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  • Articles  (454)
  • Oxford University Press  (421)
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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: 2024-01-18
    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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  • 15
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    American Meteorological Society
    In:  EPIC3Journal of Climate, American Meteorological Society, 34(18), pp. 7373-7388, ISSN: 0894-8755
    Publication Date: 2024-06-21
    Description: Climate variability occurs over wide ranges of spatial and temporal scales. It exhibits a complex spatial covariance structure, which depends on geographic location (e.g., tropics vs extratropics) and also consists of a superposition of (i) components with gradually decaying positive correlation functions and (ii) teleconnections that often involve anticorrelations. In addition, there are indications that the spatial covariance structure depends on frequency. Thus, a comprehensive assessment of the spatiotemporal covariance structure of climate variability would require an extensive set of statistical diagnostics. Therefore, it is often desirable to characterize the covariance structure by a simple summarizing metric that is easy to compute from datasets. Such summarizing metrics are useful, for example, in the context of comparisons between climate models or between models and observations. Here we introduce a frequency-dependent version of a simple measure of the effective spatial degrees of freedom. The measure is based on the temporal variance of the global average of some climate variable, and its novel aspect consists in its frequency dependence. We also provide a clear geometric interpretation of the measure. Its easy applicability is demonstrated using near-surface temperature and precipitation fields obtained from a paleoclimate model simulation. This application reveals a distinct scaling behavior of the spatial degrees of freedom as a function of frequency, ranging from monthly to millennial scales.
    Repository Name: EPIC Alfred Wegener Institut
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  • 16
    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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  • 17
    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.
    Print ISSN: 0305-1048
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  • 18
    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
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  • 19
    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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  • 20
    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.
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  • 21
    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.
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  • 22
    Publication Date: 2021-10-28
    Description: As humans populated the world, they adapted to many varying environmental factors, including climate, diet, and pathogens. Because many of these adaptations were mediated by multiple non-coding variants with small effects on gene regulation, it has been difficult to link genomic signals of selection to specific genes, and to describe the regulatory response to selection. To overcome this challenge, we adapted PrediXcan, a machine learning method for imputing gene regulation from genotype data, to analyze low-coverage ancient human DNA (aDNA). First, we used simulated genomes to benchmark strategies for adapting PrediXcan to increase robustness to incomplete data. Applying the resulting models to 490 ancient Eurasians, we found that genes with the strongest divergent regulation among ancient populations with hunter-gatherer, pastoralist, and agricultural lifestyles are enriched for metabolic and immune functions. Next, we explored the contribution of divergent gene regulation to two traits with strong evidence of recent adaptation: dietary metabolism and skin pigmentation. We found enrichment for divergent regulation among genes proposed to be involved in diet-related local adaptation, and the predicted effects on regulation often suggest explanations for known signals of selection, e.g. at FADS1, GPX1, and LEPR. In contrast, skin pigmentation genes show little regulatory change over a 38,000-year time series of 2999 ancient Europeans, suggesting that adaptation mainly involved large-effect coding variants. This work demonstrates that combining aDNA with present-day genomes is informative about the biological differences among ancient populations, the role of gene regulation in adaptation, and the relationship between genetic diversity and complex traits.
    Electronic ISSN: 1759-6653
    Topics: Biology
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  • 23
    Publication Date: 2021-10-28
    Description: Here, we report the new detection of three shock fronts using archival Chandra X-ray observations in Abell 1914, which also hosts a radio halo, a radio phoenix, and a head-tail galaxy. In this study, we report the X-ray shock front at the position of the radio phoenix, which further strengthens the scenario that radio phoenix traces old plasma that gets lit up when compressed by shock passage. We further analyse the thermodynamic structure of the cluster in detail. We create temperature maps of A1914 using three different techniques, Adaptive Circular Binning (ACB), Weighted Voronoi Tessellations (WVT), and Contour binning (Contbin) method. These thermodynamic maps, along with the pseudo pressure and the pseudo entropy maps for the cluster, are evidence of disturbed morphology produced by multiple merger events. These merger events create cluster-wide turbulence, which may re-accelerate the relativistic particles and result in a radio halo within the cluster. Further, comparing X-ray and radio images reveals that the radio halo is contained within two X-ray shock fronts. Our analysis suggests that A1914 has both equatorial shock and axial shock within the cluster’s ICM. We proposed a dual merging scenario based on the shock position and analysis of the thermodynamic maps obtained from the deeper Chandra X-ray observations.
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  • 24
    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
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  • 25
    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.
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  • 26
    Publication Date: 2021-10-30
    Description: Extrachromosomal circular DNA (eccDNA) are present within all eukaryotic organisms and actively contribute to gene expression changes. MicroDNA (200-1000bp) are the most abundant type of eccDNA and can amplify tRNA, microRNA, and novel si-like RNA sequences. Due to the heterogeneity of microDNA and the limited technology to directly quantify circular DNA molecules, the specific DNA repair pathways that contribute to microDNA formation have not been fully elucidated. Using a sensitive and quantitative assay that quantifies eight known abundant microDNA, we report that microDNA levels are dependent on resection after double-strand DNA break (DSB) and repair by Microhomology Mediated End Joining (MMEJ). Further, repair of DSB without resection by canonical Non-Homologous End Joining (c-NHEJ) diminishes microDNA formation. MicroDNA levels are induced locally even by a single site-directed DSB, suggesting that excision of genomic DNA by two closely spaced DSB is not necessary for microDNA formation. Consistent with all this, microDNA levels accumulate as cells undergo replication in S-phase, when DNA breaks and repair are elevated, and microDNA levels are decreased if DNA synthesis is prevented. Thus, formation of microDNA occurs during the repair of endogenous or induced DNA breaks by resection-based DNA repair pathways.
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  • 27
    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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  • 28
    Publication Date: 2021-10-30
    Description: Motivation Differential network inference is a fundamental and challenging problem to reveal gene interactions and regulation relationships under different conditions. Many algorithms have been developed for this problem; however, they do not consider the differences between the importance of genes, which may not fit the real-world situation. Different genes have different mutation probabilities, and the vital genes associated with basic life activities have less fault tolerance to mutation. Equally treating all genes may bias the results of differential network inference. Thus, it is necessary to consider the importance of genes in the models of differential network inference. Results Based on the Gaussian graphical model with adaptive gene importance regularization, we develop a novel importance-penalized joint graphical Lasso method, IPJGL, for differential network inference. The presented method is validated by the simulation experiments as well as the real datasets. Furthermore, to precisely evaluate the results of differential network inference, we propose a new metric named APC2 for the differential levels of gene pairs. We apply IPJGL to analyze the TCGA colorectal and breast cancer datasets and find some candidate cancer genes with significant survival analysis results, including SOST for colorectal cancer and RBBP8 for breast cancer. We also conduct further analysis based on the interactions in the Reactome database and confirm the utility of our method. Availability R source code of importance-penalized joint graphical lasso is freely available at https://github.com/Wu-Lab/IPJGL. Supplementary information Supplementary materials are available at Bioinformatics online.
    Print ISSN: 1367-4803
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  • 29
    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
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  • 30
    Publication Date: 2021-10-28
    Description: We present light curve analyses of two newly identified detached eclipsing binaries, HD 96609 and HD 303734, in the region of the richly populated open cluster NGC 3532. HD 96609 is composed of two main sequence stars (B9-A0V + A2V) with masses and radii of M1 = 2.66 ± 0.02M⊙, M2 = 1.84 ± 0.01M⊙, R1 = 2.740 ± 0.006R⊙, R2 = 1.697 ± 0.005R⊙. The positions of the components on log M − log R plane suggests log(age/yr) 8.55, corresponding 350 ± 40 Myr of age, which agrees with the 300 ± 100 Myr age of NGC 3532 estimated in previous studies. We find the distance of HD 96609 as 460 ± 17 pc, which is consistent with the $484^{+35}_{-30}$ pc distance of NGC 3532, estimated from GAIA parallaxes. HD 303734 is an interesting totally eclipsing binary with a quite shallow secondary eclipse. Using photometric properties of the system in conjunction with theoretical calibrations, we estimate that HD 303734 consists of A6V + K3V components. HD 96609 and HD 303734 are the second and third eclipsing binaries discovered in the region of NGC 3532, after the first one, GV Car.
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  • 31
    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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  • 32
    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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  • 33
    Publication Date: 2021-10-28
    Description: Motivation DNA Methylation plays a key role in a variety of biological processes. Recently, Nanopore long-read sequencing has enabled direct detection of these modifications. As a consequence, a range of computational methods have been developed to exploit Nanopore data for methylation detection. However, current approaches rely on a human-defined threshold to detect the methylation status of a genomic position and are not optimized to detect sites methylated at low frequency. Furthermore, most methods employ either the Nanopore signals or the basecalling errors as the model input and do not take advantage of their combination. Results Here we present DeepMP, a convolutional neural network (CNN)-based model that takes information from Nanopore signals and basecalling errors to detect whether a given motif in a read is methylated or not. Besides, DeepMP introduces a threshold-free position modification calling model sensitive to sites methylated at low frequency across cells. We comprehensively benchmarked DeepMP against state-of-the-art methods on E. coli, human and pUC19 datasets. DeepMP outperforms current approaches at read-based and position-based methylation detection across sites methylated at different frequencies in the three datasets. Availability DeepMP is implemented and freely available under MIT license at https://github.com/pepebonet/DeepMP Supplementary information Supplementary data are available at Bioinformatics online.
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  • 34
    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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  • 35
    Publication Date: 2021-10-29
    Description: Droughts are widespread disasters worldwide and are concurrently influenced by multiple large-scale climate signals. This is particularly true over Japan, where drought has strong heterogeneity due to multiple factors such as monsoon, topography, and ocean circulations. Regional heterogeneity poses challenges for drought prediction and management. To overcome this difficulty, this study provides a comprehensive analysis of teleconnection between climate signals and homogeneous drought zones over Japan. First, droughts are characterized by simulated soil moisture from land surface model during 1958-2012. The Mclust toolkit, distinct empirical orthogonal function, and wavelet coherence analysis are used, respectively, to investigate the homogeneous drought zone, principal component of each homogeneous zone, and teleconnection between climate signals and drought. Results indicate that nine homogeneous drought zones with different characteristics are defined and quantified. Among these nine zones, zone-1 is dominated by extreme drought events. Zone-2 and zone-6 are typical representatives of spring droughts, while zone-7 is wet for most of the period. The Hokkaido region is divided into wetter zone-4 and drier zone-9. Zone-3, zone-5 and zone-8 are distinguished by the topography. The analyses also reveal almost nine zones have a high level of homogeneity, with more than 60% explained variance. Also, these nine zones are dominated by different large-scale climate signals: the Arctic Oscillation has the strongest impact on zone-1, zone-7, and zone-8; the influence of the North Atlantic Oscillation on zone-3, zone-4, and zone-6 is significant; zone-2 and zone-9 are both dominated by the Pacific Decadal Oscillation; El Niño-Southern Oscillation dominates zone-5. The results will be valuable for drought management and drought prevention.
    Print ISSN: 1558-8424
    Electronic ISSN: 1558-8432
    Topics: Geography , Physics
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  • 36
    Publication Date: 2021-10-30
    Description: Over the past decade, studies of dust in the Andromeda galaxy (M31) have shown radial variations in the dust emissivity index (β). Understanding the astrophysical reasons behind these radial variations may give clues about the chemical composition of dust grains, their physical structure, and the evolution of dust. We use 12CO(J=1-0) observations taken by the Combined Array for Research in Millimeter Astronomy (CARMA) and dust maps derived from Herschel images, both with an angular resolution of 8″ and spatial resolution of 30 pc, to study variations in β across an area of ≈ 18.6 kpc2 in M31. We extract sources, which we identify as molecular clouds, by applying the astrodendro algorithm to the 12CO and dust maps, which as a byproduct allows us to compare continuum emission from dust and CO emission as alternative ways of finding molecular clouds. We then use these catalogues to investigate whether there is evidence that β is different inside and outside molecular clouds. Our results confirm the radial variations of β seen in previous studies. However, we find little difference between the average β inside molecular clouds compared to outside molecular clouds, in disagreement with models which predict an increase of β in dense environments. Finally, we find some clouds traced by dust with very little CO which may be either clouds dominated by atomic gas or clouds of molecular gas that contain little CO.
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  • 37
    Publication Date: 2021-10-30
    Description: We investigate the properties of the dark matter (DM) halo surrounding the nearby galaxy group NGC 1600. Through the use of deep (252 ks) Chandra observations and 64.3 ks of XMM–Newton observations, we construct surface brightness profiles in multiple energy bands in order to perform hydrostatic equilibrium analysis of the hot plasma within NGC 1600. Regardless of the DM model profile assumed, we measure a halo concentration (c200) that is an extreme, positive outlier of the ΛCDM c200-M200 relation. For a typical NFW DM profile, we measure c200 = 26.7 ± 1.4 and M200 = (2.0 ± 0.2) × 1013 M⊙; assuming a similar halo mass, the average concentration expected is c200 = 6 − 7 for the theoretical ΛCDM c-M relation. Such a high concentration is similar to that of well-known fossil groups MRK 1216 and NGC 6482. While NGC 1600 exhibits some properties of a fossil group, it fails to meet the X-ray luminosity threshold of LX 〉 5 × 1041 erg s−1. Whether or not it is considered a fossil group, the high concentration value makes it part of a select group of galaxy groups.
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  • 38
    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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  • 39
    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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  • 40
    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.
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  • 41
    Publication Date: 2021-10-29
    Description: Nephrops (Nephrops norvegicus) is an economically valuable target species in the North Sea. Although individual Nephrops populations are scattered, the crustacean is managed regionally by the European Union (EU). The spatial competition for fisheries in the North Sea is growing especially due to expanding offshore wind farms (OWF) and newly implemented marine protected areas (MPA). Moreover, the Brexit affects the availability of EU fishing quotas and adds to the overall uncertainty EU fishers face. We compare landings and catches to scientifically advised quantities and perform an overlap analysis of fishing grounds with current and future OWFs and MPAs. Furthermore, we explore the German Nephrops fleet using high-resolution spatial fishing effort and catch data. Our results confirm earlier studies showing that Nephrops stocks have been fished above scientific advice. Present OWFs and MPAs marginally overlap with Nephrops fishing grounds, whereas German fishing grounds are covered up to 45% in future scenarios. Co-use strategies with OWFs could mitigate the loss of fishing opportunities. Decreased cod quotas due to Brexit and worse stock conditions, lowers Germany's capability to swap Nephrops quotas with the UK. We support the call for a new management strategy of individual Nephrops populations and the promotion of selective fishing gears.
    Print ISSN: 1054-3139
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  • 42
    Publication Date: 2021-10-30
    Description: Epigenome-Wide Association Study (EWAS) has become a standard strategy to discover DNA methylation variation of different phenotypes. Since 2018, we have developed EWAS Atlas and EWAS Data Hub to integrate a growing volume of EWAS knowledge and data, respectively. Here, we present EWAS Open Platform (https://ngdc.cncb.ac.cn/ewas) that includes EWAS Atlas, EWAS Data Hub and the newly developed EWAS Toolkit. In the current implementation, EWAS Open Platform integrates 617 018 high-quality EWAS associations from 910 publications, covering 51 phenotypes, 275 diseases and 104 environmental factors. It also provides well-normalized DNA methylation array data and the corresponding metadata from 115 852 samples, which involve 707 tissues, 218 cell lines and 528 diseases. Taking advantage of integrated knowledge and data in EWAS Atlas and EWAS Data Hub, EWAS Open Platform equips with EWAS Toolkit, a powerful one-stop site for EWAS enrichment, annotation, and knowledge network construction and visualization. Collectively, EWAS Open Platform provides open access to EWAS knowledge, data and toolkit and thus bears great utility for a broader range of relevant research.
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  • 43
    Publication Date: 2021-10-30
    Description: Assessment of zooplankton abundance, distribution, community composition, and temporal variability is critical to understanding the effects of climate variability and change on lower trophic level production and availability for consumption by larger consumers. Zooplankton sampling is performed across the Canadian continental shelf system by Fisheries and Oceans Canada's Atlantic Zone Monitoring Programme (AZMP). Sampling includes semi-monthly to monthly collection of zooplankton using vertical net tows (VNTs) deployed from near-bottom to surface at stations on the central Scotian Shelf (Stn 2, 150 m depth) and Newfoundland Shelf (Stn 27, 175 m depth), and by Continuous Plankton Recorders (CPRs) in the near-surface layers along routes over the Scotian and Newfoundland shelves (0–10 m depth). Here, we compare abundance metrics for 11 copepod taxa collected using both gear types in both regions between 1999 and 2015. Seasonal cycles of VNT and CPR abundance were similar for near-surface residents. VNT: CPR abundance ratios varied year-round for vertical migrants, as ontogenetic migrants shifted their vertical distribution, and as diel migrants changed their migratory behaviour. For some taxa, differences in annual average VNT: CPR abundance ratios between regions suggest differences in vertical distribution, while for others differences in inter-annual variability for VNT and CPR abundances suggest differences in the dynamics of the near- and sub-surface components of the populations.
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  • 44
    Publication Date: 2021-10-20
    Description: An exomoon on a non-perfectly circular orbit experiences tidal heating that is capable to significantly contribute to the thermal brightness of the moon. Here we argue that the thermal heat is unevenly distributed on the moon’s surface, the emission of the tidal heat is limited to a few hotspots on the surface. A well-known example is the tidally heated Io. Due to their significantly increased temperature, the hotspots enhance the energy emission in thermal wavelengths. We made simulations using Monte Carlo method to examine this contribution, and to predict about the possible detectability of such a spotted exomoon. We found that in the case of large, Earth-sized companions to Jupiters around red dwarf stars exhibit a thermal flux that enables the direct detection of the moon, due to its photometric signal that can exceed ≈100 ppm in the most favourable configurations.
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  • 45
    Publication Date: 2021-10-13
    Description: We have carried out relativistic three-dimensional simulations of high-power radio sources propagating i,nto asymmetric cluster environments. We offset the environment by 0 or 1 core radii (equal to 144 kpc), and incline the jets by 0, 15, or 45° away from the environment centre. The different environment encountered by each radio lobe provides a unique opportunity to study the effect of environment on otherwise identical jets. We find that the jets become unstable towards the end of the simulations, even with a Lorentz factor of 5; they nevertheless develop typical Fanaroff–Riley class II radio morphology. The jets propagating into denser environments have consistently shorter lobe lengths and brighter hotspots, while the axial ratio of the two lobes is similar. We reproduce the recently reported observational anticorrelation between lobe length asymmetry and environment asymmetry, corroborating the notion that observed large-scale radio lobe asymmetry can be driven by differences in the underlying environment.
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  • 46
    Publication Date: 2021-10-28
    Description: The Repeat Expansion Diseases, a large group of human diseases that includes the fragile X-related disorders (FXDs) and Huntington's disease (HD), all result from expansion of a disease-specific microsatellite via a mechanism that is not fully understood. We have previously shown that mismatch repair (MMR) proteins are required for expansion in a mouse model of the FXDs, but that the FANCD2 and FANCI associated nuclease 1 (FAN1), a component of the Fanconi anemia (FA) DNA repair pathway, is protective. FAN1’s nuclease activity has been reported to be dispensable for protection against expansion in an HD cell model. However, we show here that in a FXD mouse model a point mutation in the nuclease domain of FAN1 has the same effect on expansion as a null mutation. Furthermore, we show that FAN1 and another nuclease, EXO1, have an additive effect in protecting against MSH3-dependent expansions. Lastly, we show that the loss of FANCD2, a vital component of the Fanconi anemia DNA repair pathway, has no effect on expansions. Thus, FAN1 protects against MSH3-dependent expansions without diverting the expansion intermediates into the canonical FA pathway and this protection depends on FAN1 having an intact nuclease domain.
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  • 47
    Publication Date: 2021-10-14
    Description: Atmospheric heavy elements have been observed in more than a quarter of white dwarfs (WDs) at different cooling ages, indicating ongoing accretion of asteroidal material, whilst only a few per cent of the WDs possess a dust disc, and all these WDs are accreting metals. Here, assuming that a rubble-pile asteroid is scattered inside a WD’s Roche lobe by a planet, we study its tidal disruption and the long-term evolution of the resulting fragments. We find that after a few pericentric passages, the asteroid is shredded into its constituent particles, forming a flat, thin ring. On a time-scale of Myr, tens of per cent of the particles are scattered on to the WD, and are therefore directly accreted without first passing through a circularized close-in disc. Fragment mutual collisions are most effective for coplanar fragments, and are thus only important in 103−104 yr before the orbital coplanarity is broken by the planet. We show that for a rubble pile asteroid with a size frequency distribution of the component particles following that of the near earth objects, it has to be roughly at least 10 km in radius such that enough fragments are generated and $ge 10{{ m per cent}}$ of its mass is lost to mutual collisions. At relative velocities of tens of km s−1, such collisions grind down the tidal fragments into smaller and smaller dust grains. The WD radiation forces may shrink those grains’ orbits, forming a dust disc. Tidal disruption of a monolithic asteroid creates large km-size fragments, and only parent bodies ≥100 km are able to generate enough fragments for mutual collisions to be significant. Hence, those large asteroids experience a disc phase before being accreted.
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  • 48
    Publication Date: 2021-10-13
    Description: The presence of planetary material in white dwarf atmospheres, thought to be accreted from a dusty debris disc produced via the tidal disruption of a planetesimal, is common. Approximately 5 per cent of these discs host a co-orbital gaseous component detectable via emission from atomic transitions  –  usually the 8600 Å Ca ii triplet. These emission profiles can be highly variable in both morphology and strength. Furthermore, the morphological variations in a few systems have been shown to be periodic, likely produced by an apsidally precessing asymmetric disc. Of the known gaseous debris discs, that around HE 1349–2305 has the most rapidly evolving emission-line morphology, and we present updated spectroscopy of the Ca ii triplet of this system. The additional observations show that the emission-line morphologies vary periodically and consistently, and we constrain the period to two aliases of 459 ± 3 and 502 ± 3 d. We produce images of the Ca ii triplet emission from the disc in velocity space using Doppler tomography  –  only the second such imaging of a white dwarf debris disc. We suggest that the asymmetric nature of these velocity images is generated by gas moving on eccentric orbits with radially dependent excitation conditions via photoionization from the white dwarf. We also obtained short-cadence (≃4 min) spectroscopy to search for variability on the time-scale of the disc’s orbital period (≃hours) due to the presence of a planetesimal, and rule out variability at a level of ≃1.4 per cent.
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  • 49
    Publication Date: 2021-10-18
    Description: The increase in detector sensitivity and availability in the past three decades has allowed us to derive knowledge of the meteoroid flux and impact energy into the Earth’s atmosphere. We present the multi-instrument detected 2018 December 22 fireball over Western Pyrenees, and compare several techniques aiming to obtain a reliable method to be used when measuring impacts of similar scale. From trajectory data alone, we found a bulk density of 3.5 g cm−3 to be the most likely value for the Pyrenean meteoroid. This allowed to further constrain the dynamic mass, which translated into a kinetic energy of 1 ton TNT (4.184 × 109 J). For the second energy derivation, via the fireball’s corrected optical radiation, we obtained a more accurate empirical relation measuring well-studied bolides. The result approximates to 1.1 ton TNT, which is notably close to the nominal dynamic result, and agrees with the lower margin of the seismic-based energy estimation, yet way lower than the infrasound estimate. Based on the relation derived in this study, we consider the nominal estimate from both the dynamic and photometric methods to be the most accurate value of deposited energy (1 ton TNT). We show that the combination of these two methods can be used to infer the meteoroid density. Among the methods presented in this paper, we found that the optical energy is the most reliable predictor of impact energy near the ton TNT-scale.
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  • 50
    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.
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  • 51
    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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  • 52
    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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  • 53
    Publication Date: 2021-10-27
    Description: In this paper we present and validate the galaxy sample used for the analysis of the Baryon Acoustic Oscillation signal (BAO) in the Dark Energy Survey (DES) Y3 data. The definition is based on a colour and redshift-dependent magnitude cut optimized to select galaxies at redshifts higher than 0.5, while ensuring a high quality determination. The sample covers ∼ 4100 square degrees to a depth of i = 22.3 (AB) at 10σ. It contains 7,031,993 galaxies in the redshift range from z= 0.6 to 1.1, with a mean effective redshift of 0.835. Redshifts are estimated with the machine learning algorithm DNF, and are validated using the VIPERS PDR2 sample. We find a mean redshift bias of zbias ∼  0.01 and a mean uncertainty, in units of 1 + z, of σ68 ∼  0.03. We evaluate the galaxy population of the sample, showing it is mostly built upon Elliptical to Sbc types. Furthermore, we find a low level of stellar contamination of $lesssim 4{{ m per cent}}$. We present the method used to mitigate the effect of spurious clustering coming from observing conditions and other large-scale systematics. We apply it to the BAO sampleand calculate weights that are used to get a robust estimate of the galaxy clustering signal. This paper is one of a series dedicated to the analysis of the BAO signal in DES Y3. In the companion papers we present the galaxy mock catalogues used to calibrate the analysis and the angular diameter distance constraints obtained through the fitting to the BAO scale.
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  • 54
    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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  • 55
    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.
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  • 56
    Publication Date: 2021-10-28
    Description: We present methods for emulating the matter power spectrum by combining information from cosmological N-body simulations at different resolutions. An emulator allows estimation of simulation output by interpolating across the parameter space of a limited number of simulations. We present the first implementation in cosmology of multi-fidelity emulation, where many low-resolution simulations are combined with a few high-resolution simulations to achieve an increased emulation accuracy. The power spectrum’s dependence on cosmology is learned from the low-resolution simulations, which are in turn calibrated using high-resolution simulations. We show that our multi-fidelity emulator predicts high-fidelity counterparts to percent-level relative accuracy when using only 3 high-fidelity simulations and outperforms a single-fidelity emulator that uses 11 simulations, although we do not attempt to produce a converged emulator with high absolute accuracy. With a fixed number of high-fidelity training simulations, we show that our multi-fidelity emulator is ≃ 100 times better than a single-fidelity emulator at k ≤ 2 hMpc−1, and ≃ 20 times better at 3 ≤ k 〈 6.4 hMpc−1. Multi-fidelity emulation is fast to train, using only a simple modification to standard Gaussian processes. Our proposed emulator shows a new way to predict non-linear scales by fusing simulations from different fidelities.
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  • 57
    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.
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  • 58
    Publication Date: 2021-10-28
    Description: To assess the number of life-bearing worlds in astrophysical environments, it is necessary to take the intertwined processes of abiogenesis (birth), extinction (death), and transfer of life (migration) into account. We construct a mathematical model that incorporates this trio of mechanisms and accordingly derive the probability distribution function and other statistical properties (e.g. mean) for the number of worlds with biospheres. We show that a given astrophysical setting may become eventually saturated with life if the rate of successful transfers of organisms is higher than the extinction rate of biospheres. Based on the available data, we suggest that this criterion might be fulfilled for star-forming clusters (and perhaps the Galactic bulge under optimal circumstances), thereby indicating that such regions could constitute promising abodes for hosting and detecting life.
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  • 59
    Publication Date: 2021-10-28
    Description: Summary We have studied the active and recent tectonics of New Guinea, using earthquake source modelling, analysis of gravity anomalies, seismic reflection profiles, and thermal and mechanical models. Our aim is to investigate the behaviour and evolution of a young continental deformation belt, and to explore the effects of lateral variations in foreland rheology on the deformation. We find that along-strike gradients in the lithosphere thickness of the southern foreland have resulted in correlated changes in seismogenic thickness, likely due to the effects on the temperature structure of the crust. The resulting variation in the strength of the foreland means that in the east, the foreland is broken through on thrust faults, whereas in the west it is relatively intact. The lack of correlation between the elevation of the mountain belt and the seismogenic thickness of the foreland is likely to be due to the time taken to thicken the crust in the mountains following changes in the rheology of the underthrusting foreland, as the thinned passive margin of northern Australia is consumed. The along-strike variation in whether the force exerted between the mountains and the lowlands is able to break the foreland crust enables us to estimate the effective coefficient of friction on foreland faults to be in the range of 0.01-0.28. We use force-balance calculations to show that the recent tectonic re-organisation in western New Guinea is likely to be due to the development of increasing curvature in the Banda Arc, and that the impingement of continental material on the subduction zone may explain the unusually low force it exerts on western New Guinea.
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  • 60
    Publication Date: 2021-10-29
    Description: Almost twenty years after its initial release, the Eukaryotic Linear Motif (ELM) resource remains an invaluable source of information for the study of motif-mediated protein-protein interactions. ELM provides a comprehensive, regularly updated and well-organised repository of manually curated, experimentally validated short linear motifs (SLiMs). An increasing number of SLiM-mediated interactions are discovered each year and keeping the resource up-to-date continues to be a great challenge. In the current update, 30 novel motif classes have been added and five existing classes have undergone major revisions. The update includes 411 new motif instances mostly focused on cell-cycle regulation, control of the actin cytoskeleton, membrane remodelling and vesicle trafficking pathways, liquid-liquid phase separation and integrin signalling. Many of the newly annotated motif-mediated interactions are targets of pathogenic motif mimicry by viral, bacterial or eukaryotic pathogens, providing invaluable insights into the molecular mechanisms underlying infectious diseases. The current ELM release includes 317 motif classes incorporating 3934 individual motif instances manually curated from 3867 scientific publications. ELM is available at: http://elm.eu.org.
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  • 61
    Publication Date: 2021-10-28
    Description: In our recent papers a non-standard quasi-molecular mechanism was suggested and applied to treat the cosmological recombination. It was assumed that, in the pre-recombination stage of evolution of the Universe, an electron combined with two neighbouring protons and created a hydrogen molecular ion, $H_2^+$ in a highly excited state, which then descended into the lower-lying state or dissociated. In this work, we implement a quantitative analysis of this quasi-molecular mechanism of recombination; namely, we elaborate the scheme of calculation for a free–bound radiative transition. We show that the quasi-molecular mechanism played a significant role in the pre-recombination and recombination stages of evolution of the early Universe, and hence must be included into the consideration of the description of a thermal history of the Universe. Together with the earlier developed treatment of bound-bound radiative transitions in $H_2^+$, the elaborated scheme of calculation can be used for the design of a rapid and complete cosmological recombination code.
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  • 62
    Publication Date: 2021-10-28
    Description: We present a search for disturbed, candidate ram pressure stripping galaxies across more than 50 spectroscopically selected SDSS groups and clusters. Forty-eight ram pressure candidates are visually identified in these systems using high quality UNIONS imaging from the Canada-France Hawaii Telescope, covering ∼6200 deg2 and ∼2800 deg2 in the u- and r-bands respectively. Ram pressure candidates are found in groups and clusters spanning a wide range in halo mass and include ∼30 ram pressure candidates in the group regime (Mh 〈 1014). The observed frequency of ram pressure candidates shows substantial scatter with group/cluster mass, but on average is larger in clusters (Mh ≥ 1014 M⊙) than groups (Mh 〈 1014 M⊙) by a factor of ∼2. We find that ram pressure candidates are most commonly low-mass galaxies and have enhanced star formation rates relative to star-forming field galaxies. The enhancement in star formation is largely independent of galaxy mass and strongest for galaxies in clusters. As a result of the large survey footprint and excellent image quality from UNIONS, we are able to identify disturbed galaxies, potentially affected by ram pressure stripping, across a wide range of host environment.
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  • 63
    Publication Date: 2021-10-30
    Description: Motivation Coiled-coil is composed of two or more helices that are wound around each other. It widely exists in proteins and has been discovered to play a variety of critical roles in biology processes. Generally, there are three types of structural features in coiled-coil: coiled-coil domain (CCD), oligomeric state, and register. However, most of the existing computational tools only focus on one of them. Results Here, we describe a new deep learning model, CoCoPRED, which is based on convolutional layers, bidirectional long short-term memory, and attention mechanism. It has three networks, i.e., CCD network, oligomeric state network, and register network, corresponding to the three types of structural features in coiled-coil. This means CoCoPRED has the ability of fulfilling comprehensive prediction for coiled-coil proteins. Through the 5-fold cross-validation experiment, we demonstrate that CoCoPRED can achieve better performance than the state-of-the-art models on both CCD prediction and oligomeric state prediction. Further analysis suggests the CCD prediction may be a performance indicator of the oligomeric state prediction in CoCoPRED. The attention heads in CoCoPRED indicate that registers a, b, and e are more crucial for the oligomeric state prediction. Availability CoCoPRED is available at http://www.csbio.sjtu.edu.cn/bioinf/CoCoPRED. Supplementary information Supplementary data are available at Bioinformatics online.
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  • 64
    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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  • 65
    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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  • 66
    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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  • 67
    Publication Date: 2021-10-28
    Description: Summary This article proposes the use of geostatistical techniques to estimate dispersion curves between other known ones. To do it, we introduce two novel methodologies: the stacking method and the group-velocity mapping method. We obtain our set of group-velocity fundamental mode dispersion curves from seismic noise correlation. Consequently, we first assign their attribution point at the mid-distance between the stations used for the dispersion curves calculation. The stacking method uses the range of the omnidirectional semivariogram of a regionalized variable that quantifies the similarity between dispersion curves to stack them according to their spatial correlation. We test this technique with dispersion curves obtained in Mexico City and get a range of ∼400 m for the omnidirectional semivariogram. We also calculate directional semivariograms and observe a maximum range (∼500 m) in the NW-SE direction, agreeing with the city's spatial distribution of natural periods. On the other hand, the group-velocity mapping method uses the ordinary kriging estimator in the group velocities for all the ranges of periods to generate maps and then dispersion curves. Estimated dispersion curves retrieved from both, the stacking and the group-velocity mapping method, were compared with those obtained with the fast marching tomographic method. We also establish analogies between getting group-velocity maps with the tomographic method and with the group-velocity mapping method. Finally, we observe that the range of the omnidirectional semivariogram used in the stacking method may be related to the tomographic method resolution.
    Print ISSN: 0956-540X
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    Topics: Geosciences
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  • 68
    Publication Date: 2021-10-28
    Description: Gravitational waves provide a unique and powerful opportunity to constrain the dynamics in the interior of proto-neutron stars during core collapse supernovae. Convective motions play an important role in generating neutron stars magnetic fields, which could explain magnetar formation in the presence of fast rotation. We compute the gravitational wave emission from proto-neutron star convection and its associated dynamo, by post-processing three-dimensional MHD simulations of a model restricted to the convective zone in the anelastic approximation. We consider two different proto-neutron star structures representative of early times (with a convective layer) and late times (when the star is almost entirely convective). In the slow rotation regime, the gravitational wave emission follows a broad spectrum peaking at about three times the turnover frequency. In this regime, the inclusion of magnetic fields slightly decreases the amplitude without changing the spectrum significantly compared to a non-magnetised simulation. Fast rotation changes both the amplitude and spectrum dramatically. The amplitude is increased by a factor of up to a few thousands. The spectrum is characterized by several peaks associated to inertial modes, whose frequency scales with the rotation frequency. Using simple physical arguments, we derive scalings that reproduce quantitatively several aspects of these numerical results. We also observe an excess of low-frequency gravitational waves, which appears at the transition to a strong field dynamo characterized by a strong axisymmetric toroidal magnetic field. This signature of dynamo action could be used to constrain the dynamo efficiency in a proto-neutron star with future gravitational wave detections.
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  • 69
    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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  • 70
    Publication Date: 2021-10-30
    Description: Spectroscopy from the final internal data release of the Gaia-ESO Survey (GES) has been combined with Gaia EDR3 to assign membership probabilities to targets observed towards 63 Galactic open clusters and 7 globular clusters. The membership probabilities are based chiefly on maximum likelihood modelling of the 3D kinematics of the targets, separating them into cluster and field populations. From 43211 observed targets, 13985 are identified as highly probable cluster members (P 〉 0.9), with an average membership probability of 0.993. The addition of GES radial velocities successfully drives down the fraction of false positives and we achieve better levels of discrimination in most clusters over the use of astrometric data alone, especially those at larger distances. Since the membership selection is almost purely kinematic, the union of this catalogue with GES and Gaia is ideal for investigating the photometric and chemical properties of clusters as a function of stellar mass, age and Galactic position.
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  • 71
    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.
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  • 72
    Publication Date: 2021-10-29
    Description: Investigations of some type Iax supernovae have led to the suggestion that their ejecta must be layered to some degree. Such an ejecta structure has been argued as inconsistent with the well-mixed composition predicted by pure deflagrations. Based on explosion models, we create toy models in which the ejecta are artificially stratified and progressively mixed until a uniform composition is obtained. We find that models that are heavily mixed, containing burned and unburned material at all velocities, produce reasonably good agreement with SN 2012Z, for which a layered structure has been suggested. We also discuss how existing ejecta compositions determined for type Iax supernovae do not necessarily contradict pure deflagration models and may be consistent with a steeper density profile. We investigate previous claims that differences in line profile shapes may be due to strong blending, by presenting a series of models with different plasma states. These models indicate that blending could indeed explain differences in the observed profiles. Alternatively, stratification could also explain such differences, however all of our models indicate that this does not necessarily require stratification in abundance. Sufficient stratification in ionisation state can be achieved even for a well-mixed model. Based on our analysis, we demonstrate that there is insufficient evidence to suggest the ejecta of type Iax supernovae must be layered and therefore argue the pure deflagration scenario is not ruled out, even for the brightest type Iax supernovae. Our analysis does not indicate the ejecta cannot be layered to some degree, but observations within days of explosion are necessary to determine the extent to which the outer ejecta could be layered.
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  • 73
    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.
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 74
    Publication Date: 2021-10-27
    Description: We describe a modified version of the nbody6 code for simulating star clusters which greatly improves computational efficiency while sacrificing little in the way of accuracy. The distant force calculator is replaced by a GPU-enabled Barnes-Hut code, and integration is done with a standard leap frog scheme. Short-range forces continue to use the CPU-based fourth-order Hermite predictor-corrector scheme of nbody6. Our code outperforms nbody6 for systems with more than 3 × 105 particles and runs more than a factor 2 faster for systems of 106 particles with similar energy conservation. Our code should be useful for simulating realistic dense stellar clusters, such as globular clusters or galactic nuclei.
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  • 75
    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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  • 76
    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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  • 77
    Publication Date: 2021-10-28
    Description: Since the first report of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019, over 100 million people have been infected by COVID-19, millions of whom have died. In the latest year, a large number of omics data have sprung up and helped researchers broadly study the sequence, chemical structure and function of SARS-CoV-2, as well as molecular abnormal mechanisms of COVID-19 patients. Though some successes have been achieved in these areas, it is necessary to analyze and mine omics data for comprehensively understanding SARS-CoV-2 and COVID-19. Hence, we reviewed the current advantages and limitations of the integration of omics data herein. Firstly, we sorted out the sequence resources and database resources of SARS-CoV-2, including protein chemical structure, potential drug information and research literature resources. Next, we collected omics data of the COVID-19 hosts, including genomics, transcriptomics, microbiology and potential drug information data. And subsequently, based on the integration of omics data, we summarized the existing data analysis methods and the related research results of COVID-19 multi-omics data in recent years. Finally, we put forward SARS-CoV-2 (COVID-19) multi-omics data integration research direction and gave a case study to mine deeper for the disease mechanisms of COVID-19.
    Print ISSN: 1467-5463
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  • 78
    Publication Date: 2021-10-28
    Description: The European Variation Archive (EVA; https://www.ebi.ac.uk/eva/) is a resource for sharing all types of genetic variation data (SNPs, indels, and structural variants) for all species. The EVA was created in 2014 to provide FAIR access to genetic variation data and has since grown to be a primary resource for genomic variants hosting 〉3 billion records. The EVA and dbSNP have established a compatible global system to assign unique identifiers to all submitted genetic variants. The EVA is active within the Global Alliance of Genomics and Health (GA4GH), maintaining, contributing and implementing standards such as VCF, Refget and Variant Representation Specification (VRS). In this article, we describe the submission and permanent accessioning services along with the different ways the data can be retrieved by the scientific community.
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  • 79
    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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  • 80
    Publication Date: 2021-10-19
    Description: The feedback from young stars (i.e. pre-supernova) is thought to play a crucial role in molecular cloud destruction. In this paper, we assess the feedback mechanisms acting within a sample of 5810 H ii regions identified from the PHANGS-MUSE survey of 19 nearby ( 1, and expanding, yet there is a small sample of compact H ii regions with Ptot,max/Pde 〈 1 (∼1 per cent of the sample). These mostly reside in galaxy centres (Rgal 〈 1 kpc), or, specifically, environments of high gas surface density; log(Σgas/M⊙ pc−2) ∼ 2.5 (measured on kpc-scales). Lastly, we compare to a sample of literature measurements for Ptherm and Prad to investigate how dominant pressure term transitions over around 5 dex in spatial dynamic range and 10 dex in pressure.
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  • 81
    Publication Date: 2021-10-21
    Description: Summary Eukaryotic gene expression requires coordination among hundreds of transcriptional regulators. To characterize a specific transcriptional regulator, identifying how it shares genomic-binding profiles with others can generate important insights into its action. As genomic data such as ChIP-Seq are being rapidly generated from individual labs, there is a demand for timely integration and analysis of these new data. We have developed an R package, GPSmatch (Genomic-binding Profile Similarity match), for calculating the Jaccard index to compare ChIP-Seq peaks from one experiment to the peaks of other ChIP-Seq experiments stored in a user-supplied customizable database. GPSmatch also evaluates the statistical significance of the calculated Jaccard index using a nonparametric Monte Carlo procedure. We show that GPSmatch is suitable for identifying transcriptional regulators that share similar genomic-binding profiles, which may unravel potential mechanistic actions of gene regulation. Availability The software is freely available at https://github.com/Bao-Lab/GPSmatch.
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  • 82
    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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  • 83
    Publication Date: 2021-10-28
    Description: Quantifying inter-specific variations of tree resilience to drought and revealing the underlying mechanisms are of great importance to the understanding of forest functionality particularly in water-limited regions. So far, comprehensive studies incorporating investigations in inter-specific variations of long-term growth patterns of trees and the underlying physiological mechanisms are very limited. Here, in a semi-arid site of northern China, tree radial growth rate, inter-annual tree-ring growth responses to climate variability, as well as physiological characteristics pertinent to xylem hydraulics, carbon assimilation and drought tolerance were analyzed in seven pine species growing in a common environment. Considerable inter-specific variations in radial growth rate, growth response to drought and physiological characteristics were observed among the studied species. Differently, the studied species exhibited similar degrees of resistance to drought-induced branch xylem embolism with water potential corresponding to 50% loss hydraulic conductivity ranged from −2.31 to −2.96 MPa. We found that higher branch hydraulic efficiency is related to greater leaf photosynthetic capacity, smaller hydraulic safety margin and lower woody density (P  0.05). Rather, species with higher hydraulic conductivity and photosynthetic capacity was more sensitive to drought stress and tended to show weaker growth resistance to extreme drought events as quantified by tree-ring analyses, which is at least partially due to a trade-off between hydraulic efficiency and safety across species. This study thus demonstrates the importance of drought resilience rather than instantaneous water and carbon flux capacity in determining tree growth in water-limited environments.
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    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 84
    Publication Date: 2021-10-13
    Description: The question of what determines the width of Kuiper belt analogues (exoKuiper belts) is an open one. If solved, this understanding would provide valuable insights into the architecture, dynamics, and formation of exoplanetary systems. Recent observations by ALMA have revealed an apparent paradox in this field, the presence of radially narrow belts in protoplanetary discs that are likely the birthplaces of planetesimals, and exoKuiper belts nearly four times as wide in mature systems. If the parent planetesimals of this type of debris disc indeed form in these narrow protoplanetary rings via streaming instability where dust is trapped, we propose that this width dichotomy could naturally arise if these dust traps form planetesimals whilst migrating radially, e.g. as caused by a migrating planet. Using the dust evolution software dustpy, we find that if the initial protoplanetary disc and trap conditions favour planetesimal formation, dust can still effectively accumulate and form planetesimals as the trap moves. This leads to a positive correlation between the inward radial speed and final planetesimal belt width, forming belts up to ∼100au over 10 Myr of evolution. We show that although planetesimal formation is most efficient in low-viscosity (α = 10−4) discs with steep dust traps to trigger the streaming instability, the large widths of most observed planetesimal belts constrain α to values ≥4 × 10−4 at tens of au, otherwise the traps cannot migrate far enough. Additionally, the large spread in the widths and radii of exoKuiper belts could be due to different trap migration speeds (or protoplanetary disc lifetimes) and different starting locations, respectively. Our work serves as a first step to link exoKuiper belts and rings in protoplanetary discs.
    Print ISSN: 0035-8711
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  • 85
    Publication Date: 2021-10-18
    Description: The radio quasar luminosity function exhibits an upturn around $L_{6 m :GHz}=10^{23}$ W Hz−1 that is well-modelled by a star-forming host galaxy population. This distribution leads some authors to cite star formation as the main radio emission mechanism in so-called radio-quiet quasars (RQQs). Understanding the origin of RQQ radio emission is crucial for our understanding of quasar feedback mechanisms – responsible for the regulation of star formation in the host galaxy – and for understanding galaxy evolution as a whole. By observing RQQs that have been magnified by strong gravitational lensing, we have direct access to the RQQ population out to cosmic noon, where evidence for twin mini-jets has recently been found in a sub-$mu$Jy RQQ. Here we present radio observations of two lensed RQQs using the VLA at 5 GHz, the latest objects to be observed in a sample of quadruply-imaged RQQs above −30°. In SDSS J1004+4112 we find strong evidence for AGN-related radio emission in the variability of the source. In PG 1115+080 we find tentative evidence for AGN-related emission, determined by comparing the radio luminosity with modelled dust components. If confirmed in the case of PG 1115+080, which lies on the radio–FIR correlation, the result would reinforce the need for caution when applying the correlation to rule out jet activity and when assuming no AGN heating of FIR-emitting dust when calculating star formation rates. Our programme so far has shown that the two of the faintest radio sources ever imaged show strong evidence for AGN-dominated radio emission.
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  • 86
    Publication Date: 2021-10-30
    Description: Post-transcriptional processes mediated by mRNA binding proteins represent important control points in gene expression. In eukaryotes, mRNAs containing specific AU-rich motifs are regulated by binding of tristetraprolin (TTP) family tandem zinc finger proteins, which promote mRNA deadenylation and decay, partly through interaction of a conserved C-terminal CNOT1 binding (CNB) domain with CCR4–NOT protein complexes. The social ameba Dictyostelium discoideum shared a common ancestor with humans more than a billion years ago, and expresses only one TTP family protein, TtpA, in contrast to three members expressed in humans. Evaluation of ttpA null-mutants identified six transcripts that were consistently upregulated compared to WT during growth and early development. The 3′-untranslated regions (3′-UTRs) of all six ‘TtpA-target’ mRNAs contained multiple TTP binding motifs (UUAUUUAUU), and one 3′-UTR conferred TtpA post-transcriptional stability regulation to a heterologous mRNA that was abrogated by mutations in the core TTP-binding motifs. All six target transcripts were upregulated to similar extents in a C-terminal truncation mutant, in contrast to less severe effects of analogous mutants in mice. All six target transcripts encoded probable membrane proteins. In Dictyostelium, TtpA may control an ‘RNA regulon’, where a single RNA binding protein, TtpA, post-transcriptionally co-regulates expression of several functionally related proteins.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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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: 2021-10-27
    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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  • 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
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  • 91
    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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  • 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
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  • 93
    Publication Date: 2021-10-28
    Description: The long-term evolutionary impacts of whole genome duplication (WGD) are strongly influenced by the ensuing rediploidization process. Following autopolyploidization, rediploidization involves a transition from tetraploid to diploid meiotic pairing, allowing duplicated genes (ohnologues) to diverge genetically and functionally. Our understanding of autopolyploid rediploidization has been informed by a WGD event ancestral to salmonid fishes, where large genomic regions are characterized by temporally delayed rediploidization, allowing lineage-specific ohnologue sequence divergence in the major salmonid clades. Here, we investigate the long-term outcomes of autopolyploid rediploidization at genome-wide resolution, exploiting a recent ‘explosion’ of salmonid genome assemblies, including a new genome sequence for the huchen (Hucho hucho). We developed a genome alignment approach to capture duplicated regions across multiple species, allowing us to create 121,864 phylogenetic trees describing genome-wide ohnologue divergence across salmonid evolution. Using molecular clock analysis, we show that 61% of the ancestral salmonid genome experienced an initial ‘wave’ of rediploidization in the late Cretaceous (85-106 Mya). This was followed by a period of relative genomic stasis lasting 17-39 My, where much of the genome remained tetraploid. A second rediploidization wave began in the early Eocene and proceeded alongside species diversification, generating predictable patterns of lineage-specific ohnologue divergence, scaling in complexity with the number of speciation events. Using gene set enrichment, gene expression, and codon-based selection analyses, we provide insights into potential functional outcomes of delayed rediploidization. This study enhances our understanding of delayed autopolyploid rediploidization and has broad implications for future studies of WGD events.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
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  • 94
    Publication Date: 2021-10-29
    Description: SIRT3 is an NAD+-dependent protein deacetylase localized in mitochondria. Several studies reported localization of SIRT3 in the cytoplasm or nucleus, but data of these studies were not consistent. We detected expression of mitochondrial (SIRT3mt) and cytoplasmic (SIRT3ct) Sirt3 mRNAs in the mouse brain, and we also found SIRT3 immunostaining of mitochondria and cytoplasm in the brain and cultured neural cells. However, expression levels of SIRT3ct in COS cells transfected with SIRT3ct cDNA were much lower than those of SIRT3mt. We found that SIRT3ct but not SIRT3mt was promptly degraded by ubiquitin-dependent degradation, in which SIRT3ct degradation was mediated mainly by ubiquitination of NH2-terminal methionine and partly by that of lysine residues of SIRT3ct. SIRT3ct expression level was significantly enhanced by treatment of cells with staurosporine or H2O2. H2O2 treatment promoted nuclear translocation of SIRT3ct and induced histone H3 deacetylation and superoxide dismutase 2 expression. Overexpression of SIRT3ct decreased cell death caused by H2O2 at levels similar to those achieved by overexpression of SIRT3mt. Knockdown of Sirt3 mRNA increased cell death caused by amyloid-β (Aβ), and overexpression of SIRT3ct suppressed the toxic function of Aβ in PC12 cells. These results indicate that SIRT3ct promotes cell survival under physiological and pathological conditions.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
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  • 95
    Publication Date: 2021-10-28
    Description: Summary On 2020 December 29, the Mw 6.4 Petrinja earthquake hit the Kupa Valley region and set a record for the largest earthquake in northwestern (NW) Croatia. The coseismic surface displacements are well obtained on three pairs of interferometric synthetic aperture radar (InSAR) images from Sentinel-1 satellites. The interferograms exhibit coseismic ground deformation with a maximum line-of-sight (LOS) displacement of 0.4 m. Based on the coseismic deformation field, we investigate both the fault geometry and the coseismic slip distribution. The results show a dextral event with a peak slip of 3.50 m at a depth of 3.47 km. The shallow depth and unusually large coseismic slip correspond to obvious ground deformation and serious damage in the epicentral zone. The 2020 earthquake highlights an unmapped, steeply dipping strike-slip fault, which possibly enabled a potential ‘curve cut-off’ process on the bending segment of the Pokupsko fault in the context of ∼N-S compression in NW Croatia. The large coseismic slip and high stress drop associated with the Mw 6.4 Petrinja earthquake are likely products of the geometrically complex fault zones and immature seismotectonic environment in NW Croatia.
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  • 96
    Publication Date: 2021-10-28
    Description: Pathogenic variants that disrupt human mitochondrial protein synthesis are associated with a clinically heterogenous group of diseases. Despite an impairment in oxidative phosphorylation being a common phenotype, the underlying molecular pathogenesis is more complex than simply a bioenergetic deficiency. Currently, we have limited mechanistic understanding on the scope by which a primary defect in mitochondrial protein synthesis contributes to organelle dysfunction. Since the proteins encoded in the mitochondrial genome are hydrophobic and need co-translational insertion into a lipid bilayer, responsive quality control mechanisms are required to resolve aberrations that arise with the synthesis of truncated and misfolded proteins. Here, we show that defects in the OXA1L-mediated insertion of MT-ATP6 nascent chains into the mitochondrial inner membrane are rapidly resolved by the AFG3L2 protease complex. Using pathogenic MT-ATP6 variants, we then reveal discrete steps in this quality control mechanism and the differential functional consequences to mitochondrial gene expression. The inherent ability of a given cell type to recognize and resolve impairments in mitochondrial protein synthesis may in part contribute at the molecular level to the wide clinical spectrum of these disorders.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 97
    Publication Date: 2021-10-30
    Description: Summary Objective assessment of seismic hazard and understanding of the Himalayan arc's tectonics requires detailed information on the crustal structure and geometry of the underthrusting Indian Plate beneath the Himalaya. Here, we present high-resolution three-dimensional P- wave velocity (Vp) and P-to-S wave velocity ratio (Vp/Vs) images of the Kumaun-Garhwal Himalaya, a proposed potential region for the future great earthquake. We generate these images by inverting arrival times of 515 local earthquakes recorded by 41 broadband stations during November 2006-June 2008. The tomographic images show a heterogeneous structure in the upper-mid crust. These images, along with available geophysical and geological information, indicate the presence of quartz-rich felsic rocks in the uppermost crust; and the occurrence of saline-rich aqueous fluid/partial melt in the upper-mid crust. We propose that the Main Himalayan Thrust (MHT), having a flat-ramp-flat geometry, lies at the base of these fluid zones. The small and moderate-to-strong magnitude earthquakes are mainly confined to the fluid-rich zones along the MHT and quartz-rich rocks in the upper crust. Such an interpretation implies that the earthquake occurrence in the Kumaun-Garhwal Himalaya is largely controlled by the geometry of the MHT and crustal lithology.
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  • 98
    Publication Date: 2021-10-28
    Description: Motivation Inference of Identity-by-descent (IBD) sharing along the genome between pairs of individuals has important uses. But all existing inference methods are based on genotypes, which is not ideal for low-depth Next Generation Sequencing (NGS) data from which genotypes can only be called with high uncertainty. Results We present a new probabilistic software tool, LocalNgsRelate, for inferring IBD sharing along the genome between pairs of individuals from low-depth NGS data. Its inference is based on genotype likelihoods instead of genotypes, and thereby it takes the uncertainty of the genotype calling into account. Using real data from the 1000 Genomes project, we show that LocalNgsRelate provides more accurate IBD inference for low-depth NGS data than two state-of-the-art genotype based methods, Albrechtsen et al. (2009) and hap-IBD. We also show that the method works well for NGS data down to a depth of 2X. Availability LocalNgsRelate is freely available at https://github.com/idamoltke/LocalNgsRelate Supplementary Data Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 99
    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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  • 100
    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.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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