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  • Articles  (144,868)
  • Oxford University Press  (144,868)
  • 2020-2024  (476)
  • 2010-2014  (78,357)
  • 1990-1994  (29,989)
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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
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
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    Source mechanisms and induced seismicity in the Val d'Agri Basin (Italy) (2024)
    Oxford University Press
    Details
    Publication Date: 2024-03-12
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2023. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved.
    Description: We present the results from a fully unconstrained moment tensor inversion of induced seismic events in a complex and high seismic hazard region (Val d’Agri basin, Southern Italy). The study area hosts two well-documented cases of induced microseismicity linked to (i) a wastewater injection well of a giant oilfield (the largest in onshore Europe), and (ii) severe seasonal level changes of an artificial lake. In order to gather information on the non-doublecouple components of the source and to better understand the rupture mechanisms, we analyse seismic events recorded during daily injection tests in the disposal well. The computed moment tensors have significant non-double-couple components that correlate with the well-head injection pressure. The injection parameters strongly influence the rupture mechanism that can be interpreted as due to the opening/closing of a fracture network inside a fault zone of a pre-existing thrust fault. For the case of the reservoir-induced seismicity, no direct correlations are observed with the loading/unloading of the reservoir.
    Description: Published
    Description: 1617–1627
    Description: OST3 Vicino alla faglia
    Description: JCR Journal
    Keywords: 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 7
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    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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    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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  • 14
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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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    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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  • 16
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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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  • 18
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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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  • 19
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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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  • 20
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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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  • 21
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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
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 22
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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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  • 23
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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
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 24
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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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  • 25
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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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  • 26
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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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    Dancing in the void: Hydrodynamical N-body simulations of the extremely metal poor galaxy DDO 68 (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-27
    Description: Using hydrodynamical N-body simulations, we show that the observed structure and kinematics of the extremely metal-poor, dwarf irregular galaxy DDO 68 is compatible with a merger event with at least two smaller satellite galaxies. We were able to obtain a self-consistent model that simultaneously reproduces several of its observed features, including: the very asymmetric and disturbed shape of the stellar component, the overall ${ m H, small {I}}$ distribution and its velocity field, the arc-like stellar structure to the west, the low-surface brightness stellar stream to the north. The model implies the interaction of the main progenitor of DDO 68 with two systems with dynamical masses 7 × 108 M⊙ and almost 108 M⊙ – 1/20 and 1/150 times the dynamical mass of DDO 68, respectively. We show that the merger between DDO 68 and the most massive of its satellites offers a route to explain the large offset of DDO 68 from the mass-metallicity relation. Assuming that the interacting galaxies have metallicities prior to the merger compatible with those of galaxies with similar stellar masses, we provide quantitative evidence that gas mixing alone does not suffice at diluting the gas of the two components; according to our simulations, the ${ m H, small {II}}$ regions observed along the Cometary Tail trace the low metallicity of the accreted satellite rather than that of DDO 68’s main body. In this case, the mass corresponding to the low metallicity is that of the secondary body and DDO 68 becomes consistent with the mass-metallicity relation.
    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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    A persistent double nuclear structure in 3C 84 (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-27
    Description: 3C 84 (NGC 1275) is the radio source at the center of the Perseus Cluster and exhibits a bright radio jet. We observed the source with the Global Millimeter VLBI Array (GMVA) between 2008 and 2015, with a typical angular resolution of ∼50 μas. The observations revealed a consistent double nuclear structure separated by ∼770 gravitational radii assuming a Black Hole mass of 3.2 × 108 M⊙. The region is likely too broad and bright to be the true jet base anchored in the accretion disk or Black Hole ergosphere. A cone and parabola were fit to the stacked (time averaged) image of the nuclear region. The data did not strongly prefer either fit, but combined with a jet/counter-jet ratio analysis, an upper limit on the viewing angle to the inner jet region of ≤35○ was found. This provides evidence for a variation of the viewing angle along the jet (and therefore a bent jet) within ∼0.5 parsec of the jet launching region. In the case of a conical jet, the apex is located ∼2400 gravitational radii upstream of the bright nuclear region and up to ∼600 gravitational radii upstream in the parabolic case. We found a possible correlation between the brightness temperature and relative position angle of the double nuclear components, which may indicate rotation within the jet.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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    Full waveform inversion based on the non-parametric estimate of the probability distribution of the residuals (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-27
    Description: Summary In an attempt to overcome the difficulties of the full waveform inversion (FWI), several alternative objective functions have been proposed over the last few years. Many of them are based on the assumption that the residuals (differences between modelled and observed seismic data) follow specific probability distributions when, in fact, the true probability distribution is unknown. This leads FWI to converge to an incorrect probability distribution if the assumed probability distribution is different from the real one and, consequently it may lead the FWI to achieve biased models of the subsurface. In this work, we propose an objective function which does not force the residuals to follow a specific probability distribution. Instead, we propose to use the non-parametric kernel density estimation technique (KDE) (which imposes the least possible assumptions about the residuals) to explore the probability distribution that may be more suitable. As evidenced by the results obtained in a synthetic model and in a typical P-wave velocity model of the Brazilian pre-salt fields, the proposed FWI reveals a greater potential to overcome more adverse situations (such as cycle-skipping) and also a lower sensitivity to noise in the observed data than conventional L2 and L1-norm objective functions and thus making it possible to obtain more accurate models of the subsurface. This greater potential is also illustrated by the smoother and less sinuous shape of the proposed objective function with fewer local minima compared with the conventional objective functions.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
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    Characterising the distinct crustal protoliths of Roberts Victor Type I and II eclogites (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-27
    Description: The origin of the eclogites that reside in cratonic mantle roots has long been debated. In the classic Roberts Victor kimberlite locality in South Africa, the strongly contrasting textural and geochemical features of two types of eclogites have led to different genetic models. We studied a new suite of 63 eclogite xenoliths from the former Roberts Victor Mine. In addition to major- and trace-element compositions for all new samples, we determined 18O/16O for garnet from 34 eclogites. Based on geochemical and textural characteristics we identify a large suite of Type I eclogites (n = 53) consistent with previous interpretations that these rocks originate from metamorphosed basaltic-picritic lavas or gabbroic cumulates from oceanic crust, crystallised from melts of depleted MORB mantle. We identify a smaller set of Type II eclogites (n = 10) based on geochemical and textural similarity to eclogites in published literature. We infer their range to very low δ18O values combined with their varied, often very low Zr/Hf ratios and LREE-depleted nature to indicate a protolith origin via low-pressure clinopyroxene-bearing oceanic cumulates formed from melts that were more depleted in incompatible elements than N-MORB. These compositions are indicative of derivation from a residual mantle source that experienced preferential extraction of incompatible elements and fractionation of Zr-Hf during previous melting.
    Print ISSN: 0022-3530
    Electronic ISSN: 1460-2415
    Topics: Geosciences
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    Well-log facies classification using an active semi-supervised algorithm with pairwise constraints (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-27
    Description: Summary We present a technique for lithofacies classification of well-log data using an active semi-supervised algorithm. This method considers both the input of domain experts and the distribution characteristics of well-log properties. It aims to obtain lithofacies that are more geologically meaningful and seismically interpretable than the conventional clustering methods. We impose guidance from experts (e.g., geologist, petrophysicist and seismic interpreter) as pairwise constraints. The acquired constraints were incorporated into facies classification in two ways: modification of the objective function and optimization of the classification subspace. An iterative expectation-maximization (EM) algorithm was used to minimize the objective function. We applied the method to a set of well logs from the Glitne field, North Sea, where six lithofacies had been defined initially. Classification results illustrated that facies predicted with the semi-supervised approach achieved good matches with true labels. Comparisons among different methods (semi-supervised method, quadratic determinant analysis and expectation-maximization with Gaussian mixture model algorithm) also demonstrated that the proposed method significantly outperformed the others. We also tested a scenario with five facies, where we combined silty shale and shale into one group due to significant overlap in the elastic domain. Results demonstrated that the semi-supervised approach produced facies that were more consistent with expert intention, and they were more geologically interpretable. The techniques and results illustrated here could be performed in different types of reservoir facies classification, and the facies classified using semi-supervised algorithm honors the input of the users and data characteristics.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
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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
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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
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    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
    Published by Oxford University Press
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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
    Print ISSN: 0035-8711
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    3-D seismic velocity structure of the Kumaun-Garhwal (Central) Himalaya: Insight into the Main Himalayan Thrust and earthquake occurrence (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-30
    Description: Summary Objective assessment of seismic hazard and understanding of the Himalayan arc's tectonics requires detailed information on the crustal structure and geometry of the underthrusting Indian Plate beneath the Himalaya. Here, we present high-resolution three-dimensional P- wave velocity (Vp) and P-to-S wave velocity ratio (Vp/Vs) images of the Kumaun-Garhwal Himalaya, a proposed potential region for the future great earthquake. We generate these images by inverting arrival times of 515 local earthquakes recorded by 41 broadband stations during November 2006-June 2008. The tomographic images show a heterogeneous structure in the upper-mid crust. These images, along with available geophysical and geological information, indicate the presence of quartz-rich felsic rocks in the uppermost crust; and the occurrence of saline-rich aqueous fluid/partial melt in the upper-mid crust. We propose that the Main Himalayan Thrust (MHT), having a flat-ramp-flat geometry, lies at the base of these fluid zones. The small and moderate-to-strong magnitude earthquakes are mainly confined to the fluid-rich zones along the MHT and quartz-rich rocks in the upper crust. Such an interpretation implies that the earthquake occurrence in the Kumaun-Garhwal Himalaya is largely controlled by the geometry of the MHT and crustal lithology.
    Print ISSN: 0956-540X
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    Topics: Geosciences
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    Predictors of Pain Reduction in Trials of Interventions for Aromatase Inhibitor-Associated Musculoskeletal Symptoms (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-30
    Description: Background Almost half of aromatase inhibitor (AI)-treated breast cancer patients experience AI-associated musculoskeletal symptoms (AIMSS); 20-30% discontinue treatment because of severe symptoms. We hypothesized that we could identify predictors of pain reduction in AIMSS intervention trials by combining data from previously conducted trials. Methods We pooled patient-level data from 3 randomized trials testing interventions (omega-3 fatty acids, acupuncture, and duloxetine) for AIMSS that had similar eligibility criteria and the same patient-reported outcome measures. Only patients with baseline Brief Pain Inventory (BPI) average pain score of ≥ 4 of 10 were included. The primary outcome examined was 2-point reduction in average pain from baseline to week 12. Variable cut-point selection and logistic regression were used. Risk models were built by summing the number of factors statistically significantly associated with pain reduction. Analyses were stratified by study and adjusted for treatment arm. Results For the 583 analyzed patients, the four factors statistically significantly associated with pain reduction were FACT Functional Well-Being 〉24 and Physical Well-Being 〉14 (higher scores reflect better function), and WOMAC
    Electronic ISSN: 2515-5091
    Topics: Chemistry and Pharmacology , Medicine
    Published by Oxford University Press on behalf of National Cancer Institute.
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    Phylogenetic articulation of uric acid evolution in mammals and how it informs a therapeutic uricase (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-28
    Description: The role of uric acid during primate evolution has remained elusive ever since it was discovered over 100 years ago that humans have unusually high levels of the small molecule in our serum. It has been difficult to generate a neutral or adaptive explanation in part because the uricase enzyme evolved to become a pseudogene in apes thus masking typical signals of sequence evolution. Adding to the difficulty is a lack of clarity on the functional role of uric acid in apes. One popular hypothesis proposes that uric acid is a potent antioxidant that increased in concentration to compensate for the lack of vitamin C synthesis in primate species ∼65 million years ago (Mya). Here, we have expanded on our previous work with resurrected ancient uricase proteins to better resolve the reshaping of uricase enzymatic activity prior to ape evolution. Our results suggest that the pivotal death-knell to uricase activity occurred between 20-30 Mya despite small sequential modifications to its catalytic efficiency for the tens of millions of years since primates lost their ability to synthesize vitamin C, and thus the two appear uncorrelated. We also use this opportunity to demonstrate how molecular evolution can contribute to biomedicine by presenting ancient uricases to human immune cells that assay for innate reactivity against foreign antigens. A highly stable and highly catalytic ancient uricase is shown to elicit a lower immune response in more human haplotypes than other uricases currently in therapeutic development.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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    Fast cooling and internal heating in hyperon stars (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: Neutron star models with maximum mass close to 2 M⊙ reach high central densities, which may activate nucleonic and hyperon direct Urca neutrino emission. To alleviate the tension between fast theoretical cooling rates and thermal luminosity observations of moderately magnetized, isolated thermally-emitting stars (with Lγ ≳ 1031 erg s−1 at t ≳ 105.3 yr), some internal heating source is required. The power supplied by the internal heater is estimated for both a phenomenological source in the inner crust and Joule heating due to magnetic field decay, assuming different superfluidity models and compositions of the outer stellar envelope. It is found that a thermal power of W(t) ≈ 1034 erg s−1 allows neutron star models to match observations of moderately magnetized, isolated stars with ages t ≳ 105.3 yr. The requisite W(t) can be supplied by Joule heating due to crust-confined initial magnetic configurations with (i) mixed poloidal-toroidal fields, with surface strength Bdip = 1013 G at the pole of the dipolar poloidal component and ∼90 per cent of the magnetic energy stored in the toroidal component; and (ii) poloidal-only configurations with Bdip = 1014 G.
    Print ISSN: 0035-8711
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    Topics: Physics
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    White dwarfs identified in LAMOST Data Release 5 (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: In this paper, we report white dwarfs identified in the 5th Data Release of the Large Area Multi-Object fibre Spectroscopic Telescope, including spectral types of DA, DB, DC, DZ, and so on. There are 2 625 DA spectra of 2 281 DA stars, 182 DB spectra of 166 DB stars, 62 DC spectra of 58 DC stars, 36 DZ spectra of 33 DZ stars and many other types identified, in addition to our previous paper (Data Release 2). Among those sources, 393 DA stars and 46 DB stars are new identifications after cross-matching with the literature. In order to select DA candidates, we use the classification result from the LAMOST pipeline, colour-colour cut method and a random forest machine learning method. For DBs, since there is no template for DB in the pipeline model, a random forest machine learning method is chosen to select candidates. All the WD candidates have been visually checked individually. The parameters of effective temperature, surface gravity, mass, and cooling age have been estimated for relatively high signal-to-noise ratio DAs and DBs. The peaks of the DA and DB mass distributions are found to be around 0.62 M⊙ and 0.65 M⊙, respectively. Finally, the data and method we used to select white dwarf candidates for the second phase of LAMOST survey are also addressed in this paper.
    Print ISSN: 0035-8711
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    Topics: Physics
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    Bayesian slip inversion with automatic differentiation variational inference (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: Summary The Bayesian slip inversion offers a powerful tool for modeling the earthquake source mechanism. It can provide a fully probabilistic result and thus permits us to quantitively assess the inversion uncertainty. The Bayesian problem is usually solved with Monte Carlo methods, but they are computationally expensive and are inapplicable for high-dimensional and large-scale problems. Variational inference is an alternative solver to the Bayesian problem. It turns Bayesian inference into an optimization task and thus enjoys better computational performances. In this study, we introduce a general variational inference algorithm, automatic differentiation variational inference (ADVI), to the Bayesian slip inversion and compare it with the classic Metropolis-Hastings (MH) sampling method. The synthetic test shows that the two methods generate nearly identical mean slip distributions and standard deviation maps. In the real case study, the two methods produce highly consistent mean slip distributions, but the ADVI-derived standard deviation map differs from that produced by the MH method, possibly because of the limitation of the Gaussian approximation in the ADVI method. In both cases, ADVI can give comparable results to the MH method but with a significantly lower computational cost. Our results show that ADVI is a promising and competitive method for the Bayesian slip inversion.
    Print ISSN: 0956-540X
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    Topics: Geosciences
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    Internal kinematics of GAIA eDR3 wide binaries (2021)
    Oxford University Press
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    Publication Date: 2021-10-27
    Description: Using the recent GAIA eDR3 catalogue we construct a sample of solar neighbourhood isolated wide binaries satisfying a series of strict signal-to-noise data cuts, exclusion of random association criteria and detailed colour-magnitude diagram selections, to minimize the presence of any kinematic contaminating effects having been discussed in the literature to date. Our final high-purity sample consists of 423 binary pairs within 130 pc of the sun and in all cases high-quality GAIA single-stellar fits for both components of each binary (final average RUWE values of 0.99), both also restricted to the cleanest region of the main sequence. We find kinematics fully consistent with Newtonian expectations for separations, s, below 0.009 pc, with relative velocities scaling with ΔV∝s−1/2 and a total binary mass, Mb, velocity scaling consistent with $Delta V propto M_{b}^{1/2}$. For the separation region of s 〉 0.009 pc we obtain significantly different results, with a separation independent ΔV ≈ 0.5 km/s and a $Delta V propto M_{b}^{0.24 pm 0.21}$. This situation is reminiscent of the low acceleration galactic baryonic Tully-Fisher phenomenology, and indeed, the change from the two regimes we find closely corresponds to the a ≲ a0 transition. These results are at odds not only with Newtonian expectations, but also with MOND predictions, where the presence of an external field effect implies only small deviations from Newtonian dynamics are expected for Solar Neighbourhood wide binaries.
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    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.
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    ConVarT: a search engine for matching human genetic variants with variants from non-human species (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: The availability of genetic variants, together with phenotypic annotations from model organisms, facilitates comparing these variants with equivalent variants in humans. However, existing databases and search tools do not make it easy to scan for equivalent variants, namely ‘matching variants’ (MatchVars) between humans and other organisms. Therefore, we developed an integrated search engine called ConVarT (http://www.convart.org/) for matching variants between humans, mice, and Caenorhabditis elegans. ConVarT incorporates annotations (including phenotypic and pathogenic) into variants, and these previously unexploited phenotypic MatchVars from mice and C. elegans can give clues about the functional consequence of human genetic variants. Our analysis shows that many phenotypic variants in different genes from mice and C. elegans, so far, have no counterparts in humans, and thus, can be useful resources when evaluating a relationship between a new human mutation and a disease.
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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.
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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.
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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.
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    Influences of accreting primordial black holes on the global 21 cm signal in the dark ages (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: Baryonic matter can be accreted on to primordial back holes (PBHs) formed in the early Universe. The radiation from accreting PBHs is capable of altering the evolution of the intergalactic medium (IGM), leaving marks on the global 21 cm signal in the dark ages. For accreting PBHs with mass MPBH = 103(104) M⊙ and mass fraction fPBH = 10−1(10−3), the brightness temperature deviation ΔδTb reaches $sim 18~(26)~ m mK$ at redshift z ∼ 90 ($ u sim 16~ m MHz$), and the gradient of the brightness temperature dδTb/dν reaches $sim 0.8~(0.5)~ m mK~MHz^{-1}$ at frequency $ u sim 28~ m MHz$ (z ∼ 50). For larger PBHs with higher mass fraction, the brightness temperature deviation is larger in the redshift range z ∼ 30–300 ($ u sim 5!-!46~ m MHz$), and the gradient is lower at the frequency range $ u sim 20!-!60~ m MHz$ (z ∼ 23–70). It is impossible to detect these low-frequency radio signals from the Earth due to the influence of the Earth’s ionosphere. However, after taking care of the essential factors properly, e.g. the foreground and interference, a future radio telescope in lunar orbit or on the farside surface of the Moon has a chance of detecting the global 21 cm signals impacted by accreting PBHs and distinguishing them from the standard model.
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    Using strong lensing to understand the microJy radio emission in two radio quiet quasars at redshift 1.7 (2021)
    Oxford University Press
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    Publication Date: 2021-10-18
    Description: The radio quasar luminosity function exhibits an upturn around $L_{6 m :GHz}=10^{23}$ W Hz−1 that is well-modelled by a star-forming host galaxy population. This distribution leads some authors to cite star formation as the main radio emission mechanism in so-called radio-quiet quasars (RQQs). Understanding the origin of RQQ radio emission is crucial for our understanding of quasar feedback mechanisms – responsible for the regulation of star formation in the host galaxy – and for understanding galaxy evolution as a whole. By observing RQQs that have been magnified by strong gravitational lensing, we have direct access to the RQQ population out to cosmic noon, where evidence for twin mini-jets has recently been found in a sub-$mu$Jy RQQ. Here we present radio observations of two lensed RQQs using the VLA at 5 GHz, the latest objects to be observed in a sample of quadruply-imaged RQQs above −30°. In SDSS J1004+4112 we find strong evidence for AGN-related radio emission in the variability of the source. In PG 1115+080 we find tentative evidence for AGN-related emission, determined by comparing the radio luminosity with modelled dust components. If confirmed in the case of PG 1115+080, which lies on the radio–FIR correlation, the result would reinforce the need for caution when applying the correlation to rule out jet activity and when assuming no AGN heating of FIR-emitting dust when calculating star formation rates. Our programme so far has shown that the two of the faintest radio sources ever imaged show strong evidence for AGN-dominated radio emission.
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    Nanomechanics of negatively supercoiled diaminopurine-substituted DNA (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: Single molecule experiments have demonstrated a progressive transition from a B- to an L-form helix as DNA is gently stretched and progressively unwound. The particular sequence of a DNA segment defines both base stacking and hydrogen bonding that affect the partitioning and conformations of the two phases. Naturally or artificially modified bases alter H-bonds and base stacking and DNA with diaminopurine (DAP) replacing adenine was synthesized to produce linear fragments with triply hydrogen-bonded DAP:T base pairs. Both unmodified and DAP-substituted DNA transitioned from a B- to an L-helix under physiological conditions of mild tension and unwinding. This transition avoids writhing and the ease of this transition may prevent cumbersome topological rearrangements in genomic DNA that would require topoisomerase activity to resolve. L-DNA displayed about tenfold lower persistence length than B-DNA. However, left-handed DAP-substituted DNA was twice as stiff as unmodified L-DNA. Unmodified DNA and DAP-substituted DNA have very distinct mechanical characteristics at physiological levels of negative supercoiling and tension.
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    Energy signature of ton TNT-class impacts: analysis of the 2018 December 22 fireball over Western Pyrenees (2021)
    Oxford University Press
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    Publication Date: 2021-10-18
    Description: The increase in detector sensitivity and availability in the past three decades has allowed us to derive knowledge of the meteoroid flux and impact energy into the Earth’s atmosphere. We present the multi-instrument detected 2018 December 22 fireball over Western Pyrenees, and compare several techniques aiming to obtain a reliable method to be used when measuring impacts of similar scale. From trajectory data alone, we found a bulk density of 3.5 g cm−3 to be the most likely value for the Pyrenean meteoroid. This allowed to further constrain the dynamic mass, which translated into a kinetic energy of 1 ton TNT (4.184 × 109 J). For the second energy derivation, via the fireball’s corrected optical radiation, we obtained a more accurate empirical relation measuring well-studied bolides. The result approximates to 1.1 ton TNT, which is notably close to the nominal dynamic result, and agrees with the lower margin of the seismic-based energy estimation, yet way lower than the infrasound estimate. Based on the relation derived in this study, we consider the nominal estimate from both the dynamic and photometric methods to be the most accurate value of deposited energy (1 ton TNT). We show that the combination of these two methods can be used to infer the meteoroid density. Among the methods presented in this paper, we found that the optical energy is the most reliable predictor of impact energy near the ton TNT-scale.
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    RNAPhaSep: a resource of RNAs undergoing phase separation (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: Liquid-liquid phase separation (LLPS) partitions cellular contents, underlies the formation of membraneless organelles and plays essential biological roles. To date, most of the research on LLPS has focused on proteins, especially RNA-binding proteins. However, accumulating evidence has demonstrated that RNAs can also function as ‘scaffolds’ and play essential roles in seeding or nucleating the formation of granules. To better utilize the knowledge dispersed in published literature, we here introduce RNAPhaSep (http://www.rnaphasep.cn), a manually curated database of RNAs undergoing LLPS. It contains 1113 entries with experimentally validated RNA self-assembly or RNA and protein co-involved phase separation events. RNAPhaSep contains various types of information, including RNA information, protein information, phase separation experiment information and integrated annotation from multiple databases. RNAPhaSep provides a valuable resource for exploring the relationship between RNA properties and phase behaviour, and may further enhance our comprehensive understanding of LLPS in cellular functions and human diseases.
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    RNAInter v4.0: RNA interactome repository with redefined confidence scoring system and improved accessibility (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: Establishing an RNA-associated interaction repository facilitates the system-level understanding of RNA functions. However, as these interactions are distributed throughout various resources, an essential prerequisite for effectively applying these data requires that they are deposited together and annotated with confidence scores. Hence, we have updated the RNA-associated interaction database RNAInter (RNA Interactome Database) to version 4.0, which is freely accessible at http://www.rnainter.org or http://www.rna-society.org/rnainter/. Compared with previous versions, the current RNAInter not only contains an enlarged data set, but also an updated confidence scoring system. The merits of this 4.0 version can be summarized in the following points: (i) a redefined confidence scoring system as achieved by integrating the trust of experimental evidence, the trust of the scientific community and the types of tissues/cells, (ii) a redesigned fully functional database that enables for a more rapid retrieval and browsing of interactions via an upgraded user-friendly interface and (iii) an update of entries to 〉47 million by manually mining the literature and integrating six database resources with evidence from experimental and computational sources. Overall, RNAInter will provide a more comprehensive and readily accessible RNA interactome platform to investigate the regulatory landscape of cellular RNAs.
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    The Natural Products Atlas 2.0: a database of microbially-derived natural products (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: Within the natural products field there is an increasing emphasis on the study of compounds from microbial sources. This has been fuelled by interest in the central role that microorganisms play in mediating both interspecies interactions and host-microbe relationships. To support the study of natural products chemistry produced by microorganisms we released the Natural Products Atlas, a database of known microbial natural products structures, in 2019. This paper reports the release of a new version of the database which includes a full RESTful application programming interface (API), a new website framework, and an expanded database that includes 8128 new compounds, bringing the total to 32 552. In addition to these structural and content changes we have added full taxonomic descriptions for all microbial taxa and have added chemical ontology terms from both NP Classifier and ClassyFire. We have also performed manual curation to review all entries with incomplete configurational assignments and have integrated data from external resources, including CyanoMetDB. Finally, we have improved the user experience by updating the Overview dashboard and creating a dashboard for taxonomic origin. The database can be accessed via the new interactive website at https://www.npatlas.org.
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    A new framework for understanding systematic errors in cluster lens modelling – I. Selection and treatment of cluster member galaxies (2021)
    Oxford University Press
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    Publication Date: 2021-10-06
    Description: With high-quality data from programs like the Hubble Frontier Fields, cluster lensing has reached the point that models are dominated by systematic rather than statistical uncertainties. We introduce a Bayesian framework to quantify systematic effects by determining how different lens modelling choices affect the results. Our framework includes a new two-sample test for quantifying the difference between posterior probability distributions that are sampled by methods like Monte Carlo Markov chains. We use the framework to examine choices related to the selection and treatment of cluster member galaxies in two of the Frontier Field clusters: Abell 2744 and MACS J0416.1–2403. When selecting member galaxies, choices about depth and area affect the models; we find that model results are robust for an I-band magnitude limit of mlim ≥ 22.5 mag and a radial cut of rlim ≥ 90 arcsec (from the centre of the field), although the radial limit likely depends on the spatial extent of lensed images. Mass is typically assigned to galaxies using luminosity/mass scaling relations. We find that the slopes of the scaling relations can have significant effects on lens model parameters but only modest effects on lensing magnifications. Interestingly, scatter in the scaling relations affects the two fields differently. This analysis illustrates how our framework can be used to analyse lens modelling choices and guide future cluster lensing programs.
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    Bringing faint active galactic nuclei (AGNs) to light: a view from large-scale cosmological simulations (2021)
    Oxford University Press
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    Publication Date: 2021-10-05
    Description: The sensitivity of X-ray facilities and our ability to detect fainter active galactic nuclei (AGNs) will increase with the upcoming Athena mission and the AXIS and Lynx concept missions, thus improving our understanding of supermassive black holes (BHs) in a luminosity regime that can be dominated by X-ray binaries. We analyse the population of faint AGNs ($L_{ m x, 2{-}10 , keV}leqslant 10^{42}, m erg,s^{ -1}$) in the Illustris, TNG100, EAGLE, and SIMBA cosmological simulations, and find that the properties of their host galaxies vary from one simulation to another. In Illustris and EAGLE, faint AGNs are powered by low-mass BHs located in low-mass star-forming galaxies. In TNG100 and SIMBA, they are mostly associated with more massive BHs in quenched massive galaxies. We model the X-ray binary (XRB) populations of the simulated galaxies, and find that AGNs often dominate the galaxy AGN + XRB hard X-ray luminosity at z 〉 2, while XRBs dominate in some simulations at z 〈 2. Whether the AGN or XRB emission dominates in star-forming and quenched galaxies depends on the simulations. These differences in simulations can be used to discriminate between galaxy formation models with future high-resolution X-ray observations. We compare the luminosity of simulated faint AGN host galaxies to observations of stacked galaxies from Chandra. Our comparison indicates that the simulations post-processed with our X-ray modelling tend to overestimate the AGN + XRB X-ray luminosity; luminosity that can be strongly affected by AGN obscuration. Some simulations reveal clear AGN trends as a function of stellar mass (e.g. galaxy luminosity drop in massive galaxies), which are not apparent in the observations.
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    Proteome-pI 2.0: proteome isoelectric point database update (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: Proteome-pI 2.0 is an update of an online database containing predicted isoelectric points and pKa dissociation constants of proteins and peptides. The isoelectric point—the pH at which a particular molecule carries no net electrical charge—is an important parameter for many analytical biochemistry and proteomics techniques. Additionally, it can be obtained directly from the pKa values of individual charged residues of the protein. The Proteome-pI 2.0 database includes data for over 61 million protein sequences from 20 115 proteomes (three to four times more than the previous release). The isoelectric point for proteins is predicted by 21 methods, whereas pKa values are inferred by one method. To facilitate bottom-up proteomics analysis, individual proteomes were digested in silico with the five most commonly used proteases (trypsin, chymotrypsin, trypsin + LysC, LysN, ArgC), and the peptides’ isoelectric point and molecular weights were calculated. The database enables the retrieval of virtual 2D-PAGE plots and customized fractions of a proteome based on the isoelectric point and molecular weight. In addition, isoelectric points for proteins in NCBI non-redundant (nr), UniProt, SwissProt, and Protein Data Bank are available in both CSV and FASTA formats. The database can be accessed at http://isoelectricpointdb2.org.
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    CST does not evict elongating telomerase but prevents initiation by ssDNA binding (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: The CST complex (CTC1-STN1-TEN1) has been shown to inhibit telomerase extension of the G-strand of telomeres and facilitate the switch to C-strand synthesis by DNA polymerase alpha-primase (pol α-primase). Recently the structure of human CST was solved by cryo-EM, allowing the design of mutant proteins defective in telomeric ssDNA binding and prompting the reexamination of CST inhibition of telomerase. The previous proposal that human CST inhibits telomerase by sequestration of the DNA primer was tested with a series of DNA-binding mutants of CST and modeled by a competitive binding simulation. The DNA-binding mutants had substantially reduced ability to inhibit telomerase, as predicted from their reduced affinity for telomeric DNA. These results provide strong support for the previous primer sequestration model. We then tested whether addition of CST to an ongoing processive telomerase reaction would terminate DNA extension. Pulse-chase telomerase reactions with addition of either wild-type CST or DNA-binding mutants showed that CST has no detectable ability to terminate ongoing telomerase extension in vitro. The same lack of inhibition was observed with or without pol α-primase bound to CST. These results suggest how the switch from telomerase extension to C-strand synthesis may occur.
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    Inferring primase-DNA specific recognition using a data driven approach (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: DNA–protein interactions play essential roles in all living cells. Understanding of how features embedded in the DNA sequence affect specific interactions with proteins is both challenging and important, since it may contribute to finding the means to regulate metabolic pathways involving DNA–protein interactions. Using a massive experimental benchmark dataset of binding scores for DNA sequences and a machine learning workflow, we describe the binding to DNA of T7 primase, as a model system for specific DNA–protein interactions. Effective binding of T7 primase to its specific DNA recognition sequences triggers the formation of RNA primers that serve as Okazaki fragment start sites during DNA replication.
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    The NuSTAR extragalactic survey of the James Webb Space Telescope North Ecliptic Pole time-domain field (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-06
    Description: We present the NuSTAR extragalactic survey of the James Webb Space Telescope (JWST) North Ecliptic Pole (NEP) Time-Domain Field. The survey covers a ∼0.16 deg2 area with a total exposure of 681 ks acquired in a total of nine observations from three epochs. The survey sensitivities at 20 per cent of the area are 2.39, 1.14, 2.76, 1.52, and 5.20 × 10−14 erg cm−2 s−1 in the 3–24, 3–8, 8–24, 8–16, and 16–24 keV bands, respectively. The NEP survey is one of the most sensitive extragalactic surveys with NuSTAR so far. A total of 33 sources were detected above 95 per cent reliability in at least one of the five bands. We present the number counts, logN-logS, measured in the hard X-ray 8–24 and 8–16 keV bands, uniquely accessible by NuSTAR down to such faint fluxes. We performed source detection on the XMM–Newton and Chandra observations of the same field to search for soft X-ray counterparts of each NuSTAR detection. The soft band positions were used to identify optical and infrared associations. We present the X-ray properties (hardness ratio and luminosity) and optical-to-X-ray properties of the detected sources. The measured fraction of candidate Compton-thick (N$ m _Hge 10^{24}, cm^{-2}$) active galactic nuclei, derived from the hardness ratio, is between 3 and 27 per cent. As this survey was designed to have variability as its primary focus, we present preliminary results on multiepoch flux variability in the 3–24 keV band.
    Print ISSN: 0035-8711
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    Topics: Physics
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    GVDTI: graph convolutional and variational autoencoders with attribute-level attention for drug–protein interaction prediction (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-27
    Description: Motivation Identifying proteins that interact with drugs plays an important role in the initial period of developing drugs, which helps to reduce the development cost and time. Recent methods for predicting drug–protein interactions mainly focus on exploiting various data about drugs and proteins. These methods failed to completely learn and integrate the attribute information of a pair of drug and protein nodes and their attribute distribution. Results We present a new prediction method, GVDTI, to encode multiple pairwise representations, including attention-enhanced topological representation, attribute representation and attribute distribution. First, a framework based on graph convolutional autoencoder is constructed to learn attention-enhanced topological embedding that integrates the topology structure of a drug–protein network for each drug and protein nodes. The topological embeddings of each drug and each protein are then combined and fused by multi-layer convolution neural networks to obtain the pairwise topological representation, which reveals the hidden topological relationships between drug and protein nodes. The proposed attribute-wise attention mechanism learns and adjusts the importance of individual attribute in each topological embedding of drug and protein nodes. Secondly, a tri-layer heterogeneous network composed of drug, protein and disease nodes is created to associate the similarities, interactions and associations across the heterogeneous nodes. The attribute distribution of the drug–protein node pair is encoded by a variational autoencoder. The pairwise attribute representation is learned via a multi-layer convolutional neural network to deeply integrate the attributes of drug and protein nodes. Finally, the three pairwise representations are fused by convolutional and fully connected neural networks for drug–protein interaction prediction. The experimental results show that GVDTI outperformed other seven state-of-the-art methods in comparison. The improved recall rates indicate that GVDTI retrieved more actual drug–protein interactions in the top ranked candidates than conventional methods. Case studies on five drugs further confirm GVDTI’s ability in discovering the potential candidate drug-related proteins. Contact zhang@hlju.edu.cn  Supplementary information: Supplementary data are available at Briefings in Bioinformatics online.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
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    Targeting 3′ and 5′ untranslated regions with antisense oligonucleotides to stabilize frataxin mRNA and increase protein expression (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: Friedreich’s ataxia (FRDA) is a severe multisystem disease caused by transcriptional repression induced by expanded GAA repeats located in intron 1 of the Frataxin (FXN) gene encoding frataxin. FRDA results from decreased levels of frataxin; thus, stabilization of the FXN mRNA already present in patient cells represents an attractive and unexplored therapeutic avenue. In this work, we pursued a novel approach based on oligonucleotide-mediated targeting of FXN mRNA ends to extend its half-life and availability as a template for translation. We demonstrated that oligonucleotides designed to bind to FXN 5′ or 3′ noncoding regions can increase FXN mRNA and protein levels. Simultaneous delivery of oligonucleotides targeting both ends increases efficacy of the treatment. The approach was confirmed in several FRDA fibroblast and induced pluripotent stem cell-derived neuronal progenitor lines. RNA sequencing and single-cell expression analyses confirmed oligonucleotide-mediated FXN mRNA upregulation. Mechanistically, a significant elongation of the FXN mRNA half-life without any changes in chromatin status at the FXN gene was observed upon treatment with end-targeting oligonucleotides, indicating that transcript stabilization is responsible for frataxin upregulation. These results identify a novel approach toward upregulation of steady-state mRNA levels via oligonucleotide-mediated end targeting that may be of significance to any condition resulting from transcription downregulation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    A new framework for understanding systematic errors in cluster lens modelling – II. Constraint selection (2021)
    Oxford University Press
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    Publication Date: 2021-10-06
    Description: Cluster lens models are affected by a variety of choices in the lens modelling process. We have begun a programme to develop a systematic error budget for cluster lens modelling. Here, we examine the selection of image constraints as a potential systematic effect. For constraining the mass model, we find that it is more important to have images be spatially distributed around the cluster than to have them distributed in redshift. We also find that some image sets appear to be more important than others in terms of how well they constrain the models; the ‘important’ image sets typically include an image that lies close to a lensing critical curve as well as an image that is relatively isolated from other images (providing constraints in a region that would otherwise lack lensing information). These conclusions can help guide observing programmes that seek follow-up data for candidate lensed images.
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    Topics: Physics
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    isymba: a symplectic massive bodies integrator with planets interpolation (2021)
    Oxford University Press
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    Publication Date: 2021-10-06
    Description: A planetary instability occurring at time
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    New strategies to improve minimap2 alignment accuracy (2021)
    Oxford University Press
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    Publication Date: 2021-10-08
    Description: Summary We present several recent improvements to minimap2, a versatile pairwise aligner for nucleotide sequences. Now minimap2 v2.22 can more accurately map long reads to highly repetitive regions and align through insertions or deletions up to 100 kb by default, addressing major weakness in minimap2 v2.18 or earlier. Availability and implementation https://github.com/lh3/minimap2.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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    The statistical properties of protostellar discs and their dependence on metallicity (2021)
    Oxford University Press
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    Publication Date: 2021-10-08
    Description: We present the analysis of the properties of large samples of protostellar discs formed in four radiation hydrodynamical simulations of star cluster formation. The four calculations have metallicities of 0.01, 0.1, 1, and 3 times solar metallicity. The calculations treat dust and gas temperatures separately and include a thermochemical model of the diffuse interstellar medium. We find that the radii of discs of bound protostellar systems tend to decrease with decreasing metallicity, with the median characteristic radius of discs in the 0.01 and 3 times solar metallicity calculations being ≈20 and ≈65 au, respectively. Disc masses and radii of isolated protostars also tend to decrease with decreasing metallicity. We find that the circumstellar discs and orbits of bound protostellar pairs, and the two spins of the two protostars are all less well aligned with each other with lower metallicity than with higher metallicity. These variations with metallicity are due to increased small-scale fragmentation due to lower opacities and greater cooling rates with lower metallicity, which increase the stellar multiplicity and increase dynamical interactions. We compare the disc masses and radii of protostellar systems from the solar metallicity calculation with recent surveys of discs around Class 0 and I objects in the Orion and Perseus star-forming regions. The masses and radii of the simulated discs have similar distributions to the observed Class 0 and I discs.
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    Corn ethanol in the Midwestern USA: Local competition, entry and agglomeration (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: This article analyzes the entry of corn-ethanol plants in the Midwestern USA, where the majority of corn in the USA is grown, during the second US ethanol boom. In particular, we examine whether the presence of existing ethanol plants affects ethanol plant entry decisions at the county level using discrete response panel models. There are two main channels through which existing ethanol plants may affect ethanol plant entry decisions: a competition effect and an agglomeration effect. Our results show that existing ethanol plants have a negative effect on the probability of ethanol plant entry in a given county. The net negative competition effect dissipates with distance. We also find that existing conglomerates and large ethanol producing firms in neighboring counties have a positive effect on ethanol plant entry, while existing singlet plants in neighboring counties do not. These results provide evidence for both local competition among ethanol plants within counties, as well as possible agglomeration benefits from existing conglomerates and large ethanol producing firms in neighboring counties.
    Print ISSN: 1468-2702
    Electronic ISSN: 1468-2710
    Topics: Geography , Economics
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    Analysis of an electroless plating problem (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: Electroless plating in microfluidic channels is a novel technology at the micrometer scale. As the microchannel depth varies with the flow of the chemicals, care must be taken for the channel not to run dry. Owing to the deposited chemical species the physical domain of the flow changes with time, leading to a free boundary problem. As the motion of the free boundary is small it is modelled by a transpiration approximation. With this simplification, the mathematical model consists of a Navier–Stokes flow and an equation for the concentration of the plating chemical coupled by nonstandard and nonlinear boundary conditions. Existence and uniqueness are proved for the concentration equation, assuming that the flow is given. Numerical analysis is carried out and justifies the proposed numerical schemes and the nonlinear algorithms. The numerical study is performed, in the two-dimensional case, with the finite element method and an implicit Euler time scheme for the coupled problem with the Navier–Stokes flow and the nonlinear concentration equation.
    Print ISSN: 0272-4979
    Electronic ISSN: 1464-3642
    Topics: Mathematics
    Published by Oxford University Press on behalf of Institute of Mathematics and its Applications.
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    Characterizing Amino Acid Substitution with Complete Linkage of Sites on a Lineage (2021)
    Oxford University Press
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    Publication Date: 2021-09-28
    Description: Amino acid substitution models are commonly used for phylogenetic inference, for ancestral sequence reconstruction, and for the inference of positive selection. All commonly used models explicitly assume that each site evolves independently, an assumption that is violated by both linkage and protein structural and functional constraints. We introduce two new models for amino acid substitution which incorporate linkage between sites, each based on the (population-genetic) Moran model. The first model is a generalized population process tracking arbitrarily many sites which undergo mutation, with individuals replaced according to their fitnesses. This model provides a reasonably complete framework for simulations but is numerically and analytically intractable. We also introduce a second model which includes several simplifying assumptions but for which some theoretical results can be derived. We analyze the simplified model to determine conditions where linkage is likely to have meaningful effects on sitewise substitution probabilities, as well as conditions under which the effects are likely to be negligible. These findings are an important step in the generation of tractable phylogenetic models that parameterize selective coefficients for amino acid substitution while accounting for linkage of sites leading to both hitchhiking and background selection.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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    Pair-regulated Klein–Nishina relativistic magnetic reconnection with applications to blazars and accreting black holes (2021)
    Oxford University Press
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    Publication Date: 2021-07-25
    Description: Relativistic magnetic reconnection is a powerful agent through which magnetic energy can be tapped in astrophysics, energizing particles that then produce observed radiation. In some systems, the highest energy photons come from particles Comptonizing an ambient radiation bath supplied by an external source. If the emitting particle energies are high enough, this inverse Compton (IC) scattering enters the Klein–Nishina regime, which differs from the low-energy Thomson IC limit in two significant ways. First, radiative losses become inherently discrete, with particles delivering an order-unity fraction of their energies to single photons. Secondly, Comptonized photons may pair produce with the ambient radiation, opening up another channel for radiative feedback on magnetic reconnection. We analytically study externally illuminated highly magnetized reconnecting systems for which both of these effects are important. We identify a universal (initial magnetization-independent) quasi-steady state in which gamma-rays emitted from the reconnection layer are absorbed in the upstream region, and the resulting hot pairs dominate the energy density of the inflow plasma. However, a true pair cascade is unlikely, and the number density of created pairs remains subdominant to that of the original plasma for a wide parameter range. Future particle-in-cell simulation studies may test various aspects. Pair-regulated Klein–Nishina reconnection may explain steep spectra (quiescent and flaring) from flat-spectrum radio quasars and black hole accretion disc coronae.
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    Topics: Physics
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    Outflows from starburst galaxies with various driving mechanisms and their X-ray properties (2021)
    Oxford University Press
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    Publication Date: 2021-09-24
    Description: Outflows in starburst galaxies driven by thermal-mechanical energy, cosmic rays, and their mix are investigated with 1D and 2D hydrodynamic simulations. We show that these outflows could reach a stationary state, after which their hydrodynamic profiles asymptotically approach previous results obtained semi-analytically for stationary outflow configurations. The X-rays from the simulated outflows are computed, and high-resolution synthetic spectra and broad-band light curves are constructed. The simulated outflows driven by thermal mechanical pressure and CRs have distinguishable spectral signatures, in particular, in the sequence of the keV K α lines of various ions and in the L-shell Fe emission complex. We demonstrate that broad-band colour analysis in X-rays is a possible alternative means to probe outflow driving mechanisms for distant galaxies, where observations may not be able to provide sufficient photons for high-resolution spectroscopic analyses.
    Print ISSN: 0035-8711
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    Topics: Physics
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    An unbiased estimator of the full-sky CMB angular power spectrum at large scales using neural networks (2021)
    Oxford University Press
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    Publication Date: 2021-09-24
    Description: Accurate estimation of the cosmic microwave background (CMB) angular power spectrum is enticing due to the prospect for precision cosmology it presents. Galactic foreground emissions, however, contaminate the CMB signal and need to be subtracted reliably in order to lessen systematic errors on the CMB temperature estimates. Typically, bright foregrounds in a region lead to further uncertainty in temperature estimates in the area even after some foreground removal technique is performed and hence determining the underlying full-sky angular power spectrum poses a challenge. We explore the feasibility of utilizing artificial neural networks to predict the angular power spectrum of the full-sky CMB temperature maps from the observed angular power spectrum of the partial sky in which CMB temperatures in some bright foreground regions are masked. We present our analysis at large angular scales with two different masks. We produce unbiased predictions of the full-sky angular power spectrum and recover the underlying theoretical power spectrum using neural networks. Our predictions are also uncorrelated to a large extent. We further show that the multipole-space covariances of the predictions of full-sky spectra made by the artificial neural networks are much smaller than those of the estimates obtained using the pseudo-Cℓ method.
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    The impact of pre-supernova feedback and its dependence on environment (2021)
    Oxford University Press
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    Publication Date: 2021-09-25
    Description: Integral field units enable resolved studies of a large number of star-forming regions across entire nearby galaxies, providing insight on the conversion of gas into stars and the feedback from the emerging stellar populations over unprecedented dynamic ranges in terms of spatial scale, star-forming region properties, and environments. We use the Very Large Telescope (VLT) MUSE (Multi Unit Spectroscopic Explorer) legacy data set covering the central 35 arcmin2 (∼12 kpc2) of the nearby galaxy NGC 300 to quantify the effect of stellar feedback as a function of the local galactic environment. We extract spectra from emission line regions identified within dendrograms, combine emission line ratios and line widths to distinguish between ${ m H, small {II}}$ regions, planetary nebulae, and supernova remnants, and compute their ionized gas properties, gas-phase oxygen abundances, and feedback-related pressure terms. For the ${ m H, small {II}}$ regions, we find that the direct radiation pressure (Pdir) and the pressure of the ionized gas ($P_{{ m H, small {II}}}$) weakly increase towards larger galactocentric radii, i.e. along the galaxy’s (negative) abundance and (positive) extinction gradients. While the increase of $P_{{ m H, small {II}}}$ with galactocentric radius is likely due to higher photon fluxes from lower-metallicity stellar populations, we find that the increase of Pdir is likely driven by the combination of higher photon fluxes and enhanced dust content at larger galactocentric radii. In light of the above, we investigate the effect of increased pre-supernova feedback at larger galactocentric distances (lower metallicities and increased dust mass surface density) on the ISM, finding that supernovae at lower metallicities expand into lower-density environments, thereby enhancing the impact of supernova feedback.
    Print ISSN: 0035-8711
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    Topics: Physics
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    Metal-enriched halo gas across galaxy overdensities over the last 10 billion years (2021)
    Oxford University Press
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    Publication Date: 2021-09-25
    Description: We present a study of metal-enriched halo gas traced by Mg ii and C iv absorption at z 〈 2 in the MUSE Analysis of Gas around Galaxies survey and the Quasar Sightline and Galaxy Evolution survey. Using these large and complete galaxy surveys in quasar fields, we study the dependence of the metal distribution on galaxy properties and overdensities, out to physical projected separations of 750 kpc. We find that the cool, low-ionization gas is significantly affected by the environment across the full redshift range probed, with ≈2–3 times more prevalent and stronger Mg ii absorption in higher overdensity group environments and in regions with greater overall stellar mass and star formation rates. Complementary to these results, we have further investigated the more highly ionized gas as traced by C iv absorption, and found that it is likely to be more extended than the Mg ii gas, with ≈2 times higher covering fraction at a given distance. We find that the strength and covering fraction of C iv absorption show less significant dependence on galaxy properties and environment than the Mg ii absorption, but more massive and star-forming galaxies nevertheless also show ≈2 times higher incidence of C iv absorption. The incidence of Mg ii and C iv absorption within the virial radius shows a tentative increase with redshift, being higher by a factor of ≈1.5 and ≈4, respectively, at z 〉 1. It is clear from our results that environmental processes have a significant impact on the distribution of metals around galaxies and need to be fully accounted for when analysing correlations between gaseous haloes and galaxy properties.
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    Structure, stability, and optical absorption spectra of small TinCx clusters: a first-principles approach (2021)
    Oxford University Press
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    Publication Date: 2021-09-24
    Description: Titanium carbide molecular clusters are thought to form in the circumstellar envelopes of carbon-rich asymptotic giant branch (AGB) stars but, to date, their detection has remained elusive. To facilitate the astrophysical identification of those clusters in AGB and post-AGB environments, the molecular structures and optical absorption spectra of small TinCx clusters, with n = 1–4 and x = 1–4, and some selected larger clusters, Ti3C8, Ti4C8, Ti6C13, Ti7C13, Ti8C12, Ti9C15, and Ti13C22, have been calculated. The density functional formalism, within the B3LYP approximation for electronic exchange and correlation, was used to find the lowest energy structures. Except the clusters having a single Ti atom, the rest exhibit three-dimensional structures. Those are formed by a Ti fragment surrounded in general by carbon dimers. The optical spectra of TinCx, computed by time-dependent density functional theory, using the corrected CAM-B3LYP functional, show absorption features in the visible and near-infrared regions which may help in the identification of these clusters in space. In addition, most of the clusters have sizable electric dipole moments, allowing their detection by radioastronomical observations.
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    A Hybrid Machine Learning Approach for Performance Modeling of Cloud-Based Big Data Applications (2021)
    Oxford University Press
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    Publication Date: 2021-09-20
    Description: Nowadays, Apache Hadoop and Apache Spark are two of the most prominent distributed solutions for processing big data applications on the market. Since in many cases these frameworks are adopted to support business critical activities, it is often important to predict with fair confidence the execution time of submitted applications, for instance when service-level agreements are established with end-users. In this work, we propose and validate a hybrid approach for the performance prediction of big data applications running on clouds, which exploits both analytical modeling and machine learning (ML) techniques and it is able to achieve a good accuracy without too many time consuming and costly experiments on a real setup. The experimental results show how the proposed approach attains improvement in accuracy, number of experiments to be run on the operational system and cost over applying ML techniques without any support from analytical models. Moreover, we compare our approach with Ernest, an ML-based technique proposed in the literature by the Spark inventors. Experiments show that Ernest can accurately estimate the performance in interpolating scenarios while it fails to predict the performance when configurations with increasing number of cores are considered. Finally, a comparison with a similar hybrid approach proposed in the literature demonstrates how our approach significantly reduce prediction errors especially when few experiments on the real system are performed.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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    RdRp or RT, That is the Question (2021)
    Oxford University Press
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    Publication Date: 2021-08-05
    Description: The RNA-dependent RNA polymerase (RdRp) of all known double-stranded RNA viruses is located within the viral particle and is responsible for the transcription and replication of the viral genome. Through an RT-PCR assay, we determined that purified virions, in vitro translated RdRp proteins, and purified recombinant RdRp proteins of partitiviruses also have reverse transcriptase (RT) function. We show that partitivirus RdRps 1) synthesized DNA from homologous and heterologous dsRNA templates; 2) are active using both ssRNA and dsRNA templates; and 3) are active at lower temperatures compared to an optimal reaction temperature of commercial RT enzymes. This finding poses an intriguing question: why do partitiviruses, with dsRNA genomes, have a polymerase with RT functions? In comparison, 3Dpol, the RdRp of poliovirus, did not show any RT activity. Our findings lead us to propose a new evolutionary model for RNA viruses where the RdRp of dsRNA viruses could be the ancestor of RdRps.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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    Functional Evolution of a Bark Beetle Odorant Receptor Clade Detecting Monoterpenoids of Different Ecological Origins (2021)
    Oxford University Press
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    Publication Date: 2021-07-22
    Description: Insects detect odors using an array of odorant receptors (ORs), which may expand through gene duplication. How and which new functions may evolve among related ORs within a species remain poorly investigated. We addressed this question by functionally characterizing ORs from the Eurasian spruce bark beetle Ips typographus, in which physiological and behavioral responses to pheromones, volatiles from host and nonhost trees, and fungal symbionts are well described. In contrast, knowledge of OR function is restricted to two receptors detecting the pheromone compounds (S)-(–)-ipsenol (ItypOR46) and (R)-(–)-ipsdienol (ItypOR49). These receptors belong to an Ips-specific OR-lineage comprising seven ItypORs. To gain insight into the functional evolution of related ORs, we characterized the five remaining ORs in this clade using Xenopus oocytes. Two receptors responded primarily to the host tree monoterpenes (+)-3-carene (ItypOR25) and p-cymene (ItypOR27). Two receptors responded to oxygenated monoterpenoids produced in larger relative amounts by the beetle-associated fungi, with ItypOR23 specific for (+)-trans-(1R, 4S)-4-thujanol, and ItypOR29 responding to (+)-isopinocamphone and similar ketones. ItypOR28 responded to the pheromone E-myrcenol from the competitor Ips duplicatus. Overall, the OR responses match well with those of previously characterized olfactory sensory neuron classes except that neurons detecting E-myrcenol have not been identified. The characterized ORs are under strong purifying selection and demonstrate a shared functional property in that they all primarily respond to monoterpenoids. The variation in functional groups among OR ligands and their diverse ecological origins suggest that neofunctionalization has occurred early in the evolution of this OR-lineage following gene duplication.
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    Electronic ISSN: 1537-1719
    Topics: Biology
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    The influence of trawl efficiency assumptions on survey-based population metrics (2021)
    Oxford University Press
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    Publication Date: 2021-09-03
    Description: Catch data from bottom trawl surveys are used in various ways (e.g. stock assessments, fisheries management, and ecosystem studies) to represent trends in fish populations across space, time, season, or size. Relative abundance indices assume constant capture efficiency, and area-swept abundance requires an estimate of capture efficiency. Therefore, it is important to develop a predictive understanding of the interaction between fish and survey gear. We conducted experiments to test two primary factors that influence the efficiency of survey trawls at capturing demersal groundfish: (1) footrope escapement—estimated by attaching a collection bag beneath the primary trawl, and (2) herding of the sweeps/doors—estimated by varying sweep length. Random forest models were used to disentangle the herding effect from patterns caused by environmental variables. Contrary to common assumptions, footrope efficiency was incomplete (〈 100%) and herding was non-trivial (〉 0%), which introduces a bias in population metrics that rely on such assumptions. This bias varied by species and depended upon the relative strength of the counteracting effects of footrope escapement and herding. Our findings suggest that trawl efficiency should be estimated (not assumed) to derive area-swept abundance, and relative abundance indices should account for size-based efficiency and changing size compositions.
    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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    Is the Genetic Code Optimized for Resource Conservation? (2021)
    Oxford University Press
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    Publication Date: 2021-08-12
    Description: The causes and consequences of the nonrandom structure of the standard genetic code (SGC) have been of long-standing interest. A recent study reported that mutations in present-day protein-coding sequences are less likely to increase proteomic nitrogen and carbon uses under the SGC than under random genetic codes, concluding that the SGC has been selectively optimized for resource conservation. If true, this finding might offer important information on the environment in which the SGC and some of the earliest life forms evolved. However, we here show that the hypothesis of optimization of a genetic code for resource conservation is theoretically untenable. We discover that the aforementioned study estimated the expected mutational effect by inappropriately excluding mutations lowering resource consumptions and including mutations involving stop codons. After remedying these problems, we find no evidence that the SGC is optimized for nitrogen or carbon conservation.
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    Electronic ISSN: 1537-1719
    Topics: Biology
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    Maximization of non-idle enzymes improves the coverage of the estimated maximal in vivo enzyme catalytic rates in Escherichia coli (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-06
    Description: Motivation Constraint-based modeling approaches allow the estimation of maximal in vivo enzyme catalytic rates that can serve as proxies for enzyme turnover numbers. Yet, genome-scale flux profiling remains a challenge in deploying these approaches to catalogue proxies for enzyme catalytic rates across organisms. Results Here, we formulate a constraint-based approach, termed NIDLE-flux, to estimate fluxes at a genome-scale level by using the principle of efficient usage of expressed enzymes. Using proteomics data from Escherichia coli, we show that the fluxes estimated by NIDLE-flux and the existing approaches are in excellent qualitative agreement (Pearson correlation 〉 0.9). We also find that the maximal in vivo catalytic rates estimated by NIDLE-flux exhibits a Pearson correlation of 0.74 with in vitro enzyme turnover numbers. However, NIDLE-flux results in a 1.4-fold increase in the size of the estimated maximal in vivo catalytic rates in comparison to the contenders. Integration of the maximum in vivo catalytic rates with publically available proteomics and metabolomics data provide a better match to fluxes estimated by NIDLE-flux. Therefore, NIDLE-flux facilitates more effective usage of proteomics data to estimate proxies for kcatomes. Availability and implementation https://github.com/Rudan-X/NIDLE-flux-code. 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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    Deterrents and nudges improve compliance in Greenland's Atlantic salmon (Salmo salar) fishery (2021)
    Oxford University Press
    Details
    Publication Date: 2021-09-04
    Description: Fishers reporting all of their catch is key to estimating population viabilities of vulnerable, highly migratory fish stocks. However, fishery managers find it difficult to ensure that this reporting behavior takes place consistently. Wild Atlantic salmon (Salmo salar) are a highly migratory and internationally contested species with a threatened conservation status. Greenland manages a fishery for Atlantic salmon, and its coastline serves as a key feeding ground in the life history of Atlantic salmon. However, salmon catch is underreported by fishers, even though they are required to report. Deterring noncompliant behavior with penalties and sending short message service (SMS) messages have been shown to increase compliance, but no known studies test their effect on compliance with catch reporting requirements. We evaluated two interventions for their effect on salmon catch reporting behavior among Greenland's salmon fishers. Salmon fishers were 41% more likely to report (p
    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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    Use of food web knowledge in environmental conservation and management of living resources in the Baltic Sea (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-19
    Description: Food webs are central entities mediating processes and external pressures in marine ecosystems. They are essential to understand and predict ecosystem dynamics and provision of ecosystem services. Paradoxically, utilization of food web knowledge in marine environmental conservation and resource management is limited. To better understand the use of knowledge and barriers to incorporation in management, we assess its application related to the management of eutrophication, chemical contamination, fish stocks, and non-indigenous species. We focus on the Baltic, a severely impacted, but also intensely studied and actively managed semi-enclosed sea. Our assessment shows food web processes playing a central role in all four areas, but application varies strongly, from formalized integration in management decisions, to support in selecting indicators and setting threshold values, to informal knowledge explaining ecosystem dynamics and management performance. Barriers for integration are complexity of involved ecological processes and that management frameworks are not designed to handle such information. We provide a categorization of the multi-faceted uses of food web knowledge and benefits of future incorporation in management, especially moving towards ecosystem-based approaches as guiding principle in present marine policies and directives. We close with perspectives on research needs to support this move considering global and regional change.
    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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    Comparative Analysis of Mammal Genomes Unveils Key Genomic Variability for Human Life Span (2021)
    Oxford University Press
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    Publication Date: 2021-07-23
    Description: The enormous mammal’s lifespan variation is the result of each species’ adaptations to their own biological trade-offs and ecological conditions. Comparative genomics have demonstrated that genomic factors underlying both, species lifespans and longevity of individuals, are in part shared across the tree of life. Here, we compared protein-coding regions across the mammalian phylogeny to detect individual amino acid (AA) changes shared by the most long-lived mammals and genes whose rates of protein evolution correlate with longevity. We discovered a total of 2,737 AA in 2,004 genes that distinguish long- and short-lived mammals, significantly more than expected by chance (P = 0.003). These genes belong to pathways involved in regulating lifespan, such as inflammatory response and hemostasis. Among them, a total 1,157 AA showed a significant association with maximum lifespan in a phylogenetic test. Interestingly, most of the detected AA positions do not vary in extant human populations (81.2%) or have allele frequencies below 1% (99.78%). Consequently, almost none of these putatively important variants could have been detected by genome-wide association studies. Additionally, we identified four more genes whose rate of protein evolution correlated with longevity in mammals. Crucially, SNPs located in the detected genes explain a larger fraction of human lifespan heritability than expected, successfully demonstrating for the first time that comparative genomics can be used to enhance interpretation of human genome-wide association studies. Finally, we show that the human longevity-associated proteins are significantly more stable than the orthologous proteins from short-lived mammals, strongly suggesting that general protein stability is linked to increased lifespan.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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    Five centuries of cod catches in Eastern Canada (2021)
    Oxford University Press
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    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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    Botanical drugs: a new strategy for structure-based target prediction (2021)
    Oxford University Press
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    Publication Date: 2021-10-26
    Description: Target identification of small molecules is an important and still changeling work in the area of drug discovery, especially for botanical drug development. Indistinct understanding of the relationships of ligand–protein interactions is one of the main obstacles for drug repurposing and identification of off-targets. In this study, we collected 9063 crystal structures of ligand-binding proteins released from January, 1995 to April, 2021 in PDB bank, and split the complexes into 5133 interaction pairs of ligand atoms and protein fragments (covalently linked three heavy atoms) with interatomic distance ≤5 Å. The interaction pairs were grouped into ligand atoms with the same SYBYL atom type surrounding each type of protein fragment, which were further clustered via Bayesian Gaussian Mixture Model (BGMM). Gaussian distributions with ligand atoms ≥20 were identified as significant interaction patterns. Reliability of the significant interaction patterns was validated by comparing the difference of number of significant interaction patterns between the docked poses with higher and lower similarity to the native crystal structures. Fifty-one candidate targets of brucine, strychnine and icajine involved in Semen Strychni (Mǎ Qián Zǐ) and eight candidate targets of astragaloside-IV, formononetin and calycosin-7-glucoside involved in Astragalus (Huáng Qí) were predicted by the significant interaction patterns, in combination with docking, which were consistent with the therapeutic effects of Semen Strychni and Astragalus for cancer and chronic pain. The new strategy in this study improves the accuracy of target identification for small molecules, which will facilitate discovery of botanical drugs.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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    The impact of the FMR and starburst galaxies on the (low metallicity) cosmic star formation history (2021)
    Oxford University Press
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    Publication Date: 2021-09-24
    Description: The question how much star formation is occurring at low metallicity throughout the cosmic history appears crucial for the discussion of the origin of various energetic transients, and possibly double black hole mergers. We revisit the observation-based distribution of birth metallicities of stars (fSFR(Z,z)), focusing on several factors that strongly affect its low metallicity part: (i) the method used to describe the metallicity distribution of galaxies (redshift-dependent mass metallicity relation – MZR, or redshift-invariant fundamental metallicity relation – FMR), (ii) the contribution of starburst galaxies and (iii) the slope of the MZR. We empirically construct the FMR based on the low-redshift scaling relations, which allows us to capture the systematic differences in the relation caused by the choice of metallicity and star formation rate (SFR) determination techniques and discuss the related fSFR(Z,z) uncertainty. We indicate factors that dominate the fSFR(Z,z) uncertainty in different metallicity and redshift regimes. The low metallicity part of the distribution is poorly constrained even at low redshifts (even a factor of ∼200 difference between the model variations) The non-evolving FMR implies a much shallower metallicity evolution than the extrapolated MZR, however, its effect on the low metallicity part of the fSFR(Z,z) is counterbalanced by the contribution of starbursts (assuming that they follow the FMR). A non-negligible fraction of starbursts in our model may be necessary to satisfy the recent high-redshift SFR density constraints.
    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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    Effective Resource Allocation and Load Balancing in Hierarchical HetNets: Toward QoS-Aware Multi-Access Edge Computing (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: Mobile edge computing (MEC) is a key feature of next-generation heterogeneous networks aimed at providing a variety of services for different applications by performing related processing tasks closer to the user equipment. In this research, we investigated on connection management approaches in multi-access edge computing systems. This paper presents joint radio resource allocation and MEC optimization in a multi-layer NOMA HetNet in order to maximize system’s energy efficiency. The continues carrier allocation and handoff decision variables, in addition to the interference incorporated in the goal function, modifies the primary optimization problem to a mixed integer nonlinear programming. Network selection is done statically based on the Analytic Hierarchy Process, and station selection is done dynamically based on the Data Envelope Analysis method. Also, an effective feedback mechanism has been designed in collaboration with the server resource manager to solve a global optimization problem in order to load balancing and meet the users quality of service constraints simultaneously. To reduce the computational complexity and to achieve a locally optimal solution, we applied variable relaxation and majorization minimization approach in which offloading decision and multi-part Markov noise analysis have been developed to model users’ preferences without the need for explicit information from the users. Based on the simulations, the proposed approach not only results in a significant increase of system’s energy efficiency but also enhances the system throughput in multiple-source scenarios.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 92
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    Organic nitrogen enhances nitrogen nutrition and early growth of Pinus sylvestris seedlings (2021)
    Oxford University Press
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    Publication Date: 2021-09-28
    Description: Boreal trees are capable of taking up organic nitrogen (N) as effectively as inorganic N. Depending on the abundance of soil N forms, plants may adjust physiological and morphological traits to optimize N uptake. However, the link between these traits and N uptake in response to soil N sources is poorly understood. We examined Pinus sylvestris seedlings’ biomass growth and allocation, transpiration, and N uptake in response to additions of organic (the amino acid arginine) or inorganic N (ammonium-nitrate). We also monitored in-situ soil N fluxes in the pots following an addition of N, using a microdialysis system. Supplying organic N resulted in a stable soil N flux, whereas the inorganic N resulted in a sharp increase of nitrate flux followed by a rapid decline, demonstrating a fluctuating N supply and a risk for loss of nitrate from the growth medium. Seedlings supplied with organic N achieved a greater biomass with a higher N content, thus reaching a higher N recovery compared with those supplied inorganic N. In spite of a higher N concentration in organic N seedlings, root-to-shoot ratio and transpiration per unit leaf area were similar to those of inorganic N seedlings. We conclude that enhanced seedlings’ nutrition and growth under the organic N source may be attributed to a stable supply of N, owing to a strong retention rate in the soil medium.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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  • 93
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    Phenotype bias determines how natural RNA structures occupy the morphospace of all possible shapes (2021)
    Oxford University Press
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    Publication Date: 2021-09-20
    Description: Morphospaces –representations of phenotypic characteristics– are often populated unevenly, leaving large parts unoccupied. Such patterns are typically ascribed to contingency, or else to natural selection disfavouring certain parts of the morphospace. The extent to which developmental bias, the tendency of certain phenotypes to preferentially appear as potential variation, also explains these patterns is hotly debated. Here we demonstrate quantitatively that developmental bias is the primary explanation for the occupation of the morphospace of RNA secondary structure (SS) shapes. Upon random mutations, some RNA SS shapes (the frequent ones) are much more likely to appear than others. By using the RNAshapes method to define coarse-grained SS classes, we can directly compare the frequencies that non-coding RNA SS shapes appear in the RNAcentral database to frequencies obtained upon random sampling of sequences. We show that: a) Only the most frequent structures appear in nature; the vast majority of possible structures in the morphospace have not yet been explored. b) Remarkably small numbers of random sequences are needed to produce all the RNA SS shapes found in nature so far. c) Perhaps most surprisingly, the natural frequencies are accurately predicted, over several orders of magnitude in variation, by the likelihood that structures appear upon uniform random sampling of sequences. The ultimate cause of these patterns is not natural selection, but rather strong phenotype bias in the RNA genotype-phenotype map, a type of developmental bias or “findability constraint”, which limits evolutionary dynamics to a hugely reduced subset of structures that are easy to “find”.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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    Corrigendum to: Geonomics: Forward-Time, Spatially Explicit, and Arbitrarily Complex Landscape Genomic Simulations (2021)
    Oxford University Press
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    Publication Date: 2021-09-14
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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    DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria (2021)
    Oxford University Press
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    Publication Date: 2021-09-15
    Description: Summary Recent efforts to identify novel bacterial structured noncoding RNA (ncRNA) motifs through searching long, GC-rich intergenic regions (IGRs) have revealed several new classes, including the recently validated HMP-PP riboswitch. The DIMPL (Discovery of Intergenic Motifs PipeLine) discovery pipeline described herein enables rapid extraction and selection of bacterial IGRs that are enriched for structured ncRNAs. Moreover, DIMPL automates the subsequent computational steps necessary for their functional identification. Availability and implementation The DIMPL pipeline is freely available as a Docker image with an accompanying set of Jupyter notebooks. Full instructions for download and use are available at https://github.com/breakerlab/dimpl. 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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    Light and shade of citizen science for less charismatic invertebrate groups: quality assessment of iNaturalist nonmarine mollusc observations in central Italy (2021)
    Oxford University Press
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    Publication Date: 2021-09-01
    Description: Citizen science has grown in importance in recent years: many projects have been launched and records are being collected on an unprecedented scale. However, certain less charismatic invertebrate groups are still underreported and the accuracy and quality of their records in crowd-sourced citizen-science projects have rarely been investigated. Here, we used expert review to conduct quality control of nonmarine mollusc observations from central Italy on the online citizen-science platform iNaturalist (https://www.inaturalist.org/). As of December 2019, c. 400 observations of nonmarine molluscs had been reported from Tuscany on iNaturalist. Most records (59.4%) were identified to species level by the iNaturalist community and included a total of 90 taxa, providing interesting new chorological data of certain entities. Although identification of more than half the observations uploaded by the community was confirmed by expert malacologists, some major issues emerged: low quality of photographic vouchers; bias in favour of a few large common species; poor taxonomic knowledge producing incorrect identifications; and difficulty of identifying many taxa without anatomical study. Expert review remains an essential tool for verification and improvement of data quality in citizen-science projects. In this regard, information on the main diagnostic characters of the more common species (e.g. certain medium–large-sized snails and slugs) as well as tips on how to take good quality photographic images could be provided to volunteers in the form of simple guides and tutorials. High-quality training resources to support recorders and regular feedback and teamwork between scientists and citizens could prevent unverified or inaccurate records from impairing the accuracy of citizen-science datasets and offer a real opportunity to discover and conserve less charismatic taxa.
    Print ISSN: 0260-1230
    Electronic ISSN: 1464-3766
    Topics: Biology
    Published by Oxford University Press
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    Quartic Lp-convergence of cubic Riemannian splines (2021)
    Oxford University Press
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    Publication Date: 2021-10-27
    Description: We prove quartic convergence of cubic spline interpolation for curves into Riemannian manifolds as the grid size of the interpolation grid tends to zero. In contrast to cubic spline interpolation in Euclidean space, where this result is classical, the interpolation operator is no longer linear. Still, concepts from the linear setting may be generalized to the Riemannian case, where we try to use intrinsic Riemannian formulations and avoid charts as much as possible.
    Print ISSN: 0272-4979
    Electronic ISSN: 1464-3642
    Topics: Mathematics
    Published by Oxford University Press on behalf of Institute of Mathematics and its Applications.
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    Are hierarchically formed embedded star clusters surviving gas expulsion depending on their initial conditions? (2021)
    Oxford University Press
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    Publication Date: 2021-09-17
    Description: We investigate the dissolution process of young embedded star clusters with different primordial mass segregation levels using fractal distributions by means of N-body simulations. We combine several star clusters in virial and subvirial global states with Plummer and uniform density profiles to mimic the gas. The star clusters have masses of Mstars = 500 M⊙ that follow an initial mass function where the stars have maximum distance from the centre of r = 1.5 pc. The clusters are placed in clouds that at the same radius have masses of Mcloud = 2000 M⊙, resulting in star formation efficiency of 0.2. We remove the background potential instantaneously at a very early phase, mimicking the most destructive scenario of gas expulsion. The evolution of the fraction of bound stellar mass is followed for a total of 16 Myr for simulations with stellar evolution and without. We compare our results with previous works using equal-mass particles where an analytical physical model was used to estimate the bound mass fraction after gas expulsion. We find that independent of the initial condition, the fraction of bound stellar mass can be well predicted just right after the gas expulsion but tends to be lower at later stages, as these systems evolve due to the stronger two-body interactions resulting from the inclusion of a realistic initial mass function. This discrepancy is independent of the primordial mass segregation level.
    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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    Genetic modeling of GNAO1 disorder delineates mechanisms of Gαo dysfunction (2021)
    Oxford University Press
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    Publication Date: 2021-09-11
    Description: GNAO1 encephalopathy is a neurodevelopmental disorder with a spectrum of symptoms that include dystonic movements, seizures and developmental delay. While numerous GNAO1 mutations are associated with this disorder, the functional consequences of pathological variants are not completely understood. Here, we deployed the invertebrate C. elegans as a whole-animal behavioral model to study the functional effects of GNAO1 disorder-associated mutations. We tested several pathological GNAO1 mutations for effects on locomotor behaviors using a combination of CRISPR/Cas9 gene editing and transgenic overexpression in vivo. We report that all three mutations tested (G42R, G203R and R209C) result in strong loss of function defects when evaluated as homozygous CRISPR alleles. In addition, mutations produced dominant negative effects assessed using both heterozygous CRISPR alleles and transgenic overexpression. Experiments in mice confirmed dominant negative effects of GNAO1 G42R, which impaired numerous motor behaviors. Thus, GNAO1 pathological mutations result in conserved functional outcomes across animal models. Our study further establishes the molecular genetic basis of GNAO1 encephalopathy, and develops a CRISPR-based pipeline for functionally evaluating mutations associated with neurodevelopmental disorders.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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    Optimal sizing and financial analysis of a stand-alone SPV-micro-hydropower hybrid system considering generation uncertainty (2021)
    Oxford University Press
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    Publication Date: 2021-10-20
    Description: Stand-alone hybrid energy systems are an enticing option for electrification in remote areas in several aspects such as grid extension difficulty, economic feasibility and reliability. The use of existing micro-hydropower (MHP) with other renewable resources in rural areas has not been well studied. Moreover, it is challenging to use mathematical optimization algorithms for these kinds of real-world problems, so the derivative-free algorithm is highly sought. In this paper, a methodology has been proposed to perform the optimal sizing, financial and generation uncertainty analysis of solar photovoltaic (SPV) based on an MHP that is proposed to handle the intermittent power output of the SPV. The analysis is performed in two cases: using storage and without storage. The optimal sizing is performed using the least present value cost and reliability constraint using different derivative-free algorithms. The storage-based hybrid system has been found to generate reliable electricity at minimal cost than without a storage-based one. This study would be helpful to propose electrification and existing micro-hydro reinforcement policies to provide reliable electricity in rural areas.
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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