of the accretion rate distribution is relatively insensitive. We compute a current nova rate of approximately 33 novae per year for the Milky Way, a result consistent with observational estimates relying on extra-Galactic novae but an under-prediction relative to observational estimates relying on Galactic novae. However, the shape of our predicted Galactic white dwarf mass distribution differs significantly to existing observationally derived distributions, likely due to our underlying physical assumptions. In M31, we compute a current nova rate of approximately 36 novae per year, under-predicting the most recent observational estimate of $65^{+15}_{-16}$. Finally, we conclude that when making predictions about currently observable nova rates in spiral galaxies, or stellar environments where star formation has ceased in the distant past, metallicity can likely be considered of secondary importance compared to uncertainties in binary stellar evolution.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
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  • 95
    Publication Date: 2021-10-28
    Description: The Mediterranean Basin has experienced extensive change in geology and climate over the past six million years. Yet, the relative importance of key geological events for the distribution and genetic structure of the Mediterranean fauna remains poorly understood. Here, we use population genomic and phylogenomic analyses to establish the evolutionary history and genetic structure of common wall lizards (Podarcis muralis). This species is particularly informative because, in contrast to other Mediterranean lizards, it is widespread across the Iberian, Italian, and Balkan peninsulas, and in extra-Mediterranean regions. We found strong support for six major lineages within P. muralis, which were largely discordant with the phylogenetic relationship of mitochondrial DNA. The most recent common ancestor of extant P. muralis was likely distributed in the Italian Peninsula, and experienced an “Out-of-Italy” expansion following the Messinian salinity crisis (∼5 Mya), resulting in the differentiation into the extant lineages on the Iberian, Italian and Balkan peninsulas. Introgression analysis revealed that both inter- and intraspecific gene flows have been pervasive throughout the evolutionary history of P. muralis. For example, the Southern Italy lineage has a hybrid origin, formed through admixture between the Central Italy lineage and an ancient lineage that was the sister to all other P. muralis. More recent genetic differentiation is associated with the onset of the Quaternary glaciations, which influenced population dynamics and genetic diversity of contemporary lineages. These results demonstrate the pervasive role of Mediterranean geology and climate for the evolutionary history and population genetic structure of extant species.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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  • 96
    Publication Date: 2021-10-28
    Description: Summary Finite-difference (FD) modeling of seismic waves in the vicinity of dipping interfaces gives rise to artifacts. Examples are phase and amplitude errors, as well as staircase diffractions. Such errors can be reduced in two general ways. In the first approach, the interface can be anti-aliased (i.e., with an anti-aliased step-function, or a lowpass filter). Alternatively, the interface may be replaced with an equivalent medium (i.e., using Schoenberg & Muir (SM) calculus or orthorhombic averaging). We test these strategies in acoustic, elastic isotropic, and elastic anisotropic settings. Computed FD solutions are compared to analytical solutions. We find that in acoustic media, anti-aliasing methods lead to the smallest errors. Conversely, in elastic media, the SM calculus provides the best accuracy. The downside of the SM calculus is that it requires an anisotropic FD solver even to model an interface between two isotropic materials. As a result, the computational cost increases compared to when using isotropic FD solvers. However, since coarser grid spacings can be used to represent the dipping interfaces, the two effects (an expensive FD solver on a coarser FD grid) equal out. Hence, the SM calculus can provide an efficient means to reduce errors, also in elastic isotropic media.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
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  • 97
    Publication Date: 2021-10-28
    Description: We explore, using numerical simulations, the influence of mass and distance on the evolution of triple black hole systems. Following in the direction of Burrau’s famous 3,4,5 problem, black holes are initially placed at the vertices of Pythagorean triangles. Numerical integration of orbits was conducted using relativistic corrections (post-Newtonian) up to the 2.5th order with ARCcode. As a descriptor of the evolution of the systems, the lifetimes, the number of two-body encounters and the number of mergers were all analysed. We found that as the mass unit of the black holes increased there was strong positive correlation with the fraction of mergers (0.9868), strong negative correlation with the average number of two-body encounters (-0.9016) and the average lifetimes of the triple systems decayed exponentially (determination coefficient of 0.9986). Around the mass unit range of 105.5M⊙-105.6M⊙, there was a transition from escape dominated dynamics to merger dominated dynamics. However, in the mass unit range of 106 M⊙ − 109M⊙ with 1 pc distance unit, we find that 25 per cent of cases resulted in the escape of a supermassive black hole (SMBH) which may be a cause for wandering SMBH’s found in some galaxies/galactic merger remnants.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 98
    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.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 99
    Publication Date: 2021-10-27
    Description: The form of Charcot–Marie-Tooth type 4B (CMT4B) disease caused by mutations in myotubularin-related 5 (MTMR5; also called SET Binding Factor 1; SBF1) shows a spectrum of axonal and demyelinating nerve phenotypes. This contrasts with the CMT4B subtypes caused by MTMR2 or MTMR13 (SBF2) mutations, which are characterized by myelin outfoldings and classic demyelination. Thus, it is unclear whether MTMR5 plays an analogous or distinct role from that of its homolog, MTMR13, in the peripheral nervous system (PNS). MTMR5 and MTMR13 are pseudophosphatases predicted to regulate endosomal trafficking by activating Rab GTPases and binding to the phosphoinositide 3-phosphatase MTMR2. In the mouse PNS, Mtmr2 was required to maintain wild type levels of Mtmr5 and Mtmr13, suggesting that these factors function in discrete protein complexes. Genetic elimination of both Mtmr5 and Mtmr13 in mice led to perinatal lethality, indicating that the two proteins have partially redundant functions during embryogenesis. Loss of Mtmr5 in mice did not cause CMT4B-like myelin outfoldings. However, adult Mtmr5−/− mouse nerves contained fewer myelinated axons than control nerves, likely as a result of axon radial sorting defects. Consistently, Mtmr5 levels were highest during axon radial sorting and fell sharply after postnatal day seven. Our findings suggest that Mtmr5 and Mtmr13 ensure proper axon radial sorting and Schwann cell myelination, respectively, perhaps through their direct interactions with Mtmr2. This study enhances our understanding of the non-redundant roles of the endosomal regulators MTMR5 and MTMR13 during normal peripheral nerve development and disease.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 100
    Publication Date: 2021-10-29
    Description: Epigenetic therapy has significant potential for cancer treatment. However, few small potent molecules have been identified against DNA or RNA modification regulatory proteins. Current approaches for activity detection of DNA/RNA methyltransferases and demethylases are time-consuming and labor-intensive, making it difficult to subject them to high-throughput screening. Here, we developed a fluorescence polarization-based ‘High-Throughput Methyl Reading’ (HTMR) assay to implement large-scale compound screening for DNA/RNA methyltransferases and demethylases-DNMTs, TETs, ALKBH5 and METTL3/METTL14. This assay is simple to perform in a mix-and-read manner by adding the methyl-binding proteins MBD1 or YTHDF1. The proteins can be used to distinguish FAM-labelled substrates or product oligonucleotides with different methylation statuses catalyzed by enzymes. Therefore, the extent of the enzymatic reactions can be coupled with the variation of FP binding signals. Furthermore, this assay can be effectively used to conduct a cofactor competition study. Based on the assay, we identified two natural products as candidate compounds for DNMT1 and ALKBH5. In summary, this study outlines a powerful homogeneous approach for high-throughput screening and evaluating enzymatic activity for DNA/RNA methyltransferases and demethylases that is cheap, easy, quick, and highly sensitive.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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