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  • Articles  (274,517)
  • American Institute of Physics (AIP)  (139,455)
  • Oxford University Press  (135,062)
  • 2020-2024  (477)
  • 2010-2014  (139,911)
  • 1990-1994  (76,182)
  • 1985-1989  (54,998)
  • 1950-1954  (2,949)
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  • 1
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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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  • 2
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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)
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  • 3
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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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  • 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
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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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    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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  • 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 Influence of Undercooling and Sector Zoning on Clinopyroxene–Melt Equilibrium and Thermobarometry (2024)
    Oxford University Press
    Details
    Publication Date: 2024-06-17
    Description: Thermobarometry provides a critical means of assessing locations of magma storage and dynamics in the lead-up to volcanic eruptions and crustal growth. A common approach is to utilise minerals that have compositions sensitive to changes in pressure and/or temperature, such as clinopyroxene, which is ubiquitous in mafic to intermediate magmas. However, clinopyroxene thermobarometry may carry significant uncertainty and require an appropriate equilibrium melt composition. In addition, the degree of magma undercooling (ΔT) affects clinopyroxene composition and zoning, with common sector zoning potentially obfuscating thermobarometry results. Here, we use a set of crystallisation experiments on a primitive trachybasalt from Mt. Etna (Italy) at ΔT = 25–233 °C, P = 400–800 MPa, H2O = 0–4 wt % and fO2 = NNO + 2, with clinopyroxene crystals defined by Al-rich zones (prisms and skeletons) and Al-poor zones (hourglass and overgrowths) to assess common equilibrium models and thermobarometric approaches. Under the studied conditions, our data suggest that the commonly applied Fe–Mg exchange (cpx-meltKdFe–Mg) is insensitive to increasing ΔT and may not be a reliable indicator of equilibrium. The combined use of DiHd (CaMgSi2O6 + CaFeSi2O6) and EnFs (Mg2Si2O6 + Fe2Si2O6) models indicate the attainment of equilibrium in both Al-rich and Al-poor zones for almost all investigated ΔT. In contrast, CaTs (CaAl2SiO6) and CaTi (CaTiAl2O6) models reveal substantial deviations from equilibrium with increasing ΔT, particularly in Al-rich zones. We postulate that this reflects slower diffusion of Al and Ti in the melt compared with Ca and Mg and recommend the concurrent application of these four models to evaluate equilibrium between clinopyroxene and melt, particularly for sector-zoned crystals. Thermobarometers calibrated with only isothermal–isobaric experiments closely reproduce experimental P–T at low ΔT, equivalent to natural phenocrysts cores and sector-zoned mantles. Models that also consider decompression experiments are most accurate at high ΔT and are therefore suitable for outermost phenocryst rims and groundmass microlites. Recent machine learning approaches reproduce P–T conditions across all ΔT conditions. Applying our experimental constraints to sector-zoned microphenocrysts and groundmass microlites erupted during the 1974 eccentric eruption at Mt. Etna, we highlight that both hourglass and prism sectors are suitable for thermobarometry, given that equilibrium is sufficiently tested for. The combination of DiHd, EnFs, CaTs and CaTi models identifies compositions closest to equilibrium with the bulk melt composition, and results in smaller differences in P–T calculated for hourglass and prism sectors compared with applying only DiHd and EnFs equilibrium models. This provides a framework to assess crystallisation conditions recorded by sector-zoned clinopyroxene crystals in mafic alkaline settings.
    Description: Published
    Description: egad074
    Description: OSV2: Complessità dei processi vulcanici: approcci multidisciplinari e multiparametrici
    Description: JCR Journal
    Keywords: Experimental Petrology ; Petrology ; Clinopyroxene ; Thermobarometry ; Experimental Petrology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 13
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    Mass-change And Geosciences International Constellation (MAGIC) expected impact on science and applications (2024)
    Oxford University Press
    Details
    Publication Date: 2024-07-02
    Description: The joint ESA/NASA Mass-change And Geosciences International Constellation (MAGIC) has the objective to extend time-series from previous gravity missions, including an improvement of accuracy and spatio-temporal resolution. The long-term monitoring of Earth’s gravity field carries information on mass change induced by water cycle, climate change and mass transport processes between atmosphere, cryosphere, oceans and solid Earth. MAGIC will be composed of two satellite pairs flying in different orbit planes. The NASA/DLR-led first pair (P1) is expected to be in a near-polar orbit around 500 km of altitude; while the second ESA-led pair (P2) is expected to be in an inclined orbit of 65°–70° at approximately 400 km altitude. The ESA-led pair P2 Next Generation Gravity Mission shall be launched after P1 in a staggered manner to form the MAGIC constellation. The addition of an inclined pair shall lead to reduction of temporal aliasing effects and consequently of reliance on de-aliasing models and post-processing. The main novelty of the MAGIC constellation is the delivery of mass-change products at higher spatial resolution, temporal (i.e. subweekly) resolution, shorter latency and higher accuracy than the Gravity Recovery and Climate Experiment (GRACE) and Gravity Recovery and Climate Experiment Follow-On (GRACE-FO). This will pave the way to new science applications and operational services. In this paper, an overview of various fields of science and service applications for hydrology, cryosphere, oceanography, solid Earth, climate change and geodesy is provided. These thematic fields and newly enabled applications and services were analysed in the frame of the initial ESA Science Support activities for MAGIC. The analyses of MAGIC scenarios for different application areas in the field of geosciences confirmed that the double-pair configuration will significantly enlarge the number of observable mass-change phenomena by resolving smaller spatial scales with an uncertainty that satisfies evolved user requirements expressed by international bodies such as IUGG. The required uncertainty levels of dedicated thematic fields met by MAGIC unfiltered Level-2 products will benefit hydrological applications by recovering more than 90 per cent of the major river basins worldwide at 260 km spatial resolution, cryosphere applications by enabling mass change signal separation in the interior of Greenland from those in the coastal zones and by resolving small-scale mass variability in challenging regions such as the Antarctic Peninsula, oceanography applications by monitoring meridional overturning circulation changes on timescales of years and decades, climate applications by detecting amplitude and phase changes of Terrestrial Water Storage after 30 yr in 64 and 56 per cent of the global land areas and solid Earth applications by lowering the Earthquake detection threshold from magnitude 8.8 to magnitude 7.4 with spatial resolution increased to 333 km.
    Description: Published
    Description: 1288–1308
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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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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  • 15
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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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  • 16
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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
    Repository Name: Woods Hole Open Access Server
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  • 17
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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
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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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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  • 19
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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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    Fault imaging at Mt Pollino (Italy) from relative location of microearthquakes (2021)
    Oxford University Press
    Details
    Publication Date: 2023-10-26
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2021. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved.
    Description: Relative location of microearthquakes that occurred at Mt Pollino (Italy) from 2011 to 2013 have been analyzed with the aim of a detailed imaging of the geometry of active faults. We identified 27 clusters composed of a number of earthquakes from 9 to 33, with local magnitude in the range 0.6–2.7. The relative location shows that the distribution of hypocentres in each cluster is characterized by extension from few tens of meters to at most 350 m. For each cluster the hypocentre distribution was fitted by a plane to infer the fault orientation, and results were compared with the fault plane solutions corresponding to the focal mechanism of earthquakes of the same cluster. The comparison shows a good agreement in most of the cases. The relative location analysis, generally applied to earthquakes with similar waveform, has been improved to permit also the relative location of earthquakes characterized by not similar signals. To achieve this purpose a modified procedure that overcome the condition of very similar waveforms has been applied to estimate the time delay between first pulses of the master events. The relative location of master events of all clusters shows a precise imaging of the relative position of all analysed sources and allows also to follow with high accuracy the evolution in time of the seismic swarm within the selected periods. The hypocentre position of master events and the nearly parallel fitting planes of any clusters suggest that most of the analyzed earthquakes were produced by different patches of the same fault. The final results depict a main fault plane characterized by NW–SE strike, dip of about 35–45° and depth between 4.5 and 6.5 km b.s.l. Focal mechanisms, used also to evaluate the local stress field, are mostly of normal type with few strike slip solutions for the shallowest events. This result is in good agreement with the local tectonic stress regime that is characterized by predominant NE–SW transtension, as inferred from structural, seismological and geophysical data.
    Description: Published
    Description: 637–648
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: Persistence, memory, correlations, clustering, Spatial analysis, Crustal imaging, Earthquake source observations, Seismicity and tectonics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 21
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    Upper mantle deformation signatures of craton–orogen interaction in the Carpathian–Pannonian region from SKS anisotropy analysis (2021)
    Oxford University Press
    Details
    Publication Date: 2023-10-31
    Description: Since the Mesozoic, central and eastern European tectonics have been dominated by the closure of the Tethyan Ocean as the African and European plates collided. In the Miocene, the edge of the East European Craton and Moesian Platform were reworked in collision during the Carpathian orogeny and lithospheric extension formed the Pannonian Basin. To investigate the mantle deformation signatures associated with this complex collisional-extensional system, we carry out SKS splitting analysis at 123 broad-band seismic stations in the region. We compare our measurements with estimates of lithospheric thickness and recent seismic tomography models to test for correlation with mantle heterogeneities. Reviewing splitting delay times in light of xenolith measurements of anisotropy yields estimates of anisotropic layer thickness. Fast polarization directions are mostly NW–SE oriented across the seismically slow West Carpathians and Pannonian Basin and are independent of geological boundaries, absolute plate motion direction or an expected palaeo-slab roll-back path. Instead, they are systematically orthogonal to maximum stress directions, implying that the indenting Adria Plate, the leading deformational force in Central Europe, reset the upper-mantle mineral fabric in the past 5 Ma beneath the Pannonian Basin, overprinting the anisotropic signature of earlier tectonic events. Towards the east, fast polarization directions are perpendicular to steep gradients of lithospheric thickness and align along the edges of fast seismic anomalies beneath the Precambrian-aged Moesian Platform in the South Carpathians and the East European Craton, supporting the idea that craton roots exert a strong influence on the surrounding mantle flow. Within the Moesian Platform, SKS measurements become more variable with Fresnel zone arguments indicating a shallow fossil lithospheric source of anisotropy likely caused by older tectonic deformation frozen in the Precambrian. In the Southeast Carpathian corner, in the Vrancea Seismic Zone, a lithospheric fragment that sinks into the mantle is sandwiched between two slow anomalies, but smaller SKS delay times reveal weaker anisotropy occurs mainly to the NW side, consistent with asymmetric upwelling adjacent to a slab, slower mantle velocities and recent volcanism.
    Description: Published
    Description: 2105–2118
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: Seismic anisotropy ; geodynamics ; Seismic anisotropy and geodynamics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 22
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    Broad-band ground-motion simulation of 2016 Amatrice earthquake, Central Italy (2021)
    Oxford University Press
    Details
    Publication Date: 2023-11-21
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2021. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved.
    Description: On 24 August 2016 at 01:36 UTC a ML6.0 earthquake struck several villages in central Italy, among which Accumoli, Amatrice and Arquata del Tronto. The earthquake was recorded by about 350 seismic stations, causing 299 fatalities and damage with macroseismic intensities up to 11. The maximum acceleration was observed at Amatrice station (AMT) reaching 916 cm s–2 on E–W component, with epicentral distance of 15 km and Joyner and Boore distance to the fault surface (RJB) of less than a kilometre. Motivated by the high levels of observed ground motion and damage, we generate broad-band seismograms for engineering purposes by adopting a hybrid method. To infer the low frequency seismograms, we considered the kinematic slip model by Tinti et al . The high frequency seismograms were produced using a stochastic finite-fault model approach based on dynamic corner-frequency. Broadband synthetic time-series were therefore obtained by merging the low and high frequency seismograms. Simulated hybrid ground motions were compared both with the observed ground motions and the ground-motion prediction equations (GMPEs), to explore their performance and to retrieve the region-specific parameters endorsed for the simulations. In the near-fault area we observed that hybrid simulations have a higher capability to detect near source effects and to reproduce the source complexity than the use of GMPEs. Indeed, the general good consistency found between synthetic and observed ground motion (both in the time and frequency domain), suggests that the use of regional-specific source scaling and attenuation parameters together with the source complexity in hybrid simulations improves ground motion estimations. To include the site effect in stochastic simulations at selected stations, we tested the use of amplification curves derived from HVRSs (horizontal-to-vertical response spectra) and from HVSRs (horizontal-to-vertical spectral ratios) rather than the use of generic curves according to NTC18 Italian seismic design code. We generally found a further reduction of residuals between observed and simulated both in terms of time histories and spectra.
    Description: Published
    Description: 1753–1779
    Description: 6T. Studi di pericolosità sismica e da maremoto
    Description: JCR Journal
    Keywords: 04.06. Seismology
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  • 23
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    Rapid Prediction of Earthquake Ground Shaking Intensity Using Raw Waveform Data and a Convolutional Neural Network (2021)
    Oxford University Press
    Details
    Publication Date: 2023-11-16
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2020. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved
    Description: This study describes a deep convolutional neural network (CNN) based technique for the prediction of intensity measurements (IMs) of ground shaking. The input data to the CNN model consists of multistation 3C broadband and accelerometric waveforms recorded during the 2016 Central Italy earthquake sequence for M $\ge$ 3.0. We find that the CNN is capable of predicting accurately the IMs at stations far from the epicenter and that have not yet recorded the maximum ground shaking when using a 10 s window starting at the earthquake origin time. The CNN IM predictions do not require previous knowledge of the earthquake source (location and magnitude). Comparison between the CNN model predictions and the predictions obtained with Bindi et al. (2011) GMPE (which require location and magnitude) has shown that the CNN model features similar error variance but smaller bias. Although the technique is not strictly designed for earthquake early warning, we found that it can provide useful estimates of ground motions within 15-20 sec after earthquake origin time depending on various setup elements (e.g., times for data transmission, computation, latencies). The technique has been tested on raw data without any initial data pre-selection in order to closely replicate real-time data streaming. When noise examples were included with the earthquake data, the CNN was found to be stable predicting accurately the ground shaking intensity corresponding to the noise amplitude.
    Description: Published
    Description: 1379–1389
    Description: 8T. Sismologia in tempo reale
    Description: JCR Journal
    Keywords: Physics - Geophysics; Physics - Geophysics ; 04.06. Seismology
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    Understanding seismic path biases and magmatic activity at Mount St Helens volcano before its 2004 eruption (2021)
    Oxford University Press
    Details
    Publication Date: 2023-11-16
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2020. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved.
    Description: In volcanoes, topography, shallow heterogeneity and even shallow morphology can substan- tially modify seismic coda signals. Coda waves are an essential tool to monitor eruption dynamics and model volcanic structures jointly and independently from velocity anomalies: it is thus fundamental to test their spatial sensitivity to seismic path effects. Here, we apply the Multiple Lapse Time Window Analysis (MLTWA) to measure the relative importance of scattering attenuation vs absorption at Mount St Helens volcano before its 2004 erup- tion. The results show the characteristic dominance of scattering attenuation in volcanoes at lower frequencies (3–6 Hz), while absorption is the primary attenuation mechanism at 12 and 18 Hz. Scattering attenuation is similar but seismic absorption is one order of magnitude lower than at open-conduit volcanoes, like Etna and Kilauea, a typical behaviour of a (rela- tively) cool magmatic plumbing system. Still, the seismic albedo (measuring the ratio between seismic energy emitted and received from the area) is anomalously high (0.95) at 3 Hz. A radiative-transfer forward model of far- and near-field envelopes confirms this is due to strong near-receiver scattering enhancing anomalous phases in the intermediate and late coda across the 1980 debris avalanche and central crater. Only above this frequency and in the far-field diffusion onsets at late lapse times. The scattering and absorption parameters derived from MLTWA are used as inputs to construct 2-D frequency-dependent bulk sensitivity kernels for the S-wave coda in the multiple-scattering (using the Energy Transport Equations—ETE) and diffusive (AD, independent of MLTWA results) regimes. At 12 Hz, high coda-attenuation anomalies characterize the eastern side of the volcano using both kernels, in spatial correla- tion with low-velocity anomalies from literature. At 3 Hz, the anomalous albedo, the forward modelling, and the results of the tomographic imaging confirm that shallow heterogeneity beneath the extended 1980 debris-avalanche and crater enhance anomalous intermediate and late coda phases, mapping shallow geological contrasts. We remark the effect this may have on coda-dependent source inversion and tomography, currently used across the world to image and monitor volcanoes. At Mount St Helens, higher frequencies and deep borehole data are necessary to reconstruct deep volcanic structures with coda waves.
    Description: Scottish Alliance for Geosciences Environment and Society and the Kleinman Grant for Volcano Research
    Description: Published
    Description: 169-188
    Description: 1T. Struttura della Terra
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: 3IT. Calcolo scientifico
    Description: JCR Journal
    Keywords: NorthAmerica ; Wave scattering and diffraction. ; Codawaves ; Seismicattenuation ; Seismic tomography ; Volcano seismology ; 04.06. Seismology
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  • 25
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    Methodology to identify the reference rock sites in regions of medium-to-high seismicity: an application in Central Italy (2021)
    Oxford University Press
    Details
    Publication Date: 2023-11-14
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2020. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved.
    Description: To evaluate the site response using both empirical approaches (e.g. standard spectral ratio, ground motion models (GMMs), generalized inversion techniques, etc.) and numerical 1-D/2-D analyses, the definition of the reference motion, that is the ground motion recorded at stations unaffected by site-effects due to topographic, stratigraphic or basin effects, is needed. The main objective of this work is to define a robust strategy to identify the seismic stations that can be considered as reference rock sites, using six proxies for the site response: three proxies are related to the analysis of geophysical and seismological data (the repeatable site term from the residual analysis, the resonance frequencies from horizontal-to-vertical spectral ratios on noise or earthquake signals, the average shear wave velocity in the first 30 m); the remaining ones concern geomorphological and installation features (outcropping rocks or stiff soils, flat topography and absence of interaction with structures). We introduce a weighting scheme to take into account the availability and the quality of the site information, as well as the fulfillment of the criterion associated to each proxy. We also introduce a hierarchical index, to take into account the relevance of the proposed proxies in the description of the site effects, and an acceptance threshold for reference rock sites identification. The procedure is applied on a very large data set, composed by accelerometric and velocimetric waveforms, recorded in Central Italy in the period 2008–2018. This data set is composed by more than 30 000 waveforms relative to 450 earthquakes in the magnitude range 3.2–6.5 and recorded by more than 450 stations. A total of 36 out of 133 candidate stations are identified as reference sites: the majority of them are installed on rock with flat topography, but this condition is not sufficient to guarantee the absence of amplifications, especially at high frequencies. Seismological analyses are necessary to exclude stations affected by resonances. We test the impact of using these sites by calibrating a GMMs. The results show that for reference rock sites the median predictions are reduced down to about 45 per cent at short periods in comparison to the generic rock motions.
    Description: Published
    Description: 2053–2067
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Arrival-angle effects on two-receiver measurements of phase velocity (2021)
    Oxford University Press
    Details
    Publication Date: 2023-11-14
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2020. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved.
    Description: We compile a data set of Rayleigh-wave phase velocities between pairs of stations, based on teleseismic events located on the same great circle as the two stations. We validate our observations against dispersion estimates based on ambient-noise cross correlations at the same station pairs. Discrepancies between the results of the two methods can in principle be explained by deviations in the wave propagation path between earthquake and receivers, due to lateral heterogeneity in the Earth’s structure, but the latter effect has, so far, not been precisely quantified nor corrected for. We implement an algorithm to measure the arrival angle of earthquake-generated surface waves and correct the dispersion measurements accordingly. Application to a data set from the Central-Western Mediterranean shows that the arrival-angle correction almost entirely accounts for the discrepancy in question, decreasing significantly the velocity bias for a wide range of periods.
    Description: Published
    Description: 1838–1844
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    3-D Q-coda attenuation structure at Mt. Etna (Italy) (2021)
    Oxford University Press
    Details
    Publication Date: 2023-11-16
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2021. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2021. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved.
    Description: Three dimensional attenuation images of Mt Etna volcano obtained by the analysis of Q-coda from local volcano-tectonic earthquakes are presented in this work. Seismic sources are confined inside the Etna structure with a maximum focal depth of 35 km below the sea level. The space distribution of the attenuation values was calculated by using 3-D weighting functions derived by the sensitivity kernels of Pacheco & Snieders and approximated by a polynomial interpolation, represented in the maps by using a backprojection method. Data were analyzed in four bands with central frequency placed at 1.5, 3, 6 and 12 Hz, respectively. We observed a frequency dependence of Q-coda with values that range from 55 at 1.5 Hz to 218 at 12 Hz. Q-coda space distribution in the Etna area shows almost uniformity in the average attenuation in the first 35 km below the surface. The images were derived with a resolution of 5 km. We observe as one of our main conclusions that Q-coda attenuation space anomalies are correlated with the areas of highest structural heterogeneities and are distributed along the well-known tectonic structures which characterize the crust in Mt Etna region. Previous and numerous velocity and attenuation images describing the structure of Mt Etna support our main conclusion: high Q-coda volumes almost coincide with the zones marked by high velocity and relative low total attenuation for direct waves.
    Description: Published
    Description: 544–558
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Source modelling and strong ground motion simulations for the 24 January 2020, Mw 6.8 Elazığ earthquake, Turkey (2021)
    Oxford University Press
    Details
    Publication Date: 2023-11-29
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2020. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved.
    Description: On 24 January 2020 an Mw 6.8 earthquake occurred at 20:55 local time (17:55 UTC) in eastern Turkey, close to the town of Sivrice in the Elazığ province, causing widespread considerable seismic damage in buildings. In this study, we analyse the main features of the rupture process and the seismic ground shaking during the Elazığ earthquake. We first use Interferometric Synthetic Aperture Radar (InSAR) interferograms (Sentinel-1 satellites) to constrain the fault geometry and the coseismic slip distribution of the causative fault segment. Then, we utilize this information to analyse the ground motion characteristics of the main shock in terms of peak ground acceleration (PGA), peak ground velocity (PGV) and spectral accelerations. The absence of seismic registrations in near-field for this earthquake imposes major constraints on the computation of seismic ground motion estimations in the study area. To do this, we have used a stochastic finite-fault simulation method to generate high-frequency ground motions synthetics for the Mw 6.8 Elazığ 2020 earthquake. Finally, we evaluate the potential state of stress of the unruptured portions of the causative fault segment as well as of adjacent segments, using the Coulomb stress failure function variations. Modelling of geodetic data shows that the 2020 Elazığ earthquake ruptured two major slip patches (for a total length of about 40 km) located along the Pütürge segment of the well-known left-lateral strike-slip East Anatolian Fault Zone (EAFZ), with up to 2.3 m of slip and an estimated geodetic moment of 1.70 × 1019 Nm (equivalent to a Mw 6.8). The position of the hypocentre supports the evidence of marked WSW rupture directivity during the main shock. In terms of ground motion characteristics, we observe that the high-frequency stochastic ground motion simulations have a good capability to reproduce the source complexity and capture the ground motion attenuation decay as a function of distance, up to the 200 km. We also demonstrate that the design spectra corresponding to 475 yr return period, provided by the new Turkish building code is not exceeded by the simulated seismograms in the epicentral area where there are no strong motion stations and no recordings available. Finally, based on the Coulomb stress distribution computation, we find that the Elazığ main shock increased the stress level of the westernmost part of the Pütürge fault and of the adjacent Palu segment and as a result of an off-fault lobe.
    Description: Published
    Description: 1054–1068
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Ontogeny of osmoregulation of the Asian shore crab Hemigrapsus sanguineus at an invaded site of Europe (2021)
    Oxford University Press
    In:  EPIC3Conservation Physiology, Oxford University Press, 9(1), ISSN: 2051-1434
    Details
    Publication Date: 2024-01-01
    Description: We studied the ontogeny of osmoregulation of the Asian shore crab Hemigrapsus sanguineus at an invaded area in the North Sea. H. sanguineus is native to Japan and China but has successfully invaded the Atlantic coast of North America and Europe. In the invaded areas, H. sanguineus is becoming a keystone species as driver of community structure and the adults compete with the shore crab Carcinus maenas. Strong osmoregulatory abilities may confer the potential to use and invade coastal areas already earlier in the life cycle. We reared larvae and first juveniles at 24°C in seawater from hatching to intermoult of each developmental stage (zoea I-V, megalopa, crab I). We exposed each stage to a range of salinities (0–39 ppt) for 24 h, and then we quantified haemolymph osmolality, using nano-osmometry. In addition, we quantified osmolality in field-collected adults after acclimation to the test salinities for 6 days. Larvae of H. sanguineus were able to hyper-osmoregulate at low salinities (15 and 20 ppt) over the complete larval development, although the capacity was reduced at the zoeal stage V; at higher salinities (25–39 ppt), all larval stages were osmoconformers. The capacity to slightly hypo-regulate at high salinity appeared in the first juvenile. Adults were able to hyper-osmoregulate at low salinities and hypo-regulate at concentrated seawater (39 ppt). H. sanguineus showed a strong capacity to osmoregulate as compared to its native competitor C. maenas, which only hyper-regulates at the first and last larval stages and does not hypo-regulate at the juvenile-adult stages. The capacity of H. sanguineus to osmoregulate over most of the life cycle should underpin the potential to invade empty niches in the coastal zone (characterized by low salinity and high temperatures). Osmoregulation abilities over the whole life cycle also constitute a strong competitive advantage over C. maenas.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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    Eccentric millisecond pulsars by resonant convection (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-26
    Description: Eccentric millisecond pulsars (eMSPs) with white dwarf companions exhibit orbital eccentricities orders of magnitude larger than predicted by turbulent convection in the white dwarfs’ red giant progenitors. The orbital periods of eMSPs cluster around P = 20–30 d, remarkably close to the red giant convective eddy turnover time teddy. We propose that the anomalously large eccentricities are resonantly driven by convective flows somehow made coherent when the turnover time matches the tidally locked red giant’s spin period, which is also the tidal forcing period. Numerical simulations of rotating red giants and magnetic field studies of stars show some evidence for especially ordered flow patterns when the convective Rossby number P/teddy is of order unity. We show that resonant convection boosts eccentricities by a factor of (tnuc/P)1/2 ≈ 3 × 103 over the random-walk values that characterize conventional MSPs, in good agreement with observations (tnuc is the giant’s nuclear burning time-scale). We also show how variations in the eddy turnover time arising from red giant metallicity variations can reproduce the observed effective width of the resonance, ΔP/P ≈ 0.4.
    Print ISSN: 1745-3925
    Electronic ISSN: 1745-3933
    Topics: Physics
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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    Genome-wide reconstruction of rediploidization following autopolyploidization across one hundred million years of salmonid evolution (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-28
    Description: The long-term evolutionary impacts of whole genome duplication (WGD) are strongly influenced by the ensuing rediploidization process. Following autopolyploidization, rediploidization involves a transition from tetraploid to diploid meiotic pairing, allowing duplicated genes (ohnologues) to diverge genetically and functionally. Our understanding of autopolyploid rediploidization has been informed by a WGD event ancestral to salmonid fishes, where large genomic regions are characterized by temporally delayed rediploidization, allowing lineage-specific ohnologue sequence divergence in the major salmonid clades. Here, we investigate the long-term outcomes of autopolyploid rediploidization at genome-wide resolution, exploiting a recent ‘explosion’ of salmonid genome assemblies, including a new genome sequence for the huchen (Hucho hucho). We developed a genome alignment approach to capture duplicated regions across multiple species, allowing us to create 121,864 phylogenetic trees describing genome-wide ohnologue divergence across salmonid evolution. Using molecular clock analysis, we show that 61% of the ancestral salmonid genome experienced an initial ‘wave’ of rediploidization in the late Cretaceous (85-106 Mya). This was followed by a period of relative genomic stasis lasting 17-39 My, where much of the genome remained tetraploid. A second rediploidization wave began in the early Eocene and proceeded alongside species diversification, generating predictable patterns of lineage-specific ohnologue divergence, scaling in complexity with the number of speciation events. Using gene set enrichment, gene expression, and codon-based selection analyses, we provide insights into potential functional outcomes of delayed rediploidization. This study enhances our understanding of delayed autopolyploid rediploidization and has broad implications for future studies of WGD events.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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    A birth-death-migration model for life in astrophysical environments (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-28
    Description: To assess the number of life-bearing worlds in astrophysical environments, it is necessary to take the intertwined processes of abiogenesis (birth), extinction (death), and transfer of life (migration) into account. We construct a mathematical model that incorporates this trio of mechanisms and accordingly derive the probability distribution function and other statistical properties (e.g. mean) for the number of worlds with biospheres. We show that a given astrophysical setting may become eventually saturated with life if the rate of successful transfers of organisms is higher than the extinction rate of biospheres. Based on the available data, we suggest that this criterion might be fulfilled for star-forming clusters (and perhaps the Galactic bulge under optimal circumstances), thereby indicating that such regions could constitute promising abodes for hosting and detecting life.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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    Ram pressure candidates in UNIONS (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-28
    Description: We present a search for disturbed, candidate ram pressure stripping galaxies across more than 50 spectroscopically selected SDSS groups and clusters. Forty-eight ram pressure candidates are visually identified in these systems using high quality UNIONS imaging from the Canada-France Hawaii Telescope, covering ∼6200 deg2 and ∼2800 deg2 in the u- and r-bands respectively. Ram pressure candidates are found in groups and clusters spanning a wide range in halo mass and include ∼30 ram pressure candidates in the group regime (Mh 〈 1014). The observed frequency of ram pressure candidates shows substantial scatter with group/cluster mass, but on average is larger in clusters (Mh ≥ 1014 M⊙) than groups (Mh 〈 1014 M⊙) by a factor of ∼2. We find that ram pressure candidates are most commonly low-mass galaxies and have enhanced star formation rates relative to star-forming field galaxies. The enhancement in star formation is largely independent of galaxy mass and strongest for galaxies in clusters. As a result of the large survey footprint and excellent image quality from UNIONS, we are able to identify disturbed galaxies, potentially affected by ram pressure stripping, across a wide range of host environment.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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    AstroSat observations of Long-duration X-ray superflares on active M-dwarf binary EQ Peg (2021)
    Oxford University Press
    Details
    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
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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    Links between foreland rheology and the growth and evolution of a young mountain belt in New Guinea (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-28
    Description: Summary We have studied the active and recent tectonics of New Guinea, using earthquake source modelling, analysis of gravity anomalies, seismic reflection profiles, and thermal and mechanical models. Our aim is to investigate the behaviour and evolution of a young continental deformation belt, and to explore the effects of lateral variations in foreland rheology on the deformation. We find that along-strike gradients in the lithosphere thickness of the southern foreland have resulted in correlated changes in seismogenic thickness, likely due to the effects on the temperature structure of the crust. The resulting variation in the strength of the foreland means that in the east, the foreland is broken through on thrust faults, whereas in the west it is relatively intact. The lack of correlation between the elevation of the mountain belt and the seismogenic thickness of the foreland is likely to be due to the time taken to thicken the crust in the mountains following changes in the rheology of the underthrusting foreland, as the thinned passive margin of northern Australia is consumed. The along-strike variation in whether the force exerted between the mountains and the lowlands is able to break the foreland crust enables us to estimate the effective coefficient of friction on foreland faults to be in the range of 0.01-0.28. We use force-balance calculations to show that the recent tectonic re-organisation in western New Guinea is likely to be due to the development of increasing curvature in the Banda Arc, and that the impingement of continental material on the subduction zone may explain the unusually low force it exerts on western New Guinea.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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    The Eukaryotic Linear Motif resource: 2022 release (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-29
    Description: Almost twenty years after its initial release, the Eukaryotic Linear Motif (ELM) resource remains an invaluable source of information for the study of motif-mediated protein-protein interactions. ELM provides a comprehensive, regularly updated and well-organised repository of manually curated, experimentally validated short linear motifs (SLiMs). An increasing number of SLiM-mediated interactions are discovered each year and keeping the resource up-to-date continues to be a great challenge. In the current update, 30 novel motif classes have been added and five existing classes have undergone major revisions. The update includes 411 new motif instances mostly focused on cell-cycle regulation, control of the actin cytoskeleton, membrane remodelling and vesicle trafficking pathways, liquid-liquid phase separation and integrin signalling. Many of the newly annotated motif-mediated interactions are targets of pathogenic motif mimicry by viral, bacterial or eukaryotic pathogens, providing invaluable insights into the molecular mechanisms underlying infectious diseases. The current ELM release includes 317 motif classes incorporating 3934 individual motif instances manually curated from 3867 scientific publications. ELM is available at: http://elm.eu.org.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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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
    Details
    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.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
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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
    Details
    Publication Date: 2021-10-28
    Description: Pathogenic variants that disrupt human mitochondrial protein synthesis are associated with a clinically heterogenous group of diseases. Despite an impairment in oxidative phosphorylation being a common phenotype, the underlying molecular pathogenesis is more complex than simply a bioenergetic deficiency. Currently, we have limited mechanistic understanding on the scope by which a primary defect in mitochondrial protein synthesis contributes to organelle dysfunction. Since the proteins encoded in the mitochondrial genome are hydrophobic and need co-translational insertion into a lipid bilayer, responsive quality control mechanisms are required to resolve aberrations that arise with the synthesis of truncated and misfolded proteins. Here, we show that defects in the OXA1L-mediated insertion of MT-ATP6 nascent chains into the mitochondrial inner membrane are rapidly resolved by the AFG3L2 protease complex. Using pathogenic MT-ATP6 variants, we then reveal discrete steps in this quality control mechanism and the differential functional consequences to mitochondrial gene expression. The inherent ability of a given cell type to recognize and resolve impairments in mitochondrial protein synthesis may in part contribute at the molecular level to the wide clinical spectrum of these disorders.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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    CoCoPRED: coiled-coil protein structural feature prediction from amino acid sequence using deep neural networks (2021)
    Oxford University Press
    Details
    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.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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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
    Details
    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.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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    Two newly identified eclipsing binaries in open cluster NGC 3532 (2021)
    Oxford University Press
    Details
    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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    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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    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
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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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.
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    Topics: Biology , Computer Science , 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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    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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    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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    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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    Spectropolarimetry of the Type Ia SN 2019ein rules out significant global asphericity of the ejecta (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: Detailed spectropolarimetric studies may hold the key to probing the explosion mechanisms and the progenitor scenarios of Type Ia supernovae (SNe Ia). We present multi-epoch spectropolarimetry and imaging polarimetry of SN 2019ein, an SN Ia showing high expansion velocities at early phases. The spectropolarimetry sequence spans from ∼−11 to +10 days relative to peak brightness in the B-band. We find that the level of the continuum polarization of SN 2019ein, after subtracting estimated interstellar polarization, is in the range 0.0–0.3%, typical for SNe Ia. The polarization position angle remains roughly constant before and after the SN light-curve peak, implying that the inner regions share the same axisymmetry as the outer layers. We observe high polarization ($sim 1\%$) across both the Si ii λ6355 and Ca ii near-infrared triplet features. These two lines also display complex polarization modulations. The spectropolarimetric properties of SN 2019ein rule out a significant departure from spherical symmetry of the ejecta for up to a month after the explosion. These observations disfavour merger-induced and double-detonation models for SN 2019ein. The imaging polarimetry shows weak evidence for a modest increase in polarization after ∼20 days since the B-band maximum. If this rise is real and is observed in other SNe Ia at similar phases, we may have seen, for the first time, an aspherical interior similar to what has been previously observed for SNe IIP. Future polarization observations of SNe Ia extending to post-peak epochs will help to examine the inner structure of the explosion.
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    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.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
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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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    Noncoding Variation and Transcriptional Plasticity Promote Thermal Adaptation in Oysters by Altering Energy Metabolism (2021)
    Oxford University Press
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    Publication Date: 2021-08-15
    Description: Genetic variation and phenotypic plasticity are both important to adaptive evolution. However, how they act together on particular traits remains poorly understood. Here, we integrated phenotypic, genomic, and transcriptomic data from two allopatric but closely related congeneric oyster species, Crassostrea angulata from southern/warm environments and Crassostrea gigas from northern/cold environments, to investigate the roles of genetic divergence and plasticity in thermal adaptation. Reciprocal transplantation experiments showed that both species had higher fitness in their native habitats than in nonnative environments, indicating strong adaptive divergence. The southern species evolved higher transcriptional plasticity, and the plasticity was adaptive, suggesting that increased plasticity is important for thermal adaptation to warm climates. Genome-wide comparisons between the two species revealed that genes under selection tended to respond to environmental changes and showed higher sequence divergence in noncoding regions. All genes under selection and related to energy metabolism exhibited habitat-specific expression with genes involved in ATP production and lipid catabolism highly expressed in warm/southern habitats, and genes involved in ATP consumption and lipid synthesis were highly expressed in cold/northern habitats. The gene for acyl-CoA desaturase, a key enzyme for lipid synthesis, showed strong selective sweep in the upstream noncoding region and lower transcription in the southern species. These results were further supported by the lower free fatty acid (FFA) but higher ATP content in southern species and habitat, pointing to significance of ATP/FFA trade-off. Our findings provide evidence that noncoding variation and transcriptional plasticity play important roles in shaping energy metabolism for thermal adaptation in oysters.
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    The Chicken Pan-Genome Reveals Gene Content Variation and a Promoter Region Deletion in IGF2BP1 Affecting Body Size (2021)
    Oxford University Press
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    Publication Date: 2021-07-30
    Description: Domestication and breeding have reshaped the genomic architecture of chicken, but the retention and loss of genomic elements during these evolutionary processes remain unclear. We present the first chicken pan-genome constructed using 664 individuals, which identified an additional approximately 66.5-Mb sequences that are absent from the reference genome (GRCg6a). The constructed pan-genome encoded 20,491 predicated protein-coding genes, of which higher expression levels are observed in conserved genes relative to dispensable genes. Presence/absence variation (PAV) analyses demonstrated that gene PAV in chicken was shaped by selection, genetic drift, and hybridization. PAV-based genome-wide association studies identified numerous candidate mutations related to growth, carcass composition, meat quality, or physiological traits. Among them, a deletion in the promoter region of IGF2BP1 affecting chicken body size is reported, which is supported by functional studies and extra samples. This is the first time to report the causal variant of chicken body size quantitative trait locus located at chromosome 27 which was repeatedly reported. Therefore, the chicken pan-genome is a useful resource for biological discovery and breeding. It improves our understanding of chicken genome diversity and provides materials to unveil the evolution history of chicken domestication.
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    Learning Representation From Concurrence-Words Graph For Aspect Sentiment Classification (2021)
    Oxford University Press
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    Publication Date: 2021-07-01
    Description: Aspect sentiment classification is an important research topic in natural language processing and computational linguistics, assisting in automatically review analysis and emotional tendency judgement. Different from extant methods that focus on text sequence representations, this paper presents a network framework to learn representation from concurrence-words relation graph (LRCWG), so as to improve the Macro-F1 and accuracy. The LRCWG first employs the multi-head attention mechanism to capture the sentiment representation from the sentences which can learn the importance of text sequence representation. And then, it leverages the priori sentiment dictionary information to construct the concurrence relations of sentiment words with Graph Convolution Network (GCN). This assists in that the learnt context representation can keep both the semantics integrity and the features of sentiment concurrence-words relations. The designed algorithm is experimentally evaluated with all the five benchmark datasets and demonstrated that the proposed aspect sentiment classification can significantly improve the prediction performance of learning task.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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    An Ancient Clade of Penelope-Like Retroelements with Permuted Domains Is Present in the Green Lineage and Protists, and Dominates Many Invertebrate Genomes (2021)
    Oxford University Press
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    Publication Date: 2021-07-28
    Description: Penelope-like elements (PLEs) are an enigmatic clade of retrotransposons whose reverse transcriptases (RTs) share a most recent common ancestor with telomerase RTs. The single ORF of canonical endonuclease (EN)+ PLEs encodes RT and a C-terminal GIY–YIG EN that enables intrachromosomal integration, whereas EN− PLEs lack EN and are generally restricted to chromosome termini. EN+ PLEs have only been found in animals, except for one case of horizontal transfer to conifers, whereas EN− PLEs occur in several kingdoms. Here, we report a new, deep-branching PLE clade with a permuted domain order, whereby an N-terminal GIY–YIG EN is linked to a C-terminal RT by a short domain with a characteristic CxC motif. These N-terminal EN+ PLEs share a structural organization, including pseudo-LTRs and complex tandem/inverted insertions, with canonical EN+ PLEs from Penelope/Poseidon, Neptune, and Nematis clades, and show insertion bias for microsatellites, but lack canonical hammerhead ribozyme motifs. However, their phylogenetic distribution is much broader. The Naiads, found in numerous invertebrate phyla, can reach tens of thousands of copies per genome. In spiders and clams, Naiads independently evolved to encode selenoproteins containing multiple selenocysteines. Chlamys, which lack the CCHH motif universal to PLE ENs, occur in green algae, spike mosses (targeting ribosomal DNA), and slime molds. Unlike canonical PLEs, RTs of N-terminal EN+ PLEs contain the insertion-in-fingers domain (IFD), strengthening the link between PLEs and telomerases. Additionally, we describe Hydra, a novel metazoan C-terminal EN+ clade. Overall, we conclude that PLE diversity, taxonomic distribution, and abundance are comparable with non-LTR and LTR-retrotransposons.
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    Endogenous Retroviruses Drive Lineage-Specific Regulatory Evolution across Primate and Rodent Placentae (2021)
    Oxford University Press
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    Publication Date: 2021-07-28
    Description: In mammals, the placenta mediates maternal–fetal nutrient and waste exchange and acts in an immunomodulatory way to facilitate maternal–fetal tolerance. The placenta is highly diverse across mammalian species, yet the molecular mechanisms that distinguish the placenta of human from other mammals are not fully understood. Using an interspecies transcriptomic comparison of human, macaque, and mouse late-gestation placentae, we identified hundreds of genes with lineage-specific expression—including dozens that are placentally enriched and potentially related to pregnancy. We further annotated the enhancers for different human tissues using epigenomic data and demonstrate that the placenta and chorion are unique in that their enhancers display the least conservation. We identified numerous lineage-specific human placental enhancers and found they highly overlap with specific families of endogenous retroviruses (ERVs), including MER21A, MER41A/B, and MER39B that were previously linked to immune response and placental function. Among these ERV families, we further demonstrate that MER41A/B insertions create dozens of lineage-specific serum response factor-binding loci in human, including one adjacent to FBN2, a placenta-specific gene with increased expression in humans that produces the peptide hormone placensin to stimulate glucose secretion and trophoblast invasion. Overall, our results demonstrate the prevalence of lineage-specific placental enhancers which are frequently associated with ERV insertions and likely facilitate the lineage-specific evolution of the mammalian placenta.
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    Two Reference-Quality Sea Snake Genomes Reveal Their Divergent Evolution of Adaptive Traits and Venom Systems (2021)
    Oxford University Press
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    Publication Date: 2021-07-28
    Description: True sea snakes (Hydrophiini) are among the last and most successful clades of vertebrates that show secondary marine adaptation, exhibiting diverse phenotypic traits and lethal venom systems. To better understand their evolution, we generated the first chromosome-level genomes of two representative Hydrophiini snakes, Hydrophis cyanocinctus and H. curtus. Through comparative genomics we identified a great expansion of the underwater olfaction-related V2R gene family, consisting of more than 1,000 copies in both snakes. A series of chromosome rearrangements and genomic structural variations were recognized, including large inversions longer than 30 megabase (Mb) on sex chromosomes which potentially affect key functional genes associated with differentiated phenotypes between the two species. By integrating multiomics we found a significant loss of the major weapon for elapid predation, three-finger toxin genes, which displayed a dosage effect in H. curtus. These genetic changes may imply mechanisms that drove the divergent evolution of adaptive traits including prey preferences between the two closely related snakes. Our reference-quality sea snake genomes also enrich the repositories for addressing important issues on the evolution of marine tetrapods, and provide a resource for discovering marine-derived biological products.
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    Evolution of Renal-Disease Factor APOL1 Results in Cis and Trans Orientations at the Endoplasmic Reticulum That Both Show Cytotoxic Effects (2021)
    Oxford University Press
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    Publication Date: 2021-07-29
    Description: The recent and exclusively in humans and a few other higher primates expressed APOL1 (apolipoprotein L1) gene is linked to African human trypanosomiasis (also known as African sleeping sickness) as well as to different forms of kidney diseases. Whereas APOL1’s role as a trypanolytic factor is well established, pathobiological mechanisms explaining its cytotoxicity in renal cells remain unclear. In this study, we compared the APOL family members using a combination of evolutionary studies and cell biological experiments to detect unique features causal for APOL1 nephrotoxic effects. We investigated available primate and mouse genome and transcriptome data to apply comparative phylogenetic and maximum likelihood selection analyses. We suggest that the APOL gene family evolved early in vertebrates and initial splitting occurred in ancestral mammals. Diversification and differentiation of functional domains continued in primates, including developing the two members APOL1 and APOL2. Their close relationship could be diagnosed by sequence similarity and a shared ancestral insertion of an AluY transposable element. Live-cell imaging analyses showed that both expressed proteins show a strong preference to localize at the endoplasmic reticulum (ER). However, glycosylation and secretion assays revealed that—unlike APOL2—APOL1 membrane insertion or association occurs in different orientations at the ER, with the disease-associated mutants facing either the luminal (cis) or cytoplasmic (trans) side of the ER. The various pools of APOL1 at the ER offer a novel perspective in explaining the broad spectrum of its observed toxic effects.
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    Novel Doublesex Duplication Associated with Sexually Dimorphic Development of Dogface Butterfly Wings (2021)
    Oxford University Press
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    Publication Date: 2021-07-29
    Description: Sexually dimorphic development is responsible for some of the most remarkable phenotypic variation found in nature. Alternative splicing of the transcription factor gene doublesex (dsx) is a highly conserved developmental switch controlling the expression of sex-specific pathways. Here, we leverage sex-specific differences in butterfly wing color pattern to characterize the genetic basis of sexually dimorphic development. We use RNA-seq, immunolocalization, and motif binding site analysis to test specific predictions about the role of dsx in the development of structurally based ultraviolet (UV) wing patterns in Zerene cesonia (Southern Dogface). Unexpectedly, we discover a novel duplication of dsx that shows a sex-specific burst of expression associated with the sexually dimorphic UV coloration. The derived copy consists of a single exon that encodes a DNA binding but no protein-binding domain and has experienced rapid amino-acid divergence. We propose the novel dsx paralog may suppress UV scale differentiation in females, which is supported by an excess of Dsx-binding sites at cytoskeletal and chitin-related genes with sex-biased expression. These findings illustrate the molecular flexibility of the dsx gene in mediating the differentiation of secondary sexual characteristics.
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    Five centuries of cod catches in Eastern Canada (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-28
    Description: The fishery for Northern Atlantic cod (Gadus morhua) off Newfoundland and Labrador, Eastern Canada, presents the most spectacular case of an exploited stock crashed in a few decades by an industrial bottom trawl fishery under a seemingly sophisticated management regime after half a millennium of sustainable fishing. The fishery, which had generated annual catches of 100000 to 200000 tonnes from the beginning of the 16th century to the 1950s,  peaked in 1968 at 810000 tonnes, followed by a devastating collapse and closure 24 years later. Since then, stock recovery may have been hindered by premature openings, with vessels targeting the remains of the cod population. Previous research paid little attention towards using multicentury time series to inform sustainable catches and recovery plans. Here, we show that a simple stock assessment model can be used to model the cod population trajectory for the entire period from 1508 to 2019 for which catch estimates are available. The model suggests that if fishing effort and mortality had been stabilized in the 1980s,  precautionary annual yields of about 200000 tonnes could have been sustained. Our analysis demonstrates the value of incorporating prior knowledge to counteract shifting baseline effects on reference points and contemporary perceptions of historical stock status.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press on behalf of International Council for the Exploration of the Sea.
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    Onshore biological sampling of landings by species and size category within auction sites can be more efficient than trip-based concurrent sampling (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-13
    Description: Since 1996, the European Union has required that fishery products of 35 fish species or groups of species, including crustaceans and cephalopods, be graded before being landed on the basis of commercial size-categories. A multi-stage sampling scheme to estimate catch-at-length and catch-at-age compositions of total annual landings has been conducted in Portuguese waters since 2009. All species and their size-categories are sampled concurrently from random trips within representatively selected site-days annually. In an effort to improve cost-efficiency of the biological catch sampling of commercial landings in Portugal, a size- category sampling scheme was tested during 2017, taking advantage of the stratification of horse mackerel landings, induced by the mandatory grading of landings by size-category. The total number of site-days (primary sampling units), fish boxes sampled, and specimens of horse mackerel sampled for length and age across strata during the pilot study were 30%, 57%, and 12% of the sampling carried out under the standard concurrent scheme, respectively. The assignment of horse mackerel length to the six commercial size-categories was highly consistent across site-days. Our study shows that the concurrent sampling, where trips are subsampled within site-days, could miss some size-categories by chance, resulting in poor estimates of catch-at-length especially for small fish present at the market during a site-day. The size-category sampling scheme ensured subsamples of fish from all size-categories within a site-day, and achieved data on catch-at-age that are fit-for purpose at 24% of the total cost for the standard concurrent sampling. The effect of sampling designs and sample sizes on horse mackerel stock assessment outputs showed that the onshore biological sampling to estimate catch-at-age compositions for stock assessment is optimized with the size-category sampling scheme. Pilot field experiments should be carried out for selected species that evidence consistent size grading among commercial categories.
    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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    Are glyphosate‐resistant weeds a threat to conservation agriculture? Evidence from tillage practices in soybeans (2021)
    Oxford University Press
    Details
    Publication Date: 2021-06-15
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
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    Monitoring Insect Transposable Elements in Large Double-Stranded DNA Viruses Reveals Host-to-Virus and Virus-to-Virus Transposition (2021)
    Oxford University Press
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    Publication Date: 2021-06-30
    Description: The mechanisms by which transposable elements (TEs) can be horizontally transferred between animals are unknown, but viruses are possible candidate vectors. Here, we surveyed the presence of host-derived TEs in viral genomes in 35 deep sequencing data sets produced from 11 host–virus systems, encompassing nine arthropod host species (five lepidopterans, two dipterans, and two crustaceans) and six different double-stranded (ds) DNA viruses (four baculoviruses and two iridoviruses). We found evidence of viral-borne TEs in 14 data sets, with frequencies of viral genomes carrying a TE ranging from 0.01% to 26.33% for baculoviruses and from 0.45% to 7.36% for iridoviruses. The analysis of viral populations separated by a single replication cycle revealed that viral-borne TEs originating from an initial host species can be retrieved after viral replication in another host species, sometimes at higher frequencies. Furthermore, we detected a strong increase in the number of integrations in a viral population for a TE absent from the hosts’ genomes, indicating that this TE has undergone intense transposition within the viral population. Finally, we provide evidence that many TEs found integrated in viral genomes (15/41) have been horizontally transferred in insects. Altogether, our results indicate that multiple large dsDNA viruses have the capacity to shuttle TEs in insects and they underline the potential of viruses to act as vectors of horizontal transfer of TEs. Furthermore, the finding that TEs can transpose between viral genomes of a viral species sets viruses as possible new niches in which TEs can persist and evolve.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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    Whole-Genome Duplication Facilitated the Evolution of C4 Photosynthesis in Gynandropsis gynandra (2021)
    Oxford University Press
    Details
    Publication Date: 2021-06-30
    Description: In higher plants, whole-genome duplication (WGD) is thought to facilitate the evolution of C4 photosynthesis from C3 photosynthesis. To understand this issue, we used new and existing leaf-development transcriptomes to construct two coding sequence databases for C4Gynandropsis gynandra and C3Tarenaya hassleriana, which shared a WGD before their divergence. We compared duplicated genes in the two species and found that the WGD contributed to four aspects of the evolution of C4 photosynthesis in G. gynandra. First, G. gynandra has retained the duplicates of ALAAT (alanine aminotransferase) and GOGAT (glutamine oxoglutarate aminotransferase) for nitrogen recycling to establish a photorespiratory CO2 pump in bundle sheath (BS) cells for increasing photosynthesis efficiency, suggesting that G. gynandra experienced a C3–C4 intermediate stage during the C4 evolution. Second, G. gynandra has retained almost all known vein-development-related paralogous genes derived from the WGD event, likely contributing to the high vein complexity of G. gynandra. Third, the WGD facilitated the evolution of C4 enzyme genes and their recruitment into the C4 pathway. Fourth, several genes encoding photosystem I proteins were derived from the WGD and are upregulated in G. gynandra, likely enabling the NADH dehydrogenase-like complex to produce extra ATPs for the C4 CO2 concentration mechanism. Thus, the WGD apparently played an enabler role in the evolution of C4 photosynthesis in G. gynandra. Importantly, an ALAAT duplicate became highly expressed in BS cells in G. gynandra, facilitating nitrogen recycling and transition to the C4 cycle. This study revealed how WDG may facilitate C4 photosynthesis evolution.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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    MeerKAT-64 discovers wide-spread tidal debris in the nearby NGC 7232 galaxy group (2021)
    Oxford University Press
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    Publication Date: 2021-06-02
    Description: We report the discovery of large amounts of previously undetected cold neutral atomic hydrogen (H i) around the core triplet galaxies in the nearby NGC 7232 galaxy group with MeerKAT. With a physical resolution of ∼1 kpc, we detect a complex web of low-surface-brightness H i emission down to a 4σ column density level of ∼1 × 1019 cm−2 (over 44  km s−1). The newly discovered H i streams extend over ∼20 arcmin corresponding to 140 kpc in projection. This is approximately three times the H i extent of the galaxy triplet (52 kpc). The H i debris has an H i mass of ∼6.6 × 109 M⊙, more than 50 per cent of the total H i mass of the triplet. Within the galaxy triplet, NGC 7233 and NGC 7232 have lost a significant amount of H i while NGC 7232B appears to have an excess of H i. The H i deficiency in NGC 7232 and NGC 7233 indicates that galaxy–galaxy interaction in the group concentrates on this galaxy pair while the other disc galaxies have visited them over time. In comparison to the AMIGA sample of isolated galaxies, we find that with regards to its total H i mass the NGC 7232/3 galaxy triplet is not H i-deficient. Despite the many interactions associated to the triplet galaxies, no H i seems to have been lost from the group (yet).
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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    An Optimized k-means Algorithm Based on Information Entropy (2021)
    Oxford University Press
    Details
    Publication Date: 2021-06-04
    Description: Clustering is a widely used technique in data mining applications and various pattern recognition applications, in which data objects are divided into groups. K-means algorithm is one of the most classical clustering algorithms. In this algorithm, the initial clustering centers are randomly selected, this results in unstable clustering results. To solve this problem, an optimized algorithm to select the initial centers is proposed. In the proposed algorithm, dispersion degree is defined, which is based on entropy. In the algorithm, all the objects are firstly grouped into a big cluster, and the object that has the maximum dispersion degree and the object that has the minimum dispersion degree are selected as the initial clustering centers from the initial big cluster. And then other objects in the biggest cluster are partitioned to the initial clusters to which the objects are nearest. The partition process will be repeated until the cluster number is equal to the specified value k. Finally, the partitioned k clusters and their cluster centers are applied to k-means algorithm as initial clusters and centers. Several experiments are conducted on real data sets to evaluate the proposed algorithm. The proposed algorithm is compared with traditional k-means algorithm and max-min distance clustering algorithm, and experimental results show that the improved k-means algorithm is stable in selecting initial clustering, because it can select unique initial clustering centers. The optimized algorithm’s effectiveness and feasibility are also verified by experiments, and the algorithm can reduce the times of iterations and has more stable clustering results and higher accuracy.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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    Analysis of Genomic DNA from Medieval Plague Victims Suggests Long-Term Effect of Yersinia pestis on Human Immunity Genes (2021)
    Oxford University Press
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    Publication Date: 2021-05-18
    Description: Pathogens and associated outbreaks of infectious disease exert selective pressure on human populations, and any changes in allele frequencies that result may be especially evident for genes involved in immunity. In this regard, the 1346-1353 Yersinia pestis-caused Black Death pandemic, with continued plague outbreaks spanning several hundred years, is one of the most devastating recorded in human history. To investigate the potential impact of Y. pestis on human immunity genes, we extracted DNA from 36 plague victims buried in a mass grave in Ellwangen, Germany in the 16th century. We targeted 488 immune-related genes, including HLA, using a novel in-solution hybridization capture approach. In comparison with 50 modern native inhabitants of Ellwangen, we find differences in allele frequencies for variants of the innate immunity proteins Ficolin-2 and NLRP14 at sites involved in determining specificity. We also observed that HLA-DRB1*13 is more than twice as frequent in the modern population, whereas HLA-B alleles encoding an isoleucine at position 80 (I-80+), HLA C*06:02 and HLA-DPB1 alleles encoding histidine at position 9 are half as frequent in the modern population. Simulations show that natural selection has likely driven these allele frequency changes. Thus, our data suggest that allele frequencies of HLA genes involved in innate and adaptive immunity responsible for extracellular and intracellular responses to pathogenic bacteria, such as Y. pestis, could have been affected by the historical epidemics that occurred in Europe.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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    HyRAD-X Exome Capture Museomics Unravels Giant Ground Beetle Evolution (2021)
    Oxford University Press
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    Publication Date: 2021-05-14
    Description: Advances in phylogenomics contribute toward resolving long-standing evolutionary questions. Notwithstanding, genetic diversity contained within more than a billion biological specimens deposited in natural history museums remains recalcitrant to analysis owing to challenges posed by its intrinsically degraded nature. Yet that tantalizing resource could be critical in overcoming taxon sampling constraints hindering our ability to address major evolutionary questions. We addressed this impediment by developing phyloHyRAD, a new bioinformatic pipeline enabling locus recovery at a broad evolutionary scale from HyRAD-X exome capture of museum specimens of low DNA integrity using a benchtop RAD-derived exome-complexity-reduction probe set developed from high DNA integrity specimens. Our new pipeline can also successfully align raw RNAseq transcriptomic and ultraconserved element reads with the RAD-derived probe catalog. Using this method, we generated a robust timetree for Carabinae beetles, the lack of which had precluded study of macroevolutionary trends pertaining to their biogeography and wing-morphology evolution. We successfully recovered up to 2,945 loci with a mean of 1,788 loci across the exome of specimens of varying age. Coverage was not significantly linked to specimen age, demonstrating the wide exploitability of museum specimens. We also recovered fragmentary mitogenomes compatible with Sanger-sequenced mtDNA. Our phylogenomic timetree revealed a Lower Cretaceous origin for crown group Carabinae, with the extinct Aplothorax Waterhouse, 1841 nested within the genus Calosoma Weber, 1801 demonstrating the junior synonymy of Aplothorax syn. nov., resulting in the new combination Calosomaburchellii (Waterhouse, 1841) comb. nov. This study compellingly illustrates that HyRAD-X and phyloHyRAD efficiently provide genomic-level data sets informative at deep evolutionary scales.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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    Adaptive Laplacian Support Vector Machine for Semi-supervised Learning (2021)
    Oxford University Press
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    Publication Date: 2021-04-30
    Description: Laplacian support vector machine (LapSVM) is an extremely popular classification method and relies on a small number of labels and a Laplacian regularization to complete the training of the support vector machine (SVM). However, the training of SVM model and Laplacian matrix construction are usually two independent process. Therefore, In this paper, we propose a new adaptive LapSVM method to realize semi-supervised learning with a primal solution. Specifically, the hinge loss of unlabelled data is considered to maximize the distance between unlabelled samples from different classes and the process of dealing with labelled data are similar to other LapSVM methods. Besides, the proposed method embeds the Laplacian matrix acquisition into the SVM training process to improve the effectiveness of Laplacian matrix and the accuracy of new SVM model. Moreover, a novel optimization algorithm considering primal solver is proposed to our adaptive LapSVM model. Experimental results showed that our method outperformed all comparison methods in terms of different evaluation metrics on both real datasets and synthetic datasets.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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    Global and Local Structure Preservation for Nonlinear High-dimensional Spectral Clustering (2021)
    Oxford University Press
    Details
    Publication Date: 2021-05-14
    Description: Spectral clustering is widely applied in real applications, as it utilizes a graph matrix to consider the similarity relationship of subjects. The quality of graph structure is usually important to the robustness of the clustering task. However, existing spectral clustering methods consider either the local structure or the global structure, which can not provide comprehensive information for clustering tasks. Moreover, previous clustering methods only consider the simple similarity relationship, which may not output the optimal clustering performance. To solve these problems, we propose a novel clustering method considering both the local structure and the global structure for conducting nonlinear clustering. Specifically, our proposed method simultaneously considers (i) preserving the local structure and the global structure of subjects to provide comprehensive information for clustering tasks, (ii) exploring the nonlinear similarity relationship to capture the complex and inherent correlation of subjects and (iii) embedding dimensionality reduction techniques and a low-rank constraint in the framework of adaptive graph learning to reduce clustering biases. These constraints are considered in a unified optimization framework to result in one-step clustering. Experimental results on real data sets demonstrate that our method achieved competitive clustering performance in comparison with state-of-the-art clustering methods.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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    BAli-Phy version 3: model-based co-estimation of alignment and phylogeny (2021)
    Oxford University Press
    Details
    Publication Date: 2021-03-02
    Description: Summary We describe improvements to BAli-Phy, a Markov chain Monte Carlo (MCMC) program that jointly estimates phylogeny, alignment and other parameters from unaligned sequence data. Version 3 is substantially faster for large trees, and implements covarion models, additional codon models and other new models. It implements ancestral state reconstruction, allows prior selection for all model parameters, and can also analyze multiple genes simultaneously. Availability and implementation Software is available for download at http://www.bali-phy.org. C++ source code is freely available on Github under the GPL2 License. Supplementary information Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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    The biology of thermoacidophilic archaea from the order Sulfolobales (2021)
    Oxford University Press
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    Publication Date: 2021-01-21
    Description: Thermoacidophilic archaea belonging to the order Sulfolobales thrive in extreme biotopes, such as sulfuric hot springs and ore deposits. These microorganisms have been model systems for understanding life in extreme environments, as well as for probing the evolution of both molecular genetic processes and central metabolic pathways. Thermoacidophiles, such as the Sulfolobales, use typical microbial responses to persist in hot acid (e.g. motility, stress response, biofilm formation), albeit with some unusual twists. They also exhibit unique physiological features, including iron and sulfur chemolithoautotrophy, that differentiate them from much of the microbial world. Although first discovered 〉50 years ago, it was not until recently that genome sequence data and facile genetic tools have been developed for species in the Sulfolobales. These advances have not only opened up ways to further probe novel features of these microbes but also paved the way for their potential biotechnological applications. Discussed here are the nuances of the thermoacidophilic lifestyle of the Sulfolobales, including their evolutionary placement, cell biology, survival strategies, genetic tools, metabolic processes and physiological attributes together with how these characteristics make thermoacidophiles ideal platforms for specialized industrial processes.
    Print ISSN: 0168-6445
    Electronic ISSN: 1574-6976
    Topics: Biology
    Published by Oxford University Press on behalf of Federation of European Microbiological Societies.
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    An analysis of core-mantle boundary Stoneley mode sensitivity and sources of uncertainty (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: Summary Stoneley modes are a special subset of normal modes whose energy is confined along the core-mantle boundary. As such, they offer a unique glimpse into Earth structure at the base of the mantle. They are often observed through coupling with mantle modes due to rotation, ellipticity and lateral heterogeneity, though they can be detected without such coupling. In this study, we explore the relative sensitivities of seismic spectra of two low-frequency Stoneley modes to several factors, taking as reference the fully coupled computation up to 3 mHz in model S20RTS. The factors considered are (i) theoretical, by exploring the extent to which various coupling approximations can accurately reproduce reference spectra; and (ii) model-based, by exploring how various Earth parameters such as core-mantle boundary topography, attenuation, and S-wave and P-wave structures, and the seismic source solution may influence the spectra. We find that mode-pair coupling is insufficiently accurate, but coupling modes within a range of ±0.1 mHz produces acceptable spectra, compared to full coupling. This has important implications for splitting function measurements, which are computed under the assumption of isolated modes or at best, mode-pair or group coupling. We find that uncertainties in the P-wave velocity mantle model dominate compared to other model parameters. In addition, we also test several hypothetical models of mantle density structure against real data. These tests indicate that, with the low-frequency Stoneley mode spectral data considered here, it is difficult to make any firm statement on whether the large-low-shear-velocity-provinces are denser or lighter than their surroundings. We conclude that better constraints on long wavelength elastic mantle structure, particularly P-wave velocity, need to be obtained, before making further statements on deep mantle density heterogeneity. In particular, a dense anomaly confined to a thin layer at the base of the mantle (less than ∼100-200 km) may not be resolvable using the two Stoneley modes tested here, while the ability of higher frequency Stoneley modes to resolve it requires further investigations.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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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.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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    The Two-Dimensional Metallicity Distribution and Mixing Scales of Nearby Galaxies (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: Understanding the spatial distribution of metals within galaxies allows us to study the processes of chemical enrichment and mixing in the interstellar medium (ISM). In this work, we map the two-dimensional distribution of metals using a Gaussian Process Regression (GPR) for 19 star-forming galaxies observed with the Very Large Telescope/Multi Unit Spectroscopic Explorer (VLT–MUSE) as part of the PHANGS–MUSE survey. We find that 12 of our 19 galaxies show significant two-dimensional metallicity variation. Those without significant variations typically have fewer metallicity measurements, indicating this is due to the dearth of H ii regions in these galaxies, rather than a lack of higher-order variation. After subtracting a linear radial gradient, we see no enrichment in the spiral arms versus the disc. We measure the 50 per cent correlation scale from the two-point correlation function of these radially-subtracted maps, finding it to typically be an order of magnitude smaller than the fitted GPR kernel scale length. We study the dependence of the two-point correlation scale length with a number of global galaxy properties. We find no relationship between the 50 per cent correlation scale and the overall gas turbulence, in tension with existing theoretical models. We also find more actively star forming galaxies, and earlier type galaxies have a larger 50 per cent correlation scale. The size and stellar mass surface density do not appear to correlate with the 50 per cent correlation scale, indicating that perhaps the evolutionary state of the galaxy and its current star formation activity is the strongest indicator of the homogeneity of the metal distribution.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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    WGA-LP: a pipeline for whole genome assembly of contaminated reads (2021)
    Oxford University Press
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    Publication Date: 2021-10-20
    Description: Summary Whole genome assembly (WGA) of bacterial genomes with short reads is a quite common task as DNA sequencing has become cheaper with the advances of its technology. The process of assembling a genome has no absolute golden standard and it requires to perform a sequence of steps each of which can involve combinations of many different tools. However, the quality of the final assembly is always strongly related to the quality of the input data. With this in mind we built WGA-LP, a package that connects state-of-the-art programs for microbial analysis and novel scripts to check and improve the quality of both samples and resulting assemblies. WGA-LP, with its conservative decontamination approach, has shown to be capable of creating high quality assemblies even in the case of contaminated reads. Availability and implementation WGA-LP is available on GitHub (https://github.com/redsnic/WGA-LP) and Docker Hub (https://hub.docker.com/r/redsnic/wgalp). The web app for node visualization is hosted by shinyapps.io (https://redsnic.shinyapps.io/ContigCoverageVisualizer/). Supplementary information Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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    Enhanced thermal radiation from a tidally heated exomoon with a single hotspot (2021)
    Oxford University Press
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    Publication Date: 2021-10-20
    Description: An exomoon on a non-perfectly circular orbit experiences tidal heating that is capable to significantly contribute to the thermal brightness of the moon. Here we argue that the thermal heat is unevenly distributed on the moon’s surface, the emission of the tidal heat is limited to a few hotspots on the surface. A well-known example is the tidally heated Io. Due to their significantly increased temperature, the hotspots enhance the energy emission in thermal wavelengths. We made simulations using Monte Carlo method to examine this contribution, and to predict about the possible detectability of such a spotted exomoon. We found that in the case of large, Earth-sized companions to Jupiters around red dwarf stars exhibit a thermal flux that enables the direct detection of the moon, due to its photometric signal that can exceed ≈100 ppm in the most favourable configurations.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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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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    Plankton monitoring in the Northwest Atlantic: a comparison of zooplankton abundance estimates from vertical net tows and Continuous Plankton Recorder sampling on the Scotian and Newfoundland shelves, 1999–2015 (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-30
    Description: Assessment of zooplankton abundance, distribution, community composition, and temporal variability is critical to understanding the effects of climate variability and change on lower trophic level production and availability for consumption by larger consumers. Zooplankton sampling is performed across the Canadian continental shelf system by Fisheries and Oceans Canada's Atlantic Zone Monitoring Programme (AZMP). Sampling includes semi-monthly to monthly collection of zooplankton using vertical net tows (VNTs) deployed from near-bottom to surface at stations on the central Scotian Shelf (Stn 2, 150 m depth) and Newfoundland Shelf (Stn 27, 175 m depth), and by Continuous Plankton Recorders (CPRs) in the near-surface layers along routes over the Scotian and Newfoundland shelves (0–10 m depth). Here, we compare abundance metrics for 11 copepod taxa collected using both gear types in both regions between 1999 and 2015. Seasonal cycles of VNT and CPR abundance were similar for near-surface residents. VNT: CPR abundance ratios varied year-round for vertical migrants, as ontogenetic migrants shifted their vertical distribution, and as diel migrants changed their migratory behaviour. For some taxa, differences in annual average VNT: CPR abundance ratios between regions suggest differences in vertical distribution, while for others differences in inter-annual variability for VNT and CPR abundances suggest differences in the dynamics of the near- and sub-surface components of the populations.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press on behalf of International Council for the Exploration of the Sea.
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    Eureka! A Petroleum Transactions Guide that Delivers (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Print ISSN: 1754-9957
    Electronic ISSN: 1754-9965
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Law , Economics
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    Quantifying bycatch risk factors for the Chinese distant water fishery (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: Mitigating bycatch of non-target fish species is a common objective in fisheries management that may be supported by the gathering of data from fishery observer programs and quantitative analysis of bycatch risk factors. We build three GLM models based on Chinese tuna longline fishery observer data in terms of analysis of total bycatch rate (TB rate), total bycatch ratio (TB ratio), and species-specific bycatch rate, respectively. The positive log-linear models assumed a Gaussian observation error model and a linear combination of categorical independent variables, including area, year, month, depth, and bycatch species. Results show that distributions of TB rate and TB ratio followed different trends and a latitudinal decrease was observed from both the northern and southern hemisphere of the equator. Comprehensively, the Pacific is a better place to fish compared to the Indian and Atlantic Oceans in terms of relatively lower TB rate and TB ratio. Fishing in open oceans can somehow avoid a high TB ratio than fishing in coastal waters. As a result, we recommend area 2SW, 2SE, 2 NW, 14SW, 14SE, and 14 NW as appropriate fishing ground for Albacore (Thunnus alalunga) while area 11N,  11S, 18SW, and 18SE to be appropriate fishing ground for fishing bigeye tuna (Thunnus obesus). Setting fishing gears deeper than 500 m would also help to get a low TB rate and TB ratio.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
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    The European Variation Archive: a FAIR resource of genomic variation for all species (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: The European Variation Archive (EVA; https://www.ebi.ac.uk/eva/) is a resource for sharing all types of genetic variation data (SNPs, indels, and structural variants) for all species. The EVA was created in 2014 to provide FAIR access to genetic variation data and has since grown to be a primary resource for genomic variants hosting 〉3 billion records. The EVA and dbSNP have established a compatible global system to assign unique identifiers to all submitted genetic variants. The EVA is active within the Global Alliance of Genomics and Health (GA4GH), maintaining, contributing and implementing standards such as VCF, Refget and Variant Representation Specification (VRS). In this article, we describe the submission and permanent accessioning services along with the different ways the data can be retrieved by the scientific community.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    Galaxy-galaxy lensing with the DES-CMASS catalogue: measurement and constraints on the galaxy-matter cross-correlation (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: The DMASS sample is a photometric sample from the DES Year 1 data set designed to replicate the properties of the CMASS sample from BOSS, in support of a joint analysis of DES and BOSS beyond the small overlapping area. In this paper, we present the measurement of galaxy-galaxy lensing using the DMASS sample as gravitational lenses in the DES Y1 imaging data. We test a number of potential systematics that can bias the galaxy-galaxy lensing signal, including those from shear estimation, photometric redshifts, and observing conditions. After careful systematic tests, we obtain a highly significant detection of the galaxy-galaxy lensing signal, with total S/N = 25.7. With the measured signal, we assess the feasibility of using DMASS as gravitational lenses equivalent to CMASS, by estimating the galaxy-matter cross-correlation coefficient rcc. By jointly fitting the galaxy-galaxy lensing measurement with the galaxy clustering measurement from CMASS, we obtain $r_{ m cc}=1.09^{+0.12}_{-0.11}$ for the scale cut of 4h−1 Mpc and $r_{ m cc}=1.06^{+0.13}_{-0.12}$ for 12h−1 Mpc in fixed cosmology. By adding the angular galaxy clustering of DMASS, we obtain rcc = 1.06 ± 0.10 for the scale cut of 4h−1 Mpc and rcc = 1.03 ± 0.11 for 12h−1 Mpc. The resulting values of rcc indicate that the lensing signal of DMASS is statistically consistent with the one that would have been measured if CMASS had populated the DES region within the given statistical uncertainty. The measurement of galaxy-galaxy lensing presented in this paper will serve as part of the data vector for the forthcoming cosmology analysis in preparation.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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    DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: Eukaryotic genome and methylome encode DNA fragments’ propensity to form nucleosome particles. Although the mechanical properties of DNA possibly orchestrate such encoding, the definite link between ‘omics’ and DNA energetics has remained elusive. Here, we bridge the divide by examining the sequence-dependent energetics of highly bent DNA. Molecular dynamics simulations of 42 intact DNA minicircles reveal that each DNA minicircle undergoes inside-out conformational transitions with the most likely configuration uniquely prescribed by the nucleotide sequence and methylation of DNA. The minicircles’ local geometry consists of straight segments connected by sharp bends compressing the DNA’s inward-facing major groove. Such an uneven distribution of the bending stress favors minimum free energy configurations that avoid stiff base pair sequences at inward-facing major grooves. Analysis of the minicircles’ inside-out free energy landscapes yields a discrete worm-like chain model of bent DNA energetics that accurately account for its nucleotide sequence and methylation. Experimentally measuring the dependence of the DNA looping time on the DNA sequence validates the model. When applied to a nucleosome-like DNA configuration, the model quantitatively reproduces yeast and human genomes’ nucleosome occupancy. Further analyses of the genome-wide chromatin structure data suggest that DNA bending energetics is a fundamental determinant of genome architecture.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    The formation of wide exoKuiper belts from migrating dust traps (2021)
    Oxford University Press
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    Publication Date: 2021-10-13
    Description: The question of what determines the width of Kuiper belt analogues (exoKuiper belts) is an open one. If solved, this understanding would provide valuable insights into the architecture, dynamics, and formation of exoplanetary systems. Recent observations by ALMA have revealed an apparent paradox in this field, the presence of radially narrow belts in protoplanetary discs that are likely the birthplaces of planetesimals, and exoKuiper belts nearly four times as wide in mature systems. If the parent planetesimals of this type of debris disc indeed form in these narrow protoplanetary rings via streaming instability where dust is trapped, we propose that this width dichotomy could naturally arise if these dust traps form planetesimals whilst migrating radially, e.g. as caused by a migrating planet. Using the dust evolution software dustpy, we find that if the initial protoplanetary disc and trap conditions favour planetesimal formation, dust can still effectively accumulate and form planetesimals as the trap moves. This leads to a positive correlation between the inward radial speed and final planetesimal belt width, forming belts up to ∼100au over 10 Myr of evolution. We show that although planetesimal formation is most efficient in low-viscosity (α = 10−4) discs with steep dust traps to trigger the streaming instability, the large widths of most observed planetesimal belts constrain α to values ≥4 × 10−4 at tens of au, otherwise the traps cannot migrate far enough. Additionally, the large spread in the widths and radii of exoKuiper belts could be due to different trap migration speeds (or protoplanetary disc lifetimes) and different starting locations, respectively. Our work serves as a first step to link exoKuiper belts and rings in protoplanetary discs.
    Print ISSN: 0035-8711
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    Topics: Physics
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    The IUPHAR/BPS guide to PHARMACOLOGY in 2022: curating pharmacology for COVID-19, malaria and antibacterials (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb; www.guidetopharmacology.org) is an open-access, expert-curated database of molecular interactions between ligands and their targets. We describe expansion in content over nine database releases made during the last two years, which has focussed on three main areas of infection. The COVID-19 pandemic continues to have a major impact on health worldwide. GtoPdb has sought to support the wider research community to understand the pharmacology of emerging drug targets for SARS-CoV-2 as well as potential targets in the host to block viral entry and reduce the adverse effects of infection in patients with COVID-19. We describe how the database rapidly evolved to include a new family of Coronavirus proteins. Malaria remains a global threat to half the population of the world. Our database content continues to be enhanced through our collaboration with Medicines for Malaria Venture (MMV) on the IUPHAR/MMV Guide to MALARIA PHARMACOLOGY (www.guidetomalariapharmacology.org). Antibiotic resistance is also a growing threat to global health. In response, we have extended our coverage of antibacterials in partnership with AntibioticDB.
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    Topics: Biology
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    Dynamics of relativistic radio jets in asymmetric environments (2021)
    Oxford University Press
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    Publication Date: 2021-10-13
    Description: We have carried out relativistic three-dimensional simulations of high-power radio sources propagating i,nto asymmetric cluster environments. We offset the environment by 0 or 1 core radii (equal to 144 kpc), and incline the jets by 0, 15, or 45° away from the environment centre. The different environment encountered by each radio lobe provides a unique opportunity to study the effect of environment on otherwise identical jets. We find that the jets become unstable towards the end of the simulations, even with a Lorentz factor of 5; they nevertheless develop typical Fanaroff–Riley class II radio morphology. The jets propagating into denser environments have consistently shorter lobe lengths and brighter hotspots, while the axial ratio of the two lobes is similar. We reproduce the recently reported observational anticorrelation between lobe length asymmetry and environment asymmetry, corroborating the notion that observed large-scale radio lobe asymmetry can be driven by differences in the underlying environment.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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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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    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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    Topics: Physics
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    Paired analysis of tree ring width and carbon isotopes indicate when controls on tropical tree growth change from light to water limitations (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: Light and water availability are likely to vary over the lifespan of closed-canopy forest trees with understory trees experiencing greater limitations to growth by light and canopy trees greater limitation due to drought. As drought and shade have opposing effects on isotope discrimination (Δ13C), paired measurement of ring width and Δ13C can potentially be used to differentiate between water and light limitations on tree growth. We tested this approach for Cedrela trees from three tropical forests in Bolivia and Mexico that differ in rainfall and canopy structure. Using lifetime ring width and Δ13C data for trees of up to and over 200 years old, we assessed how controls on tree growth changed from understory to the canopy. Growth and Δ13C are mostly anti-correlated in the understory but this anti-correlation disappeared or weakened when trees reached the canopy, especially at the wettest site. This indicates that understory growth variation is controlled by photosynthetic carbon assimilation (A) due to variation in light levels. Once trees reached the canopy, inter-annual variation in growth and Δ13C at one of the dry sites showed positive correlations, indicating inter-annual variation in growth is driven by variation in water stress affecting stomatal conductance (gs). Paired analysis of ring widths and carbon isotopes provides significant insight to discerning between environmental factors controlling growth over trees’ life; strong light limitations for understory trees in closed-canopy moist forests switched to drought stress for (sub)canopy trees in dry forests. We show that combined isotope and ring width measurements can significantly improve our insights in tree functioning and be used to disentangle limitations due to shade from those due to drought.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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    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.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
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    Chromosome level genome assembly and annotation of highly invasive Japanese stiltgrass (Microstegium vimineum) (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: The invasive Japanese stiltgrass (Microstegium vimineum) affects a wide range of ecosystems and threatens biodiversity across the eastern USA. However, the mechanisms underlying rapid adaptation, plasticity, and epigenetics in the invasive range are largely unknown. We present a chromosome-level assembly for M. vimineum to investigate genome dynamics, evolution, adaptation, and the genomics of phenotypic plasticity. We generated a 1.12 Gb genome with scaffold N50 length of 53.44 Mb respectively, taking a de novo assembly approach that combined PacBio and Dovetail Genomics Omni-C sequencing. The assembly contains 23 pseudochromosomes, representing 99.96% of the genome. BUSCO assessment indicated that 80.3% of Poales gene groups are present in the assembly. The genome is predicted to contain 39,604 protein-coding genes, of which 26,288 are functionally annotated. Furthermore, 66.68% of the genome is repetitive, of which unclassified (35.63%) and long terminal repeat (LTR) retrotransposons (26.90%) are predominant. Similar to other grasses, Gypsy (41.07%) and Copia (32%) are the most abundant LTR-retrotransposon families. The majority of LTR-retrotransposons are derived from a significant expansion in the past 1-2 million years, suggesting the presence of relatively young LTR-retrotransposon lineages. We find corroborating evidence from Ks plots for a stiltgrass-specific duplication event, distinct from the more ancient grass-specific duplication event. The assembly and annotation of M. vimineum will serve as an essential genomic resource facilitating studies of the invasion process, the history and consequences of polyploidy in grasses, and provides a crucial tool for natural resource managers.
    Electronic ISSN: 1759-6653
    Topics: Biology
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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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    The density distributions of cosmic structures: impact of the local environment on weak-lensing convergence (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: Whilst the underlying assumption of the Friedman-Lemaître-Robertson-Walker (FLRW) cosmological model is that matter is homogeneously distributed throughout the universe, gravitational influences over the life of the universe have resulted in mass clustered on a range of scales. Hence we expect that, in our inhomogeneous universe, the view of an observer will be influenced by the location and local environment. Here we analyse the one-point probability distribution functions and angular power spectra of weak-lensing (WL) convergence and magnification numerically to investigate the influence of our local environment on WL statistics in relativistic N-body simulations. To achieve this, we numerically solve the null geodesic equations which describe the propagation of light bundles backwards in time from today, and develop a ray-tracing algorithm, and from these calculate various WL properties. Our findings demonstrate how cosmological observations of large-scale structure through WL can be impacted by the locality of the observer. We also calculate the constraints on the cosmological parameters as a function of redshift from the theoretical and numerical study of the angular power spectrum of WL convergence. This study concludes the minimal redshift for the constraint on the parameter Ωm (H0) is z ∼ 0.2 (z ∼ 0.6) beyond which the local environment’s effect is negligible and the data from WL surveys are more meaningful above that redshift. The outcomes of this study will have direct consequences for future surveys, where percent-level-precision is necessary.
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    Comparing the pre-SNe feedback and environmental pressures for 6000 H ii regions across 19 nearby spiral galaxies (2021)
    Oxford University Press
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    Publication Date: 2021-10-19
    Description: The feedback from young stars (i.e. pre-supernova) is thought to play a crucial role in molecular cloud destruction. In this paper, we assess the feedback mechanisms acting within a sample of 5810 H ii regions identified from the PHANGS-MUSE survey of 19 nearby ( 1, and expanding, yet there is a small sample of compact H ii regions with Ptot,max/Pde 〈 1 (∼1 per cent of the sample). These mostly reside in galaxy centres (Rgal 〈 1 kpc), or, specifically, environments of high gas surface density; log(Σgas/M⊙ pc−2) ∼ 2.5 (measured on kpc-scales). Lastly, we compare to a sample of literature measurements for Ptherm and Prad to investigate how dominant pressure term transitions over around 5 dex in spatial dynamic range and 10 dex in pressure.
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    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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    Accurate inference of gene regulatory interactions from spatial gene expression with deep contrastive learning (2021)
    Oxford University Press
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    Publication Date: 2021-10-19
    Description: Motivation Reverse engineering of gene regulatory networks (GRNs) has long been an attractive research topic in system biology. Computational prediction of gene regulatory interactions has remained a challenging problem due to the complexity of gene expression and scarce information resources. The high-throughput spatial gene expression data, like in situ hybridization images that exhibit temporal and spatial expression patterns, has provided abundant and reliable information for the inference of GRNs. However, computational tools for analyzing the spatial gene expression data are highly underdeveloped. Results In this study, we develop a new method for identifying gene regulatory interactions from gene expression images, called ConGRI. The method is featured by a contrastive learning scheme and deep Siamese convolutional neural network architecture, which automatically learns high-level feature embeddings for the expression images and then feeds the embeddings to an artificial neural network to determine whether or not the interaction exists. We apply the method to a Drosophila embryogenesis dataset and identify GRNs of eye development and mesoderm development. Experimental results show that ConGRI outperforms previous traditional and deep learning methods by a large margin, which achieves accuracies of 76.7% and 68.7% for the GRNs of early eye development and mesoderm development, respectively. It also reveals some master regulators for Drosophila eye development. Availabilityand implementation https://github.com/lugimzheng/ConGRI. Supplementary information Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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    Weaving of bacterial cellulose by the Bcs secretion systems (2021)
    Oxford University Press
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    Publication Date: 2021-10-11
    Description: Cellulose is the most abundant biological compound on Earth and while it is the predominant building constituent of plants, it is also a key extracellular matrix component in many diverse bacterial species. While bacterial cellulose was first described in the 19th century, it was not until this last decade that a string of structural works provided insights into how the cellulose synthase BcsA, assisted by its inner-membrane partner BcsB, senses c-di-GMP to simultaneously polymerize its substrate and extrude the nascent polysaccharide across the inner bacterial membrane. It is now established that bacterial cellulose can be produced by several distinct types of cellulose secretion systems and that in addition to BcsAB, they can feature multiple accessory subunits, often indispensable for polysaccharide production. Importantly, the last years mark significant progress in our understanding not only of cellulose polymerization per se but also of the bigger picture of bacterial signaling, secretion system assembly, biofilm formation and host tissue colonization, as well as of structural and functional parallels of this dominant biosynthetic process between the bacterial and eukaryotic domains of life. Here, we review current mechanistic knowledge on bacterial cellulose secretion with focus on the structure, assembly and cooperativity of Bcs secretion system components.
    Print ISSN: 0168-6445
    Electronic ISSN: 1574-6976
    Topics: Biology
    Published by Oxford University Press on behalf of Federation of European Microbiological Societies.
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    Differential rotation in a 3D simulation of oxygen shell burning (2021)
    Oxford University Press
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    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
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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    The Power of Word-Frequency Based Alignment-Free Functions: a Comprehensive Large-Scale Experimental Analysis (2021)
    Oxford University Press
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    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
    Published by Oxford University Press
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