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  • Journals
  • Articles  (475)
  • Oxford University Press  (475)
  • MDPI Publishing
  • 2020-2024  (475)
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  • 1
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    New constraints on the shear wave velocity structure of the Ivrea geophysical body from seismic ambient noise tomography (Ivrea-Verbano Zone, Alps) (2024)
    Oxford University Press
    Details
    Publication Date: 2024-01-19
    Description: We performed seismic ambient noise tomography to investigate the shallow crustal structure around the Ivrea geophysical body (IGB) in the Ivrea-Verbano Zone (IVZ). We achieved higher resolution with respect to previous tomographic works covering the Western Alps, by processing seismic data collected by both permanent and temporary seismic networks (61 broad-band seismic stations in total). This included IvreaArray, a temporary, passive seismic experiment designed to investigate the IVZ crustal structure. Starting from continuous seismic ambient noise recordings, we measured and inverted the dispersion of the group velocity of surface Rayleigh waves (fundamental mode) in the period range 4–25 s. We obtained a new, 3-D vS model of the IVZ crust via the stochastic neighbourhood algorithm (NA), with the highest resolution between 3 to 40 km depth. The fast and shallow shear wave velocity anomaly associated with the IGB presents velocities of 3.6 km s−1 directly at the surface, in remarkable agreement with the location of the exposed lower-to-middle crustal and mantle outcrops. This suggests a continuity between the surface geological observations and the subsurface geophysical anomalies. The fast IGB structure reaches vS of 4 km s−1 at 20–25 km depth, at the boundary between the European and Adriatic tectonic plates, and in correspondence with the earlier identified Moho jump in the same area. The interpretation of a very shallow reaching IGB is further supported by the comparison of our new results with recent geophysical investigations, based on receiver functions and gravity anomaly data. By combining the new geophysical constraints and the geological observations at the surface, we provide a new structural interpretation of the IGB, which features lower crustal and mantle rocks at upper crustal depths. The comparison of the obtained vS values with the physical properties from laboratory analysis of local rock samples suggests that the bulk of the IGB consists of a combination of mantle peridotite, ultramafic and lower crustal rocks, bound in a heterogeneous structure. These new findings, based on vS tomography, corroborate the recent interpretation for which the Balmuccia peridotite outcrops are continuously linked to the IGB structure beneath. The new outcomes contribute to a multidisciplinary framework for the interpretation of the forthcoming results of the scientific drilling project DIVE. DIVE aims at probing the lower continental crust and its transition to the mantle, with two ongoing and one future boreholes (down to 4 km depth) in the IVZ area, providing new, complementary information on rock structure and composition across scales. In this framework, we constrain the upper crustal IGB geometries and lithology based on new evidence for vS, connecting prior crustal knowledge to recent active seismic investigations.
    Description: Published
    Description: 1089–1105
    Description: OST1 Alla ricerca dei Motori Geodinamici
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 2
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    Implications for the geometry of plate boundaries in NE Asia based on the geodetic analysis of the 2020Mw 6.4 Koryak event (2024)
    Oxford University Press
    Details
    Publication Date: 2024-01-23
    Description: On the 9th of January 2020, an Mw 6.4 strike-slip earthquake took place north of the Asian margin of the Bering Sea. The earthquake occurred within the known reverse-right-lateral active fault zone, called Khatyrka–Vyvenka, which transverses the Koryak Highland from SE to NW and is thought to be a surface manifestation of the Asian portion of either the Bering plate boundary or the northern edge of the Alaskan stream. No other strong earthquake has ever been recorded in this remote uninhabited area and the few existing seismic stations provide poor quality earthquake locations.We adopt SAR interferometry (InSAR) technique to define an improved location of the Koryak 2020 earthquake and constrain the seismic source. The analysis of the 2020 event revealed a previously unknown active fault of left-lateral kinematics that is possibly hidden and strikes NWtransversely to the Khatyrka–Vyvenka fault zone. Although several mechanisms could account for left-lateral kinematics of this fault, we propose that the structure is part of a more extended NW fault structure, that formed in pre-neotectonic times and has played a role of a pre-existing rheological discontinuity. This revived NW structure together with a similar structure located easterly, so far aseismic, make the plate/stream boundary segmented, step-like in plan view. The step-like boundary geometry may be the result of internal transform deformation of a rigid plate, but it is better explained by deflections of the Alaskan stream edge at local crustal asperities, which are pre-Cenozoic terrains.
    Description: Published
    Description: 1412–1421
    Description: OST2 Deformazione e Hazard sismico e da maremoto
    Description: JCR Journal
    Keywords: Plate motion ; Radar interferometry ; Seismic cycle ; Asia
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
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    High frequency attenuation of S waves in alluvial deposits of the central Po Plain (northern Italy) (2024)
    Oxford University Press
    Details
    Publication Date: 2024-04-03
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2023. 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: Estimation of local seismic response plays a key role in assessing local seismic hazard and particularly in the design of shaking scenarios. Modelling local seismic response involves knowing of the shear wave velocity (Vs) and quality factor (Qs) profiles for the site in question. The many techniques that have been developed to assess Vs in surface deposits produce reliable measurements of Vs , but these rarely correspond to direct measurements of Qs . The latter is often considered through damping measures from laboratory tests on small-scale soil samples, which can provide information primarily on intrinsic attenuation, neglecting the contribution of scattering effects. In this paper, using seismic recordings obtained at the surface and in boreholes at 100 m depth, we estimate an average value of Qs of some characteristic alluvial deposits of the Po Plain (northern Italy). Data come from a microseismic network which sampled an almost uniform lithology in the central Po Plain and consisted of three surface and four borehole stations with an interstation distance of about 2 km. The average value of Qs of the shallowest 100 m of the sedimentary strata, Qs100, is estimated by considering: (1) the high-frequency attenuation of seismic waves due to propagation through the corresponding stratigraphy and (2) the interference between incident and surface-reflected waves observed at borehole stations. We parametrize the first through k0_100, the difference between the values of the spectral decay parameter kappa (k) estimated at the surface and at the boreholes depth, respectively. We use the second in order to compute Vs100, the time-averaged Vs referred to the uppermost 100 m stratigraphy. We obtain: k0_100 = (11 ± 3) ms, Vs100 = (309 ± 11) m s −1 and Qs100 = 31 ± 10. At the surface, the estimated values of the site-specific kappa, k0, are found to range from 75 to 79 ms. As expected, these results are in good agreement with studies performed in other sites characterized by sandy or clayey lithologies, and can be usefully used in site response analysis at sites where the rigidity is mainly controlled by lithostatic pressure.
    Description: Comune di Minerbio (grant: “Sperimentazione ILG Minerbio”; grant number: 0913.010).
    Description: Published
    Description: 2075–2094
    Description: OST2 Deformazione e Hazard sismico e da maremoto
    Description: JCR Journal
    Keywords: Earthquake ground motions ; Seismic attenuation ; Site effects ; Wave propagation ; Wave scattering and diffraction ; 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
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    Moment magnitude for earthquakes in the Etna volcano area (2024)
    Oxford University Press
    Details
    Publication Date: 2024-03-19
    Description: Accurate quantification of seismic activity in volcanic regions is an important asset for im- proving hazard and risk assessment. This is especially true for densely populated areas, as in the case of Etna volcano (Southern Italy). There, the volcanic hazard is amplified by the seismic risk of acti ve faults, especiall y on the eastern flank of the volcano. In such a context, it is common to rely on moment magnitude ( M W ) to characterize seismicity and monitor the energy released during an eruption. In this study, we calculate the moment-based magnitude ( M W ) for selected seismic data sets, using different approaches in distinct magnitude ranges to cover the widest possible range of magnitude that characterizes Etna’s seismicity . Specifically , we computed the M W from a data set of moment tensor solutions of earthquakes that occurred in the magnitude range 3.4 ≤M L ≤4.8 during 2005–2020; we created a data set of seismic moment and associated M W for earthquakes 1.0 ≤M L 〈 3.4 obtained by analysing source spectra; we fine-tuned two relationships, for shallow and deep earthquakes, to obtain M W from response spectra. Finally, we calibrated a specific relationship between M W and M L for the Etna area earthquakes in the range 1.0 ≤M L ≤4.8. All the empirical relationships obtained in this study can be applied in real-time analysis of the seismicity to provide fast and robust information on the released seismic energy.
    Description: INGV-DPC 2012- 2021 agreement; B2 DPC-INGV 2019-2021 project; IMPACT Department strategic project ; ‘Project PE0000005–RETURN (NRRP)
    Description: Published
    Description: 2520-2534
    Description: OST2 Deformazione e Hazard sismico e da maremoto
    Description: JCR Journal
    Keywords: Earthquak e source observations ; Earthquake hazards ; Time series analysis ; Full moment tensor
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 5
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    A statistical framework for detection of b-value anomalies in Italy (2024)
    Oxford University Press
    Details
    Publication Date: 2024-03-12
    Description: This study presents a new robust statistical framework, in which to measure relative differences, or deviations from a hypothetical reference value, of Gutenberg-Richter b-value. Moreover, it applies this method to recent seismicity in Italy, to find possible changes of earthquake magnitude distribution in time and space. The method uses bootstrap techniques, which have no prior assumptions about the distribution of data, keeping their basic features. Excluding Central Italy, no significative b-value variation is found, revealing that the frequency-magnitude distribution exponent is substantially stable or that data are not able to reveal hidden variations. Considering the small size of examined magnitude samples, we cannot definitively decide if the higher b-values in Central Italy, consistently founded by all applied tests, have a physical origin or result from a statistical bias. In any case, they indicate short-lived excursions which have a temporary nature and, therefore, cannot be associated solely to spatial variations in tectonic framework. Both the methodological issues and the results of the application to seismicity in Italy show that a correct assessing of b-value changes requests appropriate statistics, that accurately quantify the low accuracy and precision of b-value estimation for small magnitude samples.
    Description: Published
    Description: 729–740
    Description: OST4 Descrizione in tempo reale del terremoto, del maremoto, loro predicibilità e impatto
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
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    Source mechanisms and induced seismicity in the Val d'Agri Basin (Italy) (2024)
    Oxford University Press
    Details
    Publication Date: 2024-03-12
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2023. 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 present the results from a fully unconstrained moment tensor inversion of induced seismic events in a complex and high seismic hazard region (Val d’Agri basin, Southern Italy). The study area hosts two well-documented cases of induced microseismicity linked to (i) a wastewater injection well of a giant oilfield (the largest in onshore Europe), and (ii) severe seasonal level changes of an artificial lake. In order to gather information on the non-doublecouple components of the source and to better understand the rupture mechanisms, we analyse seismic events recorded during daily injection tests in the disposal well. The computed moment tensors have significant non-double-couple components that correlate with the well-head injection pressure. The injection parameters strongly influence the rupture mechanism that can be interpreted as due to the opening/closing of a fracture network inside a fault zone of a pre-existing thrust fault. For the case of the reservoir-induced seismicity, no direct correlations are observed with the loading/unloading of the reservoir.
    Description: Published
    Description: 1617–1627
    Description: OST3 Vicino alla faglia
    Description: JCR Journal
    Keywords: 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 7
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    Fabric controls fault stability in serpentinite gouges (2024)
    Oxford University Press
    Details
    Publication Date: 2024-04-09
    Description: Serpentinites are polymineralic rocks distributed almost ubiquitously across the globe in active tectonic regions. Magnetite-rich serpentinites are found in the low-strain domains of serpen- tinite shear zones, which act as potential sites of nucleation of unstable slip. To assess the potential of earthquake nucleation in these materials, we investigate the link between me- chanical properties and fabric of these rocks through a suite of laboratory shear experiments. Our experiments were done at room temperature and cover a range of normal stress and slip velocity from 25 to 100 MPa and 0.3 to 300 μm s −1 , respecti vel y. We show that magnetite-rich serpentinites are ideal materials since they display strong sensitivity to the loading rate and are susceptible to nucleation of unstable slip, especially at low forcing slip velocities. We also aim at the integration of mechanical and microstructural results to describe the underlying mechanisms that produce the macroscopic behaviour. We show that mineralogical composi- tion and mineral structure dictates the coexistence of two deformation mechanisms leading to stable and unstable slip. The weakness of phyllosilicates allows for creep during the interseis- mic phase of the laboratory seismic cycle while favouring the restoration of a load-bearing granular framework, responsible of the nucleation of unstable events. During dynamic slip, fault zone shear fabric determines the mode of slip, producing either asymmetric or Gaussian slip time functions for either fast or slow events. We report rate/state friction parameters and integrate our mechanical data with microstructural observations to shed light on the mech- anisms dictating the complexity of laborator y ear thquakes. We show that mineralogical and fabric heterogeneities control fault slip behaviour.
    Description: Published
    Description: 1778–1797
    Description: OST3 Vicino alla faglia
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 8
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    Comparison between alarm-based and probability-based earthquake forecasting methods (2024)
    Oxford University Press
    Details
    Publication Date: 2024-05-09
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2023. 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 a recent work, we applied the every earthquake a precursor according to scale (EEPAS) probabilistic model to the pseudo-prospective forecasting of shallow earthquakes with magni- tude M 5.0 in the Italian region. We compared the forecasting performance of EEPAS with that of the epidemic type aftershock sequences (ETAS) forecasting model, using the most recent consistency tests developed within the collaboratory for the study of earthquake predictabil- ity (CSEP). The application of such models for the forecasting of Italian target earthquakes seems to show peculiar characteristics for each of them. In particular, the ETAS model showed higher performance for short-term forecasting, in contrast, the EEPAS model showed higher forecasting performance for the medium/long-term. In this work, we compare the performance of EEPAS and ETAS models with that obtained by a deterministic model based on the occur- rence of strong foreshocks (FORE model) using an alarm-based approach. We apply the two rate-based models (ETAS and EEPAS) estimating the best probability threshold above which we issue an alarm. The model parameters and probability thresholds for issuing the alarms are calibrated on a learning data set from 1990 to 2011 during which 27 target earthquakes have occurred within the analysis region. The pseudo-prospective forecasting performance is as- sessed on a validation data set from 2012 to 2021, which also comprises 27 target earthquakes. Tests to assess the forecasting capability demonstrate that, even if all models outperform a purely random method, which trivially forecast earthquake proportionally to the space–time occupied by alarms, the EEPAS model exhibits lower forecasting performance than ETAS and FORE models. In addition, the relative performance comparison of the three models demonstrates that the forecasting capability of the FORE model appears slightly better than ETAS, but the difference is not statistically significant as it remains within the uncertainty level. However, truly prospective tests are necessary to validate such results, ideally using new testing procedures allowing the analysis of alarm-based models, not yet available within the CSEP.
    Description: Published
    Description: 1541–1551
    Description: OST4 Descrizione in tempo reale del terremoto, del maremoto, loro predicibilità e impatto
    Description: JCR Journal
    Keywords: Computational seismology ; Earthquake interaction, forecasting and prediction ; Statistical seismology ; Comparison betwee earthquake forecasting methods
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 9
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    Low-strength shear zone in the western Makran subduction zone, southeastern Iran: insights from a receiver function analysis (2024)
    Oxford University Press
    Details
    Publication Date: 2024-05-09
    Description: To understand the seismic hazard of a subduction zone, it is necessary to know the geometry, location and mechanical characteristics of the interplate boundary below which an oceanic plate is thrust downward. By considering the azimuthal dependence of converted P-to-S (Ps) amplitudes in receiver functions, we have detected the interplate boundary in the Makran subduction zone, revealing significant seismic anisotropy at the base of the accretionary wedge above the slab before it bends down beneath the Jaz Murian basin. This anisotropic feature aligns with a zone of reduced seismic velocity and a high primary/secondary wave velocity ratio (Vp/Vs), as documented in previous studies. The presence of this low-velocity highly anisotropic layer at the base of the accretionary wedge, likely representing a low-strength shear zone, could possibly explain the unusually wide accretionary wedge in Makran. Additionally, it may impact the location and width of the locked zone along the interplate boundary.
    Description: Iranian National Science Foundation (INSF)
    Description: Published
    Description: 64-74
    Description: OST1 Alla ricerca dei Motori Geodinamici
    Description: JCR Journal
    Keywords: Earthquake hazards, Seismic anisotropy, Crustal structure, Subduction zone processes ; 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 10
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    Application of the EEPAS earthquake forecasting model to Italy (2024)
    Oxford University Press
    Details
    Publication Date: 2024-05-09
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2023. 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: The Every Earthquake a Precursor According to Scale (EEPAS) forecasting model is a space– time point-process model based on the precursory scale increase (ψ ) phenomenon and associated predictive scaling relations. It has been previously applied to New Zealand, Cal- ifornia and Japan earthquakes with target magnitude thresholds varying from about 5–7. In all previous application, computations were done using the computer code implemented in Fortran language by the model authors. In this work, we applied it to Italy using a suite of computing codes completely rewritten in Matlab. We first compared the two software codes to ensure the convergence and adequate coincidence between the estimated model parameters for a simple region capable of being analysed by both software codes. Then, using the rewritten codes, we optimized the parameters for a different and more complex polygon of analysis using the Homogenized Instrumental Seismic Catalogue data from 1990 to 2011. We then perform a pseudo-prospective forecasting experiment of Italian earthquakes from 2012 to 2021 with Mw ≥ 5.0 and compare the forecasting skill of EEPAS with those obtained by other time in- dependent (Spatially Uniform Poisson, Spatially Variable Poisson and PPE: Proximity to Past Earthquakes) and time dependent [Epidemic Type Aftershock Sequence (ETAS)] forecasting models using the information gain per active cell. The preference goes to the ETAS model for short time intervals (3 months) and to the EEPAS model for longer time intervals (6 months to 10 yr).
    Description: Published
    Description: 1681–1700
    Description: OST4 Descrizione in tempo reale del terremoto, del maremoto, loro predicibilità e impatto
    Description: JCR Journal
    Keywords: Computational seismology ; Earthquake interaction ; forecasting and prediction ; Statistical seismology ; Earthquake forecasting
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 11
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    Hydrological and volcano-related gravity signals at Mt. Somma–Vesuvius from ∼20 yr of time-lapse gravity monitoring: implications for volcano quiescence (2024)
    Oxford University Press
    Details
    Publication Date: 2024-05-27
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2023. 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 report on about 20 yr of relative gravity measurements, acquired on Mt. Somma–Vesuvius volcano in order to investigate the hydrological and volcano-tectonic processes controlling the present-day activity of the volcano. The retrieved long-term field of time gravity change (2003–2022) shows a pattern essentially related to the subsidence, which have affected the central part of the volcano, as detected by the permanent GNSS network and InSAR data. After reducing the observations for the effect of vertical deformation, no significant residuals are found, indicating no significant mass accumulation or loss within the volcanic system. In the north-western sector of the study area, at the border of the volcano edifice, however, significant residual positive gravity changes are detected which are associated to ground-water rebound after years of intense exploitation of the aquifers. On the seasonal timescale, we find that stations within the caldera rim are affected by the seasonal hydrological effects, while the gravity stations at the base of the Vesuvius show a less clear correlation. Furthermore, within the caldera rim a multiyear gravity transient is detected with an increase phase lasting about 4 yr followed by a slower decrease phase. Analysis of rain data seem to exclude a hydrological origin, hence, we hypothesize a deeper source related to the geothermal activity, which can be present even if the volcano is in a quiescent state. We infer the depth and volume of the source by inverting the spatial pattern of the gravity field at the peak of the transient. A volume of fluids of 9.5 × 107 m3 with density of 1000 kg m−3 at 2.3 km depth is capable to fit reasonably well the observations. To explain the gravity transient, simple synthetic models are produced, that simulate the ascent of fluids from a deep reservoir up to the depth of 2.3 km and a successive diffusion within the carbonate aquifer hosting the geothermal system. The whole process appears to not significantly affect the seismicity rate and the deformation of the volcano. This study demonstrates the importance of a 4-D gravity monitoring of a volcano to understand its complex gravity signals that cover different spatial and temporal scales. Discriminating the different contributions that mix up in the observed gravity changes, in particular those due to hydrologic/anthropogenic activities form those due to the geothermal dynamics, is fundamental for a complete and reliable evaluation of the volcano state.
    Description: Published
    Description: 1565–1580
    Description: OSV2: Complessità dei processi vulcanici: approcci multidisciplinari e multiparametrici
    Description: JCR Journal
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  • 12
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    The ground deformation of the south-eastern flank of Mount Etna monitored by GNSS and SAR interferometry from 2016 to 2019 (2023)
    Oxford University Press
    Details
    Publication Date: 2023-12-27
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2023. 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: The south-eastern sector of the Mount Etna, Italy, is characterized by numerous active faults, in particular the Belpasso–Ognina lineament, the Tremestieri–San Gregorio–Acitrezza fault, the Trecastagni fault and the Fiandaca–Nizzeti fault including the Timpe Fault System. Their activity is the result of both volcanism and tectonics. Here, we analyse the ground deformation occurred from 2016 to 2019 across those active faults by using the GNSS data acquired at 22 permanent stations and 35 campaign points observed by the Etna Observatory (INGV) and by the University of Catania. We also use the time-series of line of sight displacement of permanent scatterers SENTINEL-1 A-DInSAR obtained by using the P-SBAS tool of the ESA GEP-TEP (Geohazards Thematic Exploitation Platform) service. We discriminate the contributions of the regional tectonic strain, the inflations, the deflations of the volcano and the gravitational sliding in order to analyse the deformation along the faults of the south-eastern flank of Etna. The shallow and destructive Mw = 4.9 earthquake of 2018 December 26 occurred within the studied area two days after a dyke intrusion, that propagated beneath the centre of the volcano accompanied by a short eruption. Both GNSS and InSAR time-series document well those events and allow to investigate the post-seismic sliding across the faults of south-eastern flank. We analyse the slow slip events (SSE) that are observed in the GNSS and InSAR time-series in the vicinity of the Acitrezza fault. We quantify and discuss the tectonic origin of the Belpasso–Ognina lineament that we interpreted as a tear fault.
    Description: Published
    Description: 664–682
    Description: OST3 Vicino alla faglia
    Description: JCR Journal
    Keywords: Satellite geodesy ; Transient deformation ; Interferometry ; Fractures ; fault ; Volcano monitoring
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 13
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    Strong ground-motion prediction equations from induced earthquakes in St. Gallen geothermal field, Switzerland (2023)
    Oxford University Press
    Details
    Publication Date: 2023-03-15
    Description: Ground shaking, whether it is due to natural or induced earthquakes, has always been a matter of concern since it correlates with structural/non-structural damage and can culminate in human anxiety. Industrial activities such as water injection, gas sequestration and waste fluid disposals, promote induced seismicity and consequent ground shaking that can hinder ongoing activities. Therefore, keeping in mind the importance of timely evaluation of a seismic hazard and its mitigation for societal benefits, the present study proposes specifically designed ground-motion prediction equations (GMPEs) from induced earthquakes in the St. Gallen geothermal area, Switzerland. The data analysed in this study consist of 343 earthquakes with magnitude −1.17 ≤ ML, corr ≤ 3.5 and hypocentral distance between 4 and 15 km. The proposed study is one of the first to incorporate ground motions from negative magnitude earthquakes for the development of GMPEs. The GMPEs are inferred with a two-phase approach. In the first phase, a reference model is obtained by considering the effect of source and medium properties on the ground motion. In the second phase the final model is obtained by including a site/station effect. The comparison between the GMPEs obtained in the present study with GMPEs developed for the other induced seismicity environments highlights a mismatch that is ascribed to differences in regional seismic environment and local site conditions of the respective regions. This suggests that, when dealing with induced earthquakes, GMPEs specific for the study should be inferred and used for both monitoring purposes and seismic hazard analyses.
    Description: Published
    Description: 820–832
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
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  • 14
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    Cross-site comparisons of dryland ecosystem response to climate change in the US long-term ecological research network (2023)
    Oxford University Press
    Details
    Publication Date: 2023-02-25
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hudson, A. R., Peters, D. P. C., Blair, J. M., Childers, D. L., Doran, P. T., Geil, K., Gooseff, M., Gross, K. L., Haddad, N. M., Pastore, M. A., Rudgers, J. A., Sala, O., Seabloom, E. W., & Shaver, G. Cross-site comparisons of dryland ecosystem response to climate change in the US long-term ecological research network. Bioscience, 72(9), (2022): 889–907, https://doi.org/10.1093/biosci/biab134.
    Description: Long-term observations and experiments in diverse drylands reveal how ecosystems and services are responding to climate change. To develop generalities about climate change impacts at dryland sites, we compared broadscale patterns in climate and synthesized primary production responses among the eight terrestrial, nonforested sites of the United States Long-Term Ecological Research (US LTER) Network located in temperate (Southwest and Midwest) and polar (Arctic and Antarctic) regions. All sites experienced warming in recent decades, whereas drought varied regionally with multidecadal phases. Multiple years of wet or dry conditions had larger effects than single years on primary production. Droughts, floods, and wildfires altered resource availability and restructured plant communities, with greater impacts on primary production than warming alone. During severe regional droughts, air pollution from wildfire and dust events peaked. Studies at US LTER drylands over more than 40 years demonstrate reciprocal links and feedbacks among dryland ecosystems, climate-driven disturbance events, and climate change.
    Description: Funding was provided by the USDA-ARS SCINet Big Data Project (grant no. 0500–00093–001–00-D), and the National Science Foundation US LTER Program to New Mexico State University for the Jornada Basin (grant no. DEB 20–25166), Kansas State University for the Konza Prairie (grant no. DEB 2025849), the Kellogg Biological Station (grant no. DEB 1832042), Cedar Creek Ecosystem Science Reserve (grants no. DEB-1234162 and no. DEB-1831944), ARC (grant no. DEB-1637459), MCM (grant no. OPP-1637708), CAP (grant no. DEB-1832016), and SEV (grant no. DEB-1655499). Support was also provided by the Minnesota Supercomputer Institute and the University of Minnesota, Michigan State University AgBioResearch.
    Repository Name: Woods Hole Open Access Server
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    Mechanism of the 2017 M-w 6.3 Pasni earthquake and its significance for future major earthquakes in the eastern Makran (2023)
    Oxford University Press
    Details
    Publication Date: 2023-02-17
    Description: Author Posting. © The Author(s), 2022. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 231(2),(2022): 1434–1445, https://doi.org/10.1093/gji/ggac257.
    Description: Makran subduction zone is very active with ∼38 mm yr−1 convergence rate and has experienced great earthquakes in the past. The latest great earthquake of 1945 Mw 8.1 event also triggered a large tsunami and led to ∼4000 casualties. However, due to incomplete historical seismicity records and poor modern instrumentation, earthquake mechanism, co-seismic slip and tsunami characteristics in Makran remain unclear. On 2017 February 17, an Mw 6.3 earthquake rattled offshore Pasni of Pakistan in the eastern Makran, marking the largest event after the 1945 Mw 8.1 earthquake with good geodetic and geophysical data coverage. We use a combination of seismicity, multibeam bathymetry, seismic profile, InSAR measurements and tide-gauge observation to investigate the seismogenic structure, co-seismic deformation, tsunami characteristics of this event and its implication for future major earthquakes. Our results indicate that (1) the earthquake occurred on the shallow-dipping (3°–4°) megathrust; (2) the megathrust co-seismically slipped 15 cm and caused ∼2–4 cm ground subsidence and uplift at Pasni; (3) our tsunami modelling reproduces the observed 5-cm-high small tsunami waveforms. The Pasni earthquake rupture largely overlaps the 1945 slip patch and disturbs the west and east megathrust segments that have not ruptured yet at least since 1765. With such stress perturbation and possible stress evolution effect from the 1945 earthquake, the unruptured patches may fail in the future. This study calls for more preparedness in mitigating earthquake and associated hazards in the eastern Makran.
    Description: his study is financially supported by the National Natural Science Foundation of China (Nos. 42076059, 41890813, 41976066 and 41976064), the Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) (No. GML2019ZD0205), Chinese Academy of Sciences (Nos. Y4SL021001, QYZDY-SSW-DQC005, 131551KYSB20200021, ISEE2021PY03, 133244KYSB20180029 and E1SL3C02), Guangdong Basic and Applied Basic Research Foundation (No. 2021B1515020098) and China–Pakistan Joint Research Centre on Earth Sciences.
    Keywords: Tsunamis ; Earthquake dynamics ; Earthquake hazards ; Seismicity and tectonics ; Subduction zone processes
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  • 16
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    Genesis of Oceanic Oxide Gabbros and Gabbronorites During Reactive Melt Migration at Transform Walls (Doldrums Megatransform System; 7–8°N Mid-Atlantic Ridge) (2023)
    Oxford University Press
    Details
    Publication Date: 2023-01-25
    Description: The Doldrums Megatransform System (~7–8°N, Mid-Atlantic Ridge) shows a complex architecture including four intra-transform ridge segments bounded by five active transform faults. Lower crustal rocks are exposed along the Doldrums and Vernadsky transform walls that bound the northernmost intra-transform ridge segment. The recovered gabbros are characterized by variably evolved chemical compositions, ranging from olivine gabbros to gabbronorites and oxide gabbros, and lack the most primitive gabbroic endmembers (troctolites, dunites). Notably, the numerous recovered gabbronorites show up to 20 vol. % of coarse-grained orthopyroxene. Although covariations in mineral and bulk-rock chemical compositions of the olivine and oxide gabbros define trends of crystallization from a common parental melt, the gabbronorites show elevated light over heavy rare earth elements (LREE/HREE) ratios in both bulk-rock and mineral compositions. These features are not consistent with a petrological evolution driven solely by fractional crystallization, which cannot produce the preferential enrichments in highly incompatible elements documented in the orthopyroxene-bearing lithologies. We suggest that gabbronorites crystallized from evolved melts percolating and partly assimilating a pre-existing olivine gabbro matrix. Saturation in orthopyroxene and selective enrichments in LREE relative to M-HREE are both triggered by an increase in assimilated crystal mass, which ranges from negligible in the oxide-gabbros to abundant in the gabbronorites. This melt–rock reaction process has been related to lateral melt migration beneath ridge-transform intersections, where variably evolved melts injected from the peripheral parts of the melting region towards the transform zone may interact with a gabbroic crystal mush to form abundant oxide-bearing gabbronoritic associations.
    Description: Published
    Description: egac086
    Description: 3A. Geofisica marina e osservazioni multiparametriche a fondo mare
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Metagenomic survey of the microbiome of ancient Siberian permafrost and modern Kamchatkan cryosols (2022)
    Oxford University Press
    In:  EPIC3microLife, Oxford University Press, 3(1), pp. 1-15, ISSN: 2633-6693
    Details
    Publication Date: 2024-01-30
    Description: In the context of global warming, the melting of arctic permafrost raises the threat of a re-emergence of microorganisms some of which were shown to remain viable in ancient frozen soils for up to half a million years. In order to evaluate this risk, it is of interest to acquire a better knowledge of the composition of the microbial communities found in this understudied environment. Here we present a metagenomics analysis of 12 soil samples from Russian Arctic and subarctic pristine areas: Chukotka, Yakutia, and Kamchatka, including 9 permafrost samples collected at various depths. These large datasets (9.2 1011 total bp) were assembled (525,313 contigs 〉 5kb), their encoded protein contents predicted, then used to perform taxonomical assignments of bacterial, archaeal, and eukaryotic organisms, as well as DNA viruses. The various samples exhibited variable DNA contents and highly diverse taxonomic profiles showing no obvious relationship with their locations, depths or deposit ages. Bacteria represented the largely dominant DNA fraction (95%) in all samples, followed by archaea (3.2%), surprisingly little eukaryotes (0.5%), and viruses (0.4%). Although no common taxonomic pattern was identified, the samples shared unexpected high frequencies of β-lactamase genes, almost 0.9 copy/bacterial genome. In addition of known environmental threats, the particularly intense warming of the Arctic might thus enhance the spread of bacterial antibiotic resistances, today's major challenge in public health. β-lactamases were also observed at high frequency in other types of soils, suggesting their general role in the regulation of bacterial populations.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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    Full waveform inversion based on the non-parametric estimate of the probability distribution of the residuals (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-27
    Description: Summary In an attempt to overcome the difficulties of the full waveform inversion (FWI), several alternative objective functions have been proposed over the last few years. Many of them are based on the assumption that the residuals (differences between modelled and observed seismic data) follow specific probability distributions when, in fact, the true probability distribution is unknown. This leads FWI to converge to an incorrect probability distribution if the assumed probability distribution is different from the real one and, consequently it may lead the FWI to achieve biased models of the subsurface. In this work, we propose an objective function which does not force the residuals to follow a specific probability distribution. Instead, we propose to use the non-parametric kernel density estimation technique (KDE) (which imposes the least possible assumptions about the residuals) to explore the probability distribution that may be more suitable. As evidenced by the results obtained in a synthetic model and in a typical P-wave velocity model of the Brazilian pre-salt fields, the proposed FWI reveals a greater potential to overcome more adverse situations (such as cycle-skipping) and also a lower sensitivity to noise in the observed data than conventional L2 and L1-norm objective functions and thus making it possible to obtain more accurate models of the subsurface. This greater potential is also illustrated by the smoother and less sinuous shape of the proposed objective function with fewer local minima compared with the conventional objective functions.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
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    Phospho-Ku70 induced by DNA damage interacts with RNA Pol II and promotes the formation of phospho-53BP1 foci to ensure optimal cNHEJ (2021)
    Oxford University Press
    Details
    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
    Electronic ISSN: 1362-4962
    Topics: Biology
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    Differential rotation in a 3D simulation of oxygen shell burning (2021)
    Oxford University Press
    Details
    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.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 21
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    Characterising the distinct crustal protoliths of Roberts Victor Type I and II eclogites (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-27
    Description: The origin of the eclogites that reside in cratonic mantle roots has long been debated. In the classic Roberts Victor kimberlite locality in South Africa, the strongly contrasting textural and geochemical features of two types of eclogites have led to different genetic models. We studied a new suite of 63 eclogite xenoliths from the former Roberts Victor Mine. In addition to major- and trace-element compositions for all new samples, we determined 18O/16O for garnet from 34 eclogites. Based on geochemical and textural characteristics we identify a large suite of Type I eclogites (n = 53) consistent with previous interpretations that these rocks originate from metamorphosed basaltic-picritic lavas or gabbroic cumulates from oceanic crust, crystallised from melts of depleted MORB mantle. We identify a smaller set of Type II eclogites (n = 10) based on geochemical and textural similarity to eclogites in published literature. We infer their range to very low δ18O values combined with their varied, often very low Zr/Hf ratios and LREE-depleted nature to indicate a protolith origin via low-pressure clinopyroxene-bearing oceanic cumulates formed from melts that were more depleted in incompatible elements than N-MORB. These compositions are indicative of derivation from a residual mantle source that experienced preferential extraction of incompatible elements and fractionation of Zr-Hf during previous melting.
    Print ISSN: 0022-3530
    Electronic ISSN: 1460-2415
    Topics: Geosciences
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    Evidence for an expanding corona based on spectral-timing modelling of multiple black hole X-ray binaries (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-27
    Description: Galactic black hole X-ray binaries (BHXBs) provide excellent laboratories to study accretion, as their relatively quick evolution allows us to monitor large changes in the in-flowing and/or out-flowing material over human timescales. However, the details of how the inflow-outflow coupling evolves during a BHXB outburst remain an area of active debate. In this work we attempt to probe the physical changes underlying the system evolution, by performing a systematic analysis of the multi-wavelength data of three BHXB sources: XTE J1752-223, MAXI J1659-152, and XTE J1650-500, during hard and hard-intermediate states. Using the power spectral hue which characterises the X-ray variability properties, we identify several clusters of BHXB epochs and perform the joint multi-wavelength spectral modelling to test their commonality with a physical jet model. Under the assumption that the corona is related to the base of the jet, we find that the power spectral hue traces the variation of the coronal radius (from ∼10Rg − ∼ 40Rg) in multiple BHXBs at hard and hard-intermediate states, and that the data are consistent with moderately truncated accretion discs (
    Print ISSN: 0035-8711
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    The Power of Word-Frequency Based Alignment-Free Functions: a Comprehensive Large-Scale Experimental Analysis (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-30
    Description: Motivation Alignment-free (AF) distance/similarity functions are a key tool for sequence analysis. Experimental studies on real datasets abound and, to some extent, there are also studies regarding their control of false positive rate (Type I error). However, assessment of their power, i.e., their ability to identify true similarity, has been limited to some members of the D2 family. The corresponding experimental studies have concentrated on short sequences, a scenario no longer adequate for current applications, where sequence lengths may vary considerably. Such a State of the Art is methodologically problematic, since information regarding a key feature such as power is either missing or limited. Results By concentrating on a representative set of word-frequency based AF functions, we perform the first coherent and uniform evaluation of the power, involving also Type I error for completeness. Two Alternative models of important genomic features (CIS Regulatory Modules and Horizontal Gene Transfer), a wide range of sequence lengths from a few thousand to millions, and different values of k have been used. As a result, we provide a characterization of those AF functions that is novel and informative. Indeed, we identify weak and strong points of each function considered, which may be used as a guide to choose one for analysis tasks. Remarkably, of the fifteen functions that we have considered, only four stand out, with small differences between small and short sequence length scenarios. Finally, in order to encourage the use of our methodology for validation of future AF functions, the Big Data platform supporting it is public. Availability The software is available at: https://github.com/pipp8/power_statistics Supplementary information Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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    Dark energy survey year 3 results: Galaxy sample for BAO measurement (2021)
    Oxford University Press
    Details
    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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    Finite-difference modeling of 2-D wave propagation in the vicinity of dipping interfaces: a comparison of anti-aliasing and equivalent medium approaches (2021)
    Oxford University Press
    Details
    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
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    Topics: Geosciences
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    Relativistic effects on triple black holes: Burrau’s problem revisited (2021)
    Oxford University Press
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    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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    Deep searches for X-ray pulsations from Scorpius X-1 and Cygnus X-2 in support of continuous gravitational wave searches (2021)
    Oxford University Press
    Details
    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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    On the detection of multiple shock fronts in A1914 using deep Chandra X-ray observations (2021)
    Oxford University Press
    Details
    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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    The impact of metallicity on nova populations (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: The metallicity of a star affects its evolution in a variety of ways, changing stellar radii, luminosities, lifetimes, and remnant properties. In this work, we use the population synthesis code binary_c to study how metallicity affects novae in the context of binary stellar evolution. We compute a 16-point grid of metallicities ranging from Z = 10−4 to 0.03, presenting distributions of nova white dwarf masses, accretion rates, delay-times, and initial system properties at the two extremes of our 16-point metallicity grid. We find a clear anti-correlation between metallicity and the number of novae produced, with the number of novae at Z = 0.03 roughly half that at Z = 10−4. The white dwarf mass distribution has a strong systematic variation with metallicity, while the shape of the accretion rate distribution is relatively insensitive. We compute a current nova rate of approximately 33 novae per year for the Milky Way, a result consistent with observational estimates relying on extra-Galactic novae but an under-prediction relative to observational estimates relying on Galactic novae. However, the shape of our predicted Galactic white dwarf mass distribution differs significantly to existing observationally derived distributions, likely due to our underlying physical assumptions. In M31, we compute a current nova rate of approximately 36 novae per year, under-predicting the most recent observational estimate of $65^{+15}_{-16}$. Finally, we conclude that when making predictions about currently observable nova rates in spiral galaxies, or stellar environments where star formation has ceased in the distant past, metallicity can likely be considered of secondary importance compared to uncertainties in binary stellar evolution.
    Print ISSN: 0035-8711
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    Tracing the evolution of human gene regulation and its association with shifts in environment (2021)
    Oxford University Press
    Details
    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
    Published by Oxford University Press
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    Analysis of sex chromosome evolution in the clade Palaeognathae from phased genome assembly (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: Birds in the clade Palaeognathae, excluding Tinamiformes, have morphologically conserved karyotypes and less differentiated ZW sex chromosomes compared with those of other birds. In particular, the sex chromosomes of the ostrich and emu have exceptionally large recombining pseudoautosomal regions (PARs), while non-PARs are classified into two strata according to the date of their origins: stratum 0 (S0) and stratum 1 (S1). However, the construction and analysis of the genome sequences in these regions in the clade Palaeognathae can be challenging because assembling the S1 region is difficult owing to low sequence diversity between gametologs (Z-linked and W-linked sequences). We addressed this issue by applying the Platanus-allee assembler and successfully constructed the haplotype-resolved (phased) assembly for female emu, cassowary, and ostrich using only sequence read data derived from the Illumina platform. Comparative genomic and phylogenetic analyses based on assembled Z-linked and W-linked sequences confirmed that the S1 region of emu and cassowary formed in their common ancestor. Moreover, the interspersed repetitive sequence landscapes in the S1 regions of female emu showed an expansion of younger repetitive elements in the W-linked S1 region, suggesting an interruption in homologous recombination in the S1 region. These results provide novel insights into the trajectory of sex chromosome evolution in the clade Palaeognathae and suggest that the Illumina-based phased assembly method is an effective approach for elucidating the evolutionary process underlying the transition from homomorphic to differentiated sex chromosomes.
    Electronic ISSN: 1759-6653
    Topics: Biology
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    Multi-Fidelity Emulation for the Matter Power Spectrum using Gaussian Processes (2021)
    Oxford University Press
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    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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    Population genomics of wall lizards reflects the dynamic history of the Mediterranean Basin (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: The Mediterranean Basin has experienced extensive change in geology and climate over the past six million years. Yet, the relative importance of key geological events for the distribution and genetic structure of the Mediterranean fauna remains poorly understood. Here, we use population genomic and phylogenomic analyses to establish the evolutionary history and genetic structure of common wall lizards (Podarcis muralis). This species is particularly informative because, in contrast to other Mediterranean lizards, it is widespread across the Iberian, Italian, and Balkan peninsulas, and in extra-Mediterranean regions. We found strong support for six major lineages within P. muralis, which were largely discordant with the phylogenetic relationship of mitochondrial DNA. The most recent common ancestor of extant P. muralis was likely distributed in the Italian Peninsula, and experienced an “Out-of-Italy” expansion following the Messinian salinity crisis (∼5 Mya), resulting in the differentiation into the extant lineages on the Iberian, Italian and Balkan peninsulas. Introgression analysis revealed that both inter- and intraspecific gene flows have been pervasive throughout the evolutionary history of P. muralis. For example, the Southern Italy lineage has a hybrid origin, formed through admixture between the Central Italy lineage and an ancient lineage that was the sister to all other P. muralis. More recent genetic differentiation is associated with the onset of the Quaternary glaciations, which influenced population dynamics and genetic diversity of contemporary lineages. These results demonstrate the pervasive role of Mediterranean geology and climate for the evolutionary history and population genetic structure of extant species.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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    Five-percent measurements of the growth rate from simulation-based modelling of redshift-space clustering in BOSS LOWZ (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: We use a simulation-based modelling approach to analyse the anisotropic clustering of the BOSS LOWZ sample over the radial range 0.4 h−1 Mpc to 63 h−1 Mpc, significantly extending what is possible with a purely analytic modelling framework. Our full-scale analysis yields constraints on the growth of structure that are a factor of two more stringent than any other study on large scales at similar redshifts. We infer fσ8 = 0.471 ± 0.024 at z ≈ 0.25, and fσ8 = 0.430 ± 0.025 at z ≈ 0.40; the corresponding ΛCDM predictions of the Planck CMB analysis are 0.470 ± 0.006 and 0.476 ± 0.005, respectively. Our results are thus consistent with Planck, but also follow the trend seen in previous low-redshift measurements of fσ8 falling slightly below the ΛCDM+CMB prediction. We find that small and large radial scales yield mutually consistent values of fσ8, but there are 1 − 2.5σ hints of small scales (
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    Genome-wide reconstruction of rediploidization following autopolyploidization across one hundred million years of salmonid evolution (2021)
    Oxford University Press
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    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.
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    Ubiquitin-dependent rapid degradation conceals a cell-protective function of cytoplasmic SIRT3 against oxidative stress (2021)
    Oxford University Press
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    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
    Published by Oxford University Press on behalf of Japanese Biochemical Society.
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    The Jun-dependent axon regeneration gene program: Jun promotes regeneration over plasticity (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: The regeneration-associated gene (RAG) expression program is activated in injured peripheral neurons after axotomy and enables long-distance axon re-growth. Over 1000 genes are regulated, and many transcription factors are upregulated or activated as part of this response. However, a detailed picture of how RAG expression is regulated is lacking. In particular the transcriptional targets and specific functions of the various transcription factors are unclear. Jun was the first regeneration-associated transcription factor identified and the first shown to be functionally important. Here we fully define the role of Jun in the RAG expression program in regenerating facial motor neurons. At 1, 4, and 14 days after axotomy, Jun upregulates 11%, 23% and 44% of the RAG program, respectively. Jun functions relevant to regeneration include cytoskeleton production, metabolic functions and cell activation, and the down-regulation of neurotransmission machinery. In silico analysis of promoter regions of Jun targets identifies stronger over-representation of AP1-like sites than CRE-like sites, although CRE sites were also over-represented in regions flanking AP1 sites. Strikingly, in motor neurons lacking Jun, an alternative SRF-dependent gene expression program is initiated after axotomy. The promoters of these newly expressed genes exhibit over-representation of CRE sites in regions near to SRF target sites. This alternative gene expression program includes plasticity-associated transcription factors, and leads to an aberrant early increase in synapse density on motor neurons. Jun thus has the important function in the early phase after axotomy of pushing the injured neuron away from a plasticity response and towards a regenerative phenotype.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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    Spatiotemporal evolution of the global species diversity of Rhododendron (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: Evolutionary radiation is a widely recognized mode of species diversification, but its underlying mechanisms have not been unambiguously resolved for species-rich cosmopolitan plant genera. In particular, it remains largely unknown how biological and environmental factors have jointly driven its occurrence in specific regions. Here we use Rhododendron, the largest genus of woody plants in the Northern Hemisphere, to investigate how geographic and climatic factors, as well as functional traits, worked together to trigger plant evolutionary radiations and shape the global patterns of species richness based on a solid species phylogeny. Using 3437 orthologous nuclear genes, we reconstructed the first highly supported and dated backbone phylogeny of Rhododendron comprising 200 species that represent all subgenera, sections, and nearly all multi-species subsections, and found that most extant species originated by evolutionary radiations when the genus migrated southwards from circumboreal areas to tropical/subtropical mountains, showing rapid increases of both net diversification rate and evolutionary rate of environmental factors in the Miocene. We also found that the geographically uneven diversification of Rhododendron led to a much higher diversity in Asia than in other continents, which was mainly driven by two environmental variables, i.e., elevation range and annual precipitation, and were further strengthened by the adaptation of leaf functional traits. Our study provides a good example of integrating phylogenomic and ecological analyses in deciphering the mechanisms of plant evolutionary radiations, and sheds new light on how the intensification of the Asian monsoon has driven evolutionary radiations in large plant genera of the Himalaya-Hengduan Mountains.
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    Electronic ISSN: 1537-1719
    Topics: Biology
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    Interpreting Internal Consistency of DES Measurements (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: Bayesian evidence ratios are widely used to quantify the statistical consistency between different experiments. However, since the evidence ratio is prior dependent, the precise translation between its value and the degree of concordance/discordance requires additional information. The most commonly adopted metric, the Jeffreys scale, can falsely suggest agreement between datasets when priors are chosen to be sufficiently wide. This work examines evidence ratios in a DES-Y1 simulated analysis, focusing on the internal consistency between weak lensing and galaxy clustering. We study two scenarios using simulated data in controlled experiments. First, we calibrate the expected evidence ratio distribution given noise realizations around the best fit DES-Y1 ΛCDM cosmology. Second, we show the behavior of evidence ratios for noiseless fiducial data vectors simulated using a modified gravity model, which generates internal tension in the LCDM analysis. We find that the evidence ratio of noise realizations generated at all confidence levels was biased towards agreement and show, with a modified gravity model, that the choice of prior could conceal the discrepancies between weak lensing and galaxy clustering induced by prior effects in unlike cosmological models, concluding that the evidence ratio in a DES-Y1 study is, indeed, biased towards agreement. Boundary effects can also influence conclusions about the inconsistency induced by modified gravity, even in a noiseless data vector simulation.
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    The extreme properties of the nearby hyper-Eddington accreting Active Galactic Nucleus in IRAS 04416+1215 (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: The physical properties of the accretion flow and of the X-ray emitting plasma, in supermassive black holes accreting at extreme Eddington rates, are still very unclear. Here we present the analysis of simultaneous XMM-Newton and NuSTAR observations of the hyper-Eddington Seyfert 1 galaxy IRAS 04416+1215, carried out in 2020. The main goal of these observations is to investigate the properties of the X-ray corona, as well as the structure of the accretion flow and of the circumnuclear environment, in this regime of extreme accretion. IRAS 04416+1215 has one of the highest Eddington ratio (λEdd ≃ 472) in the local Universe. It shows an interesting spectral shape, very similar to the standard Narrow Line Seyfert 1 galaxy’s spectra, with the presence of multi-phase absorption structure composed of three phases, whose estimate of the minimum and maximum distances suggests two different interpretations, one consistent with the three X-ray winds being co-spatial, and possibly driven by magnetohydrodynamical processes, the other consistent with the multi-phase winds being also multi-scale. The X-ray spectrum of IRAS 04416+1215 also has a prominent soft excess component and a hard X-ray emission dominated by a reflection component. Moreover, our detailed spectral analysis shows that IRAS 04416+1215 has the lowest coronal temperature measured so far by NuSTAR (kTe = 3 − 22 keV, depending on the model). This is consistent with a hybrid coronal plasma, in which the primary continuum emission is driven by pair production due to high-energy tail of the energy distribution of non-thermal electrons.
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    Kinematics and structure of Ionized gas in the UCHII regions of W33 main (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: High mass proto-stars create Ultra-Compact H ii regions (UCHII) at the stage of evolution when most of the accretion is finished but the star is still heavily embedded in molecular material. The morphologies of UCHII regions reflect the interactions of stellar winds, stellar motions, and density structure in the molecular cloud; they are complex and it has been very difficult to interpret them. We here present data obtained with TEXES on the NASA IRTF of the [Nei,ii] emission line in the proto-cluster of young OB stars in W33 Main. The data cube has a spatial resolution of ∼1.4 arcsec and true velocity resolution ∼5 km s-1; with Aλ ∼ 0.02AV it is relatively unaffected by extinction. We have run 3D hydrodynamic and line profile simulations, using PLUTO and RADMC-3D, of the gas structures created by multiple windy stars moving relative to each other through the ambient cloud. By iterative comparison of the data cube and the simulations, we arrive at models that reproduce the different morphology and kinematic structure of each UCHII region in W33 Main. The results indicate that each sub-source probably holds multiple exciting stars, permitting an improved view of the stellar population, and finds the stellar trajectories, which may determine the dynamical development of the proto-cluster.
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    Data-Efficient Classification of Radio Galaxies (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: The continuum emission from radio galaxies can be generally classified into different morphological classes such as FRI, FRII, Bent, or Compact. In this paper, we explore the task of radio galaxy classification based on morphology using deep learning methods with a focus on using a small scale dataset (∼2000 samples). We apply few-shot learning techniques based on Twin Networks and transfer learning techniques using a pre-trained DenseNet model with advanced techniques like cyclical learning rate and discriminative learning to train the model rapidly. We achieve a classification accuracy of over 92% using our best performing model with the biggest source of confusion being between Bent and FRII type galaxies. Our results show that focusing on a small but curated dataset along with the use of best practices to train the neural network can lead to good results. Automated classification techniques will be crucial for upcoming surveys with next generation radio telescopes which are expected to detect hundreds of thousands of new radio galaxies in the near future.
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    Lensing of gravitational waves as a probe of compact dark matter (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: We study gravitational lensing of gravitational waves from compact object binaries as a probe of compact dark matter (DM) objects such as primordial black holes. Assuming a point mass lens, we perform parameter estimation of lensed gravitational wave signals from compact object binaries to determine the detectability of the lens with ground based laser interferometers. Then, considering binary populations that LIGO-Virgo has been probing, we derive a constraint on the abundance of compact DM from non-observation of lensed events. We find that the LIGO-Virgo observations imply that compact objects heavier than Ml = 200 M⊙ can not constitute all DM and less than $40{{ m per cent}}$ of DM can be in compact objects heavier than Ml = 400 M⊙. We also show that the DM fraction in compact objects can be probed by LIGO in its final sensitivity for Ml 〉 40 M⊙ reaching $2{{ m per cent}}$ of the DM abundance at Ml 〉 200 M⊙, and by ET for Ml 〉 1 M⊙ reaching DM fraction as low as 7 × 10−5 at Ml 〉 40 M⊙.
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    Variable star classification across the Galactic bulge and disc with the VISTA Variables in the Vía Láctea survey (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: We present VIVACE, the VIrac VAriable Classification Ensemble, a catalogue of variable stars extracted from an automated classification pipeline for the Vista Variables in the Vía Láctea (VVV) infrared survey of the Galactic bar/bulge and southern disc. Our procedure utilises a two-stage hierarchical classifier to first isolate likely variable sources using simple variability summary statistics and training sets of non-variable sources from the Gaia early third data release, and then classify candidate variables using more detailed light curve statistics and training labels primarily from OGLE and VSX. The methodology is applied to point-spread-function photometry for ∼490 million light curves from the VIRAC v2 astrometric and photometric catalogue resulting in a catalogue of ∼1.4 million likely variable stars, of which ∼39, 000 are high-confidence (classification probability 〉0.9) RR Lyrae ab stars, ∼8000 RR Lyrae c/d stars, ∼187, 000 detached/semi-detached eclipsing binaries, ∼18, 000 contact eclipsing binaries, ∼1400 classical Cepheid variables and ∼2200 Type II Cepheid variables. Comparison with OGLE-4 suggests a completeness of around 90  per cent for RRab and ≲ 60 per cent for RRc/d, and a misclassification rate for known RR Lyrae stars of around 1 per cent for the high confidence sample. We close with two science demonstrations of our new VIVACE catalogue: first, a brief investigation of the spatial and kinematic properties of the RR Lyrae stars within the disc/bulge, demonstrating the spatial elongation of bar-bulge RR Lyrae stars is in the same sense as the more metal-rich red giant population whilst having a slower rotation rate of ∼40 km s−1kpc−1; and secondly, an investigation of the Gaia EDR3 parallax zeropoint using contact eclipsing binaries across the Galactic disc plane and bulge.
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    Static and dynamic solar coronal loops with cross-sectional area variations (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: The Enthalpy Based Thermal Evolution of Loops (EBTEL) approximate model for static and dynamic coronal loops is developed to include the effect of a loop cross-sectional area which increases from the base of the transition region (TR) to the corona. The TR is defined as the part of a loop between the top of the chromosphere and the location where thermal conduction changes from an energy loss to an energy gain. There are significant differences from constant area loops due to the manner in which the reduced volume of the TR responds to conductive and enthalpy fluxes from the corona. For static loops with modest area variation the standard picture of loop energy balance is retained, with the corona and TR being primarily a balance between heating and conductive losses in the corona, and downward conduction and radiation to space in the TR. As the area at the loop apex increases, the TR becomes thicker and the density in TR and corona larger. For large apex areas, the coronal energy balance changes to one primarily between heating and radiation, with conduction playing an increasingly unimportant role, and the TR thickness becoming a significant fraction of the loop length. Approximate scaling laws are derived that give agreement with full numerical solutions for the density, but not the temperature. For non-uniform areas, dynamic loops have a higher peak temperature and are denser in the radiative cooling phase by of order 50% than the constant area case for the examples considered. They also show a final rapid cooling and draining once the temperature approaches 1 MK. Although the magnitude of the emission measure will be enhanced in the radiative phase, there is little change in the important observational diagnostic of its temperature dependence.
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    The unusually high dark matter concentration of the galaxy group NGC 1600 (2021)
    Oxford University Press
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    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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    Fast cooling and internal heating in hyperon stars (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: Neutron star models with maximum mass close to 2 M⊙ reach high central densities, which may activate nucleonic and hyperon direct Urca neutrino emission. To alleviate the tension between fast theoretical cooling rates and thermal luminosity observations of moderately magnetized, isolated thermally-emitting stars (with Lγ ≳ 1031 erg s−1 at t ≳ 105.3 yr), some internal heating source is required. The power supplied by the internal heater is estimated for both a phenomenological source in the inner crust and Joule heating due to magnetic field decay, assuming different superfluidity models and compositions of the outer stellar envelope. It is found that a thermal power of W(t) ≈ 1034 erg s−1 allows neutron star models to match observations of moderately magnetized, isolated stars with ages t ≳ 105.3 yr. The requisite W(t) can be supplied by Joule heating due to crust-confined initial magnetic configurations with (i) mixed poloidal-toroidal fields, with surface strength Bdip = 1013 G at the pole of the dipolar poloidal component and ∼90 per cent of the magnetic energy stored in the toroidal component; and (ii) poloidal-only configurations with Bdip = 1014 G.
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    An analysis of the spectroscopic signatures of layering in the ejecta of type Iax supernovae (2021)
    Oxford University Press
    Details
    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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    Topics: Physics
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    White dwarfs identified in LAMOST Data Release 5 (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: In this paper, we report white dwarfs identified in the 5th Data Release of the Large Area Multi-Object fibre Spectroscopic Telescope, including spectral types of DA, DB, DC, DZ, and so on. There are 2 625 DA spectra of 2 281 DA stars, 182 DB spectra of 166 DB stars, 62 DC spectra of 58 DC stars, 36 DZ spectra of 33 DZ stars and many other types identified, in addition to our previous paper (Data Release 2). Among those sources, 393 DA stars and 46 DB stars are new identifications after cross-matching with the literature. In order to select DA candidates, we use the classification result from the LAMOST pipeline, colour-colour cut method and a random forest machine learning method. For DBs, since there is no template for DB in the pipeline model, a random forest machine learning method is chosen to select candidates. All the WD candidates have been visually checked individually. The parameters of effective temperature, surface gravity, mass, and cooling age have been estimated for relatively high signal-to-noise ratio DAs and DBs. The peaks of the DA and DB mass distributions are found to be around 0.62 M⊙ and 0.65 M⊙, respectively. Finally, the data and method we used to select white dwarf candidates for the second phase of LAMOST survey are also addressed in this paper.
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    Bayesian slip inversion with automatic differentiation variational inference (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: Summary The Bayesian slip inversion offers a powerful tool for modeling the earthquake source mechanism. It can provide a fully probabilistic result and thus permits us to quantitively assess the inversion uncertainty. The Bayesian problem is usually solved with Monte Carlo methods, but they are computationally expensive and are inapplicable for high-dimensional and large-scale problems. Variational inference is an alternative solver to the Bayesian problem. It turns Bayesian inference into an optimization task and thus enjoys better computational performances. In this study, we introduce a general variational inference algorithm, automatic differentiation variational inference (ADVI), to the Bayesian slip inversion and compare it with the classic Metropolis-Hastings (MH) sampling method. The synthetic test shows that the two methods generate nearly identical mean slip distributions and standard deviation maps. In the real case study, the two methods produce highly consistent mean slip distributions, but the ADVI-derived standard deviation map differs from that produced by the MH method, possibly because of the limitation of the Gaussian approximation in the ADVI method. In both cases, ADVI can give comparable results to the MH method but with a significantly lower computational cost. Our results show that ADVI is a promising and competitive method for the Bayesian slip inversion.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
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    prose: A Python framework for modular astronomical images processing (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: To reduce and analyse astronomical images, astronomers can rely on a wide range of libraries providing low-level implementations of legacy algorithms. However, combining these routines into robust and functional pipelines requires a major effort which often ends up in instrument-specific and poorly maintainable tools, yielding products that suffer from a low-level of reproducibility and portability. In this context, we present prose, a Python framework to build modular and maintainable image processing pipelines. Built for astronomy, it is instrument-agnostic and allows the construction of pipelines using a wide range of building blocks, pre-implemented or user-defined. With this architecture, our package provides basic tools to deal with common tasks such as automatic reduction and photometric extraction. To demonstrate its potential, we use its default photometric pipeline to process 26 TESS candidates follow-up observations and compare their products to the ones obtained with AstroImageJ, the reference software for such endeavors. We show that prose produces light curves with lower white and red noise while requiring less user interactions and offering richer functionalities for reporting.
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    Internal kinematics of GAIA eDR3 wide binaries (2021)
    Oxford University Press
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    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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    First mitochondrial genome wide association study with metabolomics (2021)
    Oxford University Press
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    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.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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    The uncertain future of the Norway lobster fisheries in the North Sea calls for new management strategies (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: Nephrops (Nephrops norvegicus) is an economically valuable target species in the North Sea. Although individual Nephrops populations are scattered, the crustacean is managed regionally by the European Union (EU). The spatial competition for fisheries in the North Sea is growing especially due to expanding offshore wind farms (OWF) and newly implemented marine protected areas (MPA). Moreover, the Brexit affects the availability of EU fishing quotas and adds to the overall uncertainty EU fishers face. We compare landings and catches to scientifically advised quantities and perform an overlap analysis of fishing grounds with current and future OWFs and MPAs. Furthermore, we explore the German Nephrops fleet using high-resolution spatial fishing effort and catch data. Our results confirm earlier studies showing that Nephrops stocks have been fished above scientific advice. Present OWFs and MPAs marginally overlap with Nephrops fishing grounds, whereas German fishing grounds are covered up to 45% in future scenarios. Co-use strategies with OWFs could mitigate the loss of fishing opportunities. Decreased cod quotas due to Brexit and worse stock conditions, lowers Germany's capability to swap Nephrops quotas with the UK. We support the call for a new management strategy of individual Nephrops populations and the promotion of selective fishing gears.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press on behalf of International Council for the Exploration of the Sea.
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    EWAS Open Platform: integrated data, knowledge and toolkit for epigenome-wide association study (2021)
    Oxford University Press
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    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.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    Erratum: The GALAH survey: Chemical homogeneity of the Orion complex (2021)
    Oxford University Press
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    Publication Date: 2021-10-26
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    Weak lensing mass modeling bias and the impact of miscentring (2021)
    Oxford University Press
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    Publication Date: 2021-10-27
    Description: Parametric modeling of galaxy cluster density profiles from weak lensing observations leads to a mass bias, whose detailed understanding is critical in deriving accurate mass-observable relations for constraining cosmological models. Drawing from existing methods, we develop a robust framework for calculating this mass bias in one-parameter fits to simulations of dark matter haloes. We show that our approach has the advantage of being independent of the absolute noise level, so that only the number of haloes in a given simulation and the representativeness of the simulated haloes for real clusters limit the accuracy of the bias estimation. While we model the bias as a lognormal distribution and the haloes with a Navarro-Frenk-White profile, our method can be generalized to any bias distribution and parametric model of the radial mass distribution. We find that the lognormal assumption is not strictly valid in the presence of miscentring of haloes. We investigate the use of cluster centers derived from weak lensing in the context of mass bias, and tentatively find that such centroids can yield sensible mass estimates if the convergence peak has a signal-to-noise ratio approximately greater than four. In this context we also find that the standard approach to estimating the positional uncertainty of weak lensing mass peaks using bootstrapping severely underestimates the true positional uncertainty for peaks with low signal-to-noise ratios. Though we determine the mass and redshift dependence of the bias distribution for a few experimental setups, our focus remains providing a general approach to computing such distributions.
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    A persistent double nuclear structure in 3C 84 (2021)
    Oxford University Press
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    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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    FOREVER22: galaxy formation in protocluster regions (2021)
    Oxford University Press
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    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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    Dancing in the void: Hydrodynamical N-body simulations of the extremely metal poor galaxy DDO 68 (2021)
    Oxford University Press
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    Publication Date: 2021-10-27
    Description: Using hydrodynamical N-body simulations, we show that the observed structure and kinematics of the extremely metal-poor, dwarf irregular galaxy DDO 68 is compatible with a merger event with at least two smaller satellite galaxies. We were able to obtain a self-consistent model that simultaneously reproduces several of its observed features, including: the very asymmetric and disturbed shape of the stellar component, the overall ${ m H, small {I}}$ distribution and its velocity field, the arc-like stellar structure to the west, the low-surface brightness stellar stream to the north. The model implies the interaction of the main progenitor of DDO 68 with two systems with dynamical masses 7 × 108 M⊙ and almost 108 M⊙ – 1/20 and 1/150 times the dynamical mass of DDO 68, respectively. We show that the merger between DDO 68 and the most massive of its satellites offers a route to explain the large offset of DDO 68 from the mass-metallicity relation. Assuming that the interacting galaxies have metallicities prior to the merger compatible with those of galaxies with similar stellar masses, we provide quantitative evidence that gas mixing alone does not suffice at diluting the gas of the two components; according to our simulations, the ${ m H, small {II}}$ regions observed along the Cometary Tail trace the low metallicity of the accreted satellite rather than that of DDO 68’s main body. In this case, the mass corresponding to the low metallicity is that of the secondary body and DDO 68 becomes consistent with the mass-metallicity relation.
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    Dark Energy Survey Year 3 Results: Deep Field optical + near-infrared images and catalogue (2021)
    Oxford University Press
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    Publication Date: 2021-10-27
    Description: We describe the Dark Energy Survey (DES) Deep Fields, a set of images and associated multi-wavelength catalogue (ugrizJHKs) built from Dark Energy Camera (DECam) and Visible and Infrared Survey Telescope for Astronomy (VISTA) data. The DES Deep Fields comprise 11 fields (10 DES supernova fields plus COSMOS), with a total area of ∼30 square degrees in ugriz bands and reaching a maximum i-band depth of 26.75 (AB, 10σ, 2″). We present a catalogue for the DES 3-year cosmology analysis of those four fields with full 8-band coverage, totalling 5.88 sq. deg. after masking. Numbering 2.8million objects (1.6million post masking), our catalogue is drawn from images coadded to consistent depths of r = 25.7, i = 25, z = 24.3 mag. We use a new model-fitting code, built upon established methods, to deblend sources and ensure consistent colours across the u-band to Ks-band wavelength range. We further detail the tight control we maintain over the point-spread function modelling required for the model fitting, astrometry and consistency of photometry between the four fields. The catalogue allows us to perform a careful star-galaxy separation and produces excellent photometric redshift performance (NMAD = 0.023 at i 〈 23). The Deep-Fields catalogue will be made available as part of the cosmology data products release, following the completion of the DES 3-year weak lensing and galaxy clustering cosmology work.
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    High-Throughput-Methyl-Reading (HTMR) assay: a solution based on nucleotide methyl-binding proteins enables large-scale screening for DNA/RNA methyltransferases and demethylases (2021)
    Oxford University Press
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    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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    Wavefield-based evaluation of DAS instrument response and array design (2021)
    Oxford University Press
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    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.
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    Topics: Geosciences
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    Similarity-based analysis of allele frequency distribution among multiple populations identifies adaptive genomic structural variants (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: Structural variants have a considerable impact on human genomic diversity. However, their evolutionary history remains mostly unexplored. Here, we developed a new method to identify potentially adaptive structural variants based on a similarity-based analysis that incorporates genotype frequency data from 26 populations simultaneously. Using this method, we analyzed 57,629 structural variants and identified 576 structural variants that show unusual population differentiation. Of these putatively adaptive structural variants, we further showed that 24 variants are multiallelic and overlap with coding sequences, and 20 variants are significantly associated with GWAS traits. Closer inspection of the haplotypic variation associated with these putatively adaptive and functional structural variants reveals deviations from neutral expectations due to (i) population differentiation of rapidly evolving multi-allelic variants, (ii) incomplete sweeps, and (iii) recent population-specific negative selection. Overall, our study provides new methodological insights, documents hundreds of putatively adaptive variants, and introduces evolutionary models that may better explain the complex evolution of structural variants.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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    A birth-death-migration model for life in astrophysical environments (2021)
    Oxford University Press
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    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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    3-D seismic velocity structure of the Kumaun-Garhwal (Central) Himalaya: Insight into the Main Himalayan Thrust and earthquake occurrence (2021)
    Oxford University Press
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    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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    Translation of MT-ATP6 pathogenic variants reveals distinct regulatory consequences from the co-translational quality control of mitochondrial protein synthesis (2021)
    Oxford University Press
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    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.
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    AstroSat observations of Long-duration X-ray superflares on active M-dwarf binary EQ Peg (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: We present a comprehensive study of three large long-duration flares detected on an active M-dwarf binary EQ Peg using the Soft X-Ray Telescope of the AstroSat observatory. The peak X-ray luminosities of the flares in the 0.3–7 keV band are found to be within ∼5–10 ×  1030 $ m {erg}~ m {s}^{-1}$. The e-folding rise- and decay-times of the flares are derived to be in the range of 3.4–11 and 1.6–24 ks, respectively. Spectral analysis indicates the presence of three temperature corona with the first two plasma temperatures remain constant during all the flares and the post-flare observation at ∼3 and ∼9 MK. The flare temperature peaked at 26, 16, and 17 MK, which are 2, 1.3, and 1.4 times more than the minimum value, respectively. The peak emission measures are found to be 3.9–7.1 ×  1053 cm−3, whereas the abundances peaked at 0.16–0.26 times the solar abundances. Using quasi-static loop modelling, we derive loop-lengths for all the flares as 2.5±0.5 ×  1011, 2.0 ± 0.5 ×  1011, and 2.5 ± 0.9 ×  1011 cm, respectively. The density of the flaring plasma is estimated to be 4.2 ± 0.8 ×  1010, 3.0 ± 0.7 ×  1010, 2.2 ± 0.8 ×  1010 cm−3 for flares F1, F2, and F3, respectively. Whereas the magnetic field for all three flares is estimated to be
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    Five years of BRITE-Constellation photometry of the luminous blue variable P Cygni: properties of the stochastic low-frequency variability (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: Luminous Blue Variables (LBVs) are massive stars that are likely to be a transitionary phase between O stars and hydrogen-free classical Wolf-Rayet stars. The variability of these stars has been an area of study for both professional and amateur astronomers for more than a century. In this paper, we present five years of precision photometry of the classical LBV P Cygni taken with the BRITE-Constellation nanosatellites. We have analyzed these data with Fourier analysis to search for periodicities that could elucidate the drivers of variability for these stars. These data show some long-timescale variability over the course of all six calendar years of observations, but the frequencies needed to reproduce the individual light curves are not consistent from one year to the next. These results likely show that there is no periodic phenomenon present for P Cygni, meaning that the variability is largely stochastic. We interpret the data as being caused by internal gravity waves similar to those seen in other massive stars, with P Cygni exhibiting a larger amplitude and lower characteristic frequency than the main-sequence or blue supergiant stars previously studied. These results show evidence that LBVs may be an extrapolation of the blue supergiants, which have previously been shown to be an extension of main-sequence stars in the context of the stochastic low-frequency photometric variability.
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    CoCoPRED: coiled-coil protein structural feature prediction from amino acid sequence using deep neural networks (2021)
    Oxford University Press
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    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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    Zodiacal exoplanets in time (ZEIT) XIII: Planet orbits and atmospheres in the V1298 Tau system, a keystone in studies of early planetary evolution (2021)
    Oxford University Press
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    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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    Two newly identified eclipsing binaries in open cluster NGC 3532 (2021)
    Oxford University Press
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    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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    AOP-helpFinder webserver: a tool for comprehensive analysis of the literature to support adverse outcome pathways development (2021)
    Oxford University Press
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    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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    Self-similarity of k-nearest neighbor distributions in scale-free simulations (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: We use the k-nearest neighbor probability distribution function (kNN-PDF, Banerjee & Abel 2021) to assess convergence in a scale-free N-body simulation. Compared to our previous two-point analysis, the kNN-PDF allows us to quantify our results in the language of haloes and numbers of particles, while also incorporating non-Gaussian information. We find good convergence for 32 particles and greater at densities typical of haloes, while 16 particles and fewer appears unconverged. Halving the softening length extends convergence to higher densities, but not to fewer particles. Our analysis is less sensitive to voids, but we analyse a limited range of underdensities and find evidence for convergence at 16 particles and greater even in sparse voids.
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    SatGen – II. Assessing the impact of a disc potential on subhalo populations (2021)
    Oxford University Press
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    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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    Heterozygous Tropomodulin 3 mice have improved lung vascularization after chronic hypoxia. (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: The molecular mechanisms leading to high altitude pulmonary hypertension (HAPH) remains poorly understood. We previously analyzed the whole genome sequence of Kyrgyz highland population and identified eight genomic intervals having a potential role in HAPH. Tropomodulin 3 gene (TMOD3) which encodes a protein that binds and caps the pointed ends of actin filaments and inhibits cell migration, was one of the top candidates. Here we systematically sought additional evidence to validate the functional role of TMOD3. In-silico analysis reveals that some of the SNPs in HAPH associated genomic intervals were positioned in a regulatory region that could result in alternative splicing of TMOD3. In order to functionally validate the role of TMOD3 in HAPH, we exposed Tmod3−/+ mice to 4 weeks of constant hypoxia, i.e. 10% O2 and analyzed both functional (hemodynamic measurements) and structural (angiography) parameters related to HAPH. The hemodynamic measurements, such as right ventricular systolic pressure, a surrogate measure for pulmonary arterial systolic pressure, and right ventricular contractility (RV- ± dP/dt), increases with hypoxia did not separate between Tmod3−/+ and control mice. Remarkably, there was a significant increase in the number of lung vascular branches and total length of pulmonary vascular branches (p 
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    Gravitational wave signature of proto-neutron star convection: I. MHD numerical simulations (2021)
    Oxford University Press
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    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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    Phylogenetic articulation of uric acid evolution in mammals and how it informs a therapeutic uricase (2021)
    Oxford University Press
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    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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    Regulation of star formation by large scale gravito-turbulence (2021)
    Oxford University Press
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    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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    Predictors of Pain Reduction in Trials of Interventions for Aromatase Inhibitor-Associated Musculoskeletal Symptoms (2021)
    Oxford University Press
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    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
    Published by Oxford University Press on behalf of National Cancer Institute.
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    LocalNgsRelate: a software tool for inferring IBD sharing along the genome between pairs of individuals from low-depth NGS data (2021)
    Oxford University Press
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    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.
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    Spatial estimation of fundamental mode dispersion curves using geostatistical techniques (2021)
    Oxford University Press
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    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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    DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data (2021)
    Oxford University Press
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    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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    Notes on a compressible extended burgers model of rheology (2021)
    Oxford University Press
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    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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    SigTools: Exploratory Visualization For Genomic Signals (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: Motivation With the advancement of sequencing technologies, genomic data sets are constantly being expanded by high volumes of different data types. One recently introduced data type in genomic science is genomic signals, which are usually short-read coverage measurements over the genome. To understand and evaluate the results of such studies, one needs to understand and analyze the characteristics of the input data. Results SigTools is an R-based genomic signals visualization package developed with two objectives: 1) to facilitate genomic signals exploration in order to uncover insights for later model training, refinement, and development by including distribution and autocorrelation plots. 2) to enable genomic signals interpretation by including correlation, and aggregation plots. In addition, our corresponding web application, SigTools-Shiny, extends the accessibility scope of these modules to people who are more comfortable working with graphical user interfaces instead of command-line tools. Availability SigTools source code, installation guide, and manual is freely available on http://github.com/shohre73.
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    The Gaia-ESO Survey: Membership probabilities for stars in 63 open and 7 globular clusters from 3D kinematics (2021)
    Oxford University Press
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    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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    Impacts of geometric model simplifications on wave propagation - Application to ground motion simulation in the lower Var valley basin (France). (2021)
    Oxford University Press
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    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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    Topics: Geosciences
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    Search for fast radio transients using Arecibo drift-scan observations at 1.4 GHz (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: We conducted a drift-scan observation campaign using the 305-m Arecibo telescope in January and March 2020 when the observatory was temporarily closed during the intense earthquakes and the initial outbreak of the COVID-19 pandemic, respectively. The primary objective of the survey was to search for fast radio transients, including Fast Radio Bursts (FRBs) and Rotating Radio Transients (RRATs). We used the 7-beam ALFA receiver to observe different sections of the sky within the declination region ∼(10–20) deg on 23 nights and collected 160 hours of data in total. We searched our data for single-pulse transients, of covering up to a maximum dispersion measure of 11 000 pc cm−3 at which the dispersion delay across the entire bandwidth is equal to the 13 s transit length of our observations. The analysis produced more than 18 million candidates. Machine learning techniques sorted the radio frequency interference and possibly astrophysical candidates, allowing us to visually inspect and confirm the candidate transients. We found no evidence for new astrophysical transients in our data. We also searched for emission from repeated transient signals, but found no evidence for such sources. We detected single pulses from two known pulsars in our observations and their measured flux densities are consistent with the expected values. Based on our observations and sensitivity, we estimated the upper limit for the FRB rate to be
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    Accelerating NBODY6 with a GPU-enabled Particle-Particle Particle-Tree scheme (2021)
    Oxford University Press
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    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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    Well-log facies classification using an active semi-supervised algorithm with pairwise constraints (2021)
    Oxford University Press
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    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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    The z–DM distribution of fast radio bursts (2021)
    Oxford University Press
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    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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    A multiwavelength study of the H ii region G347.600+00.211 and its effects on the surrounding medium (2021)
    Oxford University Press
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    Publication Date: 2021-10-27
    Description: We present a multi-wavelength investigation of the H ii region G347.600+00.211, located at a distance of 7.9 kpc. We analyse the gas and dust properties aiming to disentangle the origin of the region as well as its role in the formation of new stars. G347.600+00.211 is very conspicuous at 1420 MHz and infrared wavelengths, showing an incomplete shell-like structure with two distinct zones of very intense emission. The infrared bubble S8 is part of the shell structure. The spatial distribution of the molecular gas shows the presence of six clouds located around the ionized region and showing a good morphological correlation with the 8 μm emission. Cold dust is coincident with the dense gas shown in the CO measurements. As for the origin of the region, we found that the massive cluster [DBS2003]179 and two Wolf–Rayet (WR) stars are located at the same distance than the ionized gas. Based on a stellar density analysis, we inferred that one of the WR stars, 1181-81L, is also a probable member of the cluster. Both the cluster and the WR stars are not only within the ring–like structure, but are also located near the two spots of very heightened emission, suggesting they may be responsible for this bright emission. Finally, as expanding H ii regions are hypothesised to trigger star formation, we used different infrared point source catalogues to search for young stellar object candidates (cYSOs). A total of 33 cYSOs and 4 CH ii regions were identified projected on to the photo–dissociation regions and molecular clouds.
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    Non-standard mechanism of recombination in the early Universe (2021)
    Oxford University Press
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    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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    The 2020 Mw 6.4 Petrinja earthquake: A dextral event with large coseismic slip highlights a complex fault system in northwestern Croatia (2021)
    Oxford University Press
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    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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    The homogeneity scale and the growth rate of cosmic structures (2021)
    Oxford University Press
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    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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    Importance-Penalized Joint Graphical Lasso (IPJGL): differential network inference via GGMs (2021)
    Oxford University Press
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    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
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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    CpG Transformer for imputation of single-cell methylomes (2021)
    Oxford University Press
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    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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    Topics: Biology , Computer Science , Medicine
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    Polycyclic Aromatic Hydrocarbons in Seyfert and star-forming galaxies (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: Polycyclic Aromatic Hydrocarbons (PAHs) are carbon-based molecules resulting from the union of aromatic rings and related species, which are likely responsible for strong infrared emission features. In this work, using a sample of 50 Seyfert galaxies (DL 〈 100 Mpc) we compare the circumnuclear (inner kpc) PAH emission of AGN to that of a control sample of star-forming galaxies (22 luminous infrared galaxies and 30 H ii galaxies), and investigate the differences between central and extended PAH emission. Using Spitzer/InfraRed Spectrograph spectral data of Seyfert and star-forming galaxies and newly developed PAH diagnostic model grids, derived from theoretical spectra, we compare the predicted and observed PAH ratios. We find that star-forming galaxies and AGN-dominated systems are located in different regions of the PAH diagnostic diagrams. This suggests that not only are the size and charge of the PAH molecules different, but also the nature and hardness of the radiation field that excite them. We find tentative evidence that PAH ratios in AGN-dominated systems are consistent with emission from larger PAH molecules (Nc 〉 300–400) as well as neutral species. By subtracting the spectrum of the central source from the total, we compare the PAH emission in the central versus extended region of a small sample of AGN. In contrast to the findings for the central regions of AGN-dominated systems, the PAH ratios measured in the extended regions of both type 1 and type 2 Seyfert galaxies can be explained assuming similar PAH molecular size distribution and ionized fractions of molecules to those seen in central regions of star-forming galaxies (100 〈 Nc 〈 300).
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    Aftershock sequence of the 2017 Mw 6.5 Jiuzhaigou, China earthquake monitored by an AsA network and its implication to fault structures and strength (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: Summary We deployed a seismic network near the source region of the 2017 Mw 6.5 Jiuzhaigou earthquake to monitor aftershock activity and to investigate the local fault structure. An aftershock deployment of Array of small Arrays (AsA) and a Geometric Mean Envelop (GME) algorithm are adopted to enhance detection performance. We also adopt a set of association, relocation, and matched-filter techniques to obtain a detailed regional catalog. 16,742 events are detected and relocated, including 1,279 aftershocks following the Mw 4.8 aftershock. We develop a joint inversion algorithm utilizing locations of event clusters and focal mechanisms to determine the geometry of planar faults. Six segments were finally determined, in which three segments are related to the Huya fault reflecting a change in fault dip direction near the mainshock hypocenter, while the other segments reflect branches showing orthogonal and conjugate geometries with the Huya fault. Aftershocks were active on branching faults between the Huya and Minjiang faults indicating that the mainshock may have ruptured both major faults. We also resolve a fault portion with ‘weak strength’ near the mainshock hypocenter, which is characterized by limited co-seismic slips, concentrated afterslip, low aftershock activities, high b-value, and high sensitivity to stress changes. These phenomena can be explained by fault frictional properties at conditional stable sliding status, which may be related to the localized high pore-fluid pressure produced by the fluid intrusion.
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    Clinical, pathological and genetic features and follow-up of 110 patients with late-onset MADD: A single-center retrospective study (2021)
    Oxford University Press
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    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
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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