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  • Articles  (7,289)
  • Oxford University Press  (7,282)
  • American Chemical Society (ACS)
  • MDPI Publishing
  • 2020-2024  (482)
  • 1965-1969  (6,807)
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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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    Significant turning point: common buzzard (Buteo buteo) exposure to second-generation anticoagulant rodenticides in the United Kingdom (2024)
    American Chemical Society (ACS)
    In:  Environmental Science & Technology vol. 2024 no. 3c09052
    Details
    Publication Date: 2024-04-04
    Description: Second-generation anticoagulant rodenticides (SGARs) are widely used to control rodent populations, resulting in the serious secondary exposure of predators to these contaminants. In the United Kingdom (UK), professional use and purchase of SGARs were revised in the 2010s. Certain highly toxic SGARs have been authorized since then to be used outdoors around buildings as resistance-breaking chemicals under risk mitigation procedures. However, it is still uncertain whether and how these regulatory changes have influenced the secondary exposure of birds of prey to SGARs. Based on biomonitoring of the UK Common Buzzard (Buteo buteo) collected from 2001 to 2019, we assessed the temporal trend of exposure to SGARs and statistically determined potential turning points. The magnitude of difenacoum decreased over time with a seasonal fluctuation, while the magnitude and prevalence of more toxic brodifacoum, authorized to be used outdoors around buildings after the regulatory changes, increased. The summer of 2016 was statistically identified as a turning point for exposure to brodifacoum and summed SGARs that increased after this point. This time point coincided with the aforementioned regulatory changes. Our findings suggest a possible shift in SGAR use to brodifacoum from difenacoum over the decades, which may pose higher risks of impacts on wildlife.
    Keywords: apex predator ; conditional inference trees ; effectiveness evaluation ; regulatory changes ; seasonal fluctuation
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 8
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    Hotspots of Floating Plastic Particles across the North Pacific Ocean (2024)
    American Chemical Society (ACS)
    In:  EPIC3Environmental Science & Technology, American Chemical Society (ACS), 58(9), pp. 4302-4313, ISSN: 0013-936X
    Details
    Publication Date: 2024-03-28
    Description: The pollution of the marine environment with plastic debris is expected to increase, where ocean currents and winds cause their accumulation in convergence zones like the North Pacific Subtropical Gyre (NPSG). Surface-floating plastic (〉330 μm) was collected in the North Pacific Ocean between Vancouver (Canada) and Singapore using a neuston catamaran and identified by Fourier-transform infrared spectroscopy (FT-IR). Baseline concentrations of 41,600–102,700 items km–2 were found, dominated by polyethylene and polypropylene. Higher concentrations (factors 4–10) of plastic items occurred not only in the NPSG (452,800 items km–2) but also in a second area, the Papaha̅naumokua̅kea Marine National Monument (PMNM, 285,200 items km–2). This second maximum was neither reported previously nor predicted by the applied ocean current model. Visual observations of floating debris (〉5 cm; 8–2565 items km–2 and 34–4941 items km–2 including smaller “white bits”) yielded similar patterns of baseline pollution (34–3265 items km–2) and elevated concentrations of plastic debris in the NPSG (67–4941 items km–2) and the PMNM (295–3748 items km–2). These findings suggest that ocean currents are not the only factor provoking plastic debris accumulation in the ocean. Visual observations may be useful to increase our knowledge of large-scale (micro)plastic pollution in the global oceans.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
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  • 9
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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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  • 10
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    Direct Analysis of Marine Dissolved Organic Matter Using LC-FT-ICR MS (2024)
    American Chemical Society (ACS)
    In:  EPIC3Environmental Science and Technology, American Chemical Society (ACS), 58(10), pp. 4637-4647, ISSN: 0013-936X
    Details
    Publication Date: 2024-04-08
    Description: Marine dissolved organic matter (DOM) is an important component of the global carbon cycle, yet its intricate composition and the sea salt matrix pose major challenges for chemical analysis. We introduce a direct injection, reversed-phase liquid chromatography ultrahigh resolution mass spectrometry approach to analyze marine DOM without the need for solid-phase extraction. Effective separation of salt and DOM is achieved with a large chromatographic column and an extended isocratic aqueous step. Postcolumn dilution of the sample flow with buffer-free solvents and implementing a counter gradient reduced salt buildup in the ion source and resulted in excellent repeatability. With this method, over 5,500 unique molecular formulas were detected from just 5.5 nmol carbon in 100 μL of filtered Arctic Ocean seawater. We observed a highly linear detector response for variable sample carbon concentrations and a high robustness against the salt matrix. Compared to solid-phase extracted DOM, our direct injection method demonstrated superior sensitivity for heteroatom-containing DOM. The direct analysis of seawater offers fast and simple sample preparation and avoids fractionation introduced by extraction. The method facilitates studies in environments, where only minimal sample volume is available e.g. in marine sediment pore water, ice cores, or permafrost soil solution. The small volume requirement also supports higher spatial (e.g., in soils) or temporal sample resolution (e.g., in culture experiments). Chromatographic separation adds further chemical information to molecular formulas, enhancing our understanding of marine biogeochemistry, chemodiversity, and ecological processes.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 11
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    Iron Promotes the Retention of Terrigenous Dissolved Organic Matter in Subtidal Permeable Sediments (2024)
    American Chemical Society (ACS)
    In:  EPIC3Environmental Science and Technology, American Chemical Society (ACS), ISSN: 0013-936X
    Details
    Publication Date: 2024-04-08
    Description: Marine permeable sediments are important sites for organic matter turnover in the coastal ocean. However, little is known about their role in trapping dissolved organic matter (DOM). Here, we examined DOM abundance and molecular compositions (9804 formulas identified) in subtidal permeable sediments along a near- to offshore gradient in the German North Sea. With the salinity increasing from 30.1 to 34.6 PSU, the DOM composition in bottom water shifts from relatively higher abundances of aromatic compounds to more highly unsaturated compounds. In the bulk sediment, DOM leached by ultrapure water (UPW) from the solid phase is 54 ± 20 times more abundant than DOM in porewater, with higher H/C ratios and a more terrigenous signature. With 0.5 M HCl, the amount of leached DOM (enriched in aromatic and oxygen-rich compounds) is doubled compared to UPW, mainly due to the dissolution of poorly crystalline Fe phases (e.g., ferrihydrite and Fe monosulfides). This suggests that poorly crystalline Fe phases promote DOM retention in permeable sediments, preferentially terrigenous, and aromatic fractions. Given the intense filtration of seawater through the permeable sediments, we posit that Fe can serve as an important intermediate storage for terrigenous organic matter and potentially accelerate organic matter burial in the coastal ocean.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 12
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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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  • 13
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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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  • 14
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    Application of the EEPAS earthquake forecasting model to Italy (2024)
    Oxford University Press
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    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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  • 15
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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
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 16
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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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  • 17
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    High Levels of Microplastics in the Arctic Sea Ice Alga 〈i〉Melosira arctica〈/i〉, a Vector to Ice-Associated and Benthic Food Webs (2023)
    American Chemical Society (ACS)
    In:  EPIC3Environmental Science & Technology, American Chemical Society (ACS), 57(17), pp. 6799-6807, ISSN: 0013-936X
    Details
    Publication Date: 2023-08-16
    Description: Plastic pollution has become ubiquitous with very high quantities detected even in ecosystems as remote as arctic sea ice and deepsea sediments. Ice algae growing underneath sea ice are released upon melting and can form fast-sinking aggregates. In this pilot study, we sampled and analyzed the ice algaeMelosira arcticaand ambient sea water from three locations in the Fram Strait to assess their microplastic content and potential as a temporary sink and pathway to the deep seafloor. Analysis by μ-Raman and fluorescence microscopy detected microplastics (≥2.2 μm) in all samples at concentrations ranging from 1.3 to 5.7 × 104 microplastics (MP) m−3 in ice algae and from 1.4 to 4.5 × 103 MP m−3 in sea water, indicating magnitude higher concentrations in algae. On average, 94% of the total microplastic particles were identified as 10 μm or smaller in size and comprised 16 polymer types without a clear dominance. The high concentrations of microplastics found in our pilot study suggest thatM. arctica could trap microplastics from melting ice and ambient sea water. The algae appear to be a temporary sink and could act as a key vector to food webs near the sea surface and on the deep seafloor, to which its fast-sinking aggregates could facilitate an important mechanism of transport.
    Repository Name: EPIC Alfred Wegener Institut
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  • 18
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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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  • 19
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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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  • 20
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    Strong ground-motion prediction equations from induced earthquakes in St. Gallen geothermal field, Switzerland (2023)
    Oxford University Press
    Details
    Publication Date: 2023-03-15
    Description: Ground shaking, whether it is due to natural or induced earthquakes, has always been a matter of concern since it correlates with structural/non-structural damage and can culminate in human anxiety. Industrial activities such as water injection, gas sequestration and waste fluid disposals, promote induced seismicity and consequent ground shaking that can hinder ongoing activities. Therefore, keeping in mind the importance of timely evaluation of a seismic hazard and its mitigation for societal benefits, the present study proposes specifically designed ground-motion prediction equations (GMPEs) from induced earthquakes in the St. Gallen geothermal area, Switzerland. The data analysed in this study consist of 343 earthquakes with magnitude −1.17 ≤ ML, corr ≤ 3.5 and hypocentral distance between 4 and 15 km. The proposed study is one of the first to incorporate ground motions from negative magnitude earthquakes for the development of GMPEs. The GMPEs are inferred with a two-phase approach. In the first phase, a reference model is obtained by considering the effect of source and medium properties on the ground motion. In the second phase the final model is obtained by including a site/station effect. The comparison between the GMPEs obtained in the present study with GMPEs developed for the other induced seismicity environments highlights a mismatch that is ascribed to differences in regional seismic environment and local site conditions of the respective regions. This suggests that, when dealing with induced earthquakes, GMPEs specific for the study should be inferred and used for both monitoring purposes and seismic hazard analyses.
    Description: Published
    Description: 820–832
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
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  • 21
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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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  • 22
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    Finding the Balance between Research and Monitoring: When Are Methods Good Enough to Understand Plastic Pollution? (2023)
    American Chemical Society (ACS)
    In:  EPIC3Environmental Science and Technology, American Chemical Society (ACS), 57(15), pp. 6033-6039, ISSN: 0013-936X
    Details
    Publication Date: 2024-04-17
    Description: Plastic pollution is an international environmental problem. Desire to act is shared from the public to policymakers, yet motivation and approaches are diverging. Public attention is directed to reducing plastic consumption, cleaning local environments, and engaging in citizen science initiatives. Policymakers and regulators are working on prevention and mitigation measures, while international, regional, and national bodies are defining monitoring recommendations. Research activities are focused on validating approaches to address goals and comparing methods. Policy and regulation are eager to act on plastic pollution, often asking questions researchers cannot answer with available methods. The purpose of monitoring will define which method is implemented. A clear and open dialogue between all actors is essential to facilitate communication on what is feasible with current methods, further research, and development needs. For example, some methods can already be used for international monitoring, yet limitations including target plastic types and sizes, sampling strategy, available infrastructure and analytical capacity, and harmonization of generated data remain. Time and resources to advance scientific understanding must be balanced against the need to answer pressing policy issues.
    Repository Name: EPIC Alfred Wegener Institut
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  • 23
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    A Call to Include Plastics in the Global Environment in the Class of Persistent, Bioaccumulative, and Toxic (PBT) Pollutants (2023)
    American Chemical Society (ACS)
    In:  EPIC3Environmental Science and Technology, American Chemical Society (ACS), 57(22), pp. 8185-8188, ISSN: 0013-936X
    Details
    Publication Date: 2024-05-03
    Repository Name: EPIC Alfred Wegener Institut
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  • 24
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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
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  • 25
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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
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  • 26
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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
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  • 27
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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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  • 28
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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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  • 29
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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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    Methodology to identify the reference rock sites in regions of medium-to-high seismicity: an application in Central Italy (2021)
    Oxford University Press
    Details
    Publication Date: 2023-11-14
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2020. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved.
    Description: To evaluate the site response using both empirical approaches (e.g. standard spectral ratio, ground motion models (GMMs), generalized inversion techniques, etc.) and numerical 1-D/2-D analyses, the definition of the reference motion, that is the ground motion recorded at stations unaffected by site-effects due to topographic, stratigraphic or basin effects, is needed. The main objective of this work is to define a robust strategy to identify the seismic stations that can be considered as reference rock sites, using six proxies for the site response: three proxies are related to the analysis of geophysical and seismological data (the repeatable site term from the residual analysis, the resonance frequencies from horizontal-to-vertical spectral ratios on noise or earthquake signals, the average shear wave velocity in the first 30 m); the remaining ones concern geomorphological and installation features (outcropping rocks or stiff soils, flat topography and absence of interaction with structures). We introduce a weighting scheme to take into account the availability and the quality of the site information, as well as the fulfillment of the criterion associated to each proxy. We also introduce a hierarchical index, to take into account the relevance of the proposed proxies in the description of the site effects, and an acceptance threshold for reference rock sites identification. The procedure is applied on a very large data set, composed by accelerometric and velocimetric waveforms, recorded in Central Italy in the period 2008–2018. This data set is composed by more than 30 000 waveforms relative to 450 earthquakes in the magnitude range 3.2–6.5 and recorded by more than 450 stations. A total of 36 out of 133 candidate stations are identified as reference sites: the majority of them are installed on rock with flat topography, but this condition is not sufficient to guarantee the absence of amplifications, especially at high frequencies. Seismological analyses are necessary to exclude stations affected by resonances. We test the impact of using these sites by calibrating a GMMs. The results show that for reference rock sites the median predictions are reduced down to about 45 per cent at short periods in comparison to the generic rock motions.
    Description: Published
    Description: 2053–2067
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Arrival-angle effects on two-receiver measurements of phase velocity (2021)
    Oxford University Press
    Details
    Publication Date: 2023-11-14
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2020. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved.
    Description: We compile a data set of Rayleigh-wave phase velocities between pairs of stations, based on teleseismic events located on the same great circle as the two stations. We validate our observations against dispersion estimates based on ambient-noise cross correlations at the same station pairs. Discrepancies between the results of the two methods can in principle be explained by deviations in the wave propagation path between earthquake and receivers, due to lateral heterogeneity in the Earth’s structure, but the latter effect has, so far, not been precisely quantified nor corrected for. We implement an algorithm to measure the arrival angle of earthquake-generated surface waves and correct the dispersion measurements accordingly. Application to a data set from the Central-Western Mediterranean shows that the arrival-angle correction almost entirely accounts for the discrepancy in question, decreasing significantly the velocity bias for a wide range of periods.
    Description: Published
    Description: 1838–1844
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    3-D Q-coda attenuation structure at Mt. Etna (Italy) (2021)
    Oxford University Press
    Details
    Publication Date: 2023-11-16
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2021. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2021. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved.
    Description: Three dimensional attenuation images of Mt Etna volcano obtained by the analysis of Q-coda from local volcano-tectonic earthquakes are presented in this work. Seismic sources are confined inside the Etna structure with a maximum focal depth of 35 km below the sea level. The space distribution of the attenuation values was calculated by using 3-D weighting functions derived by the sensitivity kernels of Pacheco & Snieders and approximated by a polynomial interpolation, represented in the maps by using a backprojection method. Data were analyzed in four bands with central frequency placed at 1.5, 3, 6 and 12 Hz, respectively. We observed a frequency dependence of Q-coda with values that range from 55 at 1.5 Hz to 218 at 12 Hz. Q-coda space distribution in the Etna area shows almost uniformity in the average attenuation in the first 35 km below the surface. The images were derived with a resolution of 5 km. We observe as one of our main conclusions that Q-coda attenuation space anomalies are correlated with the areas of highest structural heterogeneities and are distributed along the well-known tectonic structures which characterize the crust in Mt Etna region. Previous and numerous velocity and attenuation images describing the structure of Mt Etna support our main conclusion: high Q-coda volumes almost coincide with the zones marked by high velocity and relative low total attenuation for direct waves.
    Description: Published
    Description: 544–558
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Source modelling and strong ground motion simulations for the 24 January 2020, Mw 6.8 Elazığ earthquake, Turkey (2021)
    Oxford University Press
    Details
    Publication Date: 2023-11-29
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2020. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved.
    Description: On 24 January 2020 an Mw 6.8 earthquake occurred at 20:55 local time (17:55 UTC) in eastern Turkey, close to the town of Sivrice in the Elazığ province, causing widespread considerable seismic damage in buildings. In this study, we analyse the main features of the rupture process and the seismic ground shaking during the Elazığ earthquake. We first use Interferometric Synthetic Aperture Radar (InSAR) interferograms (Sentinel-1 satellites) to constrain the fault geometry and the coseismic slip distribution of the causative fault segment. Then, we utilize this information to analyse the ground motion characteristics of the main shock in terms of peak ground acceleration (PGA), peak ground velocity (PGV) and spectral accelerations. The absence of seismic registrations in near-field for this earthquake imposes major constraints on the computation of seismic ground motion estimations in the study area. To do this, we have used a stochastic finite-fault simulation method to generate high-frequency ground motions synthetics for the Mw 6.8 Elazığ 2020 earthquake. Finally, we evaluate the potential state of stress of the unruptured portions of the causative fault segment as well as of adjacent segments, using the Coulomb stress failure function variations. Modelling of geodetic data shows that the 2020 Elazığ earthquake ruptured two major slip patches (for a total length of about 40 km) located along the Pütürge segment of the well-known left-lateral strike-slip East Anatolian Fault Zone (EAFZ), with up to 2.3 m of slip and an estimated geodetic moment of 1.70 × 1019 Nm (equivalent to a Mw 6.8). The position of the hypocentre supports the evidence of marked WSW rupture directivity during the main shock. In terms of ground motion characteristics, we observe that the high-frequency stochastic ground motion simulations have a good capability to reproduce the source complexity and capture the ground motion attenuation decay as a function of distance, up to the 200 km. We also demonstrate that the design spectra corresponding to 475 yr return period, provided by the new Turkish building code is not exceeded by the simulated seismograms in the epicentral area where there are no strong motion stations and no recordings available. Finally, based on the Coulomb stress distribution computation, we find that the Elazığ main shock increased the stress level of the westernmost part of the Pütürge fault and of the adjacent Palu segment and as a result of an off-fault lobe.
    Description: Published
    Description: 1054–1068
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Ontogeny of osmoregulation of the Asian shore crab Hemigrapsus sanguineus at an invaded site of Europe (2021)
    Oxford University Press
    In:  EPIC3Conservation Physiology, Oxford University Press, 9(1), ISSN: 2051-1434
    Details
    Publication Date: 2024-01-01
    Description: We studied the ontogeny of osmoregulation of the Asian shore crab Hemigrapsus sanguineus at an invaded area in the North Sea. H. sanguineus is native to Japan and China but has successfully invaded the Atlantic coast of North America and Europe. In the invaded areas, H. sanguineus is becoming a keystone species as driver of community structure and the adults compete with the shore crab Carcinus maenas. Strong osmoregulatory abilities may confer the potential to use and invade coastal areas already earlier in the life cycle. We reared larvae and first juveniles at 24°C in seawater from hatching to intermoult of each developmental stage (zoea I-V, megalopa, crab I). We exposed each stage to a range of salinities (0–39 ppt) for 24 h, and then we quantified haemolymph osmolality, using nano-osmometry. In addition, we quantified osmolality in field-collected adults after acclimation to the test salinities for 6 days. Larvae of H. sanguineus were able to hyper-osmoregulate at low salinities (15 and 20 ppt) over the complete larval development, although the capacity was reduced at the zoeal stage V; at higher salinities (25–39 ppt), all larval stages were osmoconformers. The capacity to slightly hypo-regulate at high salinity appeared in the first juvenile. Adults were able to hyper-osmoregulate at low salinities and hypo-regulate at concentrated seawater (39 ppt). H. sanguineus showed a strong capacity to osmoregulate as compared to its native competitor C. maenas, which only hyper-regulates at the first and last larval stages and does not hypo-regulate at the juvenile-adult stages. The capacity of H. sanguineus to osmoregulate over most of the life cycle should underpin the potential to invade empty niches in the coastal zone (characterized by low salinity and high temperatures). Osmoregulation abilities over the whole life cycle also constitute a strong competitive advantage over C. maenas.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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    3D MHD simulation of a pulsationally driven MRI decretion disc (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-09
    Description: We explore the pulsationally driven orbital mass ejection mechanism for Be star disc formation using isothermal, 3D magnetohydrodynamic (MHD) and hydrodynamic simulations. Non-radial pulsations are added to a star rotating at 95 per cent of critical as an inner boundary condition that feeds gas into the domain. In MHD, the initial magnetic field within the star is weak. The hydrodynamics simulation has limited angular momentum transport, resulting in repeating cycles of mass accumulation into a rotationally supported disc at small radii followed by fall-back on to the star. The MHD simulation, conversely, has efficient (Maxwell αM ∼ 0.04) angular momentum transport provided by both turbulent and coherent magnetic fields: a slowly decreting midplane driven by the magnetorotational instability and a supersonic wind on the surface of the disc driven by global magnetic torques. The angle and time-averaged properties near the midplane agree reasonably well with a 1D viscous decretion disc model with a modified $ilde{alpha }=0.5$, in which the gas transitions from a subsonic thin disc to a supersonic spherical wind at the critical point. 1D models, however, cannot capture the multiphase decretion/angular structure seen in our simulations. Our results demonstrate that, at least under certain conditions, non-radial pulsations on the surface of a rapidly rotating, weakly magnetised star can drive a Keplerian disc with the basic properties of the viscous decretion disc paradigm, albeit coupled to a laminar wind away from the midplane. Future modelling of Be star discs should consider the possible existence of such a surface wind.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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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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    Targeting 3′ and 5′ untranslated regions with antisense oligonucleotides to stabilize frataxin mRNA and increase protein expression (2021)
    Oxford University Press
    Details
    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
    Published by Oxford University Press
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    TcoFBase: a comprehensive database for decoding the regulatory transcription co-factors in human and mouse (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-30
    Description: Transcription co-factors (TcoFs) play crucial roles in gene expression regulation by communicating regulatory cues from enhancers to promoters. With the rapid accumulation of TcoF associated chromatin immunoprecipitation sequencing (ChIP-seq) data, the comprehensive collection and integrative analyses of these data are urgently required. Here, we developed the TcoFBase database (http://tcof.liclab.net/TcoFbase), which aimed to document a large number of available resources for mammalian TcoFs and provided annotations and enrichment analyses of TcoFs. TcoFBase curated 2322 TcoFs and 6759 TcoFs associated ChIP-seq data from over 500 tissues/cell types in human and mouse. Importantly, TcoFBase provided detailed and abundant (epi) genetic annotations of ChIP-seq based TcoF binding regions. Furthermore, TcoFBase supported regulatory annotation information and various functional annotations for TcoFs. Meanwhile, TcoFBase embedded five types of TcoF regulatory analyses for users, including TcoF gene set enrichment, TcoF binding genomic region annotation, TcoF regulatory network analysis, TcoF-TF co-occupancy analysis and TcoF regulatory axis analysis. TcoFBase was designed to be a useful resource that will help reveal the potential biological effects of TcoFs and elucidate TcoF-related regulatory mechanisms.
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    isymba: a symplectic massive bodies integrator with planets interpolation (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-06
    Description: A planetary instability occurring at time
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    iNucs: inter-nucleosome interactions (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-08
    Description: Motivation Deciphering nucleosome–nucleosome interactions is an important step toward mesoscale description of chromatin organization but computational tools to perform such analyses are not publicly available. Results We developed iNucs, a user-friendly and efficient Python-based bioinformatics tool to compute and visualize nucleosome-resolved interactions using standard pairs format input generated from pairtools. Availabilityand implementation https://github.com/Karimi-Lab/inucs/. 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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    metaGEM: reconstruction of genome scale metabolic models directly from metagenomes (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-06
    Description: Metagenomic analyses of microbial communities have revealed a large degree of interspecies and intraspecies genetic diversity through the reconstruction of metagenome assembled genomes (MAGs). Yet, metabolic modeling efforts mainly rely on reference genomes as the starting point for reconstruction and simulation of genome scale metabolic models (GEMs), neglecting the immense intra- and inter-species diversity present in microbial communities. Here, we present metaGEM (https://github.com/franciscozorrilla/metaGEM), an end-to-end pipeline enabling metabolic modeling of multi-species communities directly from metagenomes. The pipeline automates all steps from the extraction of context-specific prokaryotic GEMs from MAGs to community level flux balance analysis (FBA) simulations. To demonstrate the capabilities of metaGEM, we analyzed 483 samples spanning lab culture, human gut, plant-associated, soil, and ocean metagenomes, reconstructing over 14,000 GEMs. We show that GEMs reconstructed from metagenomes have fully represented metabolism comparable to isolated genomes. We demonstrate that metagenomic GEMs capture intraspecies metabolic diversity and identify potential differences in the progression of type 2 diabetes at the level of gut bacterial metabolic exchanges. Overall, metaGEM enables FBA-ready metabolic model reconstruction directly from metagenomes, provides a resource of metabolic models, and showcases community-level modeling of microbiomes associated with disease conditions allowing generation of mechanistic hypotheses.
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    Spurious heating of stellar motions in simulated galactic discs by dark matter halo particles (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-02
    Description: We use idealized N-body simulations of equilibrium stellar discs embedded within course-grained dark matter (DM) haloes to study the effects of spurious collisional heating on disc structure and kinematics. Collisional heating artificially increases the vertical and radial velocity dispersions of disc stars, as well as the thickness and size of discs; the effects are felt at all galacto-centric radii. The integrated effects of collisional heating are determined by the mass of DM halo particles (or equivalently, by the number of particles at fixed halo mass), their local density and characteristic velocity dispersion, but are largely insensitive to the stellar particle mass. The effects can therefore be reduced by increasing the mass resolution of DM in cosmological simulations, with limited benefits from increasing the baryonic (or stellar) mass resolution. We provide a simple empirical model that accurately captures the effects of spurious collisional heating on the structure and kinematics of simulated discs, and use it to assess the importance of disc heating for simulations of galaxy formation. We find that the majority of state-of-the-art zoom simulations, and a few of the highest-resolution, smallest-volume cosmological runs, are in principle able to resolve thin stellar discs in Milky Way-mass haloes, but most large-volume cosmological simulations cannot. For example, DM haloes resolved with fewer than ≈106 particles will collisionally heat stars near the stellar half-mass radius such that their vertical velocity dispersion increases by ≳ 10 per cent of the halo’s virial velocity in approximately one Hubble time.
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    Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-28
    Description: Non-canonical forms of nucleic acids represent challenging objects for both structure-determination and investigation of their potential role in living systems. In this work, we uncover a structure adopted by GA repetition locked in a parallel homoduplex by an i-motif. A series of DNA oligonucleotides comprising GAGA segment and C3 clip is analyzed by NMR and CD spectroscopies to understand the sequence–structure–stability relationships. We demonstrate how the relative position of the homopurine GAGA segment and the C3 clip as well as single-base mutations (guanine deamination and cytosine methylation) affect base pairing arrangement of purines, i-motif topology and overall stability. We focus on oligonucleotides C3GAGA and methylated GAGAC3 exhibiting the highest stability and structural uniformity which allowed determination of high-resolution structures further analyzed by unbiased molecular dynamics simulation. We describe sequence-specific supramolecular interactions on the junction between homoduplex and i-motif blocks that contribute to the overall stability of the structures. The results show that the distinct structural motifs can not only coexist in the tight neighborhood within the same molecule but even mutually support their formation. Our findings are expected to have general validity and could serve as guides in future structure and stability investigations of nucleic acids.
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    Topics: Biology
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    Standardizing reverberation-measured Mg II time-lag quasars, by using the radius–luminosity relation, and constraining cosmological model parameters (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-02
    Description: We use 78 reverberation-measured Mg II time-lag quasars (QSOs) in the redshift range 0.0033 ≤ z ≤ 1.89 to constrain cosmological parameters in six different cosmological models. The basis of our method is the use of the radius–luminosity or R−L relation to standardize these 78 Mg II QSOs. In each cosmological model, we simultaneously determine R−L relation and cosmological model parameters, thus avoiding the circularity problem. We find that the R−L relation parameter values are independent of the cosmological model used in the analysis, thus, establishing that current Mg II QSOs are standardizable candles. Cosmological constraints obtained using these QSOs are significantly weaker than, but consistent with, those obtained from a joint analysis of baryon acoustic oscillation (BAO) observations and Hubble parameter [H(z)] measurements. So, we also analyse these QSOs in conjunction with the BAO + H(z) data and find cosmological constraints consistent with the standard spatially flat ΛCDM model as well as with mild dark energy dynamics and a little spatial curvature. A larger sample of higher quality reverberation-measured QSOs should have a smaller intrinsic dispersion and so should provide tighter constraints on cosmological parameters.
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    ATOMS: ALMA Three-millimeter Observations of Massive Star-forming regions–VI. On the formation of the ‘L’ type filament in G286.21+0.17 (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-02
    Description: Filaments play an important role in star formation, but the formation process of filaments themselves is still unclear. The high-mass star-forming clump G286.21+0.17 (G286 for short) that contains an ‘L’ type filament was thought to undergo global collapse. Our high-resolution ALMA band 3 observations resolve the gas kinematics of G286 and reveal two sub-clumps with very different velocities inside it. We find that the ‘blue profile’ (an indicator of gas infall) of HCO+ lines in single dish observations of G286 is actually caused by gas emission from the two sub-clumps rather than gas infall. We advise great caution in interpreting gas kinematics (e.g. infall) from line profiles towards distant massive clumps in single dish observations. Energetic outflows are identified in G286 but the outflows are not strong enough to drive expansion of the two sub-clumps. The two parts of the ‘L’ type filament (‘NW–SE’ and ‘NE–SW’ filaments) show prominent velocity gradients perpendicular to their major axes, indicating that they are likely formed due to large-scale compression flows. We argue that the large-scale compression flows could be induced by the expansion of nearby giant H ii regions. The ‘NW–SE’ and ‘NE–SW’ filaments seem to be in collision, and a large amount of gas has been accumulated in the junction region where the most massive core G286c1 forms.
    Print ISSN: 0035-8711
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    Topics: Physics
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    Dissecting Genomic Determinants of Positive Selection with an Evolution-Guided Regression Model (2021)
    Oxford University Press
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    Publication Date: 2021-10-01
    Description: In evolutionary genomics, it is fundamentally important to understand how characteristics of genomic sequences, such as gene expression level, determine the rate of adaptive evolution. While numerous statistical methods, such as the McDonald–Kreitman (MK) test, are available to examine the association between genomic features and the rate of adaptation, we currently lack a statistical approach to disentangle the independent effect of a genomic feature from the effects of other correlated genomic features. To address this problem, I present a novel statistical model, the MK regression, which augments the MK test with a generalized linear model. Analogous to the classical multiple regression model, the MK regression can analyze multiple genomic features simultaneously to infer the independent effect of a genomic feature, holding constant all other genomic features. Using the MK regression, I identify numerous genomic features driving positive selection in chimpanzees. These features include well-known ones, such as local mutation rate, residue exposure level, tissue specificity, and immune genes, as well as new features not previously reported, such as gene expression level and metabolic genes. In particular, I show that highly expressed genes may have a higher adaptation rate than their weakly expressed counterparts, even though a higher expression level may impose stronger negative selection. Also, I show that metabolic genes may have a higher adaptation rate than their nonmetabolic counterparts, possibly due to recent changes in diet in primate evolution. Overall, the MK regression is a powerful approach to elucidate the genomic basis of adaptation.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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    Real-time discovery of AT2020xnd: a fast, luminous ultraviolet transient with minimal radioactive ejecta (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-09
    Description: The many unusual properties of the enigmatic AT2018cow suggested that at least some subset of the empirical class of fast blue optical transients (FBOTs) represents a genuinely new astrophysical phenomenon. Unfortunately, the intrinsic rarity and fleeting nature of these events have made it difficult to identify additional examples early enough to acquire the observations necessary to constrain theoretical models. We present here the Zwicky Transient Facility discovery of AT2020xnd (ZTF20acigmel, the ‘Camel’) at z = 0.243, the first unambiguous AT2018cow analogue to be found and confirmed in real time. AT2018cow and AT2020xnd share all key observational properties: a fast optical rise, sustained high photospheric temperature, absence of a second peak attributable to ejection of a radioactively heated stellar envelope, extremely luminous radio, millimetre, and X-ray emission, and a dwarf-galaxy host. This supports the argument that AT2018cow-like events represent a distinct phenomenon from slower-evolving radio-quiet supernovae, likely requiring a different progenitor or a different central engine. The sample properties of the four known members of this class to date disfavour tidal disruption models but are consistent with the alternative model of an accretion powered jet following the direct collapse of a massive star to a black hole. Contextual filtering of alert streams combined with rapid photometric verification using multiband imaging provides an efficient way to identify future members of this class, even at high redshift.
    Print ISSN: 0035-8711
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    Topics: Physics
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    Mean field dynamo action in shearing flows – II. Fluctuating kinetic helicity with zero mean (2021)
    Oxford University Press
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    Publication Date: 2021-10-05
    Description: Here we explore the role of temporal fluctuations in kinetic helicity on the generation of large-scale magnetic fields in the presence of a background linear shear flow. Key techniques involved here are same as in our earlier work, where we have used the renovating flow based model with shearing waves. Both the velocity and the helicity fields are treated as stochastic variables with finite correlation times, τ and τh, respectively. Growing solutions are obtained when τh 〉 τ, even when this time-scale separation, characterized by m = τh/τ, remains below the threshold for causing the turbulent diffusion to turn negative. In regimes when turbulent diffusion remains positive, and τ is of the order of eddy turnover time T, the axisymmetric modes display non-monotonic behaviour with shear rate S: both, the growth rate γ and the wavenumber k* corresponding to the fastest growing mode, first increase, reach a maximum and then decrease with |S|, with k* being always smaller than eddy-wavenumber, thus boosting growth of magnetic fields at large length-scales. The cycle period Pcyc of growing dynamo wave is inversely proportional to |S| at small shear, exactly similar to the fixed kinetic helicity case of our earlier work. This dependence becomes shallower at larger shear. Interestingly enough, various curves corresponding to different choices of m collapse on top of each other in a plot of mPcyc with |S|.
    Print ISSN: 0035-8711
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    Topics: Physics
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    First Annotated Genome of a Mandibulate Moth, Neomicropteryx cornuta, Generated Using PacBio HiFi Sequencing (2021)
    Oxford University Press
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    Publication Date: 2021-10-01
    Description: We provide a new, annotated genome assembly of Neomicropteryx cornuta, a species of the so-called mandibulate archaic moths (Lepidoptera: Micropterigidae). These moths belong to a lineage that is thought to have split from all other Lepidoptera more than 300 Ma and are consequently vital to understanding the early evolution of superorder Amphiesmenoptera, which contains the order Lepidoptera (butterflies and moths) and its sister order Trichoptera (caddisflies). Using PacBio HiFi sequencing reads, we assembled a highly contiguous genome with a contig N50 of nearly 17 Mb. The assembled genome length of 541,115,538 bp is about half the length of the largest published Amphiesmenoptera genome (Limnephilus lunatus, Trichoptera) and double the length of the smallest (Papilio polytes, Lepidoptera). We find high recovery of universal single copy orthologs with 98.1% of BUSCO genes present and provide a genome annotation of 15,643 genes aided by resolved isoforms from PacBio IsoSeq data. This high-quality genome assembly provides an important resource for studying ecological and evolutionary transitions in the early evolution of Amphiesmenoptera.
    Electronic ISSN: 1759-6653
    Topics: Biology
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    Formation and persistence of polyglutamine aggregates in mistranslating cells (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: In neurodegenerative diseases, including pathologies with well-known causative alleles, genetic factors that modify severity or age of onset are not entirely understood. We recently documented the unexpected prevalence of transfer RNA (tRNA) mutants in the human population, including variants that cause amino acid mis-incorporation. We hypothesized that a mistranslating tRNA will exacerbate toxicity and modify the molecular pathology of Huntington's disease-causing alleles. We characterized a tRNAPro mutant that mistranslates proline codons with alanine, and tRNASer mutants, including a tRNASerAGA G35A variant with a phenylalanine anticodon (tRNASerAAA) found in ∼2% of the population. The tRNAPro mutant caused synthetic toxicity with a deleterious huntingtin poly-glutamine (polyQ) allele in neuronal cells. The tRNASerAAA variant showed synthetic toxicity with proteasome inhibition but did not enhance toxicity of the huntingtin allele. Cells mistranslating phenylalanine or proline codons with serine had significantly reduced rates of protein synthesis. Mistranslating cells were slow but effective in forming insoluble polyQ aggregates, defective in protein and aggregate degradation, and resistant to the neuroprotective integrated stress response inhibitor (ISRIB). Our findings identify mistranslating tRNA variants as genetic factors that slow protein aggregation kinetics, inhibit aggregate clearance, and increase drug resistance in cellular models of neurodegenerative disease.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    Impact of massive binary star and cosmic evolution on gravitational wave observations I: black hole–neutron star mergers (2021)
    Oxford University Press
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    Publication Date: 2021-09-23
    Description: Mergers of black hole–neutron star (BHNS) binaries have now been observed by gravitational wave (GW) detectors with the recent announcement of GW200105 and GW200115. Such observations not only provide confirmation that these systems exist but will also give unique insights into the death of massive stars, the evolution of binary systems and their possible association with gamma-ray bursts, r-process enrichment, and kilonovae. Here, we perform binary population synthesis of isolated BHNS systems in order to present their merger rate and characteristics for ground-based GW observatories. We present the results for 420 different model permutations that explore key uncertainties in our assumptions about massive binary star evolution (e.g. mass transfer, common-envelope evolution, supernovae), and the metallicity-specific star formation rate density, and characterize their relative impacts on our predictions. We find intrinsic local BHNS merger rates spanning $mathcal {R}_{ m {m}}^0 approx$ 4–830 $, m {Gpc}^{-3}$$, m {yr}^{-1}$ for our full range of assumptions. This encompasses the rate inferred from recent BHNS GW detections and would yield detection rates of $mathcal {R}_{ m {det}} approx 1$–180$, m {yr}^{-1}$ for a GW network consisting of LIGO, Virgo, and KAGRA at design sensitivity. We find that the binary evolution and metallicity-specific star formation rate density each impacts the predicted merger rates by order $mathcal {O}(10)$. We also present predictions for the GW-detected BHNS merger properties and find that all 420 model variations predict that $lesssim 5{{ m per cent}}$ of the BHNS mergers have BH masses $m_{ m {BH}} gtrsim 18, m {M}_{odot }$, total masses $m_{ m {tot}} gtrsim 20, m {M}_{odot }$, chirp masses ${mathcal {M}}_{ m {c}} gtrsim 5.5, m {M}_{odot }$, and mass ratios qf ≳ 12 or qf ≲ 2. Moreover, we find that massive NSs with $m_{ m {NS}} gt 2, m {M}_{odot }$ are expected to be commonly detected in BHNS mergers in almost all our model variations. Finally, a wide range of $sim 0{{ m per cent}}$ to $70{{ m per cent}}$ of the BHNS mergers are predicted to eject mass during the merger. Our results highlight the importance of considering variations in binary evolution and cosmological models when predicting, and eventually evaluating, populations of BHNS mergers.
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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
    Published by Oxford University Press
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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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    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.
    Print ISSN: 0035-8711
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    Topics: Physics
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    Hidden Historical Habitat-Linked Population Divergence and Contemporary Gene Flow of a Deep-Sea Patellogastropod Limpet (2021)
    Oxford University Press
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    Publication Date: 2021-09-17
    Description: Hydrothermal vents and hydrocarbon seeps in the deep ocean are rare oases fueled by chemosynthesis. Biological communities inhabiting these ecosystems are often distributed in widely separated habitats, raising intriguing questions on how these organisms achieve connectivity and whether habitat types facilitate intraspecific divergence. The deep-sea patellogastropod limpet Bathyacmaea nipponica that colonizes both vents and seeps across ∼2,400 km in the Northwest Pacific is a feasible model to answer these questions. We analyzed 123 individuals from four vents and three seeps using a comprehensive method incorporating population genomics and physical ocean modeling. Genome survey sequencing and genotyping-by-sequencing resulted in 9,838 single-nucleotide polymorphisms for population genomic analyses. Genetic divergence and demographic analyses revealed four habitat-linked (i.e., three seep and one vent) genetic groups, with the vent genetic group established via the opportunistic invasion of a few limpet larvae from a nearby seep genetic group. TreeMix analysis uncovered three historical seep-to-vent migration events. ADMIXTURE and divMigrate analyses elucidated weak contemporary gene flow from a seep genetic group to the vent genetic group. Physical ocean modeling underlined the potential roles of seafloor topography and ocean currents in shaping the genetic connectivity, contemporary migration, and local hybridization of these deep-sea limpets. Our study highlighted the power of integrating genomic and oceanographic approaches in deciphering the demography and diversification of deep-sea organisms. Given the increasing anthropogenic activities (e.g., mining and gas hydrate extraction) affecting the deep ocean, our results have implications for the conservation of deep-sea biodiversity and establishment of marine protected areas.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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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
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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
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    Topics: Biology
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    The meristem-associated endosymbiont Methylorubrum extorquens DSM13060 reprograms development and stress responses of pine seedlings (2021)
    Oxford University Press
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    Publication Date: 2021-07-29
    Description: Microbes living in plant tissues—endophytes—are mainly studied in crop plants where they typically colonize the root apoplast. Trees—a large carbon source with a high capacity for photosynthesis—provide a variety of niches for endophytic colonization. We have earlier identified a new type of plant–endophyte interaction in buds of adult Scots pine, where Methylorubrum species live inside the meristematic cells. The endosymbiont Methylorubrum extorquens DSM13060 significantly increases needle and root growth of pine seedlings without producing plant hormones, but by aggregating around host nuclei. Here, we studied gene expression and metabolites of the pine host induced by M. extorquens DSM13060 infection. Malic acid was produced by pine to potentially boost M. extorquens colonization and interaction. Based on gene expression, the endosymbiont activated the auxin- and ethylene (ET)-associated hormonal pathways through induction of CUL1 and HYL1, and suppressed salicylic and abscisic acid signaling of pine. Infection by the endosymbiont had an effect on pine meristem and leaf development through activation of GLP1-7 and ALE2, and suppressed flowering, root hair and lateral root formation by downregulation of AGL8, plantacyanin, GASA7, COW1 and RALFL34. Despite of systemic infection of pine seedlings by the endosymbiont, the pine genes CUL1, ETR2, ERF3, HYL, GLP1-7 and CYP71 were highly expressed in the shoot apical meristem, rarely in needles and not in stem or root tissues. Low expression of MERI5, CLH2, EULS3 and high quantities of ononitol suggest that endosymbiont promotes viability and protects pine seedlings against abiotic stress. Our results indicate that the endosymbiont positively affects host development and stress tolerance through mechanisms previously unknown for endophytic bacteria, manipulation of plant hormone signaling pathways, downregulation of senescence and cell death-associated genes and induction of ononitol biosynthesis.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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    Mistranslation Reduces Mutation Load in Evolving Proteins through Negative Epistasis with DNA Mutations (2021)
    Oxford University Press
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    Publication Date: 2021-07-13
    Description: Translational errors during protein synthesis cause phenotypic mutations that are several orders of magnitude more frequent than DNA mutations. Such phenotypic mutations may affect adaptive evolution through their interactions with DNA mutations. To study how mistranslation may affect the adaptive evolution of evolving proteins, we evolved populations of green fluorescent protein (GFP) in either high-mistranslation or low-mistranslation Escherichia coli hosts. In both hosts, we first evolved GFP under purifying selection for the ancestral phenotype green fluorescence, and then under directional selection toward the new phenotype yellow fluorescence. High-mistranslation populations evolved modestly higher yellow fluorescence during each generation of evolution than low-mistranslation populations. We demonstrate by high-throughput sequencing that elevated mistranslation reduced the accumulation of deleterious DNA mutations under both purifying and directional selection. It did so by amplifying the fitness effects of deleterious DNA mutations through negative epistasis with phenotypic mutations. In contrast, mistranslation did not affect the incidence of beneficial mutations. Our findings show that phenotypic mutations interact epistatically with DNA mutations. By reducing a population’s mutation load, mistranslation can affect an important determinant of evolvability.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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    Genomic Signatures Supporting the Symbiosis and Formation of Chitinous Tube in the Deep-Sea Tubeworm Paraescarpia echinospica (2021)
    Oxford University Press
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    Publication Date: 2021-07-13
    Description: Vestimentiferan tubeworms are iconic animals that present as large habitat-forming chitinized tube bushes in deep-sea chemosynthetic ecosystems. They are gutless and depend entirely on their endosymbiotic sulfide-oxidizing chemoautotrophic bacteria for nutrition. Information on the genomes of several siboglinid endosymbionts has improved our understanding of their nutritional supplies. However, the interactions between tubeworms and their endosymbionts remain largely unclear due to a paucity of host genomes. Here, we report the chromosome-level genome of the vestimentiferan tubeworm Paraescarpia echinospica. We found that the genome has been remodeled to facilitate symbiosis through the expansion of gene families related to substrate transfer and innate immunity, suppression of apoptosis, regulation of lysosomal digestion, and protection against oxidative stress. Furthermore, the genome encodes a programmed cell death pathway that potentially controls the endosymbiont population. Our integrated genomic, transcriptomic, and proteomic analyses uncovered matrix proteins required for the formation of the chitinous tube and revealed gene family expansion and co-option as evolutionary mechanisms driving the acquisition of this unique supporting structure for deep-sea tubeworms. Overall, our study provides novel insights into the host’s support system that has enabled tubeworms to establish symbiosis, thrive in deep-sea hot vents and cold seeps, and produce the unique chitinous tubes in the deep sea.
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    Topics: Biology
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    MeerKAT-64 discovers wide-spread tidal debris in the nearby NGC 7232 galaxy group (2021)
    Oxford University Press
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    Publication Date: 2021-06-02
    Description: We report the discovery of large amounts of previously undetected cold neutral atomic hydrogen (H i) around the core triplet galaxies in the nearby NGC 7232 galaxy group with MeerKAT. With a physical resolution of ∼1 kpc, we detect a complex web of low-surface-brightness H i emission down to a 4σ column density level of ∼1 × 1019 cm−2 (over 44  km s−1). The newly discovered H i streams extend over ∼20 arcmin corresponding to 140 kpc in projection. This is approximately three times the H i extent of the galaxy triplet (52 kpc). The H i debris has an H i mass of ∼6.6 × 109 M⊙, more than 50 per cent of the total H i mass of the triplet. Within the galaxy triplet, NGC 7233 and NGC 7232 have lost a significant amount of H i while NGC 7232B appears to have an excess of H i. The H i deficiency in NGC 7232 and NGC 7233 indicates that galaxy–galaxy interaction in the group concentrates on this galaxy pair while the other disc galaxies have visited them over time. In comparison to the AMIGA sample of isolated galaxies, we find that with regards to its total H i mass the NGC 7232/3 galaxy triplet is not H i-deficient. Despite the many interactions associated to the triplet galaxies, no H i seems to have been lost from the group (yet).
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    Topics: Physics
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    An Independent Evolutionary Origin for Insect Deterrent Cucurbitacins in Iberis amara (2021)
    Oxford University Press
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    Publication Date: 2021-07-15
    Description: Pieris rapae and Phyllotreta nemorum are Brassicaceae specialists, but do not feed on Iberis amara spp. that contain cucurbitacins. The cucurbitacins are highly oxygenated triterpenoid, occurring widespread in cucurbitaceous species and in a few other plant families. Using de novo assembled transcriptomics from I. amara, gene co-expression analysis and comparative genomics, we unraveled the evolutionary origin of the insect deterrent cucurbitacins in I. amara. Phylogenetic analysis of five oxidosqualene cyclases and heterologous expression allowed us to identify the first committed enzyme in cucurbitacin biosynthesis in I. amara, cucurbitadienol synthase (IaCPQ). In addition, two species-specific cytochrome P450s (CYP708A16 and CYP708A15) were identified that catalyze the unique C16 and C22 hydroxylation of the cucurbitadienol backbone, enzymatic steps that have not been reported before. Furthermore, the draft genome assembly of I. amara showed that the IaCPQ was localized to the same scaffold together with CYP708A15 but spanning over 100 kb, this contrasts with the highly organized cucurbitacin gene cluster in the cucurbits. These results reveal that cucurbitacin biosynthesis has evolved convergently via different biosynthetic routes in different families rather than through divergence from an ancestral pathway. This study thus provides new insight into the mechanism of recurrent evolution and diversification of a plant defensive chemical.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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    Local border reforms and economic activity (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-30
    Description: In this article, we make use of large-scale municipal border changes in Germany to provide the first evidence on the effect of local border changes on the distribution of activity in space. To allow for a comparison of economic activity within unique geographical units over time, we use geo-coded light data as well as local land-use data. Applying a difference-in-differences approach, we find evidence that municipalities absorbing their merger partners and hosting the new administrative center experience a significant increase in local activity, while the municipalities that are being absorbed and are losing the administrative center experience a decrease in such activity. The difference between the gains in activity from absorbing municipalities and the losses from absorbed ones is positive. These previously undocumented results point to the importance of distance to the administrative center as a determinant of the spatial distribution of economic activity.
    Print ISSN: 1468-2702
    Electronic ISSN: 1468-2710
    Topics: Geography , Economics
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    LEDet: A Single-Shot Real-Time Object Detector Based on Low-Light Image Enhancement (2021)
    Oxford University Press
    Details
    Publication Date: 2021-05-14
    Description: Recently, significant breakthroughs have been achieved in the field of object detection. However, existing methods mostly focus on the generic object detection task. Performance degradation can be unavoidable when applying the existing methods to some specific situations directly, e.g. a low-light environment. To address this issue, we propose a single-shot real-time object Detector based on Low-light image Enhancement, namely LEDet. LEDet adapts itself to the low-light detection task in three aspects. First, a low-light enhancement module is introduced as the image preprocessor, producing the augmented inputs from the low-light images. Second, two modules, i.e. low-light and enhanced features fusion module and the scale-aware channel attention dilated convolution module are designed. These two modules aim at learning robust and discriminative features from objects of various sizes hidden in the darkness. In experiments, we validate the effectiveness of each part of our LEDet model via several ablation studies. We also compare LEDet with various methods on the Exclusively Dark dataset, showing that our model achieves the state-of-the-art performance on the balance between speed and accuracy.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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    Global and Local Structure Preservation for Nonlinear High-dimensional Spectral Clustering (2021)
    Oxford University Press
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    Publication Date: 2021-05-14
    Description: Spectral clustering is widely applied in real applications, as it utilizes a graph matrix to consider the similarity relationship of subjects. The quality of graph structure is usually important to the robustness of the clustering task. However, existing spectral clustering methods consider either the local structure or the global structure, which can not provide comprehensive information for clustering tasks. Moreover, previous clustering methods only consider the simple similarity relationship, which may not output the optimal clustering performance. To solve these problems, we propose a novel clustering method considering both the local structure and the global structure for conducting nonlinear clustering. Specifically, our proposed method simultaneously considers (i) preserving the local structure and the global structure of subjects to provide comprehensive information for clustering tasks, (ii) exploring the nonlinear similarity relationship to capture the complex and inherent correlation of subjects and (iii) embedding dimensionality reduction techniques and a low-rank constraint in the framework of adaptive graph learning to reduce clustering biases. These constraints are considered in a unified optimization framework to result in one-step clustering. Experimental results on real data sets demonstrate that our method achieved competitive clustering performance in comparison with state-of-the-art clustering methods.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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    Robust gene coexpression networks using signed distance correlation (2021)
    Oxford University Press
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    Publication Date: 2021-02-01
    Description: Motivation Even within well-studied organisms, many genes lack useful functional annotations. One way to generate such functional information is to infer biological relationships between genes/proteins, using a network of gene coexpression data that includes functional annotations. However, the lack of trustworthy functional annotations can impede the validation of such networks. Hence, there is a need for a principled method to construct gene coexpression networks that capture biological information and are structurally stable even in the absence of functional information. Results We introduce the concept of signed distance correlation as a measure of dependency between two variables, and apply it to generate gene coexpression networks. Distance correlation offers a more intuitive approach to network construction than commonly used methods, such as Pearson correlation and mutual information. We propose a framework to generate self-consistent networks using signed distance correlation purely from gene expression data, with no additional information. We analyse data from three different organisms to illustrate how networks generated with our method are more stable and capture more biological information compared to networks obtained from Pearson correlation or mutual information. Availability and implementation Code is available online (https://github.com/javier-pardodiaz/sdcorGCN). Supplementary information Supplementary data are available at Bioinformatics online.
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    Topics: Biology , Computer Science , Medicine
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    Chromosomal-Level Genome Assembly of a True Bug, Aspongopus chinensis Dallas, 1851 (Hemiptera: Dinidoridae) (2021)
    Oxford University Press
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    Publication Date: 2021-10-01
    Description: The true bug, Aspongopus chinensis Dallas, 1851 (Hemiptera: Dinidoridae), is a fascinating insect with prolonged diapause and medicinal properties but also a notorious pest. However, because of the lack of genomic resources, an in-depth understanding of its biological characteristics is lacking. Here, we report the first genome assembly of A. chinensis anchored to 10 pseudochromosomes, which was achieved by combining PacBio long reads and Hi-C sequencing data. This chromosome-level genome assembly was 1.55 Gb in size with a scaffold N50 of 156 Mb. The benchmarking universal single-copy ortholog (BUSCO) analysis of the assembly captured 96.6% of the BUSCO genes. A total of 686,888,052 bp of repeat sequences, 18,511 protein-coding genes, and 1,749 noncoding RNAs were annotated. By comparing the A. chinensis genome with that of 8 homologous insects and 2 model organisms, 213 rapidly evolving gene families were identified, including 83 expanded and 130 contracted gene families. The functional enrichment of Gene Ontology and KEGG pathways showed that the significantly expanded gene families were primarily involved in metabolism, immunity, detoxification, and DNA/RNA replication associated with stress responses. The data reported here shed light on the ecological adaptation of A. chinensis and further expanded our understanding of true bug evolution in general.
    Electronic ISSN: 1759-6653
    Topics: Biology
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    Improving IGM temperature constraints using wavelet analysis on high-redshift quasars (2021)
    Oxford University Press
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    Publication Date: 2021-10-09
    Description: The thermal state of the intergalactic medium contains vital information about the epoch of reionization, one of the most transformative yet poorly understood periods in the young Universe. This thermal state is encoded in the small-scale structure of Lyman-α (Ly α) absorption in quasar spectra. The 1D flux power spectrum measures the average small-scale structure along quasar sightlines. At high redshifts, where the opacity is large, averaging mixes high signal-to-noise ratio transmission spikes with noisy absorption troughs. Wavelet amplitudes are an alternate statistic that maintains spatial information while quantifying fluctuations at the same spatial frequencies as the power spectrum, giving them the potential to more sensitively measure the small-scale structure. Previous Ly α forest studies using wavelet amplitude probability density functions (PDFs) used limited spatial frequencies and neglected strong correlations between PDF bins and across wavelets scales, resulting in suboptimal and unreliable parameter inference. Here we present a novel method for performing statistical inference using wavelet amplitude PDFs that spans the full range of spatial frequencies probed by the power spectrum and that fully accounts for these correlations. We applied this procedure to realistic mock data drawn from a simple thermal model parametrized by the temperature at mean density, T0, and find that wavelets deliver 1σ constraints on T0 that are on average 7 per cent more sensitive at z = 5 (12 per cent at z = 6) than those from the power spectrum. We consider the possibility of combing wavelet PDFs with the power, but find that this does not lead to improved sensitivity.
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    Topics: Physics
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    SDSS-IV MaNGA: drivers of stellar metallicity in nearby galaxies (2021)
    Oxford University Press
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    Publication Date: 2021-10-09
    Description: The distribution of stellar metallicities within and across galaxies is an excellent relic of the chemical evolution across cosmic time. We present a detailed analysis of spatially resolved stellar populations based on 〉2.6 million spatial bins from 7439 nearby galaxies in the Sloan Digital Sky Survey-IV (SDSS-IV) Mapping Nearby Galaxies at APO (MaNGA) survey. To account for accurate inclination corrections, we derive an equation for morphology-dependent determination of galaxy inclinations. Our study goes beyond the well-known global mass–metallicity relation and radial metallicity gradients by providing a statistically sound exploration of local relations between stellar metallicity [Z/H], stellar surface mass density Σ⋆, and galactocentric distance in the global mass–morphology plane. We find a significant resolved mass density–metallicity relation $rSigma _star ZR$ for galaxies of all types and masses above $10^{9.8}, mathrm{M_odot }$. Different radial distances make an important contribution to the spread of the relation. Particularly, in low- and intermediate-mass galaxies, we find that at fixed Σ⋆ metallicity increases with radius independently of morphology. For high masses, this radial dependence is only observed in high Σ⋆ regions of spiral galaxies. This result calls for a driver of metallicity, in addition to Σ⋆ that promotes chemical enrichment in the outer parts of galaxies more strongly than in the inner parts. We discuss gas accretion, outflows, recycling, and radial migration as possible scenarios.
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    Proper motions of OB stars in the far Carina Arm (2021)
    Oxford University Press
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    Publication Date: 2021-10-11
    Description: In large-scale maps of the Galactic disc, the Carina Arm stands out as a clear spiral feature, hosting prominent star clusters and associations rich in massive stars. We study the proper motions of 4199 O and early B most likely in the far Carina Arm, at distances mainly in excess of 4 kpc from the Sun, within the sky region, 282° 〈 ℓ 〈 294° and −3° 〈 b 〈 +1° (Galactic coordinates). The sample is constructed by extending an existing blue-selected catalogue, and cross-matching with Gaia EDR3 astrometry. The observed pattern of proper motions is modulated into a saw-tooth pattern, with full amplitude approaching 1 mas yr−1, recurring roughly every 2–3 degrees of longitude (200–300 pc at the median OB-star distance of 5.8 kpc). Kinematic perturbation of underlying circular rotation is most likely present. The data also reveal a moving group containing 〉50 OB stars at ℓ ∼ 286°, b ∼ −1.4° behind the main run of the far arm. An analysis of relative proper motions is performed that yields an incidence of runaway O stars of at least 10 per cent (potentially 〉20 per cent when full space motions become available). To map where runaways have run away from, we set up simulations for the region that assume linear trajectories and test for trajectory impact parameter in order to identify likely ejection hot spots. We find the method currently gives good results for times of flight of up to ∼4 Myr. It shows convincingly that only NGC 3603 and Westerlund 2 have ejected OB stars in significant numbers. Indeed, both clusters have experienced intense spells of ejection between 0.6–0.9 and 0.5–0.8 Myr ago, respectively.
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    Action-based distribution function modelling for constraining the shape of the Galactic dark matter halo (2021)
    Oxford University Press
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    Publication Date: 2021-10-08
    Description: We estimate the 3D density profile of the Galactic dark matter (DM) halo within r ≲ 30 kpc from the Galactic centre by using the astrometric data for halo RR Lyrae stars from Gaia DR2. We model both the stellar halo distribution function and the Galactic potential, fully taking into account the survey selection function, the observational errors, and the missing line-of-sight velocity data for RR Lyrae stars. With a Bayesian method, we infer the model parameters, including the density flattening of the DM halo q, which is assumed to be constant as a function of radius. We find that 99 per cent of the posterior distribution of q is located at q 〉 0.963, which strongly disfavours a flattened DM halo. We cannot draw any conclusions as to whether the Galactic DM halo at $r lesssim 30 , mathrm{kpc}$ is prolate, because we restrict ourselves to axisymmetric oblate halo models with q ≤ 1. Our DM density profile might be biased especially in the inner few kpc, due to the uncertainty in the baryonic distribution. Our result is in tension with predictions from cosmological hydrodynamical simulations that advocate more oblate (〈q〉 ∼ 0.8 ± 0.15) DM haloes within ${sim}15{{ m per cent}}$ of the virial radius for Milky-Way-sized galaxies. An alternative possibility, based on our validation tests with a cosmological simulation, is that the true value q of the Galactic halo could be consistent with cosmological simulations but that disequilibrium in the Milky Way potential is inflating our measurement of q by 0.1–0.2. As a by-product, our model constrains the DM density in the Solar neighbourhood to be $ ho _{mathrm{DM},odot } = (9.01^{+0.18}_{-0.20})imes 10^{-3}{, m M_odot} mathrm{pc}^{-3} = 0.342^{+0.007}_{-0.007}$ GeVcm−3, consistent with other recent measurements.
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    BrainBase: a curated knowledgebase for brain diseases (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: Brain is the central organ of the nervous system and any brain disease can seriously affect human health. Here we present BrainBase (https://ngdc.cncb.ac.cn/brainbase), a curated knowledgebase for brain diseases that aims to provide a whole picture of brain diseases and associated genes. Specifically, based on manual curation of 2768 published articles along with information retrieval from several public databases, BrainBase features comprehensive collection of 7175 disease–gene associations spanning a total of 123 brain diseases and linking with 5662 genes, 16 591 drug–target interactions covering 2118 drugs/chemicals and 623 genes, and five types of specific genes in light of expression specificity in brain tissue/regions/cerebrospinal fluid/cells. In addition, considering the severity of glioma among brain tumors, the current version of BrainBase incorporates 21 multi-omics datasets, presents molecular profiles across various samples/conditions and identifies four groups of glioma featured genes with potential clinical significance. Collectively, BrainBase integrates not only valuable curated disease–gene associations and drug–target interactions but also molecular profiles through multi-omics data analysis, accordingly bearing great promise to serve as a valuable knowledgebase for brain diseases.
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    Topics: Biology
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    SMILE: Mutual Information Learning for Integration of Single-cell Omics Data (2021)
    Oxford University Press
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    Publication Date: 2021-10-08
    Description: Motivation Deep learning approaches have empowered single-cell omics data analysis in many ways and generated new insights from complex cellular systems. As there is an increasing need for single cell omics data to be integrated across sources, types, and features of data, the challenges of integrating single-cell omics data are rising. Here, we present an unsupervised deep learning algorithm that learns discriminative representations for single-cell data via maximizing mutual information, SMILE (Single-cell Mutual Information Learning). Results Using a unique cell-pairing design, SMILE successfully integrates multi-source single-cell transcriptome data, removing batch effects and projecting similar cell types, even from different tissues, into the shared space. SMILE can also integrate data from two or more modalities, such as joint profiling technologies using single-cell ATAC-seq, RNA-seq, DNA methylation, Hi-C, and ChIP data. When paired cells are known, SMILE can integrate data with unmatched feature, such as genes for RNA-seq and genome wide peaks for ATAC-seq. Integrated representations learned from joint profiling technologies can then be used as a framework for comparing independent single source data. Supplementary information Supplementary data are available at Bioinformatics online. The source code of SMILE including analyses of key results in the study can be found at: https://github.com/rpmccordlab/SMILE.
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    Topics: Biology , Computer Science , Medicine
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    RBM6 splicing factor promotes homologous recombination repair of double-strand breaks and modulates sensitivity to chemotherapeutic drugs (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: RNA-binding proteins regulate mRNA processing and translation and are often aberrantly expressed in cancer. The RNA-binding motif protein 6, RBM6, is a known alternative splicing factor that harbors tumor suppressor activity and is frequently mutated in human cancer. Here, we identify RBM6 as a novel regulator of homologous recombination (HR) repair of DNA double-strand breaks (DSBs). Mechanistically, we show that RBM6 regulates alternative splicing-coupled nonstop-decay of a positive HR regulator, Fe65/APBB1. RBM6 knockdown leads to a severe reduction in Fe65 protein levels and consequently impairs HR of DSBs. Accordingly, RBM6-deficient cancer cells are vulnerable to ATM and PARP inhibition and show remarkable sensitivity to cisplatin. Concordantly, cisplatin administration inhibits the growth of breast tumor devoid of RBM6 in mouse xenograft model. Furthermore, we observe that RBM6 protein is significantly lost in metastatic breast tumors compared with primary tumors, thus suggesting RBM6 as a potential therapeutic target of advanced breast cancer. Collectively, our results elucidate the link between the multifaceted roles of RBM6 in regulating alternative splicing and HR of DSBs that may contribute to tumorigenesis, and pave the way for new avenues of therapy for RBM6-deficient tumors.
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    BioVAE: a pre-trained latent variable language model for biomedical text mining (2021)
    Oxford University Press
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    Publication Date: 2021-10-12
    Description: Summary Large scale pre-trained language models (PLMs) have advanced state-of-the-art (SOTA) performance on various biomedical text mining tasks. The power of such PLMs can be combined with the advantages of deep generative models. These are examples of these combinations. However, they are trained only on general domain text, and biomedical models are still missing. In this work, we describe BioVAE, the first large scale pre-trained latent variable language model for the biomedical domain, which uses the OPTIMUS framework to train on large volumes of biomedical text. The model shows SOTA performance on several biomedical text mining tasks when compared to existing publicly available biomedical PLMs. Additionally, our model can generate more accurate biomedical sentences than the original OPTIMUS output. Availability Our source code and pre-trained models are freely available: https://github.com/aistairc/BioVAE Supplementary information Supplementary data are available at Bioinformatics online.
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    VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports 〉500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate 〉1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC.
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    FlyAtlas 2 in 2022: enhancements to the Drosophila melanogaster expression atlas (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: FlyAtlas 2 (flyatlas2.org) is a database and web application for studying the expression of the genes of Drosophila melanogaster in different tissues of adults and larvae. It is based on RNA-Seq data, and incorporates both genes encoding proteins and microRNAs. We have now completed the population of the database with 13 tissues from both male and female adults, five sex-specific tissues, and eight larval tissues. Larval garland cell nephrocytes have also been included. Major enhancements have been made to the application. First, a facility has been added for a ‘Profile’ search for genes with a similar pattern of tissue expression as a query gene. This may help establish the function of genes for which this is currently unknown. Second, a facility has been added dedicated to the larval midgut, where the difference in gene expression in the five regions of different pH can be explored. A variety of further improvements to the interface are described.
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    Radiative energy from a reconnection region around massive black hole (2021)
    Oxford University Press
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    Publication Date: 2021-10-11
    Description: In the previous numerical study, we find the blob formation and ejection in the presence of magnetic reconnection in the environment of the hot flow of the accretion disc. Based on those encouraging results, in the present work, we calculate the energy and the spectrum of the emission in the different bands around sagittarius A* (Sgr A*). We assume the electrons in the magnetic reconnection region are non-thermal and emit synchrotron radiation. The electrons in the other region are thermal, which follows the thermal distribution, and the thermal electron emission mechanism is thermal synchrotron radiation. During the whole process of the magnetic evolution and reconnection, we find two peaks in the temporal light curve in the recently observed radio frequencies (230 and 43 GHz) and near-infrared (NIR) wavelengths (3.8 and 2.2 μm). Although the light curve of the NIR band is most prominent in a single peak. The first peak appears because of the blob in the plasma flow, which is formed due to the magnetic reconnection. The second peak appears due to the production of the non-thermal electrons with the evolution of the magnetic flux. Both peaks reach luminosity of more than 1026 erg s−1 for a single plasmoid/blob. For the NIR band, the highest luminosity can reach more than 1028 erg s−1. These luminosities can be high for the large simulation area and the stronger magnetic field with the multiple blobs. We infer that the observed flares are a group of magnetic reconnection phenomena, not a single one.
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    ImmuCellAI-mouse: a tool for comprehensive prediction of mouse immune cell abundance and immune microenvironment depiction (2021)
    Oxford University Press
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    Publication Date: 2021-10-12
    Description: Motivation Immune cells are important components of the immune system and are crucial for disease initiation, progression, prognosis, and survival. Although several computational methods have been designed for predicting the abundance of immune cells, very few tools are applicable to mouse. Given that mouse is the most widely used animal model in biomedical research, there is an urgent need to develop a precise algorithm for predicting mouse immune cells. Results We developed a tool named ImmuCellAI-mouse (Immune Cell Abundance Identifier for mouse), for estimating the abundance of 36 immune cell (sub)types from gene expression data in a hierarchical strategy of three layers. Reference expression profile and robust marker gene sets of immune cell types were curated. The abundance of cells in three layers was predicted separately by calculating the ssGSEA enrichment score of the expression deviation profile per cell type. Benchmark results showed high accuracy of ImmuCellAI-mouse in predicting most immune cell types, with correlation coefficients between predicted value and real cell proportion of most cell types being larger than 0.8. We applied ImmuCellAI-mouse to a mouse breast tumor dataset and revealed the dynamic change of immune cell infiltration during treatment, which is consistent with the findings of the original study but with more details. We also constructed an online server for ImmuCellAI-mouse, on which users can upload expression matrices for analysis. ImmuCellAI-mouse will be a useful tool for studying the immune microenvironment, cancer immunology, and immunotherapy in mouse models, providing an indispensable supplement for human disease studies. Availability Software is available at http://bioinfo.life.hust.edu.cn/ImmuCellAI-mouse/ Supplementary information Supplementary data are available at Bioinformatics online.
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    Detecting Selection in Multiple Populations by Modeling Ancestral Admixture Components (2021)
    Oxford University Press
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    Publication Date: 2021-10-09
    Description: One of the most powerful and commonly used approaches for detecting local adaptation in the genome is the identification of extreme allele frequency differences between populations. In this article, we present a new maximum likelihood method for finding regions under positive selection. It is based on a Gaussian approximation to allele frequency changes and it incorporates admixture between populations. The method can analyze multiple populations simultaneously and retains power to detect selection signatures specific to ancestry components that are not representative of any extant populations. Using simulated data, we compare our method to related approaches, and show that it is orders of magnitude faster than the state-of-the-art, while retaining similar or higher power for most simulation scenarios. We also apply it to human genomic data and identify loci with extreme genetic differentiation between major geographic groups. Many of the genes identified are previously known selected loci relating to hair pigmentation and morphology, skin, and eye pigmentation. We also identify new candidate regions, including various selected loci in the Native American component of admixed Mexican-Americans. These involve diverse biological functions, such as immunity, fat distribution, food intake, vision, and hair development.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
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    Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022 (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support global research in both academia and industry. With the explosively accumulated multi-omics data at ever-faster rates, CNCB-NGDC is constantly scaling up and updating its core database resources through big data archive, curation, integration and analysis. In the past year, efforts have been made to synthesize the growing data and knowledge, particularly in single-cell omics and precision medicine research, and a series of resources have been newly developed, updated and enhanced. Moreover, CNCB-NGDC has continued to daily update SARS-CoV-2 genome sequences, variants, haplotypes and literature. Particularly, OpenLB, an open library of bioscience, has been established by providing easy and open access to a substantial number of abstract texts from PubMed, bioRxiv and medRxiv. In addition, Database Commons is significantly updated by cataloguing a full list of global databases, and BLAST tools are newly deployed to provide online sequence search services. All these resources along with their services are publicly accessible at https://ngdc.cncb.ac.cn.
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    FindNonCoding: rapid and simple detection of non-coding RNAs in genomes (2021)
    Oxford University Press
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    Publication Date: 2021-10-12
    Description: Summary Non-coding RNAs are often neglected during genome annotation due to their difficulty of detection relative to protein coding genes. FindNonCoding takes a pattern mining approach to capture the essential sequence motifs and hairpin loops representing a non-coding RNA family and quickly identify matches in genomes. FindNonCoding was designed for ease of use and accurately finds non-coding RNAs with a low false discovery rate. Availability and implementation FindNonCoding is implemented within the DECIPHER package (v2.19.3) for R (v4.1) available from Bioconductor. Pre-trained models of common non-coding RNA families are included for bacteria, archaea and eukarya. Supplementary information Supplementary data are available at Bioinformatics online.
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    The boosted potential (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-09
    Description: The global gravitational potential, ϕ, is not commonly employed in the analysis of cosmological simulations, since its level sets do not show any clear correspondence to the underlying density field and its persistent structures. Here, we show that the potential becomes a locally meaningful quantity when considered from a boosted frame of reference, defined by subtracting a uniform gradient term $phi _{ m {boost}}( oldsymbol{x}) = phi ( oldsymbol{x}) + oldsymbol{x} cdot oldsymbol{a}_0$ with acceleration $ oldsymbol{a}_0$. We study this ‘boosted potential’ in a variety of scenarios and propose several applications: (1) The boosted potential can be used to define a binding criterion that naturally incorporates the effect of tidal fields. This solves several problems of commonly used self-potential binding checks: (i) it defines a tidal boundary for each halo, (ii) it is much less likely to misidentify caustics as haloes (specially in the context of warm dark matter cosmologies), and (iii) performs better at identifying virialized regions of haloes – yielding to the expected value of 2 for the virial ratio. (2) This binding check can be generalized to filaments and other cosmic structures. (3) The boosted potential facilitates the understanding of the disruption of satellite subhaloes. We propose a picture where most mass loss is explained through a lowering of the escape energy through the tidal field. (4) We discuss the possibility of understanding the topology of the potential field in a way that is independent of constant offsets in the first derivative $ oldsymbol{a}_0$. We foresee that this novel perspective on the potential can help to develop more accurate models and improve our understanding of structure formation.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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    3D MHD simulations of the supernova remnant CTB 109 (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-11
    Description: We examine the evolution and emission of the supernova remnant (SNR) CTB 109 using 3D magnetohydrodynamics simulations. The SNR evolves in a medium divided by a plane interface into two media with different densities and pressure equilibrium. Our results reveal that a remnant with the characteristics of CTB 109 is formed provided the supernova (SN) explosion takes place in the less dense medium and also if the interstellar magnetic field (ISMF) is almost uniform. Finally, we conclude that the quasi-parallel mechanism can explain the brightness synchrotron emission and the position angle of the projected ISMF reported in previous works.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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    MUSEQuBES: characterizing the circumgalactic medium of redshift ≈3.3 Ly α emitters (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-11
    Description: We present the first characterization of the circumgalactic medium of Ly α emitters (LAEs), using a sample of 96 z ≈ 3.3 LAEs detected with the VLT/MUSE in fields centred on eight bright background quasars. The LAEs have low Ly α luminosities ($sim 10^{42}, ext{erg}, ext{s}^{-1}$) and star formation rates (SFRs) $sim 1~ext{M}_odot , ext{yr}^{-1}$, which for main-sequence galaxies correspond to stellar masses of only $sim 10^{8.6}, ext{M}_odot$. The median transverse distance between the LAEs and the quasar sightlines is 165 proper kpc (pkpc). We stacked the high-resolution quasar spectra and measured significant excess H i and C iv absorption near the LAEs out to 500 $ext{km}, ext{s}^{-1}$ and at least ≈250 pkpc (corresponding to ≈7 virial radii). At $lesssim 30~ext{km}, ext{s}^{-1}$ from the galaxies, the median H i and C iv optical depths are enhanced by an order of magnitude. The absorption is significantly stronger around the ≈1/3 of our LAEs that are part of ‘groups’, which we attribute to the large-scale structures in which they are embedded. We do not detect any strong dependence of either the H i or C iv absorption on transverse distance (over the range ≈50–250 pkpc), redshift, or the properties of the Ly α emission line (luminosity, full width at half-maximum, or equivalent width). However, for H i, but not C iv, the absorption at $lesssim 100, ext{km}, ext{s}^{-1}$ from the LAE does increase with the SFR. This suggests that LAEs surrounded by more H i tend to have higher SFRs.
    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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    RPS: a comprehensive database of RNAs involved in liquid–liquid phase separation (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-28
    Description: Liquid–liquid phase separation (LLPS) is critical for assembling membraneless organelles (MLOs) such as nucleoli, P-bodies, and stress granules, which are involved in various physiological processes and pathological conditions. While the critical role of RNA in the formation and the maintenance of MLOs is increasingly appreciated, there is still a lack of specific resources for LLPS-related RNAs. Here, we presented RPS (http://rps.renlab.org), a comprehensive database of LLPS-related RNAs in 20 distinct biomolecular condensates from eukaryotes and viruses. Currently, RPS contains 21,613 LLPS-related RNAs with three different evidence types, including ‘Reviewed’, ‘High-throughput’ and ‘Predicted’. RPS provides extensive annotations of LLPS-associated RNA properties, including sequence features, RNA structures, RNA–protein/RNA–RNA interactions, and RNA modifications. Moreover, RPS also provides comprehensive disease annotations to help users to explore the relationship between LLPS and disease. The user-friendly web interface of RPS allows users to access the data efficiently. In summary, we believe that RPS will serve as a valuable platform to study the role of RNA in LLPS and further improve our understanding of the biological functions of LLPS.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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    Two striking head–tail galaxies in the galaxy cluster IIZW108: insights into transition to turbulence, magnetic fields, and particle re-acceleration (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-13
    Description: We present deep Jansky Very Large Array observations at 1.4 and 2.7 GHz (full polarization), as well as optical OmegaWINGS/WINGS and X-ray observations of two extended radio galaxies in the IIZW108 galaxy cluster at z = 0.04889. They show a bent tail morphology in agreement with a radio lobed galaxy falling into the cluster potential. Both galaxies are found to possess properties comparable with narrow-angle tail galaxies in the literature even though they are part of a low mass cluster. We find a spectral index steepening and an increase in fractional polarization through the galaxy jets and an ordered magnetic field component mostly aligned with the jet direction. This is likely caused by either shear due to the velocity difference of the intracluster medium and the jet fluid and/or magnetic draping of the intracluster medium across the galaxy jets. We find clear evidence that one source is showing two active galactic nuclei (AGN) outbursts from which we expect the AGN has never turned off completely. We show that pure standard electron cooling cannot explain the jet length. We demonstrate therefore that these galaxies can be used as a laboratory to study gentle re-acceleration of relativistic electrons in galaxy jets via transition from laminar to turbulent motion.
    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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    Influence of global environmental Change on plankton (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-30
    Description: Much has been published on the effects of ocean acidification on plankton since the original Royal Society 2005 report. In addition to direct effects on primary production, it is clear that ocean acidification also has profound consequences for biogeochemistry. Furthermore, although ocean acidification can have direct effects of on grazers such as copepods, acidification induces changes in nutritional value of phytoplankton which can be passed on up the food chain. There has also been recognition of the complexity of the interactions between elevated CO2 and other environmental factors and this has seen an upsurge in climate change research involving multifactorial experiments. In particular, the interaction of ocean acidification with global warming resulting from the increasing greenhouse effect has been investigated. There has also been research on acidification and warming effects in inland water plankton. These, combined with novel experimental techniques and long term studies of genetic adaptation, are providing better insights to plankton biology and communities in a future world.
    Print ISSN: 0142-7873
    Electronic ISSN: 1464-3774
    Topics: Biology
    Published by Oxford University Press
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    RNAInter v4.0: RNA interactome repository with redefined confidence scoring system and improved accessibility (2021)
    Oxford University Press
    Details
    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.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    Flexible learner or imposter? Learning A Level mathematics in England through the COVID-19 pandemic (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-26
    Description: We evidence English teacher and student perspectives on the learning of pre-university mathematics ‘A Level’ courses through the pandemic period to July 2021. Data are drawn from a 2017–21 classroom-close study of enactment of such courses in 13 fairly representative centres, using an institutional ethnographic approach. The pandemic picture was generally one of the significant and sustained negative impacts, though over the course of the study, respondents reported progress in addressing early limitations in the harnessing of digital platforms for learning. A small number of participating students reported home-based study beneficial for their mathematics learning, and a bigger group identified some wider benefits that partly offset the challenges. Most participating 16–18-year-old students, though, reported finding remote learning of mathematics both demanding and limiting. Pandemic constraints impacted most strongly on opportunities to engage with newer emphases within A Level courses: problem solving, reasoning, modelling, statistics and mechanics. Receiving academics reported that mathematical preparedness, and confidence, for mathematics-intense university courses has also been widely affected, with a bigger range of preparedness and confidence than usual. The study draws attention to the importance of studying subject-specific impact and drawing on student as well as teacher perceptions. It exposes a range of consequences of the cancellation of examinations and a need to develop and share effective pedagogies for working remotely with pre-university students.
    Print ISSN: 0268-3679
    Electronic ISSN: 1471-6976
    Topics: Mathematics
    Published by Oxford University Press on behalf of Institute of Mathematics and its Applications.
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    Controls for Phylogeny and Robust Analysis in Pareto Task Inference (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-11
    Description: Understanding the tradeoffs faced by organisms is a major goal of evolutionary biology. One of the main approaches for identifying these tradeoffs is Pareto task inference (ParTI). Two recent papers claim that results obtained in ParTI studies are spurious due to phylogenetic dependence (Mikami T, Iwasaki W. 2021. The flipping t-ratio test: phylogenetically informed assessment of the Pareto theory for phenotypic evolution. Methods Ecol Evol. 12(4):696–706) or hypothetical p-hacking and population-structure concerns (Sun M, Zhang J. 2021. Rampant false detection of adaptive phenotypic optimization by ParTI-based Pareto front inference. Mol Biol Evol. 38(4):1653–1664). Here, we show that these claims are baseless. We present a new method to control for phylogenetic dependence, called SibSwap, and show that published ParTI inference is robust to phylogenetic dependence. We show how researchers avoided p-hacking by testing for the robustness of preprocessing choices. We also provide new methods to control for population structure and detail the experimental tests of ParTI in systems ranging from ammonites to cancer gene expression. The methods presented here may help to improve future ParTI studies.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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    Prediction–variance relation in a state-space fish stock assessment model (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-27
    Description: The state-space assessment model (SAM) is extended by allowing a functional relationship between observation variance and the corresponding prediction. An estimated relationship between observation variance and predicted value for each individual observation allows the model to assign smaller (or larger) variance to predicted larger log-observations. This relation is different from the usual assumption of constant variance of log-observations within age groups. The prediction–variance link is implemented and compared to the usual constant variance assumption for the official assessments of North East Arctic cod and haddock. For both of these stocks, the prediction–variance link is found to give a significant improvement.
    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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    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.
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    Topics: Biology
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    Corrigendum to: Growth rates in a European eel Anguilla anguilla (L., 1758) population show a complex relationship with temperature over a seven-decade otolith biochronology (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-19
    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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    Fold Evolution before LUCA: Common Ancestry of SH3 Domains and OB Domains (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-12
    Description: SH3 and OB are the simplest, oldest, and most common protein domains within the translation system. SH3 and OB domains are β-barrels that are structurally similar but are topologically distinct. To transform an OB domain to a SH3 domain, β-strands must be permuted in a multistep and evolutionarily implausible mechanism. Here, we explored relationships between SH3 and OB domains of ribosomal proteins, initiation, and elongation factors using a combined sequence- and structure-based approach. We detect a common core of SH3 and OB domains, as a region of significant structure and sequence similarity. The common core contains four β-strands and a loop, but omits the fifth β-strand, which is variable and is absent from some OB and SH3 domain proteins. The structure of the common core immediately suggests a simple permutation mechanism for interconversion between SH3 and OB domains, which appear to share an ancestor. The OB domain was formed by duplication and adaptation of the SH3 domain core, or vice versa, in a simple and probable transformation. By employing the folding algorithm AlphaFold2, we demonstrated that an ancestral reconstruction of a permuted SH3 sequence folds into an OB structure, and an ancestral reconstruction of a permuted OB sequence folds into a SH3 structure. The tandem SH3 and OB domains in the universal ribosomal protein uL2 share a common ancestor, suggesting that the divergence of these two domains occurred before the last universal common ancestor.
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    Applying Bayesian model selection to determine ecological covariates for recruitment and natural mortality in stock assessment (2021)
    Oxford University Press
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    Publication Date: 2021-09-09
    Description: Incorporating ecological covariates into fishery stock assessments may improve estimates, but most covariates are estimated with error. Model selection criteria are often used to identify support for covariates, have some limitations and rely on assumptions that are often violated. For a more rigorous evaluation of ecological covariates, we used four popular selection criteria to identify covariates influencing natural mortality or recruitment in a Bayesian stock assessment of Pacific herring (Clupea pallasii) in Prince William Sound, Alaska. Within this framework, covariates were incorporated either as fixed effects or as latent variables (i.e. covariates have associated error). We found most support for pink salmon increasing natural mortality, which was selected by three of four criteria. There was ambiguous support for other fixed effects on natural mortality (walleye pollock and the North Pacific Gyre Oscillation) and recruitment (hatchery-released juvenile pink salmon and a 1989 regime shift). Generally, similar criteria values among covariates suggest no clear evidence for a consistent effect of any covariate. Models with covariates as latent variables were sensitive to prior specification and may provide potentially very different results. We recommend using multiple criteria and exploring different statistical assumptions about covariates for their use in stock assessment.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
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    Papua New Guinean Genomes Reveal the Complex Settlement of North Sahul (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-12
    Description: The settlement of Sahul, the lost continent of Oceania, remains one of the most ancient and debated human migrations. Modern New Guineans inherited a unique genetic diversity tracing back 50,000 years, and yet there is currently no model reconstructing their past population dynamics. We generated 58 new whole-genome sequences from Papua New Guinea, filling geographical gaps in previous sampling, specifically to address alternative scenarios of the initial migration to Sahul and the settlement of New Guinea. Here, we present the first genomic models for the settlement of northeast Sahul considering one or two migrations from Wallacea. Both models fit our data set, reinforcing the idea that ancestral groups to New Guinean and Indigenous Australians split early, potentially during their migration in Wallacea where the northern route could have been favored. The earliest period of human presence in Sahul was an era of interactions and gene flow between related but already differentiated groups, from whom all modern New Guineans, Bismarck islanders, and Indigenous Australians descend. The settlement of New Guinea was probably initiated from its southeast region, where the oldest archaeological sites have been found. This was followed by two migrations into the south and north lowlands that ultimately reached the west and east highlands. We also identify ancient gene flows between populations in New Guinea, Australia, East Indonesia, and the Bismarck Archipelago, emphasizing the fact that the anthropological landscape during the early period of Sahul settlement was highly dynamic rather than the traditional view of extensive isolation.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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    Exploring new netting material for fishing: the low light level of a luminous netting negatively influences species separation in trawls (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-28
    Description: We tested if a newly developed luminous netting, VISIONET, could change the vertical behaviour of six commercially important species in a Nephrops (Nephrops norvegicus) trawl fishery. We inserted a V-shaped piece of VISIONET ascending on each side of the tapered section just ahead of a divided codend. The length-based effect on the vertical separation of fishes and Nephrops was quantified, and we evaluated if the presence of VISIONET had the potential to increase the fish capture in the upper compartment. Contrary to our expectation, gadoids entered the lower compartment more frequently than in the control trawl. This was similar to that previously found when applying green LED lights in the tapered section, however opposite for haddock (Melanogrammus aeglefinus). The flatfishes did not respond. Large Nephrops significantly increased their preference for the lower compartment. Our results show that low intensity light is sufficient to alter the vertical distribution of both fishes and Nephrops. Responses of fishes to different variables, including light intensities, need to be studied in more detail to understand the underlying mechanisms and to ultimately reduce unwanted catch more efficiently. Luminous netting can be integrated in any given trawl design and does not require batteries or electronics.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
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    Little Evidence the Standard Genetic Code Is Optimized for Resource Conservation (2021)
    Oxford University Press
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    Publication Date: 2021-08-09
    Description: Selection for resource conservation can shape the coding sequences of organisms living in nutrient-limited environments. Recently, it was proposed that selection for resource conservation, specifically for nitrogen and carbon content, has also shaped the structure of the standard genetic code, such that the missense mutations the code allows tend to cause small increases in the number of nitrogen and carbon atoms in amino acids. Moreover, it was proposed that this optimization is not confounded by known optimizations of the standard genetic code, such as for polar requirement or hydropathy. We challenge these claims. We show the proposed optimization for nitrogen conservation is highly sensitive to choice of null model and the proposed optimization for carbon conservation is confounded by the known conservative nature of the standard genetic code with respect to the molecular volume of amino acids. There is therefore little evidence the standard genetic code is optimized for resource conservation. We discuss our findings in the context of null models of the standard genetic code.
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    The Chicken Pan-Genome Reveals Gene Content Variation and a Promoter Region Deletion in IGF2BP1 Affecting Body Size (2021)
    Oxford University Press
    Details
    Publication Date: 2021-07-30
    Description: Domestication and breeding have reshaped the genomic architecture of chicken, but the retention and loss of genomic elements during these evolutionary processes remain unclear. We present the first chicken pan-genome constructed using 664 individuals, which identified an additional approximately 66.5-Mb sequences that are absent from the reference genome (GRCg6a). The constructed pan-genome encoded 20,491 predicated protein-coding genes, of which higher expression levels are observed in conserved genes relative to dispensable genes. Presence/absence variation (PAV) analyses demonstrated that gene PAV in chicken was shaped by selection, genetic drift, and hybridization. PAV-based genome-wide association studies identified numerous candidate mutations related to growth, carcass composition, meat quality, or physiological traits. Among them, a deletion in the promoter region of IGF2BP1 affecting chicken body size is reported, which is supported by functional studies and extra samples. This is the first time to report the causal variant of chicken body size quantitative trait locus located at chromosome 27 which was repeatedly reported. Therefore, the chicken pan-genome is a useful resource for biological discovery and breeding. It improves our understanding of chicken genome diversity and provides materials to unveil the evolution history of chicken domestication.
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    Topics: Biology
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