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  • Articles  (471)
  • Oxford University Press  (471)
  • 2020-2024  (471)
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  • 1
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    Fault imaging at Mt Pollino (Italy) from relative location of microearthquakes (2021)
    Oxford University Press
    Details
    Publication Date: 2023-10-26
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2021. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved.
    Description: Relative location of microearthquakes that occurred at Mt Pollino (Italy) from 2011 to 2013 have been analyzed with the aim of a detailed imaging of the geometry of active faults. We identified 27 clusters composed of a number of earthquakes from 9 to 33, with local magnitude in the range 0.6–2.7. The relative location shows that the distribution of hypocentres in each cluster is characterized by extension from few tens of meters to at most 350 m. For each cluster the hypocentre distribution was fitted by a plane to infer the fault orientation, and results were compared with the fault plane solutions corresponding to the focal mechanism of earthquakes of the same cluster. The comparison shows a good agreement in most of the cases. The relative location analysis, generally applied to earthquakes with similar waveform, has been improved to permit also the relative location of earthquakes characterized by not similar signals. To achieve this purpose a modified procedure that overcome the condition of very similar waveforms has been applied to estimate the time delay between first pulses of the master events. The relative location of master events of all clusters shows a precise imaging of the relative position of all analysed sources and allows also to follow with high accuracy the evolution in time of the seismic swarm within the selected periods. The hypocentre position of master events and the nearly parallel fitting planes of any clusters suggest that most of the analyzed earthquakes were produced by different patches of the same fault. The final results depict a main fault plane characterized by NW–SE strike, dip of about 35–45° and depth between 4.5 and 6.5 km b.s.l. Focal mechanisms, used also to evaluate the local stress field, are mostly of normal type with few strike slip solutions for the shallowest events. This result is in good agreement with the local tectonic stress regime that is characterized by predominant NE–SW transtension, as inferred from structural, seismological and geophysical data.
    Description: Published
    Description: 637–648
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: Persistence, memory, correlations, clustering, Spatial analysis, Crustal imaging, Earthquake source observations, Seismicity and tectonics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 2
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    Physics-based simulation of sequences with multiple main shocks in Central Italy (2020)
    Oxford University Press
    Details
    Publication Date: 2023-10-26
    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: The application of a physics-based earthquake simulator to Central Italy allowed the compilation of a synthetic seismic catalogue spanning 100 000 yr, containing more than 300 000 M ≥ 4.0 simulated earthquakes, without the limitations that real catalogues suffer in terms of completeness, homogeneity and time duration. The seismogenic model upon which we applied the simulator code was derived from version 3.2.1 of the Database of Individual Seismogenic Sources (DISS; http://diss.rm.ingv.it/diss/), selecting, and modifying where appropriate, all the fault systems that are recognized in the portion of Central Italy considered in this study, with a total of 54 faults. Besides tectonic stress loading and static stress transfer as in the previous versions, the physical model on which the latest version of our simulation algorithm is based also includes the Rate and State constitutive law that helps to reproduce Omori’s law. One further improvement in our code was also the introduction of trapezoidalshaped faults that perform better than known faults. The resulting synthetic seismic catalogue exhibits typical magnitude, space and time features which are comparable to those in real observations. These features include the total seismic moment rate, the earthquake magnitude distribution, and the short- and medium-term earthquake clustering. A typical aspect of the observed seismicity in Central Italy, aswell as across thewhole Italian landmass and elsewhere, is the occurrence of earthquake sequences characterized by multiple main shocks of similar magnitude. These sequences are different from the usual earthquake clusters and aftershock sequences, since they have at least two main shocks of similar magnitude. Therefore, special attentionwas devoted to verifyingwhether the simulated catalogue includes this notable aspect. For this purpose, we developed a computer code especially for this work to count the number of multiple events contained in a seismic catalogue under a quantitative definition. We found that the last version of the simulator code produces a slightly larger number of multiple events than the previous versions, but not as large as in the real catalogue. A possible reason for this drawback is the lack of components such as pore-pressure changes due to fluid-diffusion in the adopted physical model.
    Description: Published
    Description: 526–542
    Description: 6T. Studi di pericolosità sismica e da maremoto
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
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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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  • 4
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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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  • 5
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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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  • 6
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    Strong ground-motion prediction equations from induced earthquakes in St. Gallen geothermal field, Switzerland (2023)
    Oxford University Press
    Details
    Publication Date: 2023-03-15
    Description: Ground shaking, whether it is due to natural or induced earthquakes, has always been a matter of concern since it correlates with structural/non-structural damage and can culminate in human anxiety. Industrial activities such as water injection, gas sequestration and waste fluid disposals, promote induced seismicity and consequent ground shaking that can hinder ongoing activities. Therefore, keeping in mind the importance of timely evaluation of a seismic hazard and its mitigation for societal benefits, the present study proposes specifically designed ground-motion prediction equations (GMPEs) from induced earthquakes in the St. Gallen geothermal area, Switzerland. The data analysed in this study consist of 343 earthquakes with magnitude −1.17 ≤ ML, corr ≤ 3.5 and hypocentral distance between 4 and 15 km. The proposed study is one of the first to incorporate ground motions from negative magnitude earthquakes for the development of GMPEs. The GMPEs are inferred with a two-phase approach. In the first phase, a reference model is obtained by considering the effect of source and medium properties on the ground motion. In the second phase the final model is obtained by including a site/station effect. The comparison between the GMPEs obtained in the present study with GMPEs developed for the other induced seismicity environments highlights a mismatch that is ascribed to differences in regional seismic environment and local site conditions of the respective regions. This suggests that, when dealing with induced earthquakes, GMPEs specific for the study should be inferred and used for both monitoring purposes and seismic hazard analyses.
    Description: Published
    Description: 820–832
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 7
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    Upper mantle deformation signatures of craton–orogen interaction in the Carpathian–Pannonian region from SKS anisotropy analysis (2021)
    Oxford University Press
    Details
    Publication Date: 2023-10-31
    Description: Since the Mesozoic, central and eastern European tectonics have been dominated by the closure of the Tethyan Ocean as the African and European plates collided. In the Miocene, the edge of the East European Craton and Moesian Platform were reworked in collision during the Carpathian orogeny and lithospheric extension formed the Pannonian Basin. To investigate the mantle deformation signatures associated with this complex collisional-extensional system, we carry out SKS splitting analysis at 123 broad-band seismic stations in the region. We compare our measurements with estimates of lithospheric thickness and recent seismic tomography models to test for correlation with mantle heterogeneities. Reviewing splitting delay times in light of xenolith measurements of anisotropy yields estimates of anisotropic layer thickness. Fast polarization directions are mostly NW–SE oriented across the seismically slow West Carpathians and Pannonian Basin and are independent of geological boundaries, absolute plate motion direction or an expected palaeo-slab roll-back path. Instead, they are systematically orthogonal to maximum stress directions, implying that the indenting Adria Plate, the leading deformational force in Central Europe, reset the upper-mantle mineral fabric in the past 5 Ma beneath the Pannonian Basin, overprinting the anisotropic signature of earlier tectonic events. Towards the east, fast polarization directions are perpendicular to steep gradients of lithospheric thickness and align along the edges of fast seismic anomalies beneath the Precambrian-aged Moesian Platform in the South Carpathians and the East European Craton, supporting the idea that craton roots exert a strong influence on the surrounding mantle flow. Within the Moesian Platform, SKS measurements become more variable with Fresnel zone arguments indicating a shallow fossil lithospheric source of anisotropy likely caused by older tectonic deformation frozen in the Precambrian. In the Southeast Carpathian corner, in the Vrancea Seismic Zone, a lithospheric fragment that sinks into the mantle is sandwiched between two slow anomalies, but smaller SKS delay times reveal weaker anisotropy occurs mainly to the NW side, consistent with asymmetric upwelling adjacent to a slab, slower mantle velocities and recent volcanism.
    Description: Published
    Description: 2105–2118
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: Seismic anisotropy ; geodynamics ; Seismic anisotropy and geodynamics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 8
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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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  • 9
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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
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 10
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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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  • 11
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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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  • 12
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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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  • 13
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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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  • 14
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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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  • 15
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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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  • 16
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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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  • 17
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    Metagenomic survey of the microbiome of ancient Siberian permafrost and modern Kamchatkan cryosols (2022)
    Oxford University Press
    In:  EPIC3microLife, Oxford University Press, 3(1), pp. 1-15, ISSN: 2633-6693
    Details
    Publication Date: 2024-01-30
    Description: In the context of global warming, the melting of arctic permafrost raises the threat of a re-emergence of microorganisms some of which were shown to remain viable in ancient frozen soils for up to half a million years. In order to evaluate this risk, it is of interest to acquire a better knowledge of the composition of the microbial communities found in this understudied environment. Here we present a metagenomics analysis of 12 soil samples from Russian Arctic and subarctic pristine areas: Chukotka, Yakutia, and Kamchatka, including 9 permafrost samples collected at various depths. These large datasets (9.2 1011 total bp) were assembled (525,313 contigs 〉 5kb), their encoded protein contents predicted, then used to perform taxonomical assignments of bacterial, archaeal, and eukaryotic organisms, as well as DNA viruses. The various samples exhibited variable DNA contents and highly diverse taxonomic profiles showing no obvious relationship with their locations, depths or deposit ages. Bacteria represented the largely dominant DNA fraction (95%) in all samples, followed by archaea (3.2%), surprisingly little eukaryotes (0.5%), and viruses (0.4%). Although no common taxonomic pattern was identified, the samples shared unexpected high frequencies of β-lactamase genes, almost 0.9 copy/bacterial genome. In addition of known environmental threats, the particularly intense warming of the Arctic might thus enhance the spread of bacterial antibiotic resistances, today's major challenge in public health. β-lactamases were also observed at high frequency in other types of soils, suggesting their general role in the regulation of bacterial populations.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 18
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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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  • 19
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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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  • 20
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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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  • 21
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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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  • 22
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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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  • 23
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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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  • 24
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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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  • 25
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    Ant Cat Swarm Optimization-Enabled Deep Recurrent Neural Network for Big Data Classification Based on Map Reduce Framework (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-27
    Description: The amount of data generated is increasing day by day due to the development in remote sensors, and thus it needs concern to increase the accuracy in the classification of the big data. Many classification methods are in practice; however, they limit due to many reasons like its nature for data loss, time complexity, efficiency and accuracy. This paper proposes an effective and optimal data classification approach using the proposed Ant Cat Swarm Optimization-enabled Deep Recurrent Neural Network (ACSO-enabled Deep RNN) by Map Reduce framework, which is the incorporation of Ant Lion Optimization approach and the Cat Swarm Optimization technique. To process feature selection and big data classification, Map Reduce framework is used. The feature selection is performed using Pearson correlation-based Black hole entropy fuzzy clustering. The classification in reducer part is performed using Deep RNN that is trained using a developed ACSO scheme. It classifies the big data based on the reduced dimension features to produce a satisfactory result. The proposed ACSO-based Deep RNN showed improved results with maximal specificity of 0.884, highest accuracy of 0.893, maximal sensitivity of 0.900 and the maximum threat score of 0.827 based on the Cleveland dataset.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 26
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    Mitochondrial enzyme GPT2 regulates metabolic mechanisms required for neuron growth and motor function in vivo (2021)
    Oxford University Press
    Details
    Publication Date: 2021-09-14
    Description: The metabolic needs for postnatal growth of the human nervous system are vast. Recessive loss-of-function mutations in the mitochondrial enzyme glutamate pyruvate transaminase 2 (GPT2) in humans cause postnatal undergrowth of brain, and cognitive and motor disability. We demonstrate that GPT2 governs critical metabolic mechanisms in neurons required for neuronal growth and survival. These metabolic processes include neuronal alanine synthesis and anaplerosis, the replenishment of tricarboxylic acid (TCA) cycle intermediates. We performed metabolomics across postnatal development in Gpt2-null mouse brain to identify the trajectory of dysregulated metabolic pathways: alterations in alanine occur earliest; followed by reduced TCA cycle intermediates and reduced pyruvate; followed by elevations in glycolytic intermediates and amino acids. Neuron-specific deletion of GPT2 in mice is sufficient to cause motor abnormalities and death pre-weaning, a phenotype identical to the germline Gpt2-null mouse. Alanine biosynthesis is profoundly impeded in Gpt2-null neurons. Exogenous alanine is necessary for Gpt2-null neuronal survival in vitro but is not needed for Gpt2-null astrocytes. Dietary alanine supplementation in Gpt2-null mice enhances animal survival and improves the metabolic profile of Gpt2-null brain but does not alone appear to correct motor function. In surviving Gpt2-null animals, we observe smaller upper and lower motor neurons in vivo. We also observe selective death of lower motor neurons in vivo with worsening motor behavior with age. In conclusion, these studies of the pathophysiology of GPT2 Deficiency have identified metabolic mechanisms that are required for neuronal growth and that potentially underlie selective neuronal vulnerabilities in motor neurons.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 27
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    A Hybrid Machine Learning Approach for Performance Modeling of Cloud-Based Big Data Applications (2021)
    Oxford University Press
    Details
    Publication Date: 2021-09-20
    Description: Nowadays, Apache Hadoop and Apache Spark are two of the most prominent distributed solutions for processing big data applications on the market. Since in many cases these frameworks are adopted to support business critical activities, it is often important to predict with fair confidence the execution time of submitted applications, for instance when service-level agreements are established with end-users. In this work, we propose and validate a hybrid approach for the performance prediction of big data applications running on clouds, which exploits both analytical modeling and machine learning (ML) techniques and it is able to achieve a good accuracy without too many time consuming and costly experiments on a real setup. The experimental results show how the proposed approach attains improvement in accuracy, number of experiments to be run on the operational system and cost over applying ML techniques without any support from analytical models. Moreover, we compare our approach with Ernest, an ML-based technique proposed in the literature by the Spark inventors. Experiments show that Ernest can accurately estimate the performance in interpolating scenarios while it fails to predict the performance when configurations with increasing number of cores are considered. Finally, a comparison with a similar hybrid approach proposed in the literature demonstrates how our approach significantly reduce prediction errors especially when few experiments on the real system are performed.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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    Quartic Lp-convergence of cubic Riemannian splines (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-27
    Description: We prove quartic convergence of cubic spline interpolation for curves into Riemannian manifolds as the grid size of the interpolation grid tends to zero. In contrast to cubic spline interpolation in Euclidean space, where this result is classical, the interpolation operator is no longer linear. Still, concepts from the linear setting may be generalized to the Riemannian case, where we try to use intrinsic Riemannian formulations and avoid charts as much as possible.
    Print ISSN: 0272-4979
    Electronic ISSN: 1464-3642
    Topics: Mathematics
    Published by Oxford University Press on behalf of Institute of Mathematics and its Applications.
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    Are hierarchically formed embedded star clusters surviving gas expulsion depending on their initial conditions? (2021)
    Oxford University Press
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    Publication Date: 2021-09-17
    Description: We investigate the dissolution process of young embedded star clusters with different primordial mass segregation levels using fractal distributions by means of N-body simulations. We combine several star clusters in virial and subvirial global states with Plummer and uniform density profiles to mimic the gas. The star clusters have masses of Mstars = 500 M⊙ that follow an initial mass function where the stars have maximum distance from the centre of r = 1.5 pc. The clusters are placed in clouds that at the same radius have masses of Mcloud = 2000 M⊙, resulting in star formation efficiency of 0.2. We remove the background potential instantaneously at a very early phase, mimicking the most destructive scenario of gas expulsion. The evolution of the fraction of bound stellar mass is followed for a total of 16 Myr for simulations with stellar evolution and without. We compare our results with previous works using equal-mass particles where an analytical physical model was used to estimate the bound mass fraction after gas expulsion. We find that independent of the initial condition, the fraction of bound stellar mass can be well predicted just right after the gas expulsion but tends to be lower at later stages, as these systems evolve due to the stronger two-body interactions resulting from the inclusion of a realistic initial mass function. This discrepancy is independent of the primordial mass segregation level.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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    Light and shade of citizen science for less charismatic invertebrate groups: quality assessment of iNaturalist nonmarine mollusc observations in central Italy (2021)
    Oxford University Press
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    Publication Date: 2021-09-01
    Description: Citizen science has grown in importance in recent years: many projects have been launched and records are being collected on an unprecedented scale. However, certain less charismatic invertebrate groups are still underreported and the accuracy and quality of their records in crowd-sourced citizen-science projects have rarely been investigated. Here, we used expert review to conduct quality control of nonmarine mollusc observations from central Italy on the online citizen-science platform iNaturalist (https://www.inaturalist.org/). As of December 2019, c. 400 observations of nonmarine molluscs had been reported from Tuscany on iNaturalist. Most records (59.4%) were identified to species level by the iNaturalist community and included a total of 90 taxa, providing interesting new chorological data of certain entities. Although identification of more than half the observations uploaded by the community was confirmed by expert malacologists, some major issues emerged: low quality of photographic vouchers; bias in favour of a few large common species; poor taxonomic knowledge producing incorrect identifications; and difficulty of identifying many taxa without anatomical study. Expert review remains an essential tool for verification and improvement of data quality in citizen-science projects. In this regard, information on the main diagnostic characters of the more common species (e.g. certain medium–large-sized snails and slugs) as well as tips on how to take good quality photographic images could be provided to volunteers in the form of simple guides and tutorials. High-quality training resources to support recorders and regular feedback and teamwork between scientists and citizens could prevent unverified or inaccurate records from impairing the accuracy of citizen-science datasets and offer a real opportunity to discover and conserve less charismatic taxa.
    Print ISSN: 0260-1230
    Electronic ISSN: 1464-3766
    Topics: Biology
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    Constraining Merging Galaxy Clusters with X-ray and Lensing Simulations & Observations: The case of Abell 2146 (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: Galaxy cluster mergers are a powerful laboratory for testing cosmological and astrophysical models. However, interpreting individual merging clusters depends crucially on their merger configuration, defined by the masses, velocities, impact parameters, and orientation of the merger axis with respect to the plane of the sky. In this work, we investigate the impact of merger parameters on the X-ray emitting intracluster medium and gravitational lensing maps using a suite of idealised simulations of binary cluster mergers performed using the GAMER-2 code. As a test case, we focus on modeling the Bullet Cluster-like merging system Abell 2146, in which deep Chandra X-ray and lensing observations revealed prominent merger shocks as well as the mass distribution and substructures associated with this merging cluster. We identify the most interesting parameter combinations, and evaluate the effects of various parameters on the properties of merger shocks observed by deep Chandra and lensing observations. We show that due to gravitational compression of the cluster halos during the merger, previous mass estimates from weak lensing are too high. The plane of the merger is tilted further from the plane of the sky than estimated previously, up to 30○ from the plane of the sky. We discuss the applicability of our results to multi-wavelength observations of merging galaxy clusters and their use as probes of cosmology and plasma physics.
    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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    DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria (2021)
    Oxford University Press
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    Publication Date: 2021-09-15
    Description: Summary Recent efforts to identify novel bacterial structured noncoding RNA (ncRNA) motifs through searching long, GC-rich intergenic regions (IGRs) have revealed several new classes, including the recently validated HMP-PP riboswitch. The DIMPL (Discovery of Intergenic Motifs PipeLine) discovery pipeline described herein enables rapid extraction and selection of bacterial IGRs that are enriched for structured ncRNAs. Moreover, DIMPL automates the subsequent computational steps necessary for their functional identification. Availability and implementation The DIMPL pipeline is freely available as a Docker image with an accompanying set of Jupyter notebooks. Full instructions for download and use are available at https://github.com/breakerlab/dimpl. Supplementary information Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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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.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    Erratum to: A Hybrid Machine Learning Approach for Performance Modeling of Cloud-Based Big Data Applications (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-28
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
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    Editorial Expression of Concern on ‘Activation of APE1/Ref-1 is dependent on reactive oxygen species generated after purinergic receptor stimulation by ATP’ (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-29
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    Classifying Liganded States in Heterogeneous Single-Particle Cryo-EM Datasets (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: A powerful aspect of single particle cryogenic electron microscopy (cryo-EM) is its ability to determine high-resolution structures from samples containing heterogeneous mixtures of the same macromolecule in different conformational or compositional states. Beyond determining structures at higher resolutions, one outstanding question is if macromolecules with only subtle conformation differences, such as the same protein bound with different ligands in the same binding pocket, can be separated reliably, and if information concerning binding kinetics can be derived from the particle distributions of different conformations obtained in classification. In this study, we address these questions by assessing the classification of synthetic heterogeneous datasets of TRPV1 generated by combining different homogeneous experimental datasets. Our results indicate that classification can isolate highly homogeneous subsets of particle for calculating high-resolution structures containing individual ligands, but with limitations.
    Print ISSN: 2050-5698
    Electronic ISSN: 2050-5701
    Topics: Electrical Engineering, Measurement and Control Technology , Natural Sciences in General , Physics
    Published by Oxford University Press on behalf of Japanese Society of Microscopy.
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    Erratum to: Assessing heterogeneity in spatial data using the HTA index with applications to spatial transcriptomics and imaging (2021)
    Oxford University Press
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    Publication Date: 2021-10-27
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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    The impact of metallicity-dependent dust destruction on the dust-to-metals ratio in galaxies (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-19
    Description: The ratio of the mass of interstellar dust to the total mass of metals (the dust-to-metals/DTM ratio) tends to increase with metallicity. This can be explained by the increasing efficiency of grain growth in the interstellar medium (ISM) at higher metallicities, with a corollary being that the low DTM ratios seen at low metallicities are due to inefficient stellar dust production. This interpretation assumes that the efficiency of dust destruction in the ISM is constant, whereas it might be expected to increase at low metallicity; the decreased cooling efficiency of low-metallicity gas should result in more post-shock dust destruction via thermal sputtering. We show that incorporating a sufficiently strong metallicity dependence into models of galaxy evolution removes the need for low stellar dust yields. The contribution of stellar sources to the overall dust budget may be significantly underestimated, and that of grain growth overestimated, by models assuming a constant destruction efficiency.
    Print ISSN: 1745-3925
    Electronic ISSN: 1745-3933
    Topics: Physics
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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    Fluid-mineral interactions: Controlling coupled mechanisms of reaction, mass transfer and deformation (2021)
    Oxford University Press
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    Publication Date: 2021-11-01
    Description: Fluid-rock interaction has profound effects on the dynamics of the lithosphere. This Perspectives article describes the catalytic effects of water on the kinetics of mineral reactions and on the strength of rocks in terms of coupled dissolution and precipitation mechanisms on a macro- and nano-scale. The length scale of coupling between the dissolution and precipitation steps depends on the fluid composition at the mineral-fluid interface and also on differential stress. Stress-induced mass transport, dependent on the generation of porosity by mineral reactions, results in dissolution-precipitation creep as the principal mechanism of rock deformation in the lithosphere. The heterogeneous distribution of fluid infiltration into dry, strong rocks in the deep crust leads to weak rocks within strong, stressed host rock and the possibility of significant local variations in pressure. Fluid-rock interaction mechanisms are discussed in terms of recrystallisation reactions whereby mass transport and the most favourable nucleation sites determine the distribution and texture of the resultant assemblages. Metamorphic differentiation is a natural consequence of dissolution-precipitation mechanisms under deviatoric stress and similar mechanisms may apply to general pattern formation in rocks.
    Print ISSN: 0022-3530
    Electronic ISSN: 1460-2415
    Topics: Geosciences
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    Characterising the distinct crustal protoliths of Roberts Victor Type I and II eclogites (2021)
    Oxford University Press
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    Publication Date: 2021-10-27
    Description: The origin of the eclogites that reside in cratonic mantle roots has long been debated. In the classic Roberts Victor kimberlite locality in South Africa, the strongly contrasting textural and geochemical features of two types of eclogites have led to different genetic models. We studied a new suite of 63 eclogite xenoliths from the former Roberts Victor Mine. In addition to major- and trace-element compositions for all new samples, we determined 18O/16O for garnet from 34 eclogites. Based on geochemical and textural characteristics we identify a large suite of Type I eclogites (n = 53) consistent with previous interpretations that these rocks originate from metamorphosed basaltic-picritic lavas or gabbroic cumulates from oceanic crust, crystallised from melts of depleted MORB mantle. We identify a smaller set of Type II eclogites (n = 10) based on geochemical and textural similarity to eclogites in published literature. We infer their range to very low δ18O values combined with their varied, often very low Zr/Hf ratios and LREE-depleted nature to indicate a protolith origin via low-pressure clinopyroxene-bearing oceanic cumulates formed from melts that were more depleted in incompatible elements than N-MORB. These compositions are indicative of derivation from a residual mantle source that experienced preferential extraction of incompatible elements and fractionation of Zr-Hf during previous melting.
    Print ISSN: 0022-3530
    Electronic ISSN: 1460-2415
    Topics: Geosciences
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    Dark energy survey year 3 results: Galaxy sample for BAO measurement (2021)
    Oxford University Press
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    Publication Date: 2021-10-27
    Description: In this paper we present and validate the galaxy sample used for the analysis of the Baryon Acoustic Oscillation signal (BAO) in the Dark Energy Survey (DES) Y3 data. The definition is based on a colour and redshift-dependent magnitude cut optimized to select galaxies at redshifts higher than 0.5, while ensuring a high quality determination. The sample covers ∼ 4100 square degrees to a depth of i = 22.3 (AB) at 10σ. It contains 7,031,993 galaxies in the redshift range from z= 0.6 to 1.1, with a mean effective redshift of 0.835. Redshifts are estimated with the machine learning algorithm DNF, and are validated using the VIPERS PDR2 sample. We find a mean redshift bias of zbias ∼  0.01 and a mean uncertainty, in units of 1 + z, of σ68 ∼  0.03. We evaluate the galaxy population of the sample, showing it is mostly built upon Elliptical to Sbc types. Furthermore, we find a low level of stellar contamination of $lesssim 4{{ m per cent}}$. We present the method used to mitigate the effect of spurious clustering coming from observing conditions and other large-scale systematics. We apply it to the BAO sampleand calculate weights that are used to get a robust estimate of the galaxy clustering signal. This paper is one of a series dedicated to the analysis of the BAO signal in DES Y3. In the companion papers we present the galaxy mock catalogues used to calibrate the analysis and the angular diameter distance constraints obtained through the fitting to the BAO scale.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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    The z–DM distribution of fast radio bursts (2021)
    Oxford University Press
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    Publication Date: 2021-10-27
    Description: We develop a sophisticated model of FRB observations, accounting for the intrinsic cosmological gas distribution and host galaxy contributions, and give the most detailed account yet of observational biases due to burst width, dispersion measure, and the exact telescope beamshape. Our results offer a significant increase in both accuracy and precision beyond those previously obtained. Using results from ASKAP and Parkes, we present our best-fit FRB population parameters in a companion paper. Here, we consider in detail the expected and fitted distributions in redshift, dispersion measure, and signal-to-noise. We estimate that the unlocalised ASKAP FRBs arise from z 〈 0.5, with between a third and a half within z 〈 0.1. Our predicted source-counts (‘logN–logS’) distribution confirms previous indications of a steepening index near the Parkes detection threshold of 1 Jy ms. We find no evidence for a minimum FRB energy, and rule out Emin 〉 1039.0 erg at 90 per cent C.L. Importantly, we find that above a certain DM, observational biases cause the Macquart (DM–z) relation to become inverted, implying that the highest-DM events detected in the unlocalised Parkes and ASKAP samples are unlikely to be the most distant. More localized FRBs will be required to quantitatively estimate this effect, though its cause is a well-understood observational bias. Works assuming a 1–1 DM–z relation may therefore derive erroneous results. Our analysis of errors suggests that limiting factors in our analysis are understanding of FRB spectral behaviour, sensitivity response of search experiments, and the treatment of the repeating population and luminosity function.
    Print ISSN: 0035-8711
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    Topics: Physics
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    On the detection of multiple shock fronts in A1914 using deep Chandra X-ray observations (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: Here, we report the new detection of three shock fronts using archival Chandra X-ray observations in Abell 1914, which also hosts a radio halo, a radio phoenix, and a head-tail galaxy. In this study, we report the X-ray shock front at the position of the radio phoenix, which further strengthens the scenario that radio phoenix traces old plasma that gets lit up when compressed by shock passage. We further analyse the thermodynamic structure of the cluster in detail. We create temperature maps of A1914 using three different techniques, Adaptive Circular Binning (ACB), Weighted Voronoi Tessellations (WVT), and Contour binning (Contbin) method. These thermodynamic maps, along with the pseudo pressure and the pseudo entropy maps for the cluster, are evidence of disturbed morphology produced by multiple merger events. These merger events create cluster-wide turbulence, which may re-accelerate the relativistic particles and result in a radio halo within the cluster. Further, comparing X-ray and radio images reveals that the radio halo is contained within two X-ray shock fronts. Our analysis suggests that A1914 has both equatorial shock and axial shock within the cluster’s ICM. We proposed a dual merging scenario based on the shock position and analysis of the thermodynamic maps obtained from the deeper Chandra X-ray observations.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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    Tracing the evolution of human gene regulation and its association with shifts in environment (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: As humans populated the world, they adapted to many varying environmental factors, including climate, diet, and pathogens. Because many of these adaptations were mediated by multiple non-coding variants with small effects on gene regulation, it has been difficult to link genomic signals of selection to specific genes, and to describe the regulatory response to selection. To overcome this challenge, we adapted PrediXcan, a machine learning method for imputing gene regulation from genotype data, to analyze low-coverage ancient human DNA (aDNA). First, we used simulated genomes to benchmark strategies for adapting PrediXcan to increase robustness to incomplete data. Applying the resulting models to 490 ancient Eurasians, we found that genes with the strongest divergent regulation among ancient populations with hunter-gatherer, pastoralist, and agricultural lifestyles are enriched for metabolic and immune functions. Next, we explored the contribution of divergent gene regulation to two traits with strong evidence of recent adaptation: dietary metabolism and skin pigmentation. We found enrichment for divergent regulation among genes proposed to be involved in diet-related local adaptation, and the predicted effects on regulation often suggest explanations for known signals of selection, e.g. at FADS1, GPX1, and LEPR. In contrast, skin pigmentation genes show little regulatory change over a 38,000-year time series of 2999 ancient Europeans, suggesting that adaptation mainly involved large-effect coding variants. This work demonstrates that combining aDNA with present-day genomes is informative about the biological differences among ancient populations, the role of gene regulation in adaptation, and the relationship between genetic diversity and complex traits.
    Electronic ISSN: 1759-6653
    Topics: Biology
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    High-Throughput-Methyl-Reading (HTMR) assay: a solution based on nucleotide methyl-binding proteins enables large-scale screening for DNA/RNA methyltransferases and demethylases (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: Epigenetic therapy has significant potential for cancer treatment. However, few small potent molecules have been identified against DNA or RNA modification regulatory proteins. Current approaches for activity detection of DNA/RNA methyltransferases and demethylases are time-consuming and labor-intensive, making it difficult to subject them to high-throughput screening. Here, we developed a fluorescence polarization-based ‘High-Throughput Methyl Reading’ (HTMR) assay to implement large-scale compound screening for DNA/RNA methyltransferases and demethylases-DNMTs, TETs, ALKBH5 and METTL3/METTL14. This assay is simple to perform in a mix-and-read manner by adding the methyl-binding proteins MBD1 or YTHDF1. The proteins can be used to distinguish FAM-labelled substrates or product oligonucleotides with different methylation statuses catalyzed by enzymes. Therefore, the extent of the enzymatic reactions can be coupled with the variation of FP binding signals. Furthermore, this assay can be effectively used to conduct a cofactor competition study. Based on the assay, we identified two natural products as candidate compounds for DNMT1 and ALKBH5. In summary, this study outlines a powerful homogeneous approach for high-throughput screening and evaluating enzymatic activity for DNA/RNA methyltransferases and demethylases that is cheap, easy, quick, and highly sensitive.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    Finite-difference modeling of 2-D wave propagation in the vicinity of dipping interfaces: a comparison of anti-aliasing and equivalent medium approaches (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: Summary Finite-difference (FD) modeling of seismic waves in the vicinity of dipping interfaces gives rise to artifacts. Examples are phase and amplitude errors, as well as staircase diffractions. Such errors can be reduced in two general ways. In the first approach, the interface can be anti-aliased (i.e., with an anti-aliased step-function, or a lowpass filter). Alternatively, the interface may be replaced with an equivalent medium (i.e., using Schoenberg & Muir (SM) calculus or orthorhombic averaging). We test these strategies in acoustic, elastic isotropic, and elastic anisotropic settings. Computed FD solutions are compared to analytical solutions. We find that in acoustic media, anti-aliasing methods lead to the smallest errors. Conversely, in elastic media, the SM calculus provides the best accuracy. The downside of the SM calculus is that it requires an anisotropic FD solver even to model an interface between two isotropic materials. As a result, the computational cost increases compared to when using isotropic FD solvers. However, since coarser grid spacings can be used to represent the dipping interfaces, the two effects (an expensive FD solver on a coarser FD grid) equal out. Hence, the SM calculus can provide an efficient means to reduce errors, also in elastic isotropic media.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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    Population genomics of wall lizards reflects the dynamic history of the Mediterranean Basin (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: The Mediterranean Basin has experienced extensive change in geology and climate over the past six million years. Yet, the relative importance of key geological events for the distribution and genetic structure of the Mediterranean fauna remains poorly understood. Here, we use population genomic and phylogenomic analyses to establish the evolutionary history and genetic structure of common wall lizards (Podarcis muralis). This species is particularly informative because, in contrast to other Mediterranean lizards, it is widespread across the Iberian, Italian, and Balkan peninsulas, and in extra-Mediterranean regions. We found strong support for six major lineages within P. muralis, which were largely discordant with the phylogenetic relationship of mitochondrial DNA. The most recent common ancestor of extant P. muralis was likely distributed in the Italian Peninsula, and experienced an “Out-of-Italy” expansion following the Messinian salinity crisis (∼5 Mya), resulting in the differentiation into the extant lineages on the Iberian, Italian and Balkan peninsulas. Introgression analysis revealed that both inter- and intraspecific gene flows have been pervasive throughout the evolutionary history of P. muralis. For example, the Southern Italy lineage has a hybrid origin, formed through admixture between the Central Italy lineage and an ancient lineage that was the sister to all other P. muralis. More recent genetic differentiation is associated with the onset of the Quaternary glaciations, which influenced population dynamics and genetic diversity of contemporary lineages. These results demonstrate the pervasive role of Mediterranean geology and climate for the evolutionary history and population genetic structure of extant species.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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    The impact of metallicity on nova populations (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: The metallicity of a star affects its evolution in a variety of ways, changing stellar radii, luminosities, lifetimes, and remnant properties. In this work, we use the population synthesis code binary_c to study how metallicity affects novae in the context of binary stellar evolution. We compute a 16-point grid of metallicities ranging from Z = 10−4 to 0.03, presenting distributions of nova white dwarf masses, accretion rates, delay-times, and initial system properties at the two extremes of our 16-point metallicity grid. We find a clear anti-correlation between metallicity and the number of novae produced, with the number of novae at Z = 0.03 roughly half that at Z = 10−4. The white dwarf mass distribution has a strong systematic variation with metallicity, while the shape of the accretion rate distribution is relatively insensitive. We compute a current nova rate of approximately 33 novae per year for the Milky Way, a result consistent with observational estimates relying on extra-Galactic novae but an under-prediction relative to observational estimates relying on Galactic novae. However, the shape of our predicted Galactic white dwarf mass distribution differs significantly to existing observationally derived distributions, likely due to our underlying physical assumptions. In M31, we compute a current nova rate of approximately 36 novae per year, under-predicting the most recent observational estimate of $65^{+15}_{-16}$. Finally, we conclude that when making predictions about currently observable nova rates in spiral galaxies, or stellar environments where star formation has ceased in the distant past, metallicity can likely be considered of secondary importance compared to uncertainties in binary stellar evolution.
    Print ISSN: 0035-8711
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    MicroDNA levels are dependent on MMEJ, repressed by c-NHEJ pathway, and stimulated by DNA damage (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: Extrachromosomal circular DNA (eccDNA) are present within all eukaryotic organisms and actively contribute to gene expression changes. MicroDNA (200-1000bp) are the most abundant type of eccDNA and can amplify tRNA, microRNA, and novel si-like RNA sequences. Due to the heterogeneity of microDNA and the limited technology to directly quantify circular DNA molecules, the specific DNA repair pathways that contribute to microDNA formation have not been fully elucidated. Using a sensitive and quantitative assay that quantifies eight known abundant microDNA, we report that microDNA levels are dependent on resection after double-strand DNA break (DSB) and repair by Microhomology Mediated End Joining (MMEJ). Further, repair of DSB without resection by canonical Non-Homologous End Joining (c-NHEJ) diminishes microDNA formation. MicroDNA levels are induced locally even by a single site-directed DSB, suggesting that excision of genomic DNA by two closely spaced DSB is not necessary for microDNA formation. Consistent with all this, microDNA levels accumulate as cells undergo replication in S-phase, when DNA breaks and repair are elevated, and microDNA levels are decreased if DNA synthesis is prevented. Thus, formation of microDNA occurs during the repair of endogenous or induced DNA breaks by resection-based DNA repair pathways.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    Genome-wide reconstruction of rediploidization following autopolyploidization across one hundred million years of salmonid evolution (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: The long-term evolutionary impacts of whole genome duplication (WGD) are strongly influenced by the ensuing rediploidization process. Following autopolyploidization, rediploidization involves a transition from tetraploid to diploid meiotic pairing, allowing duplicated genes (ohnologues) to diverge genetically and functionally. Our understanding of autopolyploid rediploidization has been informed by a WGD event ancestral to salmonid fishes, where large genomic regions are characterized by temporally delayed rediploidization, allowing lineage-specific ohnologue sequence divergence in the major salmonid clades. Here, we investigate the long-term outcomes of autopolyploid rediploidization at genome-wide resolution, exploiting a recent ‘explosion’ of salmonid genome assemblies, including a new genome sequence for the huchen (Hucho hucho). We developed a genome alignment approach to capture duplicated regions across multiple species, allowing us to create 121,864 phylogenetic trees describing genome-wide ohnologue divergence across salmonid evolution. Using molecular clock analysis, we show that 61% of the ancestral salmonid genome experienced an initial ‘wave’ of rediploidization in the late Cretaceous (85-106 Mya). This was followed by a period of relative genomic stasis lasting 17-39 My, where much of the genome remained tetraploid. A second rediploidization wave began in the early Eocene and proceeded alongside species diversification, generating predictable patterns of lineage-specific ohnologue divergence, scaling in complexity with the number of speciation events. Using gene set enrichment, gene expression, and codon-based selection analyses, we provide insights into potential functional outcomes of delayed rediploidization. This study enhances our understanding of delayed autopolyploid rediploidization and has broad implications for future studies of WGD events.
    Print ISSN: 0737-4038
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    Topics: Biology
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    A birth-death-migration model for life in astrophysical environments (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: To assess the number of life-bearing worlds in astrophysical environments, it is necessary to take the intertwined processes of abiogenesis (birth), extinction (death), and transfer of life (migration) into account. We construct a mathematical model that incorporates this trio of mechanisms and accordingly derive the probability distribution function and other statistical properties (e.g. mean) for the number of worlds with biospheres. We show that a given astrophysical setting may become eventually saturated with life if the rate of successful transfers of organisms is higher than the extinction rate of biospheres. Based on the available data, we suggest that this criterion might be fulfilled for star-forming clusters (and perhaps the Galactic bulge under optimal circumstances), thereby indicating that such regions could constitute promising abodes for hosting and detecting life.
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    Non-standard mechanism of recombination in the early Universe (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: In our recent papers a non-standard quasi-molecular mechanism was suggested and applied to treat the cosmological recombination. It was assumed that, in the pre-recombination stage of evolution of the Universe, an electron combined with two neighbouring protons and created a hydrogen molecular ion, $H_2^+$ in a highly excited state, which then descended into the lower-lying state or dissociated. In this work, we implement a quantitative analysis of this quasi-molecular mechanism of recombination; namely, we elaborate the scheme of calculation for a free–bound radiative transition. We show that the quasi-molecular mechanism played a significant role in the pre-recombination and recombination stages of evolution of the early Universe, and hence must be included into the consideration of the description of a thermal history of the Universe. Together with the earlier developed treatment of bound-bound radiative transitions in $H_2^+$, the elaborated scheme of calculation can be used for the design of a rapid and complete cosmological recombination code.
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    CpG Transformer for imputation of single-cell methylomes (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: Motivation The adoption of current single-cell DNA methylation sequencing protocols is hindered by incomplete coverage, outlining the need for effective imputation techniques. The task of imputing single-cell (methylation) data requires models to build an understanding of underlying biological processes. Results We adapt the transformer neural network architecture to operate on methylation matrices through combining axial attention with sliding window self-attention. The obtained CpG Transformer displays state-of-the-art performances on a wide range of scBS-seq and scRRBS-seq datasets. Furthermore, we demonstrate the interpretability of CpG Transformer and illustrate its rapid transfer learning properties, allowing practitioners to train models on new datasets with a limited computational and time budget. Availability and Implementation CpG Transformer is freely available at https://github.com/gdewael/cpg-transformer. Supplementary information Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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    Gravitational wave signature of proto-neutron star convection: I. MHD numerical simulations (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: Gravitational waves provide a unique and powerful opportunity to constrain the dynamics in the interior of proto-neutron stars during core collapse supernovae. Convective motions play an important role in generating neutron stars magnetic fields, which could explain magnetar formation in the presence of fast rotation. We compute the gravitational wave emission from proto-neutron star convection and its associated dynamo, by post-processing three-dimensional MHD simulations of a model restricted to the convective zone in the anelastic approximation. We consider two different proto-neutron star structures representative of early times (with a convective layer) and late times (when the star is almost entirely convective). In the slow rotation regime, the gravitational wave emission follows a broad spectrum peaking at about three times the turnover frequency. In this regime, the inclusion of magnetic fields slightly decreases the amplitude without changing the spectrum significantly compared to a non-magnetised simulation. Fast rotation changes both the amplitude and spectrum dramatically. The amplitude is increased by a factor of up to a few thousands. The spectrum is characterized by several peaks associated to inertial modes, whose frequency scales with the rotation frequency. Using simple physical arguments, we derive scalings that reproduce quantitatively several aspects of these numerical results. We also observe an excess of low-frequency gravitational waves, which appears at the transition to a strong field dynamo characterized by a strong axisymmetric toroidal magnetic field. This signature of dynamo action could be used to constrain the dynamo efficiency in a proto-neutron star with future gravitational wave detections.
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    Spatial estimation of fundamental mode dispersion curves using geostatistical techniques (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: Summary This article proposes the use of geostatistical techniques to estimate dispersion curves between other known ones. To do it, we introduce two novel methodologies: the stacking method and the group-velocity mapping method. We obtain our set of group-velocity fundamental mode dispersion curves from seismic noise correlation. Consequently, we first assign their attribution point at the mid-distance between the stations used for the dispersion curves calculation. The stacking method uses the range of the omnidirectional semivariogram of a regionalized variable that quantifies the similarity between dispersion curves to stack them according to their spatial correlation. We test this technique with dispersion curves obtained in Mexico City and get a range of ∼400 m for the omnidirectional semivariogram. We also calculate directional semivariograms and observe a maximum range (∼500 m) in the NW-SE direction, agreeing with the city's spatial distribution of natural periods. On the other hand, the group-velocity mapping method uses the ordinary kriging estimator in the group velocities for all the ranges of periods to generate maps and then dispersion curves. Estimated dispersion curves retrieved from both, the stacking and the group-velocity mapping method, were compared with those obtained with the fast marching tomographic method. We also establish analogies between getting group-velocity maps with the tomographic method and with the group-velocity mapping method. Finally, we observe that the range of the omnidirectional semivariogram used in the stacking method may be related to the tomographic method resolution.
    Print ISSN: 0956-540X
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    Topics: Geosciences
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    SatGen – II. Assessing the impact of a disc potential on subhalo populations (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: The demographics of dark matter substructure depend sensitively on the nature of dark matter. Optimally leveraging this probe requires accurate theoretical predictions regarding the abundance of subhaloes. These predictions are hampered by artificial disruption in numerical simulations, by large halo-to-halo variance, and by the fact that the results depend on the baryonic physics of galaxy formation. In particular, numerical simulations have shown that the formation of a central disc can drastically reduce the abundance of substructure compared to a dark matter-only simulation, which has been attributed to enhanced destruction of substructure due to disc shocking. We examine the impact of discs on substructure using the semi-analytical subhalo model SatGen, which accurately models the tidal evolution of substructure free of the numerical disruption that still hampers N-body simulations. Using a sample of 10,000 merger trees of Milky Way-like haloes, we study the demographics of subhaloes that are evolved under a range of composite halo–disc potentials with unprecedented statistical power. We find that the overall subhalo abundance is relatively insensitive to properties of the disc aside from its total mass. For a disc that contains 5% of Mvir, the mean subhalo abundance within rvir is suppressed by ${lesssim }10\%$ relative to the no-disc case, a difference that is dwarfed by halo-to-halo variance. For the same disc mass, the abundance of subhaloes within 50 kpc is reduced by ${sim }30\%$. We argue that the disc mainly drives excess mass loss for subhaloes with small pericentric radii and that the impact of disc shocking is negligible.
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    Heterozygous Tropomodulin 3 mice have improved lung vascularization after chronic hypoxia. (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: The molecular mechanisms leading to high altitude pulmonary hypertension (HAPH) remains poorly understood. We previously analyzed the whole genome sequence of Kyrgyz highland population and identified eight genomic intervals having a potential role in HAPH. Tropomodulin 3 gene (TMOD3) which encodes a protein that binds and caps the pointed ends of actin filaments and inhibits cell migration, was one of the top candidates. Here we systematically sought additional evidence to validate the functional role of TMOD3. In-silico analysis reveals that some of the SNPs in HAPH associated genomic intervals were positioned in a regulatory region that could result in alternative splicing of TMOD3. In order to functionally validate the role of TMOD3 in HAPH, we exposed Tmod3−/+ mice to 4 weeks of constant hypoxia, i.e. 10% O2 and analyzed both functional (hemodynamic measurements) and structural (angiography) parameters related to HAPH. The hemodynamic measurements, such as right ventricular systolic pressure, a surrogate measure for pulmonary arterial systolic pressure, and right ventricular contractility (RV- ± dP/dt), increases with hypoxia did not separate between Tmod3−/+ and control mice. Remarkably, there was a significant increase in the number of lung vascular branches and total length of pulmonary vascular branches (p 
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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    Phylogenetic articulation of uric acid evolution in mammals and how it informs a therapeutic uricase (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: The role of uric acid during primate evolution has remained elusive ever since it was discovered over 100 years ago that humans have unusually high levels of the small molecule in our serum. It has been difficult to generate a neutral or adaptive explanation in part because the uricase enzyme evolved to become a pseudogene in apes thus masking typical signals of sequence evolution. Adding to the difficulty is a lack of clarity on the functional role of uric acid in apes. One popular hypothesis proposes that uric acid is a potent antioxidant that increased in concentration to compensate for the lack of vitamin C synthesis in primate species ∼65 million years ago (Mya). Here, we have expanded on our previous work with resurrected ancient uricase proteins to better resolve the reshaping of uricase enzymatic activity prior to ape evolution. Our results suggest that the pivotal death-knell to uricase activity occurred between 20-30 Mya despite small sequential modifications to its catalytic efficiency for the tens of millions of years since primates lost their ability to synthesize vitamin C, and thus the two appear uncorrelated. We also use this opportunity to demonstrate how molecular evolution can contribute to biomedicine by presenting ancient uricases to human immune cells that assay for innate reactivity against foreign antigens. A highly stable and highly catalytic ancient uricase is shown to elicit a lower immune response in more human haplotypes than other uricases currently in therapeutic development.
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    Self-similarity of k-nearest neighbor distributions in scale-free simulations (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: We use the k-nearest neighbor probability distribution function (kNN-PDF, Banerjee & Abel 2021) to assess convergence in a scale-free N-body simulation. Compared to our previous two-point analysis, the kNN-PDF allows us to quantify our results in the language of haloes and numbers of particles, while also incorporating non-Gaussian information. We find good convergence for 32 particles and greater at densities typical of haloes, while 16 particles and fewer appears unconverged. Halving the softening length extends convergence to higher densities, but not to fewer particles. Our analysis is less sensitive to voids, but we analyse a limited range of underdensities and find evidence for convergence at 16 particles and greater even in sparse voids.
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    SigTools: Exploratory Visualization For Genomic Signals (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: Motivation With the advancement of sequencing technologies, genomic data sets are constantly being expanded by high volumes of different data types. One recently introduced data type in genomic science is genomic signals, which are usually short-read coverage measurements over the genome. To understand and evaluate the results of such studies, one needs to understand and analyze the characteristics of the input data. Results SigTools is an R-based genomic signals visualization package developed with two objectives: 1) to facilitate genomic signals exploration in order to uncover insights for later model training, refinement, and development by including distribution and autocorrelation plots. 2) to enable genomic signals interpretation by including correlation, and aggregation plots. In addition, our corresponding web application, SigTools-Shiny, extends the accessibility scope of these modules to people who are more comfortable working with graphical user interfaces instead of command-line tools. Availability SigTools source code, installation guide, and manual is freely available on http://github.com/shohre73.
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    Topics: Biology , Computer Science , Medicine
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    Galactic cosmic ray propagation through M dwarf planetary systems (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: Quantifying the flux of cosmic rays reaching exoplanets around M dwarfs is essential to understand their possible effects on exoplanet habitability. Here, we investigate the propagation of Galactic cosmic rays as they travel through the stellar winds (astrospheres) of five nearby M dwarfs, namely: GJ 15A, GJ 273, GJ 338B, GJ 411 and GJ 887. Our selected stars each have 1 or 2 detected exoplanets and they all have wind mass-loss rates constrained by Lyman-α observations. Our simulations use a combined 1D magnetohydrodynamic (MHD) Alfvén-wave-driven stellar wind model and 1D cosmic ray transport model. We find that GJ 411 and GJ 887 have Galactic cosmic rays fluxes comparable with Earth’s at their habitable zones. On the other hand, GJ 15A, GJ 273 and GJ 338B receive a lower Galactic cosmic ray flux in their habitable zones. All exoplanets in our sample, with exception of GJ 15A c and GJ 411 c, have a significantly lower flux of Galactic cosmic rays than values observed at the Earth because they orbit closer-in. The fluxes found here can be further used for chemical modelling of planetary atmospheres. Finally, we calculate the radiation dose at the surface of the habitable-zone planet GJ 273 b, assuming it has an Earth-like atmosphere. This planet receives up to 209 times less 15 MeV energy cosmic ray fluxes than values observed at Earth. However, for high-energy cosmic rays (∼ GeV), the difference in flux is only 2.3 times smaller, which contributes to GJ 273 b receiving a significant surface radiation dose of 0.13 mSv/yr (40 per cent of the annual dose on Earth’s surface).
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    Data-Efficient Classification of Radio Galaxies (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: The continuum emission from radio galaxies can be generally classified into different morphological classes such as FRI, FRII, Bent, or Compact. In this paper, we explore the task of radio galaxy classification based on morphology using deep learning methods with a focus on using a small scale dataset (∼2000 samples). We apply few-shot learning techniques based on Twin Networks and transfer learning techniques using a pre-trained DenseNet model with advanced techniques like cyclical learning rate and discriminative learning to train the model rapidly. We achieve a classification accuracy of over 92% using our best performing model with the biggest source of confusion being between Bent and FRII type galaxies. Our results show that focusing on a small but curated dataset along with the use of best practices to train the neural network can lead to good results. Automated classification techniques will be crucial for upcoming surveys with next generation radio telescopes which are expected to detect hundreds of thousands of new radio galaxies in the near future.
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    Aftershock sequence of the 2017 Mw 6.5 Jiuzhaigou, China earthquake monitored by an AsA network and its implication to fault structures and strength (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: Summary We deployed a seismic network near the source region of the 2017 Mw 6.5 Jiuzhaigou earthquake to monitor aftershock activity and to investigate the local fault structure. An aftershock deployment of Array of small Arrays (AsA) and a Geometric Mean Envelop (GME) algorithm are adopted to enhance detection performance. We also adopt a set of association, relocation, and matched-filter techniques to obtain a detailed regional catalog. 16,742 events are detected and relocated, including 1,279 aftershocks following the Mw 4.8 aftershock. We develop a joint inversion algorithm utilizing locations of event clusters and focal mechanisms to determine the geometry of planar faults. Six segments were finally determined, in which three segments are related to the Huya fault reflecting a change in fault dip direction near the mainshock hypocenter, while the other segments reflect branches showing orthogonal and conjugate geometries with the Huya fault. Aftershocks were active on branching faults between the Huya and Minjiang faults indicating that the mainshock may have ruptured both major faults. We also resolve a fault portion with ‘weak strength’ near the mainshock hypocenter, which is characterized by limited co-seismic slips, concentrated afterslip, low aftershock activities, high b-value, and high sensitivity to stress changes. These phenomena can be explained by fault frictional properties at conditional stable sliding status, which may be related to the localized high pore-fluid pressure produced by the fluid intrusion.
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    Variable star classification across the Galactic bulge and disc with the VISTA Variables in the Vía Láctea survey (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: We present VIVACE, the VIrac VAriable Classification Ensemble, a catalogue of variable stars extracted from an automated classification pipeline for the Vista Variables in the Vía Láctea (VVV) infrared survey of the Galactic bar/bulge and southern disc. Our procedure utilises a two-stage hierarchical classifier to first isolate likely variable sources using simple variability summary statistics and training sets of non-variable sources from the Gaia early third data release, and then classify candidate variables using more detailed light curve statistics and training labels primarily from OGLE and VSX. The methodology is applied to point-spread-function photometry for ∼490 million light curves from the VIRAC v2 astrometric and photometric catalogue resulting in a catalogue of ∼1.4 million likely variable stars, of which ∼39, 000 are high-confidence (classification probability 〉0.9) RR Lyrae ab stars, ∼8000 RR Lyrae c/d stars, ∼187, 000 detached/semi-detached eclipsing binaries, ∼18, 000 contact eclipsing binaries, ∼1400 classical Cepheid variables and ∼2200 Type II Cepheid variables. Comparison with OGLE-4 suggests a completeness of around 90  per cent for RRab and ≲ 60 per cent for RRc/d, and a misclassification rate for known RR Lyrae stars of around 1 per cent for the high confidence sample. We close with two science demonstrations of our new VIVACE catalogue: first, a brief investigation of the spatial and kinematic properties of the RR Lyrae stars within the disc/bulge, demonstrating the spatial elongation of bar-bulge RR Lyrae stars is in the same sense as the more metal-rich red giant population whilst having a slower rotation rate of ∼40 km s−1kpc−1; and secondly, an investigation of the Gaia EDR3 parallax zeropoint using contact eclipsing binaries across the Galactic disc plane and bulge.
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    Chromosome level genome assembly and annotation of highly invasive Japanese stiltgrass (Microstegium vimineum) (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: The invasive Japanese stiltgrass (Microstegium vimineum) affects a wide range of ecosystems and threatens biodiversity across the eastern USA. However, the mechanisms underlying rapid adaptation, plasticity, and epigenetics in the invasive range are largely unknown. We present a chromosome-level assembly for M. vimineum to investigate genome dynamics, evolution, adaptation, and the genomics of phenotypic plasticity. We generated a 1.12 Gb genome with scaffold N50 length of 53.44 Mb respectively, taking a de novo assembly approach that combined PacBio and Dovetail Genomics Omni-C sequencing. The assembly contains 23 pseudochromosomes, representing 99.96% of the genome. BUSCO assessment indicated that 80.3% of Poales gene groups are present in the assembly. The genome is predicted to contain 39,604 protein-coding genes, of which 26,288 are functionally annotated. Furthermore, 66.68% of the genome is repetitive, of which unclassified (35.63%) and long terminal repeat (LTR) retrotransposons (26.90%) are predominant. Similar to other grasses, Gypsy (41.07%) and Copia (32%) are the most abundant LTR-retrotransposon families. The majority of LTR-retrotransposons are derived from a significant expansion in the past 1-2 million years, suggesting the presence of relatively young LTR-retrotransposon lineages. We find corroborating evidence from Ks plots for a stiltgrass-specific duplication event, distinct from the more ancient grass-specific duplication event. The assembly and annotation of M. vimineum will serve as an essential genomic resource facilitating studies of the invasion process, the history and consequences of polyploidy in grasses, and provides a crucial tool for natural resource managers.
    Electronic ISSN: 1759-6653
    Topics: Biology
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    An analysis of core-mantle boundary Stoneley mode sensitivity and sources of uncertainty (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: Summary Stoneley modes are a special subset of normal modes whose energy is confined along the core-mantle boundary. As such, they offer a unique glimpse into Earth structure at the base of the mantle. They are often observed through coupling with mantle modes due to rotation, ellipticity and lateral heterogeneity, though they can be detected without such coupling. In this study, we explore the relative sensitivities of seismic spectra of two low-frequency Stoneley modes to several factors, taking as reference the fully coupled computation up to 3 mHz in model S20RTS. The factors considered are (i) theoretical, by exploring the extent to which various coupling approximations can accurately reproduce reference spectra; and (ii) model-based, by exploring how various Earth parameters such as core-mantle boundary topography, attenuation, and S-wave and P-wave structures, and the seismic source solution may influence the spectra. We find that mode-pair coupling is insufficiently accurate, but coupling modes within a range of ±0.1 mHz produces acceptable spectra, compared to full coupling. This has important implications for splitting function measurements, which are computed under the assumption of isolated modes or at best, mode-pair or group coupling. We find that uncertainties in the P-wave velocity mantle model dominate compared to other model parameters. In addition, we also test several hypothetical models of mantle density structure against real data. These tests indicate that, with the low-frequency Stoneley mode spectral data considered here, it is difficult to make any firm statement on whether the large-low-shear-velocity-provinces are denser or lighter than their surroundings. We conclude that better constraints on long wavelength elastic mantle structure, particularly P-wave velocity, need to be obtained, before making further statements on deep mantle density heterogeneity. In particular, a dense anomaly confined to a thin layer at the base of the mantle (less than ∼100-200 km) may not be resolvable using the two Stoneley modes tested here, while the ability of higher frequency Stoneley modes to resolve it requires further investigations.
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    Full waveform inversion based on the non-parametric estimate of the probability distribution of the residuals (2021)
    Oxford University Press
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    Publication Date: 2021-10-27
    Description: Summary In an attempt to overcome the difficulties of the full waveform inversion (FWI), several alternative objective functions have been proposed over the last few years. Many of them are based on the assumption that the residuals (differences between modelled and observed seismic data) follow specific probability distributions when, in fact, the true probability distribution is unknown. This leads FWI to converge to an incorrect probability distribution if the assumed probability distribution is different from the real one and, consequently it may lead the FWI to achieve biased models of the subsurface. In this work, we propose an objective function which does not force the residuals to follow a specific probability distribution. Instead, we propose to use the non-parametric kernel density estimation technique (KDE) (which imposes the least possible assumptions about the residuals) to explore the probability distribution that may be more suitable. As evidenced by the results obtained in a synthetic model and in a typical P-wave velocity model of the Brazilian pre-salt fields, the proposed FWI reveals a greater potential to overcome more adverse situations (such as cycle-skipping) and also a lower sensitivity to noise in the observed data than conventional L2 and L1-norm objective functions and thus making it possible to obtain more accurate models of the subsurface. This greater potential is also illustrated by the smoother and less sinuous shape of the proposed objective function with fewer local minima compared with the conventional objective functions.
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    A persistent double nuclear structure in 3C 84 (2021)
    Oxford University Press
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    Publication Date: 2021-10-27
    Description: 3C 84 (NGC 1275) is the radio source at the center of the Perseus Cluster and exhibits a bright radio jet. We observed the source with the Global Millimeter VLBI Array (GMVA) between 2008 and 2015, with a typical angular resolution of ∼50 μas. The observations revealed a consistent double nuclear structure separated by ∼770 gravitational radii assuming a Black Hole mass of 3.2 × 108 M⊙. The region is likely too broad and bright to be the true jet base anchored in the accretion disk or Black Hole ergosphere. A cone and parabola were fit to the stacked (time averaged) image of the nuclear region. The data did not strongly prefer either fit, but combined with a jet/counter-jet ratio analysis, an upper limit on the viewing angle to the inner jet region of ≤35○ was found. This provides evidence for a variation of the viewing angle along the jet (and therefore a bent jet) within ∼0.5 parsec of the jet launching region. In the case of a conical jet, the apex is located ∼2400 gravitational radii upstream of the bright nuclear region and up to ∼600 gravitational radii upstream in the parabolic case. We found a possible correlation between the brightness temperature and relative position angle of the double nuclear components, which may indicate rotation within the jet.
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    Dancing in the void: Hydrodynamical N-body simulations of the extremely metal poor galaxy DDO 68 (2021)
    Oxford University Press
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    Publication Date: 2021-10-27
    Description: Using hydrodynamical N-body simulations, we show that the observed structure and kinematics of the extremely metal-poor, dwarf irregular galaxy DDO 68 is compatible with a merger event with at least two smaller satellite galaxies. We were able to obtain a self-consistent model that simultaneously reproduces several of its observed features, including: the very asymmetric and disturbed shape of the stellar component, the overall ${ m H, small {I}}$ distribution and its velocity field, the arc-like stellar structure to the west, the low-surface brightness stellar stream to the north. The model implies the interaction of the main progenitor of DDO 68 with two systems with dynamical masses 7 × 108 M⊙ and almost 108 M⊙ – 1/20 and 1/150 times the dynamical mass of DDO 68, respectively. We show that the merger between DDO 68 and the most massive of its satellites offers a route to explain the large offset of DDO 68 from the mass-metallicity relation. Assuming that the interacting galaxies have metallicities prior to the merger compatible with those of galaxies with similar stellar masses, we provide quantitative evidence that gas mixing alone does not suffice at diluting the gas of the two components; according to our simulations, the ${ m H, small {II}}$ regions observed along the Cometary Tail trace the low metallicity of the accreted satellite rather than that of DDO 68’s main body. In this case, the mass corresponding to the low metallicity is that of the secondary body and DDO 68 becomes consistent with the mass-metallicity relation.
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    FOREVER22: galaxy formation in protocluster regions (2021)
    Oxford University Press
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    Publication Date: 2021-10-27
    Description: We present results from a new cosmological hydrodynamics simulation campaign of protocluster (PC) regions, FOREVER22: FORmation and EVolution of galaxies in Extremely-overdense Regions motivated by SSA22. The simulations cover a wide range of cosmological scales using three different zoom set-ups in a parent volume of $(714.2~ m cMpc)^{3}$: PCR (Proto-Cluster Region; V = (28.6 cMpc)3, SPH particle mass, mSPH = 4.1 × 106 M⊙ and final redshift, zend = 2.0), BCG (Brightest proto-Cluster Galaxy; V ∼ (10 cMpc)3, mSPH = 5.0 × 105 M⊙ and zend = 4.0 ), and First ( V ∼ (3 cMpc)3, mSPH = 7.9 × 103 M⊙ and zend = 9.5) runs, that allow to focus on different aspects of galaxy formation. In the PCR runs, we follow 10 PCs, each harbouring 1–4 SMBHs with ${ m M_{ m BH}}ge 10^{9}~{ m M_{odot }}$. One of the PC cores shows a spatially close arrangement of seven starburst galaxies with ${ m SFR} gtrsim 100~{ m { m M_{odot }}~{ m yr^{-1}}}$ each, that are dust-obscured and would appear as submillimeter galaxies with flux ≳ 1  mJy at $1.1~ m mm$ in observations. The BCG runs show that the total SFRs of haloes hosting BCGs are affected by AGN feedback, but exceed $1000~{ m { m M_{odot }}~{ m yr^{-1}}}$ at z ≲ 6. The First runs resolve mini-haloes hosting population (Pop) III stars and we show that, in PC regions, the dominant stellar population changes from Pop III to Pop II at z ≳ 20, and the first galaxies with ${ m SFR} gtrsim 18~{ m { m M_{odot }}~{ m yr^{-1}}}$ form at z ∼ 10. These can be prime targets for future observations with the James Webb Space Telescope. Our simulations successfully reproduce the global star formation activities in observed PCs and suggest that PCs can kickstart cosmic reionization.
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    Evidence for an expanding corona based on spectral-timing modelling of multiple black hole X-ray binaries (2021)
    Oxford University Press
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    Publication Date: 2021-10-27
    Description: Galactic black hole X-ray binaries (BHXBs) provide excellent laboratories to study accretion, as their relatively quick evolution allows us to monitor large changes in the in-flowing and/or out-flowing material over human timescales. However, the details of how the inflow-outflow coupling evolves during a BHXB outburst remain an area of active debate. In this work we attempt to probe the physical changes underlying the system evolution, by performing a systematic analysis of the multi-wavelength data of three BHXB sources: XTE J1752-223, MAXI J1659-152, and XTE J1650-500, during hard and hard-intermediate states. Using the power spectral hue which characterises the X-ray variability properties, we identify several clusters of BHXB epochs and perform the joint multi-wavelength spectral modelling to test their commonality with a physical jet model. Under the assumption that the corona is related to the base of the jet, we find that the power spectral hue traces the variation of the coronal radius (from ∼10Rg − ∼ 40Rg) in multiple BHXBs at hard and hard-intermediate states, and that the data are consistent with moderately truncated accretion discs (
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    A multiwavelength study of the H ii region G347.600+00.211 and its effects on the surrounding medium (2021)
    Oxford University Press
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    Publication Date: 2021-10-27
    Description: We present a multi-wavelength investigation of the H ii region G347.600+00.211, located at a distance of 7.9 kpc. We analyse the gas and dust properties aiming to disentangle the origin of the region as well as its role in the formation of new stars. G347.600+00.211 is very conspicuous at 1420 MHz and infrared wavelengths, showing an incomplete shell-like structure with two distinct zones of very intense emission. The infrared bubble S8 is part of the shell structure. The spatial distribution of the molecular gas shows the presence of six clouds located around the ionized region and showing a good morphological correlation with the 8 μm emission. Cold dust is coincident with the dense gas shown in the CO measurements. As for the origin of the region, we found that the massive cluster [DBS2003]179 and two Wolf–Rayet (WR) stars are located at the same distance than the ionized gas. Based on a stellar density analysis, we inferred that one of the WR stars, 1181-81L, is also a probable member of the cluster. Both the cluster and the WR stars are not only within the ring–like structure, but are also located near the two spots of very heightened emission, suggesting they may be responsible for this bright emission. Finally, as expanding H ii regions are hypothesised to trigger star formation, we used different infrared point source catalogues to search for young stellar object candidates (cYSOs). A total of 33 cYSOs and 4 CH ii regions were identified projected on to the photo–dissociation regions and molecular clouds.
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    Similarity-based analysis of allele frequency distribution among multiple populations identifies adaptive genomic structural variants (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: Structural variants have a considerable impact on human genomic diversity. However, their evolutionary history remains mostly unexplored. Here, we developed a new method to identify potentially adaptive structural variants based on a similarity-based analysis that incorporates genotype frequency data from 26 populations simultaneously. Using this method, we analyzed 57,629 structural variants and identified 576 structural variants that show unusual population differentiation. Of these putatively adaptive structural variants, we further showed that 24 variants are multiallelic and overlap with coding sequences, and 20 variants are significantly associated with GWAS traits. Closer inspection of the haplotypic variation associated with these putatively adaptive and functional structural variants reveals deviations from neutral expectations due to (i) population differentiation of rapidly evolving multi-allelic variants, (ii) incomplete sweeps, and (iii) recent population-specific negative selection. Overall, our study provides new methodological insights, documents hundreds of putatively adaptive variants, and introduces evolutionary models that may better explain the complex evolution of structural variants.
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    Topics: Biology
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    Links between foreland rheology and the growth and evolution of a young mountain belt in New Guinea (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: Summary We have studied the active and recent tectonics of New Guinea, using earthquake source modelling, analysis of gravity anomalies, seismic reflection profiles, and thermal and mechanical models. Our aim is to investigate the behaviour and evolution of a young continental deformation belt, and to explore the effects of lateral variations in foreland rheology on the deformation. We find that along-strike gradients in the lithosphere thickness of the southern foreland have resulted in correlated changes in seismogenic thickness, likely due to the effects on the temperature structure of the crust. The resulting variation in the strength of the foreland means that in the east, the foreland is broken through on thrust faults, whereas in the west it is relatively intact. The lack of correlation between the elevation of the mountain belt and the seismogenic thickness of the foreland is likely to be due to the time taken to thicken the crust in the mountains following changes in the rheology of the underthrusting foreland, as the thinned passive margin of northern Australia is consumed. The along-strike variation in whether the force exerted between the mountains and the lowlands is able to break the foreland crust enables us to estimate the effective coefficient of friction on foreland faults to be in the range of 0.01-0.28. We use force-balance calculations to show that the recent tectonic re-organisation in western New Guinea is likely to be due to the development of increasing curvature in the Banda Arc, and that the impingement of continental material on the subduction zone may explain the unusually low force it exerts on western New Guinea.
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    Five years of BRITE-Constellation photometry of the luminous blue variable P Cygni: properties of the stochastic low-frequency variability (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: Luminous Blue Variables (LBVs) are massive stars that are likely to be a transitionary phase between O stars and hydrogen-free classical Wolf-Rayet stars. The variability of these stars has been an area of study for both professional and amateur astronomers for more than a century. In this paper, we present five years of precision photometry of the classical LBV P Cygni taken with the BRITE-Constellation nanosatellites. We have analyzed these data with Fourier analysis to search for periodicities that could elucidate the drivers of variability for these stars. These data show some long-timescale variability over the course of all six calendar years of observations, but the frequencies needed to reproduce the individual light curves are not consistent from one year to the next. These results likely show that there is no periodic phenomenon present for P Cygni, meaning that the variability is largely stochastic. We interpret the data as being caused by internal gravity waves similar to those seen in other massive stars, with P Cygni exhibiting a larger amplitude and lower characteristic frequency than the main-sequence or blue supergiant stars previously studied. These results show evidence that LBVs may be an extrapolation of the blue supergiants, which have previously been shown to be an extension of main-sequence stars in the context of the stochastic low-frequency photometric variability.
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    Zodiacal exoplanets in time (ZEIT) XIII: Planet orbits and atmospheres in the V1298 Tau system, a keystone in studies of early planetary evolution (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: Studies of planetary systems of stars in star-forming regions and young clusters open a window on the formative stages of planetary evolution. We obtained high-cadence high-resolution infrared spectroscopy of the solar-mass Taurus association-member V1298 Tau during a transit of its 10R⊕-size ‘b’ planet. We measured the systemic radial velocity and find that the kinematics of V1298 Tau suggest an affiliation with a ≳6 Myr-old subgroup. A comparison of V1298 Tau and the nearby, co-moving star 2M0405 with stellar evolution models suggests an age of ∼10-25 Myr. We measured the projected spin-orbit angle of ‘b’ as $lambda =15_{-16}^{+15}$ and $lambda = 2_{-4}^{+12}$ degrees using the apparent RV shift and change in line profile, respectively, induced by the transient occultation of the rotating star by the planet. These values indicate a prograde orbit like that of the interior ‘c’ planet of V1298 Tau and point to a co-planar multi-planet system that formed within a disk. We also measured variation in the strength of the 1083 nm triplet of neutral orthohelium as a probe of any extended/escaping atmosphere around ‘b’. We detect a steady decrease in absorption over the transit which appears to arise from the star or its planetary system. While this variation could be ascribed to ‘b’ or possibly to the immediately preceding transit of ‘d’, we cannot rule out that this is due to rapid variation in the stellar disk-integrated flux in the triplet. The amplitude of variation (∼0.04 nm) is consistent with moderate estimates of atmospheric escape driven by XUV radiation from the central star.
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    Importance-Penalized Joint Graphical Lasso (IPJGL): differential network inference via GGMs (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: Motivation Differential network inference is a fundamental and challenging problem to reveal gene interactions and regulation relationships under different conditions. Many algorithms have been developed for this problem; however, they do not consider the differences between the importance of genes, which may not fit the real-world situation. Different genes have different mutation probabilities, and the vital genes associated with basic life activities have less fault tolerance to mutation. Equally treating all genes may bias the results of differential network inference. Thus, it is necessary to consider the importance of genes in the models of differential network inference. Results Based on the Gaussian graphical model with adaptive gene importance regularization, we develop a novel importance-penalized joint graphical Lasso method, IPJGL, for differential network inference. The presented method is validated by the simulation experiments as well as the real datasets. Furthermore, to precisely evaluate the results of differential network inference, we propose a new metric named APC2 for the differential levels of gene pairs. We apply IPJGL to analyze the TCGA colorectal and breast cancer datasets and find some candidate cancer genes with significant survival analysis results, including SOST for colorectal cancer and RBBP8 for breast cancer. We also conduct further analysis based on the interactions in the Reactome database and confirm the utility of our method. Availability R source code of importance-penalized joint graphical lasso is freely available at https://github.com/Wu-Lab/IPJGL. Supplementary information Supplementary materials are available at Bioinformatics online.
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    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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    Spatiotemporal evolution of the global species diversity of Rhododendron (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: Evolutionary radiation is a widely recognized mode of species diversification, but its underlying mechanisms have not been unambiguously resolved for species-rich cosmopolitan plant genera. In particular, it remains largely unknown how biological and environmental factors have jointly driven its occurrence in specific regions. Here we use Rhododendron, the largest genus of woody plants in the Northern Hemisphere, to investigate how geographic and climatic factors, as well as functional traits, worked together to trigger plant evolutionary radiations and shape the global patterns of species richness based on a solid species phylogeny. Using 3437 orthologous nuclear genes, we reconstructed the first highly supported and dated backbone phylogeny of Rhododendron comprising 200 species that represent all subgenera, sections, and nearly all multi-species subsections, and found that most extant species originated by evolutionary radiations when the genus migrated southwards from circumboreal areas to tropical/subtropical mountains, showing rapid increases of both net diversification rate and evolutionary rate of environmental factors in the Miocene. We also found that the geographically uneven diversification of Rhododendron led to a much higher diversity in Asia than in other continents, which was mainly driven by two environmental variables, i.e., elevation range and annual precipitation, and were further strengthened by the adaptation of leaf functional traits. Our study provides a good example of integrating phylogenomic and ecological analyses in deciphering the mechanisms of plant evolutionary radiations, and sheds new light on how the intensification of the Asian monsoon has driven evolutionary radiations in large plant genera of the Himalaya-Hengduan Mountains.
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    DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: Motivation DNA Methylation plays a key role in a variety of biological processes. Recently, Nanopore long-read sequencing has enabled direct detection of these modifications. As a consequence, a range of computational methods have been developed to exploit Nanopore data for methylation detection. However, current approaches rely on a human-defined threshold to detect the methylation status of a genomic position and are not optimized to detect sites methylated at low frequency. Furthermore, most methods employ either the Nanopore signals or the basecalling errors as the model input and do not take advantage of their combination. Results Here we present DeepMP, a convolutional neural network (CNN)-based model that takes information from Nanopore signals and basecalling errors to detect whether a given motif in a read is methylated or not. Besides, DeepMP introduces a threshold-free position modification calling model sensitive to sites methylated at low frequency across cells. We comprehensively benchmarked DeepMP against state-of-the-art methods on E. coli, human and pUC19 datasets. DeepMP outperforms current approaches at read-based and position-based methylation detection across sites methylated at different frequencies in the three datasets. Availability DeepMP is implemented and freely available under MIT license at https://github.com/pepebonet/DeepMP Supplementary information Supplementary data are available at Bioinformatics online.
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    Notes on a compressible extended burgers model of rheology (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: Summary Constitutive theory for viscoelasticity has broad application to solid mantle or ice deformations driven by tides, surface mass variations, and post-seismic flow. Geophysical models using higher order viscoelasticity can better accommodate geodetic observations than lower-order theory, typically provided by tensor versions of Maxwell, 4-parameter Burgers or standard linear (Zener) rheology. We derive, for the first time, a mathematical description of a compressible version of the extended Burgers material (EBM) model paradigm which has a distribution function of relaxation spectra. The latter model is often used for parameterizing high temperature background transient responses in the rock physics and mechanics laboratory setting and have demonstrated application to low frequency seismic wave attenuation. A new generalization of this practical anelastic model is presented and applied to the glacial isostatic adjustment momentum equations, thus providing useful guidance for generating initial-value boundary problem-solving software for quite general coding strategies. The solutions for the vertical motion response to a suddenly imposed surface load reveal a short-term transience of substantial amplitude.
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    Polycyclic Aromatic Hydrocarbons in Seyfert and star-forming galaxies (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: Polycyclic Aromatic Hydrocarbons (PAHs) are carbon-based molecules resulting from the union of aromatic rings and related species, which are likely responsible for strong infrared emission features. In this work, using a sample of 50 Seyfert galaxies (DL 〈 100 Mpc) we compare the circumnuclear (inner kpc) PAH emission of AGN to that of a control sample of star-forming galaxies (22 luminous infrared galaxies and 30 H ii galaxies), and investigate the differences between central and extended PAH emission. Using Spitzer/InfraRed Spectrograph spectral data of Seyfert and star-forming galaxies and newly developed PAH diagnostic model grids, derived from theoretical spectra, we compare the predicted and observed PAH ratios. We find that star-forming galaxies and AGN-dominated systems are located in different regions of the PAH diagnostic diagrams. This suggests that not only are the size and charge of the PAH molecules different, but also the nature and hardness of the radiation field that excite them. We find tentative evidence that PAH ratios in AGN-dominated systems are consistent with emission from larger PAH molecules (Nc 〉 300–400) as well as neutral species. By subtracting the spectrum of the central source from the total, we compare the PAH emission in the central versus extended region of a small sample of AGN. In contrast to the findings for the central regions of AGN-dominated systems, the PAH ratios measured in the extended regions of both type 1 and type 2 Seyfert galaxies can be explained assuming similar PAH molecular size distribution and ionized fractions of molecules to those seen in central regions of star-forming galaxies (100 〈 Nc 〈 300).
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    The Gaia-ESO Survey: Membership probabilities for stars in 63 open and 7 globular clusters from 3D kinematics (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: Spectroscopy from the final internal data release of the Gaia-ESO Survey (GES) has been combined with Gaia EDR3 to assign membership probabilities to targets observed towards 63 Galactic open clusters and 7 globular clusters. The membership probabilities are based chiefly on maximum likelihood modelling of the 3D kinematics of the targets, separating them into cluster and field populations. From 43211 observed targets, 13985 are identified as highly probable cluster members (P 〉 0.9), with an average membership probability of 0.993. The addition of GES radial velocities successfully drives down the fraction of false positives and we achieve better levels of discrimination in most clusters over the use of astrometric data alone, especially those at larger distances. Since the membership selection is almost purely kinematic, the union of this catalogue with GES and Gaia is ideal for investigating the photometric and chemical properties of clusters as a function of stellar mass, age and Galactic position.
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    Kinematics and structure of Ionized gas in the UCHII regions of W33 main (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: High mass proto-stars create Ultra-Compact H ii regions (UCHII) at the stage of evolution when most of the accretion is finished but the star is still heavily embedded in molecular material. The morphologies of UCHII regions reflect the interactions of stellar winds, stellar motions, and density structure in the molecular cloud; they are complex and it has been very difficult to interpret them. We here present data obtained with TEXES on the NASA IRTF of the [Nei,ii] emission line in the proto-cluster of young OB stars in W33 Main. The data cube has a spatial resolution of ∼1.4 arcsec and true velocity resolution ∼5 km s-1; with Aλ ∼ 0.02AV it is relatively unaffected by extinction. We have run 3D hydrodynamic and line profile simulations, using PLUTO and RADMC-3D, of the gas structures created by multiple windy stars moving relative to each other through the ambient cloud. By iterative comparison of the data cube and the simulations, we arrive at models that reproduce the different morphology and kinematic structure of each UCHII region in W33 Main. The results indicate that each sub-source probably holds multiple exciting stars, permitting an improved view of the stellar population, and finds the stellar trajectories, which may determine the dynamical development of the proto-cluster.
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    White dwarfs identified in LAMOST Data Release 5 (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: In this paper, we report white dwarfs identified in the 5th Data Release of the Large Area Multi-Object fibre Spectroscopic Telescope, including spectral types of DA, DB, DC, DZ, and so on. There are 2 625 DA spectra of 2 281 DA stars, 182 DB spectra of 166 DB stars, 62 DC spectra of 58 DC stars, 36 DZ spectra of 33 DZ stars and many other types identified, in addition to our previous paper (Data Release 2). Among those sources, 393 DA stars and 46 DB stars are new identifications after cross-matching with the literature. In order to select DA candidates, we use the classification result from the LAMOST pipeline, colour-colour cut method and a random forest machine learning method. For DBs, since there is no template for DB in the pipeline model, a random forest machine learning method is chosen to select candidates. All the WD candidates have been visually checked individually. The parameters of effective temperature, surface gravity, mass, and cooling age have been estimated for relatively high signal-to-noise ratio DAs and DBs. The peaks of the DA and DB mass distributions are found to be around 0.62 M⊙ and 0.65 M⊙, respectively. Finally, the data and method we used to select white dwarf candidates for the second phase of LAMOST survey are also addressed in this paper.
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    Paired analysis of tree ring width and carbon isotopes indicate when controls on tropical tree growth change from light to water limitations (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-29
    Description: Light and water availability are likely to vary over the lifespan of closed-canopy forest trees with understory trees experiencing greater limitations to growth by light and canopy trees greater limitation due to drought. As drought and shade have opposing effects on isotope discrimination (Δ13C), paired measurement of ring width and Δ13C can potentially be used to differentiate between water and light limitations on tree growth. We tested this approach for Cedrela trees from three tropical forests in Bolivia and Mexico that differ in rainfall and canopy structure. Using lifetime ring width and Δ13C data for trees of up to and over 200 years old, we assessed how controls on tree growth changed from understory to the canopy. Growth and Δ13C are mostly anti-correlated in the understory but this anti-correlation disappeared or weakened when trees reached the canopy, especially at the wettest site. This indicates that understory growth variation is controlled by photosynthetic carbon assimilation (A) due to variation in light levels. Once trees reached the canopy, inter-annual variation in growth and Δ13C at one of the dry sites showed positive correlations, indicating inter-annual variation in growth is driven by variation in water stress affecting stomatal conductance (gs). Paired analysis of ring widths and carbon isotopes provides significant insight to discerning between environmental factors controlling growth over trees’ life; strong light limitations for understory trees in closed-canopy moist forests switched to drought stress for (sub)canopy trees in dry forests. We show that combined isotope and ring width measurements can significantly improve our insights in tree functioning and be used to disentangle limitations due to shade from those due to drought.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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    prose: A Python framework for modular astronomical images processing (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-29
    Description: To reduce and analyse astronomical images, astronomers can rely on a wide range of libraries providing low-level implementations of legacy algorithms. However, combining these routines into robust and functional pipelines requires a major effort which often ends up in instrument-specific and poorly maintainable tools, yielding products that suffer from a low-level of reproducibility and portability. In this context, we present prose, a Python framework to build modular and maintainable image processing pipelines. Built for astronomy, it is instrument-agnostic and allows the construction of pipelines using a wide range of building blocks, pre-implemented or user-defined. With this architecture, our package provides basic tools to deal with common tasks such as automatic reduction and photometric extraction. To demonstrate its potential, we use its default photometric pipeline to process 26 TESS candidates follow-up observations and compare their products to the ones obtained with AstroImageJ, the reference software for such endeavors. We show that prose produces light curves with lower white and red noise while requiring less user interactions and offering richer functionalities for reporting.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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    The density distributions of cosmic structures: impact of the local environment on weak-lensing convergence (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-29
    Description: Whilst the underlying assumption of the Friedman-Lemaître-Robertson-Walker (FLRW) cosmological model is that matter is homogeneously distributed throughout the universe, gravitational influences over the life of the universe have resulted in mass clustered on a range of scales. Hence we expect that, in our inhomogeneous universe, the view of an observer will be influenced by the location and local environment. Here we analyse the one-point probability distribution functions and angular power spectra of weak-lensing (WL) convergence and magnification numerically to investigate the influence of our local environment on WL statistics in relativistic N-body simulations. To achieve this, we numerically solve the null geodesic equations which describe the propagation of light bundles backwards in time from today, and develop a ray-tracing algorithm, and from these calculate various WL properties. Our findings demonstrate how cosmological observations of large-scale structure through WL can be impacted by the locality of the observer. We also calculate the constraints on the cosmological parameters as a function of redshift from the theoretical and numerical study of the angular power spectrum of WL convergence. This study concludes the minimal redshift for the constraint on the parameter Ωm (H0) is z ∼ 0.2 (z ∼ 0.6) beyond which the local environment’s effect is negligible and the data from WL surveys are more meaningful above that redshift. The outcomes of this study will have direct consequences for future surveys, where percent-level-precision is necessary.
    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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    Search for fast radio transients using Arecibo drift-scan observations at 1.4 GHz (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-30
    Description: We conducted a drift-scan observation campaign using the 305-m Arecibo telescope in January and March 2020 when the observatory was temporarily closed during the intense earthquakes and the initial outbreak of the COVID-19 pandemic, respectively. The primary objective of the survey was to search for fast radio transients, including Fast Radio Bursts (FRBs) and Rotating Radio Transients (RRATs). We used the 7-beam ALFA receiver to observe different sections of the sky within the declination region ∼(10–20) deg on 23 nights and collected 160 hours of data in total. We searched our data for single-pulse transients, of covering up to a maximum dispersion measure of 11 000 pc cm−3 at which the dispersion delay across the entire bandwidth is equal to the 13 s transit length of our observations. The analysis produced more than 18 million candidates. Machine learning techniques sorted the radio frequency interference and possibly astrophysical candidates, allowing us to visually inspect and confirm the candidate transients. We found no evidence for new astrophysical transients in our data. We also searched for emission from repeated transient signals, but found no evidence for such sources. We detected single pulses from two known pulsars in our observations and their measured flux densities are consistent with the expected values. Based on our observations and sensitivity, we estimated the upper limit for the FRB rate to be
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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    Erratum: The GALAH survey: Chemical homogeneity of the Orion complex (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-26
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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    Eccentric millisecond pulsars by resonant convection (2021)
    Oxford University Press
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    Publication Date: 2021-10-26
    Description: Eccentric millisecond pulsars (eMSPs) with white dwarf companions exhibit orbital eccentricities orders of magnitude larger than predicted by turbulent convection in the white dwarfs’ red giant progenitors. The orbital periods of eMSPs cluster around P = 20–30 d, remarkably close to the red giant convective eddy turnover time teddy. We propose that the anomalously large eccentricities are resonantly driven by convective flows somehow made coherent when the turnover time matches the tidally locked red giant’s spin period, which is also the tidal forcing period. Numerical simulations of rotating red giants and magnetic field studies of stars show some evidence for especially ordered flow patterns when the convective Rossby number P/teddy is of order unity. We show that resonant convection boosts eccentricities by a factor of (tnuc/P)1/2 ≈ 3 × 103 over the random-walk values that characterize conventional MSPs, in good agreement with observations (tnuc is the giant’s nuclear burning time-scale). We also show how variations in the eddy turnover time arising from red giant metallicity variations can reproduce the observed effective width of the resonance, ΔP/P ≈ 0.4.
    Print ISSN: 1745-3925
    Electronic ISSN: 1745-3933
    Topics: Physics
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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    SDSS-IV DR17: Final release of MaNGA PyMorph photometric and deep learning morphological catalogs (2021)
    Oxford University Press
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    Publication Date: 2021-10-27
    Description: We present the MaNGA PyMorph photometric Value Added Catalogue (MPP-VAC-DR17) and the MaNGA Deep Learning Morphological VAC (MDLM-VAC-DR17) for the final data release of the MaNGA survey, which is part of the SDSS Data Release 17 (DR17). The MPP-VAC-DR17 provides photometric parameters from Sérsic and Sérsic+Exponential fits to the 2D surface brightness profiles of the MaNGA DR17 galaxy sample in the g, r, and i bands (e.g. total fluxes, half light radii, bulge-disk fractions, ellipticities, position angles, etc.). The MDLM-VAC-DR17 provides Deep Learning-based morphological classifications for the same galaxies. The MDLM-VAC-DR17 includes a number of morphological properties: e.g. a T-Type, a finer separation between elliptical and S0, as well as the identification of edge-on and barred galaxies. While the MPP-VAC-DR17 simply extends the MaNGA PyMorph photometric VAC published in the SDSS Data Release 15 (MPP-VAC-DR15) to now include galaxies which were added to make the final DR17, the MDLM-VAC-DR17 implements some changes and improvements compared to the previous release (MDLM-VAC-DR15): namely, the low-end of the T-Types are better recovered in this new version. The catalogue also includes a separation between Early- or Late-type (ETG, LTG), which classifies the two populations in a complementary way to the T-Type, especially at the intermediate types (-1 〈 T-Type 〈 2), where the T-Type values show a large scatter. In addition, k −fold based uncertainties on the classifications are also provided. To ensure robustness and reliability, we have also visually inspected all the images. We describe the content of the catalogues and show some interesting ways in which they can be combined.
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    Topics: Physics
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    Phospho-Ku70 induced by DNA damage interacts with RNA Pol II and promotes the formation of phospho-53BP1 foci to ensure optimal cNHEJ (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-30
    Description: Canonical non-homologous end-joining (cNHEJ) is the prominent mammalian DNA double-strand breaks (DSBs) repair pathway operative throughout the cell cycle. Phosphorylation of Ku70 at ser27-ser33 (pKu70) is induced by DNA DSBs and has been shown to regulate cNHEJ activity, but the underlying mechanism remained unknown. Here, we established that following DNA damage induction, Ku70 moves from nucleoli to the sites of damage, and once linked to DNA, it is phosphorylated. Notably, the novel emanating functions of pKu70 are evidenced through the recruitment of RNA Pol II and concomitant formation of phospho-53BP1 foci. Phosphorylation is also a prerequisite for the dynamic release of Ku70 from the repair complex through neddylation-dependent ubiquitylation. Although the non-phosphorylable ala-Ku70 form does not compromise the formation of the NHEJ core complex per se, cells expressing this form displayed constitutive and stress-inducible chromosomal instability. Consistently, upon targeted induction of DSBs by the I-SceI meganuclease into an intrachromosomal reporter substrate, cells expressing pKu70, rather than ala-Ku70, are protected against the joining of distal DNA ends. Collectively, our results underpin the essential role of pKu70 in the orchestration of DNA repair execution in living cells and substantiated the way it paves the maintenance of genome stability.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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    Differential rotation in a 3D simulation of oxygen shell burning (2021)
    Oxford University Press
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    Publication Date: 2021-10-27
    Description: We study differential rotation in late-stage shell convection in a 3D hydrodynamic simulation of a rapidly rotating 16 M⊙ helium star with a particular focus on the convective oxygen shell. We find that the oxygen shell develops a quasi-stationary pattern of differential rotation that is neither described by uniform angular velocity as assumed in current stellar evolution models of supernova progenitors, nor by uniform specific angular momentum. Instead, the oxygen shell develops a positive angular velocity gradient with faster rotation at the equator than at the pole by tens of percent. We show that the angular momentum transport inside the convection zone is not adequately captured by a diffusive mixing-length flux proportional to the angular velocity or angular momentum gradient. Zonal flow averages reveal stable large-scale meridional flow and an entropy deficit near the equator that mirrors the patterns in the angular velocity. The structure of the flow is reminiscent of simulations of stellar surface convection zones and the differential rotation of the Sun, suggesting that similar effects are involved; future simulations will need to address in more detail how the interplay of buoyancy, inertial forces, and turbulent stresses shapes differential rotation during late-stage convection in massive stars. If convective regions develop positive angular velocity gradients, angular momentum could be shuffled out of the core region more efficiently, potentially making the formation of millisecond magnetars more difficult. Our findings have implications for neutron star birth spin periods and supernova explosion scenarios that involve rapid core rotation.
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    Topics: Physics
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    An integrative NMR-SAXS approach for structural determination of large RNAs defines the substrate-free state of a trans-cleaving Neurospora Varkud Satellite ribozyme (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-28
    Description: The divide-and-conquer strategy is commonly used for protein structure determination, but its applications to high-resolution structure determination of RNAs have been limited. Here, we introduce an integrative approach based on the divide-and-conquer strategy that was undertaken to determine the solution structure of an RNA model system, the Neurospora VS ribozyme. NMR and SAXS studies were conducted on a minimal trans VS ribozyme as well as several isolated subdomains. A multi-step procedure was used for structure determination that first involved pairing refined NMR structures with SAXS data to obtain structural subensembles of the various subdomains. These subdomain structures were then assembled to build a large set of structural models of the ribozyme, which was subsequently filtered using SAXS data. The resulting NMR-SAXS structural ensemble shares several similarities with the reported crystal structures of the VS ribozyme. However, a local structural difference is observed that affects the global fold by shifting the relative orientation of the two three-way junctions. Thus, this finding highlights a global conformational change associated with substrate binding in the VS ribozyme that is likely critical for its enzymatic activity. Structural studies of other large RNAs should benefit from similar integrative approaches that allow conformational sampling of assembled fragments.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    Five-percent measurements of the growth rate from simulation-based modelling of redshift-space clustering in BOSS LOWZ (2021)
    Oxford University Press
    Details
    Publication Date: 2021-10-28
    Description: We use a simulation-based modelling approach to analyse the anisotropic clustering of the BOSS LOWZ sample over the radial range 0.4 h−1 Mpc to 63 h−1 Mpc, significantly extending what is possible with a purely analytic modelling framework. Our full-scale analysis yields constraints on the growth of structure that are a factor of two more stringent than any other study on large scales at similar redshifts. We infer fσ8 = 0.471 ± 0.024 at z ≈ 0.25, and fσ8 = 0.430 ± 0.025 at z ≈ 0.40; the corresponding ΛCDM predictions of the Planck CMB analysis are 0.470 ± 0.006 and 0.476 ± 0.005, respectively. Our results are thus consistent with Planck, but also follow the trend seen in previous low-redshift measurements of fσ8 falling slightly below the ΛCDM+CMB prediction. We find that small and large radial scales yield mutually consistent values of fσ8, but there are 1 − 2.5σ hints of small scales (
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    Ram pressure candidates in UNIONS (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: We present a search for disturbed, candidate ram pressure stripping galaxies across more than 50 spectroscopically selected SDSS groups and clusters. Forty-eight ram pressure candidates are visually identified in these systems using high quality UNIONS imaging from the Canada-France Hawaii Telescope, covering ∼6200 deg2 and ∼2800 deg2 in the u- and r-bands respectively. Ram pressure candidates are found in groups and clusters spanning a wide range in halo mass and include ∼30 ram pressure candidates in the group regime (Mh 〈 1014). The observed frequency of ram pressure candidates shows substantial scatter with group/cluster mass, but on average is larger in clusters (Mh ≥ 1014 M⊙) than groups (Mh 〈 1014 M⊙) by a factor of ∼2. We find that ram pressure candidates are most commonly low-mass galaxies and have enhanced star formation rates relative to star-forming field galaxies. The enhancement in star formation is largely independent of galaxy mass and strongest for galaxies in clusters. As a result of the large survey footprint and excellent image quality from UNIONS, we are able to identify disturbed galaxies, potentially affected by ram pressure stripping, across a wide range of host environment.
    Print ISSN: 0035-8711
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    Topics: Physics
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    The Eukaryotic Linear Motif resource: 2022 release (2021)
    Oxford University Press
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    Publication Date: 2021-10-29
    Description: Almost twenty years after its initial release, the Eukaryotic Linear Motif (ELM) resource remains an invaluable source of information for the study of motif-mediated protein-protein interactions. ELM provides a comprehensive, regularly updated and well-organised repository of manually curated, experimentally validated short linear motifs (SLiMs). An increasing number of SLiM-mediated interactions are discovered each year and keeping the resource up-to-date continues to be a great challenge. In the current update, 30 novel motif classes have been added and five existing classes have undergone major revisions. The update includes 411 new motif instances mostly focused on cell-cycle regulation, control of the actin cytoskeleton, membrane remodelling and vesicle trafficking pathways, liquid-liquid phase separation and integrin signalling. Many of the newly annotated motif-mediated interactions are targets of pathogenic motif mimicry by viral, bacterial or eukaryotic pathogens, providing invaluable insights into the molecular mechanisms underlying infectious diseases. The current ELM release includes 317 motif classes incorporating 3934 individual motif instances manually curated from 3867 scientific publications. ELM is available at: http://elm.eu.org.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    Translation of MT-ATP6 pathogenic variants reveals distinct regulatory consequences from the co-translational quality control of mitochondrial protein synthesis (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: Pathogenic variants that disrupt human mitochondrial protein synthesis are associated with a clinically heterogenous group of diseases. Despite an impairment in oxidative phosphorylation being a common phenotype, the underlying molecular pathogenesis is more complex than simply a bioenergetic deficiency. Currently, we have limited mechanistic understanding on the scope by which a primary defect in mitochondrial protein synthesis contributes to organelle dysfunction. Since the proteins encoded in the mitochondrial genome are hydrophobic and need co-translational insertion into a lipid bilayer, responsive quality control mechanisms are required to resolve aberrations that arise with the synthesis of truncated and misfolded proteins. Here, we show that defects in the OXA1L-mediated insertion of MT-ATP6 nascent chains into the mitochondrial inner membrane are rapidly resolved by the AFG3L2 protease complex. Using pathogenic MT-ATP6 variants, we then reveal discrete steps in this quality control mechanism and the differential functional consequences to mitochondrial gene expression. The inherent ability of a given cell type to recognize and resolve impairments in mitochondrial protein synthesis may in part contribute at the molecular level to the wide clinical spectrum of these disorders.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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    AOP-helpFinder webserver: a tool for comprehensive analysis of the literature to support adverse outcome pathways development (2021)
    Oxford University Press
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    Publication Date: 2021-10-30
    Description: Motivation Adverse Outcome Pathways (AOPs) are a conceptual framework developed to support the use of alternative toxicology approaches in the risk assessment. AOPs are structured linear organizations of existing knowledge illustrating causal pathways from the initial molecular perturbation triggered by various stressors, through key events (KEs) at different levels of biology, to the ultimate health or ecotoxicological adverse outcome. Results Artificial intelligence can be used to systematically explore available toxicological data that can be parsed in the scientific literature. Recently a tool called AOP-helpFinder was developed to identify associations between stressors and KEs supporting thus documentation of AOPs. To facilitate the utilization of this advanced bioinformatics tool by the scientific and the regulatory community, a webserver was created. The proposed AOP-helpFinder webserver uses better performing version of the tool which reduces the need for manual curation of the obtained results. As an example, the server was successfully applied to explore relationships of a set of endocrine disruptors with metabolic-related events. The AOP-helpFinder webserver assists in a rapid evaluation of existing knowledge stored in the PubMed database, a global resource of scientific information, to build AOPs and Adverse Outcome Networks (AONs) supporting the chemical risk assessment. Availability and implementation AOP-helpFinder is available at http://aop-helpfinder.u-paris-sciences.fr/index.php
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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    Two newly identified eclipsing binaries in open cluster NGC 3532 (2021)
    Oxford University Press
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    Publication Date: 2021-10-28
    Description: We present light curve analyses of two newly identified detached eclipsing binaries, HD 96609 and HD 303734, in the region of the richly populated open cluster NGC 3532. HD 96609 is composed of two main sequence stars (B9-A0V + A2V) with masses and radii of M1 = 2.66 ± 0.02M⊙, M2 = 1.84 ± 0.01M⊙, R1 = 2.740 ± 0.006R⊙, R2 = 1.697 ± 0.005R⊙. The positions of the components on log M − log R plane suggests log(age/yr) 8.55, corresponding 350 ± 40 Myr of age, which agrees with the 300 ± 100 Myr age of NGC 3532 estimated in previous studies. We find the distance of HD 96609 as 460 ± 17 pc, which is consistent with the $484^{+35}_{-30}$ pc distance of NGC 3532, estimated from GAIA parallaxes. HD 303734 is an interesting totally eclipsing binary with a quite shallow secondary eclipse. Using photometric properties of the system in conjunction with theoretical calibrations, we estimate that HD 303734 consists of A6V + K3V components. HD 96609 and HD 303734 are the second and third eclipsing binaries discovered in the region of NGC 3532, after the first one, GV Car.
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