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  • Articles  (495,299)
  • Oxford University Press  (428,340)
  • MDPI Publishing
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  • 1
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    New constraints on the shear wave velocity structure of the Ivrea geophysical body from seismic ambient noise tomography (Ivrea-Verbano Zone, Alps) (2024)
    Oxford University Press
    Details
    Publication Date: 2024-01-19
    Description: We performed seismic ambient noise tomography to investigate the shallow crustal structure around the Ivrea geophysical body (IGB) in the Ivrea-Verbano Zone (IVZ). We achieved higher resolution with respect to previous tomographic works covering the Western Alps, by processing seismic data collected by both permanent and temporary seismic networks (61 broad-band seismic stations in total). This included IvreaArray, a temporary, passive seismic experiment designed to investigate the IVZ crustal structure. Starting from continuous seismic ambient noise recordings, we measured and inverted the dispersion of the group velocity of surface Rayleigh waves (fundamental mode) in the period range 4–25 s. We obtained a new, 3-D vS model of the IVZ crust via the stochastic neighbourhood algorithm (NA), with the highest resolution between 3 to 40 km depth. The fast and shallow shear wave velocity anomaly associated with the IGB presents velocities of 3.6 km s−1 directly at the surface, in remarkable agreement with the location of the exposed lower-to-middle crustal and mantle outcrops. This suggests a continuity between the surface geological observations and the subsurface geophysical anomalies. The fast IGB structure reaches vS of 4 km s−1 at 20–25 km depth, at the boundary between the European and Adriatic tectonic plates, and in correspondence with the earlier identified Moho jump in the same area. The interpretation of a very shallow reaching IGB is further supported by the comparison of our new results with recent geophysical investigations, based on receiver functions and gravity anomaly data. By combining the new geophysical constraints and the geological observations at the surface, we provide a new structural interpretation of the IGB, which features lower crustal and mantle rocks at upper crustal depths. The comparison of the obtained vS values with the physical properties from laboratory analysis of local rock samples suggests that the bulk of the IGB consists of a combination of mantle peridotite, ultramafic and lower crustal rocks, bound in a heterogeneous structure. These new findings, based on vS tomography, corroborate the recent interpretation for which the Balmuccia peridotite outcrops are continuously linked to the IGB structure beneath. The new outcomes contribute to a multidisciplinary framework for the interpretation of the forthcoming results of the scientific drilling project DIVE. DIVE aims at probing the lower continental crust and its transition to the mantle, with two ongoing and one future boreholes (down to 4 km depth) in the IVZ area, providing new, complementary information on rock structure and composition across scales. In this framework, we constrain the upper crustal IGB geometries and lithology based on new evidence for vS, connecting prior crustal knowledge to recent active seismic investigations.
    Description: Published
    Description: 1089–1105
    Description: OST1 Alla ricerca dei Motori Geodinamici
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 2
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    Implications for the geometry of plate boundaries in NE Asia based on the geodetic analysis of the 2020Mw 6.4 Koryak event (2024)
    Oxford University Press
    Details
    Publication Date: 2024-01-23
    Description: On the 9th of January 2020, an Mw 6.4 strike-slip earthquake took place north of the Asian margin of the Bering Sea. The earthquake occurred within the known reverse-right-lateral active fault zone, called Khatyrka–Vyvenka, which transverses the Koryak Highland from SE to NW and is thought to be a surface manifestation of the Asian portion of either the Bering plate boundary or the northern edge of the Alaskan stream. No other strong earthquake has ever been recorded in this remote uninhabited area and the few existing seismic stations provide poor quality earthquake locations.We adopt SAR interferometry (InSAR) technique to define an improved location of the Koryak 2020 earthquake and constrain the seismic source. The analysis of the 2020 event revealed a previously unknown active fault of left-lateral kinematics that is possibly hidden and strikes NWtransversely to the Khatyrka–Vyvenka fault zone. Although several mechanisms could account for left-lateral kinematics of this fault, we propose that the structure is part of a more extended NW fault structure, that formed in pre-neotectonic times and has played a role of a pre-existing rheological discontinuity. This revived NW structure together with a similar structure located easterly, so far aseismic, make the plate/stream boundary segmented, step-like in plan view. The step-like boundary geometry may be the result of internal transform deformation of a rigid plate, but it is better explained by deflections of the Alaskan stream edge at local crustal asperities, which are pre-Cenozoic terrains.
    Description: Published
    Description: 1412–1421
    Description: OST2 Deformazione e Hazard sismico e da maremoto
    Description: JCR Journal
    Keywords: Plate motion ; Radar interferometry ; Seismic cycle ; Asia
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
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    High frequency attenuation of S waves in alluvial deposits of the central Po Plain (northern Italy) (2024)
    Oxford University Press
    Details
    Publication Date: 2024-04-03
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2023. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved.
    Description: Estimation of local seismic response plays a key role in assessing local seismic hazard and particularly in the design of shaking scenarios. Modelling local seismic response involves knowing of the shear wave velocity (Vs) and quality factor (Qs) profiles for the site in question. The many techniques that have been developed to assess Vs in surface deposits produce reliable measurements of Vs , but these rarely correspond to direct measurements of Qs . The latter is often considered through damping measures from laboratory tests on small-scale soil samples, which can provide information primarily on intrinsic attenuation, neglecting the contribution of scattering effects. In this paper, using seismic recordings obtained at the surface and in boreholes at 100 m depth, we estimate an average value of Qs of some characteristic alluvial deposits of the Po Plain (northern Italy). Data come from a microseismic network which sampled an almost uniform lithology in the central Po Plain and consisted of three surface and four borehole stations with an interstation distance of about 2 km. The average value of Qs of the shallowest 100 m of the sedimentary strata, Qs100, is estimated by considering: (1) the high-frequency attenuation of seismic waves due to propagation through the corresponding stratigraphy and (2) the interference between incident and surface-reflected waves observed at borehole stations. We parametrize the first through k0_100, the difference between the values of the spectral decay parameter kappa (k) estimated at the surface and at the boreholes depth, respectively. We use the second in order to compute Vs100, the time-averaged Vs referred to the uppermost 100 m stratigraphy. We obtain: k0_100 = (11 ± 3) ms, Vs100 = (309 ± 11) m s −1 and Qs100 = 31 ± 10. At the surface, the estimated values of the site-specific kappa, k0, are found to range from 75 to 79 ms. As expected, these results are in good agreement with studies performed in other sites characterized by sandy or clayey lithologies, and can be usefully used in site response analysis at sites where the rigidity is mainly controlled by lithostatic pressure.
    Description: Comune di Minerbio (grant: “Sperimentazione ILG Minerbio”; grant number: 0913.010).
    Description: Published
    Description: 2075–2094
    Description: OST2 Deformazione e Hazard sismico e da maremoto
    Description: JCR Journal
    Keywords: Earthquake ground motions ; Seismic attenuation ; Site effects ; Wave propagation ; Wave scattering and diffraction ; 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
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    Moment magnitude for earthquakes in the Etna volcano area (2024)
    Oxford University Press
    Details
    Publication Date: 2024-03-19
    Description: Accurate quantification of seismic activity in volcanic regions is an important asset for im- proving hazard and risk assessment. This is especially true for densely populated areas, as in the case of Etna volcano (Southern Italy). There, the volcanic hazard is amplified by the seismic risk of acti ve faults, especiall y on the eastern flank of the volcano. In such a context, it is common to rely on moment magnitude ( M W ) to characterize seismicity and monitor the energy released during an eruption. In this study, we calculate the moment-based magnitude ( M W ) for selected seismic data sets, using different approaches in distinct magnitude ranges to cover the widest possible range of magnitude that characterizes Etna’s seismicity . Specifically , we computed the M W from a data set of moment tensor solutions of earthquakes that occurred in the magnitude range 3.4 ≤M L ≤4.8 during 2005–2020; we created a data set of seismic moment and associated M W for earthquakes 1.0 ≤M L 〈 3.4 obtained by analysing source spectra; we fine-tuned two relationships, for shallow and deep earthquakes, to obtain M W from response spectra. Finally, we calibrated a specific relationship between M W and M L for the Etna area earthquakes in the range 1.0 ≤M L ≤4.8. All the empirical relationships obtained in this study can be applied in real-time analysis of the seismicity to provide fast and robust information on the released seismic energy.
    Description: INGV-DPC 2012- 2021 agreement; B2 DPC-INGV 2019-2021 project; IMPACT Department strategic project ; ‘Project PE0000005–RETURN (NRRP)
    Description: Published
    Description: 2520-2534
    Description: OST2 Deformazione e Hazard sismico e da maremoto
    Description: JCR Journal
    Keywords: Earthquak e source observations ; Earthquake hazards ; Time series analysis ; Full moment tensor
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 5
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    A statistical framework for detection of b-value anomalies in Italy (2024)
    Oxford University Press
    Details
    Publication Date: 2024-03-12
    Description: This study presents a new robust statistical framework, in which to measure relative differences, or deviations from a hypothetical reference value, of Gutenberg-Richter b-value. Moreover, it applies this method to recent seismicity in Italy, to find possible changes of earthquake magnitude distribution in time and space. The method uses bootstrap techniques, which have no prior assumptions about the distribution of data, keeping their basic features. Excluding Central Italy, no significative b-value variation is found, revealing that the frequency-magnitude distribution exponent is substantially stable or that data are not able to reveal hidden variations. Considering the small size of examined magnitude samples, we cannot definitively decide if the higher b-values in Central Italy, consistently founded by all applied tests, have a physical origin or result from a statistical bias. In any case, they indicate short-lived excursions which have a temporary nature and, therefore, cannot be associated solely to spatial variations in tectonic framework. Both the methodological issues and the results of the application to seismicity in Italy show that a correct assessing of b-value changes requests appropriate statistics, that accurately quantify the low accuracy and precision of b-value estimation for small magnitude samples.
    Description: Published
    Description: 729–740
    Description: OST4 Descrizione in tempo reale del terremoto, del maremoto, loro predicibilità e impatto
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
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    Source mechanisms and induced seismicity in the Val d'Agri Basin (Italy) (2024)
    Oxford University Press
    Details
    Publication Date: 2024-03-12
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2023. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved.
    Description: We present the results from a fully unconstrained moment tensor inversion of induced seismic events in a complex and high seismic hazard region (Val d’Agri basin, Southern Italy). The study area hosts two well-documented cases of induced microseismicity linked to (i) a wastewater injection well of a giant oilfield (the largest in onshore Europe), and (ii) severe seasonal level changes of an artificial lake. In order to gather information on the non-doublecouple components of the source and to better understand the rupture mechanisms, we analyse seismic events recorded during daily injection tests in the disposal well. The computed moment tensors have significant non-double-couple components that correlate with the well-head injection pressure. The injection parameters strongly influence the rupture mechanism that can be interpreted as due to the opening/closing of a fracture network inside a fault zone of a pre-existing thrust fault. For the case of the reservoir-induced seismicity, no direct correlations are observed with the loading/unloading of the reservoir.
    Description: Published
    Description: 1617–1627
    Description: OST3 Vicino alla faglia
    Description: JCR Journal
    Keywords: 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 7
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    Fabric controls fault stability in serpentinite gouges (2024)
    Oxford University Press
    Details
    Publication Date: 2024-04-09
    Description: Serpentinites are polymineralic rocks distributed almost ubiquitously across the globe in active tectonic regions. Magnetite-rich serpentinites are found in the low-strain domains of serpen- tinite shear zones, which act as potential sites of nucleation of unstable slip. To assess the potential of earthquake nucleation in these materials, we investigate the link between me- chanical properties and fabric of these rocks through a suite of laboratory shear experiments. Our experiments were done at room temperature and cover a range of normal stress and slip velocity from 25 to 100 MPa and 0.3 to 300 μm s −1 , respecti vel y. We show that magnetite-rich serpentinites are ideal materials since they display strong sensitivity to the loading rate and are susceptible to nucleation of unstable slip, especially at low forcing slip velocities. We also aim at the integration of mechanical and microstructural results to describe the underlying mechanisms that produce the macroscopic behaviour. We show that mineralogical composi- tion and mineral structure dictates the coexistence of two deformation mechanisms leading to stable and unstable slip. The weakness of phyllosilicates allows for creep during the interseis- mic phase of the laboratory seismic cycle while favouring the restoration of a load-bearing granular framework, responsible of the nucleation of unstable events. During dynamic slip, fault zone shear fabric determines the mode of slip, producing either asymmetric or Gaussian slip time functions for either fast or slow events. We report rate/state friction parameters and integrate our mechanical data with microstructural observations to shed light on the mech- anisms dictating the complexity of laborator y ear thquakes. We show that mineralogical and fabric heterogeneities control fault slip behaviour.
    Description: Published
    Description: 1778–1797
    Description: OST3 Vicino alla faglia
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 8
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    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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  • 9
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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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  • 10
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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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  • 11
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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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  • 12
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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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  • 13
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    3-D attenuation image of fluid storage and tectonic interactions across the Pollino fault network (2022)
    Oxford University Press
    Details
    Publication Date: 2022-03-07
    Description: The Pollino range is a region of slow deformation where earthquakes generally nucleate on low-angle normal faults. Recent studies have mapped fault structures and identified fluid related dynamics responsible for historical and recent seismicity in the area. Here, we apply the coda-normalization method at multiple frequencies and scales to image the 3-D P-wave attenuation (QP) properties of its slowly deforming fault network. The wide-scale average attenuation properties of the Pollino range are typical for a stable continental block, with a dependence of QP on frequency of Q−1 P = (0.0011   0.0008) f (0.36 0.32). Using only waveforms comprised in the area of seismic swarms, the dependence of attenuation on frequency increases [Q−1 P = (0.0373   0.0011) f (−0.59 0.01)], as expected when targeting seismically active faults. A shallow very-low-attenuation anomaly (max depth of 4–5 km) caps the seismicity recorded within the western cluster 1 of the Pollino seismic sequence (2012, maximum magnitude Mw = 5.1). High-attenuation volumes below this anomaly are likely related to fluid storage and comprise the western and northern portions of cluster 1 and the Mercure basin. These anomalies are constrained to the NW by a sharp low-attenuation interface, corresponding to the transition towards the eastern unit of the Apennine Platform under the Lauria mountains. The low-seismicity volume between cluster 1 and cluster 2 (maximum magnitude Mw = 4.3, east of the primary) shows diffuse low-to-average attenuation features. There is no clear indication of fluid-filled pathways between the two clusters resolvable at our resolution. In this volume, the attenuation values are anyway lower than in recognized low-attenuation blocks, like the Lauria Mountain and Pollino Range. As the volume develops in a region marked at surface by small-scale cross-faulting, it suggests no actual barrier between clusters, more likely a system of small locked fault patches that can break in the future. Our model loses resolution at depth, but it can still resolve a 5-to-15-km-deep high-attenuation anomaly that underlies the Castrovillari basin. This anomaly is an ideal deep source for the SE-to-NW migration of historical seismicity. Our novel deep structural maps support the hypothesis that the Pollino sequence has been caused by a mechanism of deep and lateral fluid-induced migration.
    Description: Natural Environment Research Council (NERC) Centre for Doctoral Training (CDT) in Oil and Gas. University of Aberdeen.
    Description: Published
    Description: 536–547
    Description: 4T. Sismicità dell'Italia
    Description: JCR Journal
    Keywords: body waves ; seismic attenuation ; seismic tomography ; 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 14
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    Relative relocation of earthquakes without a predefined velocity model: an example from a peculiar seismic cluster on Katla volcano's south-flank (Iceland) (2022)
    Oxford University Press
    Details
    Publication Date: 2022-10-28
    Description: Relative relocation methods are commonly used to precisely relocate earthquake clusters consisting of similar waveforms. Repeating waveforms are often recorded at volcanoes, where, however, the crust structure is expected to contain strong heterogeneities and therefore the 1D velocity model assumption that is made in most location strategies is not likely to describe reality. A peculiar cluster of repeating low-frequency seismic events was recorded on the south flank of Katla volcano (Iceland) from 2011. As the hypocentres are located at the rim of the glacier, the seismicity may be due to volcanic or glacial processes. Information on the size and shape of the cluster may help constraining the source process. The extreme similarity of waveforms points to a very small spatial distribution of hypocentres. In order to extract meaningful information about size and shape of the cluster, we minimize uncertainty by optimizing the cross-correlation measurements and relative-relocation process. With a synthetic test we determine the best parameters for differential-time measurements and estimate their uncertainties, specifically for each waveform. We design a relocation strategy to work without a predefined velocity model, by formulating and inverting the problem to seek changes in both location and slowness, thus accounting for azimuth, take-off angles and velocity deviations from a 1D model. We solve the inversion explicitly in order to propagate data errors through the calculation. With this approach we are able to resolve a source volume few tens of meters wide on horizontal directions and around 100 meters in depth. There is no suggestion that the hypocentres lie on a single fault plane and the depth distribution indicates that their source is unlikely to be related to glacial processes as the ice thickness is not expected to exceed few tens of meters in the source area.
    Description: Published
    Description: 1244–1257
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Keywords: Physics - Geophysics; Physics - Geophysics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 15
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    Estimating genotypic richness and proportion of identical multi-locus genotypes in aquatic microalgal populations (2022)
    Oxford University Press
    Details
    Publication Date: 2022-11-10
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sassenhagen, I., Erdner, D., Lougheed, B., Richlen, M., & SjÖqvist, C. Estimating genotypic richness and proportion of identical multi-locus genotypes in aquatic microalgal populations. Journal of Plankton Research, 44(4), (2022): 559-572, https://doi.org/10.1093/plankt/fbac034.
    Description: The majority of microalgal species reproduce asexually, yet population genetic studies rarely find identical multi-locus genotypes (MLG) in microalgal blooms. Instead, population genetic studies identify large genotypic diversity in most microalgal species. This paradox of frequent asexual reproduction but low number of identical genotypes hampers interpretations of microalgal genotypic diversity. We present a computer model for estimating, for the first time, the number of distinct MLGs by simulating microalgal population composition after defined exponential growth periods. The simulations highlighted the effects of initial genotypic diversity, sample size and intraspecific differences in growth rates on the probability of isolating identical genotypes. We estimated the genotypic richness for five natural microalgal species with available high-resolution population genetic data and monitoring-based growth rates, indicating 500 000 to 2 000 000 distinct genotypes for species with few observed clonal replicates (〈5%). Furthermore, our simulations indicated high variability in genotypic richness over time and among microalgal species. Genotypic richness was also strongly impacted by intraspecific variability in growth rates. The probability of finding identical MLGs and sampling a representative fraction of genotypes decreased noticeably with smaller sample sizes, challenging the detection of differences in genotypic diversity with typical isolate numbers in the field.
    Description: This work was supported by the Olle Engkvist foundation [200-0564 to I.S.]; the Swedish Research Council (Vetenskapsrådet) [2018-04992 to B.C.L.]; the Academy of Finland [321609 to C.S.]; the National Science Foundation [NSF OCE-1841811 to D.L.E. and M.L.R.]; and the National Institute of Environmental Health [NIEHS P01ES028949 to M.L.R.].
    Repository Name: Woods Hole Open Access Server
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  • 16
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    Responses of benthic calcifying algae to ocean acidification differ between laboratory and field settings (2022)
    Oxford University Press
    Details
    Publication Date: 2022-06-24
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Page, H. N., Bahr, K. D., Cyronak, T., Jewett, E. B., Johnson, M. D., & McCoy, S. J. Responses of benthic calcifying algae to ocean acidification differ between laboratory and field settings. Ices Journal of Marine Science, 79(1), (2022): 1–11, https://doi.org/10.1093/icesjms/fsab232.
    Description: Accurately predicting the effects of ocean and coastal acidification on marine ecosystems requires understanding how responses scale from laboratory experiments to the natural world. Using benthic calcifying macroalgae as a model system, we performed a semi-quantitative synthesis to compare directional responses between laboratory experiments and field studies. Variability in ecological, spatial, and temporal scales across studies, and the disparity in the number of responses documented in laboratory and field settings, make direct comparisons difficult. Despite these differences, some responses, including community-level measurements, were consistent across laboratory and field studies. However, there were also mismatches in the directionality of many responses with more negative acidification impacts reported in laboratory experiments. Recommendations to improve our ability to scale responses include: (i) developing novel approaches to allow measurements of the same responses in laboratory and field settings, and (ii) researching understudied calcifying benthic macroalgal species and responses. Incorporating these guidelines into research programs will yield data more suitable for robust meta-analyses and will facilitate the development of ecosystem models that incorporate proper scaling of organismal responses to in situ acidification. This, in turn, will allow for more accurate predictions of future changes in ecosystem health and function in a rapidly changing natural climate.
    Description: We would like to thank the Ocean Carbon and Biogeochemistry Program for organizing the fourth U.S. Ocean Acidification Principal Investigators meeting, which is where this synthesis was conceived. HNP was a postdoctoral research fellow at Mote Marine Laboratory. MDJ is a postdoctoral scholar at Woods Hole Oceanographic Institution. SJM is a Norma J. Lang early career fellow of the Phycological Society of America.
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  • 17
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    Spectral elements numerical simulation of the 2009 L’Aquila earthquake on a detailed reconstructed domain (2022)
    Oxford University Press
    Details
    Publication Date: 2022-06-22
    Description: In this paper we simulate the earthquake that hit the city of L'Aquila on the 6th of April 2009 using SPEED (SPectral Elements in Elastodynamics with Discontinuous Galerkin), an open-source code able to simulate the propagation of seismic waves in complex three-dimensional (3D) domains. Our model includes an accurate 3D recon- struction of the Quaternary deposits, according to the most up-to-date data obtained from the Microzonation studies in Central Italy and a detailed model of the topography incorporated using a newly developed tool (May et al. 2021). The sensitivity of our results with respect to dfferent kinematic seismic sources is inves- tigated. The results obtained are in good agreement with the recordings at the available seismic stations at epicentral distances within a range of 20km. Finally, a blind source prediction scenario application shows a reasonably good agreement between simulations and recordings can be obtained by simulating stochastic rupture realizations with basic input data. These results, although limited to nine simulated scenarios, demonstrate that it is possible to obtain a satisfactory reconstruction of a ground shaking scenario employing a stochastic source constrained on a limited amount of ex-ante information. A similar approach can be used to model future and past earthquakes for which little or no information is typically available, with potential relevant implications for seismic risk assessment.
    Description: Published
    Description: 29–49
    Description: 3T. Fisica dei terremoti e Sorgente Sismica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Environmental effects and seismogenic source characterization of the December 2020 earthquake sequence near Petrinja, Croatia (2022)
    Oxford University Press
    Details
    Publication Date: 2022-06-22
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2022. 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: On 29 December 2020, a shallow earthquake of magnitude Mw 6.4 struck northern Croatia, near the town of Petrinja, more than 24 hours after a strong foreshock (Ml 5). We formed a reconnaissance team of European geologists and engineers, from Croatia, Slovenia, France, Italy and Greece, rapidly deployed in the field to map the evidence of coseismic environmental effects. In the epicentral area, we recognized surface deformation, such as tectonic breaks along the earthquake source at the surface, liquefaction features (scattered in the fluvial plains of Kupa, Glina and Sava rivers), and slope failures, both caused by strong motion. Thanks to this concerted, collective and meticulous work, we were able to document and map a clear and unambiguous coseismic surface rupture associated with the main shock. The surface rupture appears discontinuous, consisting of multi-kilometer en échelon right stepping sections, along a NW-SE striking fault that we call the Petrinja-Pokupsko Fault (PPKF). The observed deformation features, in terms of kinematics and trace alignments, are consistent with slip on a right lateral fault, in agreement with the focal solution of the main shock. We found mole tracks, displacement on faults affecting natural features (e. g. drainage channels), scarplets, and more frequently breaks of anthropogenic markers (roads, fences). The surface rupture is observed over a length of ∼13 km from end-to-end, with a maximum displacement of 38 cm, and an average displacement of ∼10 cm. Moreover, the liquefaction extends over an area of nearly 600 km² around the epicenter. Typology of liquefaction features include sand blows, lateral spreading phenomenon along the road and river embankments, as well as sand ejecta of different grain size and matrix. Development of large and long fissures along the fluvial landforms, current or ancient, with massive ejections of sediments is pervasive. These features are sometimes accompanied by small horizontal displacements. Finally, the environmental effects of the earthquake appear to be reasonably consistent with the usual scaling relationships, in particular the surface faulting. This rupture of the ground occurred on or near traces of a fault that shows clear evidence of Quaternary activity. Further and detailed studies will be carried out to characterize this source and related faults in terms of future large earthquakes potential, for their integration into seismic hazard models.
    Description: Published
    Description: 1394–1418
    Description: 2T. Deformazione crostale attiva
    Description: JCR Journal
    Keywords: Seismicity and tectonics ; Earthquake hazards ; Coseismic effects ; M6.4 Petrinja earthquake (Croatia)
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 19
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    Moho depths for Antarctica Region by the inversion of ground-based gravity data (2022)
    Oxford University Press
    Details
    Publication Date: 2022-09-01
    Description: In the last years the scientific literature has been enriched with new models of the Moho depth in the Antarctica Continent derived by the seismic reflection technique and refraction profiles, receiver functions and seismic surface waves, but also by gravimetric observations over the continent. In particular, the gravity satellite missions of the last two decades have provided data in this remote region of the Earth and have allowed the investigation of the crust properties. Meanwhile, other important contributions in this direction has been given by the fourth International Polar Year (IPY, 2007–2008) which started seismographic and geodetic networks of unprecedented duration and scale, including airborne gravimetry over largely unexplored Antarctic frontiers. In this study, a new model for the Antarctica Moho depths is proposed. This new estimation is based on no satellite gravity measures, thanks to the availability of the gravity database ANTGG2015, that collects gravity data from ground-base, airborne and shipborne campaigns. In this new estimate of the Moho depths the contribution of the gravity measures has been maximized reducing any correction of the gravity measures and avoiding constraints of the solution to seismological observations and to geological evidence. With this approach a pure gravimetric solution has been determined. The model obtained is pretty in agreement with other Moho models and thanks to the use of independent data it can be exploited also for cross-validating different Moho depths solutions.
    Description: Published
    Description: 1404–1420
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: Antarctica ; Moho ; Gravity inversion ; Collocation ; ANTGG2015
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 20
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    Distribution of oceanic crust in the Enderby Basin offshore East Antarctica (2022)
    Oxford University Press
    In:  EPIC3Geophysical Journal International, Oxford University Press, 231, pp. 1959-1981
    Details
    Publication Date: 2022-09-16
    Description: Seismic reflection and refraction data were collected in 2007 and 2012 to reveal the crustal fabric on a single long composite profile offshore Prydz Bay, East Antarctica. A P-wave velocity model provides insights on the crustal fabric, and a gravity-constrained density model is used to describe the crustal and mantle structure. The models show that a 230-km- wide continent–ocean transition separates stretched continental from oceanic crust along our profile. While the oceanic crust close to the continent–ocean boundary is just 3.5–5 km thick, its thickness increases northwards towards the Southern Kerguelen Plateau to 12 km. This change is accompanied by thickening of a lower crustal layer with high P-wave velocities of up to 7.5 km s–1, marking intrusive rocks emplaced beneath the mid-ocean ridge under increasing influence of the Kerguelen plume. Joint interpretations of our crustal model, seismic reflection data and magnetic data sets constrain the age and extent of oceanic crust in the research area. Oceanic crust is shown to continue to around 160 km farther south than has been interpreted in previous data, with profound implications for plate kinematic models of the region. Finally, by combining our findings with a regional magnetic data compilation and regional seismic reflection data we propose a larger extent of oceanic crust in the Enderby Basin than previously known.
    Repository Name: EPIC Alfred Wegener Institut
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  • 21
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    TIAMMAt: leveraging biodiversity to revise protein domain models, evidence from innate immunity (2022)
    Oxford University Press
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Tassia, M. G., David, K. T., Townsend, J. P., & Halanych, K. M. TIAMMAt: leveraging biodiversity to revise protein domain models, evidence from innate immunity. Molecular Biology and Evolution, 38(12), (2021): 5806–5818, https://doi.org/10.1093/molbev/msab258.
    Description: Sequence annotation is fundamental for studying the evolution of protein families, particularly when working with nonmodel species. Given the rapid, ever-increasing number of species receiving high-quality genome sequencing, accurate domain modeling that is representative of species diversity is crucial for understanding protein family sequence evolution and their inferred function(s). Here, we describe a bioinformatic tool called Taxon-Informed Adjustment of Markov Model Attributes (TIAMMAt) which revises domain profile hidden Markov models (HMMs) by incorporating homologous domain sequences from underrepresented and nonmodel species. Using innate immunity pathways as a case study, we show that revising profile HMM parameters to directly account for variation in homologs among underrepresented species provides valuable insight into the evolution of protein families. Following adjustment by TIAMMAt, domain profile HMMs exhibit changes in their per-site amino acid state emission probabilities and insertion/deletion probabilities while maintaining the overall structure of the consensus sequence. Our results show that domain revision can heavily impact evolutionary interpretations for some families (i.e., NLR’s NACHT domain), whereas impact on other domains (e.g., rel homology domain and interferon regulatory factor domains) is minimal due to high levels of sequence conservation across the sampled phylogenetic depth (i.e., Metazoa). Importantly, TIAMMAt revises target domain models to reflect homologous sequence variation using the taxonomic distribution under consideration by the user. TIAMMAt’s flexibility to revise any subset of the Pfam database using a user-defined taxonomic pool will make it a valuable tool for future protein evolution studies, particularly when incorporating (or focusing) on nonmodel species.
    Description: This work was supported by The National Science Foundation (Grant No. IOS—1755377 to K.M.H., Rita Graze, and Elizabeth Hiltbold Schwartz), and K.T.D. was supported by The National Science Foundation’s Graduate Research Fellowship Program.
    Keywords: Protein evolution ; Domain annotation ; Animal evolution ; Innate immunity
    Repository Name: Woods Hole Open Access Server
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  • 22
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    Adaptive proteome diversification by nonsynonymous A-to-I RNA editing in coleoid cephalopods (2022)
    Oxford University Press
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Shoshan, Y., Liscovitch-Brauer, N., Rosenthal, J. J. C., & Eisenberg, E. Adaptive proteome diversification by nonsynonymous A-to-I RNA editing in coleoid cephalopods. Molecular Biology and Evolution, 38(9), (2021): 3775–3788, https://doi.org/10.1093/molbev/msab154.
    Description: RNA editing by the ADAR enzymes converts selected adenosines into inosines, biological mimics for guanosines. By doing so, it alters protein-coding sequences, resulting in novel protein products that diversify the proteome beyond its genomic blueprint. Recoding is exceptionally abundant in the neural tissues of coleoid cephalopods (octopuses, squids, and cuttlefishes), with an over-representation of nonsynonymous edits suggesting positive selection. However, the extent to which proteome diversification by recoding provides an adaptive advantage is not known. It was recently suggested that the role of evolutionarily conserved edits is to compensate for harmful genomic substitutions, and that there is no added value in having an editable codon as compared with a restoration of the preferred genomic allele. Here, we show that this hypothesis fails to explain the evolutionary dynamics of recoding sites in coleoids. Instead, our results indicate that a large fraction of the shared, strongly recoded, sites in coleoids have been selected for proteome diversification, meaning that the fitness of an editable A is higher than an uneditable A or a genomically encoded G.
    Description: This research was supported by a grants from the United States–Israel Binational Science Foundation (BSF), Jerusalem, Israel (BSF2017262 to J.J.C.R. and E.E.), the Israel Science Foundation (3371/20 to E.E.) and the National Science Foundation (IOS 1827509 and 1557748 to J.J.C.R).
    Keywords: RNA editing ; Adaptation ; Evolution
    Repository Name: Woods Hole Open Access Server
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  • 23
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    Interspecific differences in the flow regimes and drag of North Pacific skate egg cases (2022)
    Oxford University Press
    Details
    Publication Date: 2022-10-12
    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 Integrative & Comparative Biology 62(3), (2022): 805-816, https://doi.org/10.1093/icb/icac108.
    Description: Skates are a diverse group of dorso-ventrally compressed cartilaginous fish found primarily in high-latitude seas. These slow-growing oviparous fish deposit their fertilized eggs into cases, which then rest on the seafloor. Developing skates remain in their cases for 1–4 years after they are deposited, meaning the abiotic characteristics of the deposition sites, such as current and substrate type, must interact with the capsule in a way to promote long residency. Egg cases are morphologically variable and can be identified to species. Both the gross morphology and the microstructures of the egg case interact with substrate to determine how well a case stays in place on a current-swept seafloor. Our study investigated the egg case hydrodynamics of eight North Pacific skate species to understand how their morphology affects their ability to stay in place. We used a flume to measure maximum current velocity, or “break-away velocity,” each egg case could withstand before being swept off the substrate and a tilt table to measure the coefficient of static friction between each case and the substrate. We also used the programing software R to calculate theoretical drag on the egg cases of each species. For all flume trials, we found the morphology of egg cases and their orientation to flow to be significantly correlated with break-away velocity. In certain species, the morphology of the egg case was correlated with flow rate required to dislodge a case from the substrate in addition to the drag experienced in both the theoretical and flume experiments. These results effectively measure how well the egg cases of different species remain stationary in a similar habitat. Parsing out attachment biases and discrepancies in flow regimes of egg cases allows us to identify where we are likely to find other elusive species nursery sites. These results will aid predictive models for locating new nursery habitats and protective policies for avoiding the destruction of these nursery sites.
    Description: This work was supported by the NSF-REU and FHL Blinks-Beacon for funding JNE. And the Stephen and Ruth Wainwright Endowed Fellowship, BEACON and Hoag Awards, Robert T. Paine Experimental and Field Ecology Award, FHL Award, FHL Marine Science Fund, FHL Student Fund (Kohn), Patricia L. Dudley Endowment for funding KCH.
    Description: 2023-07-04
    Repository Name: Woods Hole Open Access Server
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  • 24
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    Sensitivity of sand lance to shifting prey and hydrography indicates forthcoming change to the northeast US shelf forage fish complex (2022)
    Oxford University Press
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Suca, J. J., Wiley, D. N., Silva, T. L., Robuck, A. R., Richardson, D. E., Glancy, S. G., Clancey, E., Giandonato, T., Solow, A. R., Thompson, M. A., Hong, P., Baumann, H., Kaufman, L., & Llopiz, J. K. Sensitivity of sand lance to shifting prey and hydrography indicates forthcoming change to the northeast US shelf forage fish complex. Ices Journal of Marine Science, 78(3), (2021): 1023–1037, https://doi.org/10.1093/icesjms/fsaa251.
    Description: Northern sand lance (Ammodytes dubius) and Atlantic herring (Clupea harengus) represent the dominant lipid-rich forage fish species throughout the Northeast US shelf and are critical prey for numerous top predators. However, unlike Atlantic herring, there is little research on sand lance or information about drivers of their abundance. We use intra-annual measurements of sand lance diet, growth, and condition to explain annual variability in sand lance abundance on the Northeast US Shelf. Our observations indicate that northern sand lance feed, grow, and accumulate lipids in the late winter through summer, predominantly consuming the copepod Calanus finmarchicus. Sand lance then cease feeding, utilize lipids, and begin gonad development in the fall. We show that the abundance of C. finmarchicus influences sand lance parental condition and recruitment. Atlantic herring can mute this effect through intra-guild predation. Hydrography further impacts sand lance abundance as increases in warm slope water decrease overwinter survival of reproductive adults. The predicted changes to these drivers indicate that sand lance will no longer be able to fill the role of lipid-rich forage during times of low Atlantic herring abundance—changing the Northeast US shelf forage fish complex by the end of the century.
    Description: Research was funded by the Bureau of Ocean Energy Management (IA agreement M17PG0019; DNW, LK, HB, and JKL), including a subaward via the National Marine Sanctuary Foundation (18-11-B-203). Additional support came from the National Oceanic and Atmospheric Administration Woods Hole Sea Grant Program (NA18OAR4170104, Project No. R/O-57; JKL, HB, and DNW) and a National Science Foundation Long-term Ecological Research grant for the Northeast US Shelf Ecosystem (OCE 1655686; JKL). JJS was funded by the National Science Foundation Graduate Research Fellowship programme. ARR was funded by an NOAA Nancy Foster Scholarship.
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  • 25
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    An alternative method to evaluate earthquake detection from synthetic Wood–Anderson seismograms: an application in Italy (2022)
    Oxford University Press
    Details
    Publication Date: 2022-08-26
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2022. 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: Defining the regional variability of minimum magnitude for earthquake detection is crucial for planning seismic networks. Knowing the earthquake detection magnitude values is fundamental for the optimal location of new stations and to select the priority for reactivating the stations of a seismic network in case of a breakdown. In general, the assessment of earthquake detection is performed by analysing seismic noise with spectral or more sophisticated methods. Further, to simulate amplitude values at the recording sites, spectral methods require knowledge of several geophysical parameters including rock density, S-wave velocity, corner frequency, quality factor, site specific decay parameter and so on, as well as a velocity model for the Earth's interior. The simulation results are generally expressed in terms of Mw and therefore a further conversion must be done to obtain the values of local magnitude (ML), which is the parameter commonly used for moderate and small earthquakes in seismic catalogues. Here, the relationship utilized by a seismic network to determine ML is directly applied to obtain the expected amplitude [in mm, as if it were recorded by a Wood–Anderson (WA) seismometer] at the recording site, without any additional assumptions. The station detection estimates are obtained by simply considering the ratio of the expected amplitude with respect to the background noise, also measured in mm. The seismic noise level for the station is estimated starting from four waveforms (each signal lasting 1 min) sampled at various times of the day for a period of one week. The proposed method is tested on Italian seismic events occurring in 2019 by using the locations of 16.879 earthquakes recorded by 374 stations. The first results indicate that by evaluating the station noise level with 5-s windows, a representative sample of the variability in expected noise level is generated for every station, even if only 4 min of signal per day over a week of recordings is used. The method was applied to define the detection level of the Italian National Seismic Network (RSN). The RSN detection level represents a reference for the definition and application of guidelines in the field of monitoring of subsurface industrial activities in Italy. The proposed approach can be successfully applied to define the current performance of a local seismic network (managed by private companies) and to estimate the expected further improvements, requested to fulfil the guidelines with the installation of new seismic stations. This method has been tested in Italy and can be reproduced wherever the local magnitude ML, based on synthetic WA records, is used.
    Description: Published
    Description: 1283–1297
    Description: 4T. Sismicità dell'Italia
    Description: JCR Journal
    Keywords: Time-series analysis ; Earthquake ground motions ; Seismic noise ; Induced seismicity ; 04.06. Seismology ; 05.04. Instrumentation and techniques of general interest
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 26
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    Preparing aquatic research for an extreme future: call for improved definitions and responsive, multidisciplinary approaches (2022)
    Oxford University Press
    Details
    Publication Date: 2022-08-19
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Aoki, L. R., Brisbin, M. M., Hounshell, A. G., Kincaid, D. W., Larson, E., Sansom, B. J., Shogren, A. J., Smith, R. S., & Sullivan-Stack, J. Preparing aquatic research for an extreme future: call for improved definitions and responsive, multidisciplinary approaches. Bioscience, 72(6), (2022): 508-520, https://doi.org/10.1093/biosci/biac020.
    Description: Extreme events have increased in frequency globally, with a simultaneous surge in scientific interest about their ecological responses, particularly in sensitive freshwater, coastal, and marine ecosystems. We synthesized observational studies of extreme events in these aquatic ecosystems, finding that many studies do not use consistent definitions of extreme events. Furthermore, many studies do not capture ecological responses across the full spatial scale of the events. In contrast, sampling often extends across longer temporal scales than the event itself, highlighting the usefulness of long-term monitoring. Many ecological studies of extreme events measure biological responses but exclude chemical and physical responses, underscoring the need for integrative and multidisciplinary approaches. To advance extreme event research, we suggest prioritizing pre- and postevent data collection, including leveraging long-term monitoring; making intersite and cross-scale comparisons; adopting novel empirical and statistical approaches; and developing funding streams to support flexible and responsive data collection.
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  • 27
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    Environmental drivers and trends in forage fish occupancy of the Northeast US shelf (2022)
    Oxford University Press
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Suca, J. J., Deroba, J. J., Richardson, D. E., Ji, R., & Llopiz, J. K. Environmental drivers and trends in forage fish occupancy of the Northeast US shelf. Ices Journal of Marine Science, 78(10), (2021): 3687–3708, https://doi.org/10.1093/icesjms/fsab214.
    Description: The Northeast US shelf ecosystem is undergoing unprecedented changes due to long-term warming trends and shifts in regional hydrography leading to changes in community composition. However, it remains uncertain how shelf occupancy by the region's dominant, offshore small pelagic fishes, also known as forage fishes, has changed throughout the late 20th and early 21st centuries. Here, we use species distribution models to estimate the change in shelf occupancy, mean weighted latitude, and mean weighted depth of six forage fishes on the Northeast US shelf, and whether those trends were linked to coincident hydrographic conditions. Our results suggest that observed shelf occupancy is increasing or unchanging for most species in both spring and fall, linked both to gear shifts and increasing bottom temperature and salinity. Exceptions include decreases to observed shelf occupancy by sand lance and decreases to Atlantic herring's inferred habitat suitability in the fall. Our work shows that changes in shelf occupancy and inferred habitat suitability have varying coherence, indicating complex mechanisms behind observed shelf occupancy for many species. Future work and management can use these results to better isolate the aspects of forage fish life histories that are important for determining their occupancy of the Northeast US shelf.
    Description: Funding came from the National Oceanic and Atmospheric Administration Woods Hole Sea Grant Program (NA18OAR4170104, Project number R/O-57; RJ and JKL) and a National Science Foundation Long-term Ecological Research grant for the Northeast US Shelf Ecosystem (OCE1655686; RJ and JKL). JJS was funded by the National Science Foundation Graduate Research Fellowship program.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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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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    Genomic and molecular evidence reveals novel pathways associated with cell surface polysaccharides in bacteria (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-20
    Description: Amino acid ̶ (acyl carrier protein) ligases (AALs) are a relatively new family of bacterial amino acid adenylating enzymes with unknown function(s). Here, genomic enzymology tools that employ sequence similarity networks and genome context analyses were used to hypothesize the metabolic function(s) of AALs. In over 50% of species, aal and its cognate acyl carrier protein (acp) genes, along with three more genes, formed a highly conserved AAL cassette. AAL cassettes were strongly associated with surface polysaccharide gene clusters in Proteobacteria and Actinobacteria, yet were prevalent among soil and rhizosphere-associated α- and β-Proteobacteria, including symbiotic α- and β-rhizobia and some Mycolata. Based on these associations, AAL cassettes were proposed to encode a noncanonical Acp-dependent polysaccharide modification route. Genomic-inferred predictions were substantiated by published experimental evidence, revealing a role for AAL cassettes in biosynthesis of biofilm-forming exopolysaccharide in pathogenic Burkholderia and expression of aal and acp genes in nitrogen-fixing Rhizobium bacteroids. Aal and acp genes were associated with dltBD-like homologs that modify cell wall teichoic acids with D-alanine, including in Paenibacillus and certain other bacteria. Characterization of pathways that involve AAL and Acp may lead to developing new plant and human disease-controlling agents as well as strains with improved nitrogen fixation capacity.
    Print ISSN: 0168-6496
    Electronic ISSN: 1574-6941
    Topics: Biology
    Published by Oxford University Press on behalf of Federation of European Microbiological Societies.
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    UAVs as remote sensing platforms in plant ecology: Review of applications and challenges (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-20
    Description: Aims Unmanned aerial vehicles (UAVs), i.e., drones, have recently emerged as cost-effective and flexible tools for acquiring remote sensing data with fine spatial and temporal resolution. It provides a new method and opportunity for plant ecologists to study issues from individual to regional scales. However, as a new method, UAVs remote sensing applications in plant ecology are still challenged. The needs of plant ecology research and the application development of UAVs remote sensing should be better integrated. This report provides a comprehensive review of UAV-based remote sensing applications in plant ecology to synthesize prospects of applying drones to advance plant ecology research. Important Findings Of the 400 references, 59% were published in remote sensing journals rather than in plant ecology journals, reflecting a substantial gap between the interests of remote sensing experts and plant ecologists. Most of the studies focused on UAV remote sensing's technical aspects, such as data processing and remote sensing inversion, with little attention on answering ecological questions. There were 61% of studies involved community-scale research. RGB and multispectral cameras were the most used sensors (75%). More ecologically meaningful parameters can be extracted from UAV data to better understand the canopy surface irregularity and community heterogeneity, identify geometrical characteristics of canopy gaps, and construct canopy chemical assemblies from living vegetation volumes. More cooperation between plant ecologists and remote sensing experts is needed to promote UAV remote sensing in advancing plant ecology research.
    Print ISSN: 1752-993X
    Electronic ISSN: 1752-9921
    Topics: Biology
    Published by Oxford University Press
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    Corrigendum to: Detecting Genetic Ancestry and Adaptation in the Taiwanese Han People (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-21
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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    Identification of emission-line stars in transition phase from pre-main sequence to main sequence (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-20
    Description: Pre-main sequence (PMS) stars evolve into main sequence (MS) phase over a period of time. Interestingly, we found a scarcity of studies in existing literature that examines and attempts to better understand the stars in PMS to MS transition phase. The purpose of the present study is to detect such rare stars, which we named as ‘Transition Phase’ (TP) candidates – stars evolving from the PMS to the MS phase. We identified 98 TP candidates using photometric analysis of a sample of 2167 classical Be (CBe) and 225 Herbig Ae/Be (HAeBe) stars. This identification is done by analyzing the near- and mid-infrared excess and their location in the optical colour-magnitude diagram. The age and mass of 58 of these TP candidates are determined to be between 0.1–5 Myr and 2–10.5 M⊙, respectively. The TP candidates are found to possess rotational velocity and colour excess values in between CBe and HAeBe stars, which is reconfirmed by generating a set of synthetic samples using the machine learning approach.
    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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    Robust K-means algorithm with weighted window for seismic facies analysis (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-20
    Description: Seismic facies analysis can generate a map to describe the spatial distribution characteristics of reservoirs, and therefore plays a critical role in seismic interpretation. To analyse the characteristics of the horizon of interest, it is usually necessary to extract seismic waveforms along the target horizon using a selected time window. The inaccuracy of horizon interpretation often produces some inconsistent phases and leads to inaccurate classification. Therefore, the developed adaptive phase K-means algorithm proposed a sliding time window to extract seismic waveforms. However, setting the maximum offset of the sliding window is difficult in a real data application. A value that is too large may cause the cross-layer problem, whereas a value that is too small reduces the flexibility of the algorithm. To address this disadvantage, this paper proposes a robust K-means (R-K-means) algorithm with a Gaussian-weighted sliding window for seismic waveform classification. The used weights punish those windows distant from the interpretation horizon in the objective function, consequently producing a smaller range of horizon adjustments even when using relatively large maximum offsets and benefitting the generation of stable and reliable seismic facies maps. The application of real seismic data from the F3 block proves the effectiveness of the proposed algorithm.
    Print ISSN: 1742-2132
    Electronic ISSN: 1742-2140
    Topics: Geosciences
    Published by Oxford University Press on behalf of Sinopec Geophysical Research Institute.
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    Blame it on the rain: Rainfall variability, consumption smoothing, and subjective well‐being in rural Ethiopia (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-19
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
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    Neutral CGM as damped Lyα absorbers at high redshift (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-20
    Description: Recent searches for the hosts of z ∼ 4 damped Lyα absorbers (DLAs) have detected bright galaxies at distances of tens of kpc from the DLA. Using the FIRE-2 cosmological zoom simulations, we argue that these relatively large distances are due to a predominantly cool and neutral inner circumgalactic medium (CGM) surrounding high-redshift galaxies. The inner CGM is cool because of the short cooling time of hot gas in ≲ 1012 M⊙ haloes, which implies that accretion and feedback energy are radiated quickly, while it is neutral due to high volume densities and column densities at high redshift which shield cool gas from photoionization. Our analysis predicts large DLA covering factors ($gtrsim 50{{ m per cent}}$) out to impact parameters ∼0.3((1 + z)/5)3/2Rvir from the central galaxies at z ≳ 1, equivalent to a proper distance of $sim 21, M_{12}^{1/3} left(left(1+z ight)/5 ight)^{1/2}, { m kpc}$ (Rvir and M12 are the halo virial radius and mass in units of 1012 M⊙, respectively). This implies that DLA covering factors at z ∼ 4 may be comparable to unity out to a distance ∼10 times larger than stellar half-mass radii. A predominantly neutral inner CGM in the early universe suggests that its mass and metallicity can be directly constrained by absorption surveys, without resorting to the large ionization corrections as required for ionized CGM.
    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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    Improved data sets and evaluation methods for the automatic prediction of DNA-binding proteins (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-20
    Description: Motivation Accurate automatic annotation of protein function relies on both innovative models and robust data sets. Due to their importance in biological processes, the identification of DNA-binding proteins directly from protein sequence has been the focus of many studies. However, the data sets used to train and evaluate these methods have suffered from substantial flaws. We describe some of the weaknesses of the data sets used in previous DNA-binding protein literature and provide several new data sets addressing these problems. We suggest new evaluative benchmark tasks that more realistically assess real-world performance for protein annotation models. We propose a simple new model for the prediction of DNA-binding proteins and compare its performance on the improved data sets to two previously published models. Additionally, we provide extensive tests showing how the best models predict across taxonomies. Results Our new gradient boosting model, which uses features derived from a published protein language model, outperforms the earlier models. Perhaps surprisingly, so does a baseline nearest neighbor model using BLAST percent identity. We evaluate the sensitivity of these models to perturbations of DNA-binding regions and control regions of protein sequences. The successful data-driven models learn to focus on DNA-binding regions. When predicting across taxonomies, the best models are highly accurate across species in the same kingdom and can provide some information when predicting across kingdoms. Code and Data Availability The data and results for this paper can be found at https://doi.org/10.5281/zenodo.5153906. The code for this paper can be found at https://doi.org/10.5281/zenodo.5153683. The code, data and results can also be found at https://github.com/AZaitzeff/tools_for_dna_binding_proteins.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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    Corrigendum to: ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-21
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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    Functional Diversity and Assembly Rules of Two Deciduous Seasonal Forests in Southeastern Brazil (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-21
    Description: Deciduous seasonal forests (DSFs) have a peculiar floristic composition, with species capable of surviving periods of high water deficit in a year. Our goal was to demonstrate that abiotic filters lead to the assembly of two DSF communities that have high floristic dissimilarity. For this, we characterized the environment of the areas and used the community-weighted mean (CWM), functional richness (FRic) and functional dispersion (FDis) indices for regional recognition of functional patterns. The local assessment of assembly rules was carried out using null models. We found differences in the FRic and FDis between the areas, which was attributed to the different floristic influences exercised on the communities. However, in both, the typical attributes of dry formations were dominant (CWM), indicating that, on the regional scale of study, the dry season acts as a filter in the composition of species in the communities. On a local scale, stochastic dispersion was identified as the most influential mechanism in the assembly of communities. We conclude that deterministic and stochastic processes act in the assembly of the studied communities, and the proportion of each of these depends on the scale, with abiotic filtration predominating on a regional scale and stochastic dispersion events on a local scale. Study Implications With the expansion of agriculture and climate change, tropical dry biomes, such as deciduous seasonal forests, are rapidly changing. In this study, we contribute to the recognition of functional standards and community assembly of this vegetation type to assist in management planning, restoration, and conservation. Understanding the different processes involved in building a community is crucial for anticipating how communities will behave under future environmental scenarios.
    Print ISSN: 0015-749X
    Electronic ISSN: 1938-3738
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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    Erratum to: Genomic analyses unveil helmeted guinea fowl (Numida meleagris) domestication in West Africa (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-01
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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    Erratum to: Ultrastructural, Cytochemical, and Comparative Genomic Evidence of Peroxisomes in Three Genera of Pathogenic Free-Living Amoebae, Including the First Morphological Data for the Presence of This Organelle in Heteroloboseans (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-01
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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    Variations in Soil Organic Carbon Stocks under Different Land-Use Categories in Subtropical Ecosystems of Kashmir (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-21
    Description: Quantification of soil organic carbon (SOC) stocks in different land uses holds vital significance because of its implications regarding carbon sequestration as the largest terrestrial carbon pool. The current study was conducted to quantify and compare SOC stocks in forest land, agricultural land, and barren land-use categories in the subtropical ecosystems of the Himalayan foothills in Kashmir. Results showed the highest SOC value in the forest soil (75 ± 11.1 Mg C ha−1) followed by agricultural soil (58 ± 7.0 Mg C ha−1) and barren land (44 ± 6.5 Mg C ha−1). SOC stocks in different land uses showed broad variations with values as high as 106 ± 11.3 Mg C ha−1 (forest soils) and as low as 14.1 ± 7.1 Mg C ha−1 (barren land). The forest SOC values responded significantly to species composition with the highest values in Pinus roxburghii Sarg. pure stands as compared with broad leaved forests. Multivariate ordination analyses revealed that the variations in SOC stocks were significantly correlated with vegetation type, altitude, and soil bulk density. The study has identified anthropogenic disturbances as a major factor deteriorating local SOC stocks and recommends immediate soil restoration efforts to enhance the ecological significance of soils as vital regional carbon sinks. Study Implications The current study was designed to investigate the soil organic carbon (SOC) levels in different land uses of the Kashmir Himalayas, Pakistan. Results revealed forest soils as the major carbon sinks of the region, attributed to diverse species composition having a significant quantity of organic residues, followed by agricultural soils. Barren land-use class exhibited the lowest SOC values due to minimum vegetation cover, erosion, and degradation. Significant correlations of SOC stocks with geographical and edaphic variables were identified by multivariate ordination analysis in the investigated land-use classes. Results validate the significance of forests in enhancing SOC stocks, demanding forest restoration in the area by controlling the forest losses as well as afforestation. This article provides vital information required for better understanding of SOC stocks in different land-use classes in the subtropical ecosystems of the Kashmir region.
    Print ISSN: 0015-749X
    Electronic ISSN: 1938-3738
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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    Spatio-temporal modeling of the effect of selected environmental and land-use factors on acid grassland vegetation (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-22
    Description: Aims Acid grasslands are threatened both by agricultural intensification with nutrient addition and increased livestock densities as well as by land abandonment. In order to understand and quantify the effect of selected environmental and land-use factors on the observed variation and changes in the vegetation of acid grasslands, large-scale spatial and temporal pin-point plant cover monitoring data are fitted in a structural equation model. Methods The important sources of measurement and sampling uncertainties have been included using a hierarchical model structure. Furthermore, uncertainties associated with the measurement and sampling are separated from the process uncertainty, which is important when generating ecological predictions that may feed into local conservation management decisions. Important Findings Generally, increasing atmospheric nitrogen deposition led to more grass-dominated acid grassland habitats at the expense of the cover of forbs. Sandy soils were relatively more acidic, and the effects of soil type on the vegetation include both direct effects of soil type and indirect effects mediated by the effect of soil type on soil pH. Both soil type and soil pH affected the vegetation of acid grasslands. Even though only a relatively small proportion of the temporal variation in cover was explained by the model, it would still be useful to quantify the uncertainties when using the model for generating local ecological predictions and adaptive management plans.
    Print ISSN: 1752-993X
    Electronic ISSN: 1752-9921
    Topics: Biology
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    Polysaccharide utilization by a marine heterotrophic bacterium from the SAR92 clade (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-20
    Description: SAR92 is one of the few examples of a widely distributed, abundant oligotroph that can be cultivated to study pathways of carbon oxidation in ocean systems. Genomic evidence for SAR92 suggests that this gammaproteobacterium might be a primary consumer of polysaccharides in the epipelagic zone, its main habitat. Here, we investigated cell growth, polysaccharide utilization gene expression, and carbohydrate-active enzyme abundance of a culturable SAR92 strain, HTCC2207, grown with different polysaccharides. Xylan and laminarin, two polysaccharides mainly produced by phytoplankton, supported the growth of HTCC2207 better than other polysaccharides. HTCC2207 possessed polysaccharide utilization loci (PULs) consisting of TonB-dependent receptor (TBDR) and glycoside hydrolase (GH) family genes. GH genes such as GH17 and GH3 presented no substrate-specificity and were induced by different sugar substrates, while expressions of GH16, GH10 and GH30 were enhanced in the glucose-treatment but suppressed in the polysaccharide-treatment, indicating complex polysaccharide utilization by HTCC2207. Metabolic pathways for laminarin and xylan were re-constructed in HTCC2207 based on the PULs genes and other predicted carbohydrate-active enzymes. This study reveals features of the epipelagic niche of SAR92 and provide insight into the biogeochemical cycling of labile, high-molecular carbohydrate compounds in the surface ocean.
    Print ISSN: 0168-6496
    Electronic ISSN: 1574-6941
    Topics: Biology
    Published by Oxford University Press on behalf of Federation of European Microbiological Societies.
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    Corrigendum to: Gene Similarity Networks Unveil a Potential Novel Unicellular Group Closely Related to Animals from the Tara Oceans Expedition (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-01
    Electronic ISSN: 1759-6653
    Topics: Biology
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    Moso bamboo and Japanese cedar seedlings differently affected soil N2O emissions (2021)
    Oxford University Press
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    Publication Date: 2021-08-22
    Description: Aims Moso bamboo expansions into Japanese cedar forests are common. The expansion effects on soil nitrous oxide (N2O) emissions have not been thoroughly understood, and the underlying microbial mechanisms remain unclear. Methods We studied bacterial and fungal contribution to soil N2O emissions under moso bamboo or Japanese cedar by applying bacterial or fungal inhibitors using streptomycin and iprodione, respectively. Soil N2O emissions were measured and the relative contribution of bacteria and fungi to soil N2O emissions was calculated. Important Findings N2O emission from soil with moso bamboo was significantly higher than under Japanese cedar. Compared with control, bacterial or fungal inhibitor or their combination decreased N2O emissions, indicating substantial contribution of microbial activities to N2O emissions. However, the relative contribution of bacteria and fungi to N2O emissions was not affected by plants. Soil organic carbon, total and ammonium nitrogen were lower in soil under moso bamboo than Japanese cedar, suggesting faster microbial decomposition under moso bamboo. Fungal inhibitor and plants interactively affected soil pH, total phosphorus, and ammonium nitrogen, while bacterial inhibitor and plants interactively affected total nitrogen, indicating substantial dependence of effects by microbial communities on plant species. Moso bamboo and Japanese cedar differed in their effects on soil N2O emissions with higher emissions under moso bamboo. Stimulation of N2O emission under moso bamboo might occur due to higher nitrogen mineralization and subsequent denitrification induced by high root exudation. These results highlight the need to consider the effect of species shifts on N2O emissions in forests.
    Print ISSN: 1752-993X
    Electronic ISSN: 1752-9921
    Topics: Biology
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    m6A-express: uncovering complex and condition-specific m6A regulation of gene expression (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-20
    Description: N6-methyladenosine (m6A) is the most abundant form of mRNA modification and controls many aspects of RNA metabolism including gene expression. However, the mechanisms by which m6A regulates cell- and condition-specific gene expression are still poorly understood, partly due to a lack of tools capable of identifying m6A sites that regulate gene expression under different conditions. Here we develop m6A-express, the first algorithm for predicting condition-specific m6A regulation of gene expression (m6A-reg-exp) from limited methylated RNA immunoprecipitation sequencing (MeRIP-seq) data. Comprehensive evaluations of m6A-express using simulated and real data demonstrated its high prediction specificity and sensitivity. When only a few MeRIP-seq samples may be available for the cellular or treatment conditions, m6A-express is particularly more robust than the log-linear model. Using m6A-express, we reported that m6A writers, METTL3 and METTL14, competitively regulate the transcriptional processes by mediating m6A-reg-exp of different genes in Hela cells. In contrast, METTL3 induces different m6A-reg-exp of a distinct group of genes in HepG2 cells to regulate protein functions and stress-related processes. We further uncovered unique m6A-reg-exp patterns in human brain and intestine tissues, which are enriched in organ-specific processes. This study demonstrates the effectiveness of m6A-express in predicting condition-specific m6A-reg-exp and highlights the complex, condition-specific nature of m6A-regulation of gene expression.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    A new approach of estimating the Galactic thermal dust and synchrotron polarized emission template in the microwave bands (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-20
    Description: The Internal Linear Combination (ILC) method has been extensively used to extract the cosmic microwave background (CMB) anisotropy map from foreground contaminated multi-frequency maps. However, the performance of simple ILC is limited and can be significantly improved by heavily constraint equations, dubbed constrained ILC (cILC). The standard ILC and cILC works on spin-0 fields. Recently, a generalised version of ILC has been developed, named Polarization ILC (PILC), in which Q ± iU at multiple frequencies are combined using complex coefficients to estimate Stokes Q and U maps. A statistical moment expansion method has recently been developed for high precision modelling of the Galactic foregrounds. This paper develops a semi-blind component separation method combining the moment approach of foreground modelling with a generalised version of the PILC method for heavily constraint equations. The algorithm is developed in pixel space over a spin-2 field. We demonstrate the performance of the method on three sets of absolutely calibrated simulated maps at WMAP and Planck frequencies with varying foreground models. We apply this component separation technique in simultaneous estimation of Stokes Q and U maps of the thermal dust at 353 GHz and synchrotron at 30 GHz. We also recover both dust and synchrotron maps at 100 and 143 GHz, where separating two components is challenging.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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    Differential semblance optimisation based on the adaptive quadratic Wasserstein distance (2021)
    Oxford University Press
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    Publication Date: 2021-08-20
    Description: As the robustness for the wave equation-based inversion methods, wave equation migration velocity analysis (WEMVA) is stable for overcoming the multipathing problem and has become popular in recent years. As a rapidly developed method, differential semblance optimisation (DSO) is convenient to implement and can automatically detect the moveout existing in common image gathers (CIGs). However, by implementing in the image domain with the target of minimising moveouts and improving coherence of the CIGs, the DSO method often suffers from imaging artefacts caused by uneven illumination and irregular observation geometry, which may produce poor velocity updates with artefact contamination. To deal with this issue, in this paper, by introducing Wiener-like filters, we modify the conventional image matching-based objective function to a new one by introducing the quadratic Wasserstein metric technique. The new misfit function measures the distance of two distributions obtained by the convolutional filters and target functions. With the new misfit function, the adjoint sources and the corresponding gradients are improved. We apply the new method to two numerical examples and one field dataset. The corresponding results indicate that the new method is robust to compensate low frequency components of velocity models.
    Print ISSN: 1742-2132
    Electronic ISSN: 1742-2140
    Topics: Geosciences
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    Disc tearing and Bardeen–Petterson alignment in GRMHD simulations of highly tilted thin accretion discs (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-20
    Description: Luminous active galactic nuclei and X-ray binaries often contain geometrically thin, radiatively cooled accretion discs. According to theory, these are – in many cases – initially highly misaligned with the black hole equator. In this work, we present the first general relativistic magnetohydrodynamic simulations of very thin (h/r ∼ 0.015–0.05) accretion discs around rapidly spinning (a ∼ 0.9) black holes and tilted by 45°–65°. We show that the inner regions of the discs with h/r ≲ 0.03 align with the black hole equator, though out to smaller radii than predicted by analytic work. The inner aligned and outer misaligned disc regions are separated by a sharp break in tilt angle accompanied by a sharp drop in density. We find that frame dragging by the spinning black hole overpowers the disc viscosity, which is self-consistently produced by magnetized turbulence, tearing the disc apart and forming a rapidly precessing inner sub-disc surrounded by a slowly precessing outer sub-disc. We find that the system produces a pair of relativistic jets for all initial tilt values. At small distances, the black hole launched jets precess rapidly together with the inner sub-disc, whereas at large distances they partially align with the outer sub-disc and precess more slowly. If the tearing radius can be modeled accurately in future work, emission model independent measurements of black hole spin based on precession-driven quasi-periodic oscillations may become possible.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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    Range-wide genetic assignment confirms long-distance oceanic migration in Atlantic salmon over half a century (2021)
    Oxford University Press
    Details
    Publication Date: 2021-03-13
    Description: Atlantic salmon (Salmo salar) populations throughout the North Atlantic have declined in recent decades largely due to reduced marine survival, yet our understanding of marine distribution patterns and migratory routes remains limited. Here, we assigned archived individual samples (n = 3891) collected over a half century (1968–2018) throughout the North Atlantic to region of origin using range-wide genetic assignment. In the Northwest Atlantic, the distribution of assignments reinforced the importance of the Labrador Sea as an aggregation area, with 73% of all reporting groups detected. Moreover, individuals from six European reporting groups were identified in the Northwest Atlantic, and detections decreased with decreasing latitude spanning an area from Greenland to southern Newfoundland. In the Northeast Atlantic, six North American reporting groups were detected in samples from around the Faroe Islands. Based on the distribution of samples, estimates of trans-Atlantic migration distance averaged 3861 and 2889 km for North American and European salmon respectively. Our analysis highlights the widespread importance of the Labrador Sea and Faroe Islands to the species marine distribution patterns, and the prevalence of long-distance trans-Atlantic migration. Ultimately, the results suggest that environmental conditions experienced by many Atlantic salmon populations span much of the North Atlantic Ocean.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
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    Comparative analysis of molecular fingerprints in prediction of drug combination effects (2021)
    Oxford University Press
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    Publication Date: 2021-08-17
    Description: Application of machine and deep learning methods in drug discovery and cancer research has gained a considerable amount of attention in the past years. As the field grows, it becomes crucial to systematically evaluate the performance of novel computational solutions in relation to established techniques. To this end, we compare rule-based and data-driven molecular representations in prediction of drug combination sensitivity and drug synergy scores using standardized results of 14 high-throughput screening studies, comprising 64 200 unique combinations of 4153 molecules tested in 112 cancer cell lines. We evaluate the clustering performance of molecular representations and quantify their similarity by adapting the Centered Kernel Alignment metric. Our work demonstrates that to identify an optimal molecular representation type, it is necessary to supplement quantitative benchmark results with qualitative considerations, such as model interpretability and robustness, which may vary between and throughout preclinical drug development projects.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
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    Detecting quantitative trait loci and exploring chromosomal pairing in autopolyploids using polyqtlR (2021)
    Oxford University Press
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    Publication Date: 2021-08-06
    Description: Motivation The investigation of quantitative trait loci (QTL) is an essential component in our understanding of how organisms vary phenotypically. However, many important crop species are polyploid (carrying more than two copies of each chromosome), requiring specialized tools for such analyses. Moreover, deciphering meiotic processes at higher ploidy levels is not straightforward, but is necessary to understand the reproductive dynamics of these species, or uncover potential barriers to their genetic improvement. Results Here, we present polyqtlR, a novel software tool to facilitate such analyses in (auto)polyploid crops. It performs QTL interval mapping in F1 populations of outcrossing polyploids of any ploidy level using identity-by-descent probabilities. The allelic composition of discovered QTL can be explored, enabling favourable alleles to be identified and tracked in the population. Visualization tools within the package facilitate this process, and options to include genetic co-factors and experimental factors are included. Detailed information on polyploid meiosis including prediction of multivalent pairing structures, detection of preferential chromosomal pairing and location of double reduction events can be performed. Availabilityand implementation polyqtlR is freely available from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/package=polyqtlR. Supplementary information Supplementary data are available at Bioinformatics online.
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    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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    Prediction of RBP binding sites on circRNAs using an LSTM-based deep sequence learning architecture (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-20
    Description: Circular RNAs (circRNAs) are widely expressed in highly diverged eukaryotes. Although circRNAs have been known for many years, their function remains unclear. Interaction with RNA-binding protein (RBP) to influence post-transcriptional regulation is considered to be an important pathway for circRNA function, such as acting as an oncogenic RBP sponge to inhibit cancer. In this study, we design a deep learning framework, CRPBsites, to predict the binding sites of RBPs on circRNAs. In this model, the sequences of variable-length binding sites are transformed into embedding vectors by word2vec model. Bidirectional LSTM is used to encode the embedding vectors of binding sites, and then they are fed into another LSTM decoder for decoding and classification tasks. To train and test the model, we construct four datasets that contain sequences of variable-length binding sites on circRNAs, and each set corresponds to an RBP, which is overexpressed in bladder cancer tissues. Experimental results on four datasets and comparison with other existing models show that CRPBsites has superior performance. Afterwards, we found that there were highly similar binding motifs in the four binding site datasets. Finally, we applied well-trained CRPBsites to identify the binding sites of IGF2BP1 on circCDYL, and the results proved the effectiveness of this method. In conclusion, CRPBsites is an effective prediction model for circRNA-RBP interaction site identification. We hope that CRPBsites can provide valuable guidance for experimental studies on the influence of circRNA on post-transcriptional regulation.
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    Topics: Biology , Computer Science
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    Comparison of approaches to transcriptomic analysis in multi-sampled tumors (2021)
    Oxford University Press
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    Publication Date: 2021-08-20
    Description: Intratumoral heterogeneity is a well-documented feature of human cancers and is associated with outcome and treatment resistance. However, a heterogeneous tumor transcriptome contributes an unknown level of variability to analyses of differentially expressed genes (DEGs) that may contribute to phenotypes of interest, including treatment response. Although current clinical practice and the vast majority of research studies use a single sample from each patient, decreasing costs of sequencing technologies and computing power have made repeated-measures analyses increasingly economical. Repeatedly sampling the same tumor increases the statistical power of DEG analysis, which is indispensable toward downstream analysis and also increases one’s understanding of within-tumor variance, which may affect conclusions. Here, we compared five different methods for analyzing gene expression profiles derived from repeated sampling of human prostate tumors in two separate cohorts of patients. We also benchmarked the sensitivity of generalized linear models to linear mixed models for identifying DEGs contributing to relevant prostate cancer pathways based on a ground-truth model.
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    Single molecule/particle tracking analysis program SMTracker 2.0 reveals different dynamics of proteins within the RNA degradosome complex in Bacillus subtilis (2021)
    Oxford University Press
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    Publication Date: 2021-08-20
    Description: Single-molecule (particle) tracking is a powerful method to study dynamic processes in cells at highest possible spatial and temporal resolution. We have developed SMTracker, a graphical user interface for automatic quantifying, visualizing and managing of data. Version 2.0 determines distributions of positional displacements in x- and y-direction using multi-state diffusion models, discriminates between Brownian, sub- or superdiffusive behaviour, and locates slow or fast diffusing populations in a standardized cell. Using SMTracker, we show that the Bacillus subtilis RNA degradosome consists of a highly dynamic complex of RNase Y and binding partners. We found similar changes in molecule dynamics for RNase Y, CshA, PNPase and enolase, but not for phosphofructokinase, RNase J1 and J2, to inhibition of transcription. However, the absence of PfkA or of RNase J2 affected molecule dynamics of RNase Y-mVenus, indicating that these two proteins are indeed part of the degradosome. Molecule counting suggests that RNase Y is present as a dimer in cells, at an average copy number of about 500, of which 46% are present in a slow-diffusive state and thus likely engaged within degradosomes. Thus, RNase Y, CshA, PNPase and enolase likely play central roles, and RNase J1, J2 and PfkA more peripheral roles, in degradosome architecture.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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    Academic human capital in universities: definition and proposal of a measurement scale (2021)
    Oxford University Press
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    Publication Date: 2021-08-20
    Description: Academic human capital (AHC) is a key element in the explanation of scientific productivity. However, few studies have analysed this topic in the academic context, and their conclusions about composition and measurement remain ambiguous. This study proposes a measurement scale to assess AHC, following a systemic procedure composed of two steps: qualitative and quantitative phases. First, the Delphi technique was applied to reach a consensus on the AHC factors, resulting in a scale of 22 items. Second, exploratory and confirmatory factor analyses were conducted to determine the underlying factorial structure of the scale, using a sample of 2,223 researchers in Spanish universities. The results provided a five-dimensional structure of AHC, measuring the knowledge and abilities required to perform research activities, as well as skills related to the organisation of scientific processes, alertness to research opportunities, and the openness to provide and receive criticism. This study poses interesting challenges for knowledge management in universities.
    Print ISSN: 0302-3427
    Electronic ISSN: 1471-5430
    Topics: Nature of Science, Research, Systems of Higher Education, Museum Science
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    DNAgenie: accurate prediction of DNA-type-specific binding residues in protein sequences (2021)
    Oxford University Press
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    Publication Date: 2021-08-20
    Description: Efforts to elucidate protein–DNA interactions at the molecular level rely in part on accurate predictions of DNA-binding residues in protein sequences. While there are over a dozen computational predictors of the DNA-binding residues, they are DNA-type agnostic and significantly cross-predict residues that interact with other ligands as DNA binding. We leverage a custom-designed machine learning architecture to introduce DNAgenie, first-of-its-kind predictor of residues that interact with A-DNA, B-DNA and single-stranded DNA. DNAgenie uses a comprehensive physiochemical profile extracted from an input protein sequence and implements a two-step refinement process to provide accurate predictions and to minimize the cross-predictions. Comparative tests on an independent test dataset demonstrate that DNAgenie outperforms the current methods that we adapt to predict residue-level interactions with the three DNA types. Further analysis finds that the use of the second (refinement) step leads to a substantial reduction in the cross predictions. Empirical tests show that DNAgenie’s outputs that are converted to coarse-grained protein-level predictions compare favorably against recent tools that predict which DNA-binding proteins interact with double-stranded versus single-stranded DNAs. Moreover, predictions from the sequences of the whole human proteome reveal that the results produced by DNAgenie substantially overlap with the known DNA-binding proteins while also including promising leads for several hundred previously unknown putative DNA binders. These results suggest that DNAgenie is a valuable tool for the sequence-based characterization of protein functions. The DNAgenie’s webserver is available at http://biomine.cs.vcu.edu/servers/DNAgenie/.
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    Topics: Biology , Computer Science
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    DLpTCR: an ensemble deep learning framework for predicting immunogenic peptide recognized by T cell receptor (2021)
    Oxford University Press
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    Publication Date: 2021-08-20
    Description: Accurate prediction of immunogenic peptide recognized by T cell receptor (TCR) can greatly benefit vaccine development and cancer immunotherapy. However, identifying immunogenic peptides accurately is still a huge challenge. Most of the antigen peptides predicted in silico fail to elicit immune responses in vivo without considering TCR as a key factor. This inevitably causes costly and time-consuming experimental validation test for predicted antigens. Therefore, it is necessary to develop novel computational methods for precisely and effectively predicting immunogenic peptide recognized by TCR. Here, we described DLpTCR, a multimodal ensemble deep learning framework for predicting the likelihood of interaction between single/paired chain(s) of TCR and peptide presented by major histocompatibility complex molecules. To investigate the generality and robustness of the proposed model, COVID-19 data and IEDB data were constructed for independent evaluation. The DLpTCR model exhibited high predictive power with area under the curve up to 0.91 on COVID-19 data while predicting the interaction between peptide and single TCR chain. Additionally, the DLpTCR model achieved the overall accuracy of 81.03% on IEDB data while predicting the interaction between peptide and paired TCR chains. The results demonstrate that DLpTCR has the ability to learn general interaction rules and generalize to antigen peptide recognition by TCR. A user-friendly webserver is available at http://jianglab.org.cn/DLpTCR/. Additionally, a stand-alone software package that can be downloaded from https://github.com/jiangBiolab/DLpTCR.
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    Promoting the ICT Industry for the future with fears from the past (2021)
    Oxford University Press
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    Publication Date: 2021-08-21
    Description: Unlike other developed countries, the Fourth Industrial Revolution (4IR) discourse has become the central element within technology governance in Korea. This paper examines the reasons for the discourse’s success and its political and social implications. Based on the analysis of policy documents and the media coverage, I argue that political and economic elites have actively introduced the 4IR discourse to create novel momentum for promoting Information and Communications Technology (ICT) and to justify deregulatory measures while re-enacting the developmentalist imaginary. I also highlight that the 4IR discourse’s promoters have drawn upon the dialectics between the desirable future and the nation’s shared fear to urge the Korean society to accept the measures privileging the industry as the means of making the nation a developed country and avoiding being colonized again.
    Print ISSN: 0302-3427
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    Topics: Nature of Science, Research, Systems of Higher Education, Museum Science
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    XMP gas-rich dwarfs in nearby voids: results of BTA spectroscopy (2021)
    Oxford University Press
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    Publication Date: 2021-08-20
    Description: We present the second part of results of the ongoing project aimed at searching for and studying eXtremely Metal-Poor (XMP) – adopted as those with Zgas ≲ Z⊙/30, or with 12+log (O/H) ≲ 7.21 dex − very gas-rich blue dwarfs in voids. They were first identified in the course of the ‘unbiased’ study of the galaxy population in the nearby Lynx–Cancer void. These very rare and unusual galaxies seem to be the best proxies of so-called Very Young Galaxies (VYGs) defined recently in model simulations by Tweed et al. To date, for 16 pre-selected void XMP candidates, using the Big Telescope Alt-azimuth (BTA), the SAO 6-m telescope, we have obtained spectra suitable for the determination of O/H. For majority of the observed galaxies, the principal line [O iii] λ4363 , used for the direct classical Te method of O/H determination, is undetected. Therefore, to estimate O/H, we use a new ‘strong-lines’ method by Izotov et al. This appears to be the most accurate empirical O/H estimator for the range of 12+log (O/H) ≲ 7.4–7.5. For objects with higher O/H, we use the semi-empirical method by Izotov & Thuan with our modification accounting for variance of the excitation parameter O32. Six of those 16 candidates are found, with confidence, to be XMP dwarfs. In addition, eight studied galaxies are less metal-poor, with 12+log (O/H) = 7.24–7.33, and these can also fall into the category of VYG candidates. Taking into account our recently published work and the previously known (nine prototype galaxies) XMP gas-rich void objects, the new findings increase the number of this type of galaxy known to date to a total of 19.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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    MiR-200c-based metabolic modulation in glioblastoma cells as a strategy to overcome tumor chemoresistance (2021)
    Oxford University Press
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    Publication Date: 2021-07-10
    Description: Glioblastoma (GB) is the most aggressive and common form of primary brain tumor characterized by fast proliferation, high invasion and resistance to current standard treatment. The average survival rate post-diagnosis is 14.6 months, despite the aggressive standard post-surgery radiotherapy concomitant with chemotherapy with temozolomide (TMZ). Currently, efforts are being endowed to develop new and more efficient therapeutic approaches capable to overcome chemoresistance, inhibit tumor progression and improve overall patient survival rate. Abnormal microRNA (miRNA) expression has been correlated with chemoresistance, proliferation and resistance to apoptosis, which result from their master regulatory role of gene expression. Altered cell metabolism, favoring glycolysis, was identified as an emerging cancer hallmark and has been described in GB, thus offering a new target for innovative GB therapies. In this work, we hypothesized that a gene therapy-based strategy consisting of the overexpression of a miRNA downregulated in GB and predicted to target crucial metabolic enzymes might promote a shift of GB cell metabolism, decreasing the glycolytic dependence of tumor cells and contributing to their sensitization to chemotherapy with TMZ. The increase of miR-200c levels in DBTRG cells resulted in downregulation of messenger RNA of enzymes involved in bioenergetics pathways and impaired cell metabolism and mobility. In addition, miR-200c overexpression prior to DBTRG cell exposure to TMZ resulted in cell cycle arrest. Overall, our results show that miR-200c overexpression could offer a way to overcome chemoresistance developed by GB cells in response to current standard chemotherapy, providing an improvement to current GB standard treatment, with benefit for patient outcome.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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    Constraining the sources of nitrogen fueling export production in the Gulf of Mexico using nitrogen isotope budgets (2021)
    Oxford University Press
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    Publication Date: 2021-08-19
    Description: The availability of nitrogen (N) in ocean surface waters affects rates of photosynthesis and marine ecosystem structure. In spite of low dissolved inorganic N concentrations, export production in oligotrophic waters is comparable to more nutrient replete regions. Prior observations raise the possibility that di-nitrogen (N2) fixation supplies a significant fraction of N supporting export production in the Gulf of Mexico. In this study, geochemical tools were used to quantify the relative and absolute importance of both subsurface nitrate and N2 fixation as sources of new N fueling export production in the oligotrophic Gulf of Mexico in May 2017 and May 2018. Comparing the isotopic composition (“δ15N”) of nitrate with the δ15N of sinking particulate N collected during five sediment trap deployments each lasting two to four days indicates that N2 fixation is typically not detected and that the majority (≥80%) of export production is supported by subsurface nitrate. Moreover, no gradients in upper ocean dissolved organic N and suspended particulate N concentration and/or δ15N were found that would indicate significant N2 fixation fluxes accumulated in these pools, consistent with low Trichodesmium spp. abundance. Finally, comparing the δ15N of sinking particulate N captured within vs. below the euphotic zone indicates that during late spring regenerated N is low in δ15N compared to sinking N.
    Print ISSN: 0142-7873
    Electronic ISSN: 1464-3774
    Topics: Biology
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    Optimising sampling frequency for monitoring heterotrophic protists in a marine ecosystem (2021)
    Oxford University Press
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    Publication Date: 2021-07-20
    Description: Heterotrophic protists are essential components of the marine ecosystem, yet they are often excluded from monitoring programmes. With limited resources, monitoring strategies need to be optimised considering both scientific knowledge and available resources. In doing so, it is crucial to understand how sampling frequency affects the value of the data. We analysed 11 years of weekly heterotrophic protist time-series data from Station L4 in the Western English Channel to explore how different sampling intervals impact data quality. In the L4 dataset, comprising 55 protist taxa, the reduction of sampling frequency from weekly to four times a year at specific seasons decreased the number of taxa encountered by 38% for ciliates and 29% for heterotrophic dinoflagellates while the mean annual biomass or its mean variation were not affected. Furthermore, when samples were taken only four times a year, biomass peaks of the ten most important taxa were often missed. The primary motivator for this study was furthering the development of the heterotrophic protist monitoring in temperate and subarctic marine areas, e.g. the Baltic Sea. Based on our findings, we give recommendations on sampling frequency to optimise the value of heterotrophic protist monitoring.
    Print ISSN: 1054-3139
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    Topics: Biology , Geosciences , Physics
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    Cordierite-Bearing Orbicules Record Bulk Assimilation and the Pulsating Nature of Magma Ascent: The Lafaye Orbicular Granite (France) (2021)
    Oxford University Press
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    Publication Date: 2021-07-01
    Description: The Lafaye orbicular body was emplaced in the Villatange tonalite-granodiorite unit of the Guéret magmatic complex (Massif Central, France). It consists of plagioclasic orbicules (4–35 cm diameter) embedded in homogeneous cordierite granodiorite. Orbicule cores consist mostly of residual metasedimentary xenoliths or autolithic plagioclasic cumulates. Rims (0.7–8 cm thickness) are single- or multi-layered; layers, mostly comb-textured, comprise alternating sheets dominated by cordierite (XFe = 0.32–0.37) or plagioclase (mostly An25–30). Additional mineral phases are minor biotite (XFe = 0.52; AlVI = 0.58–0.92 atoms per formula unit) and interstitial quartz. Plagioclase and cordierite morphologies (needle-like, skeletal, branching or fan-shaped) indicate growth under high initial supersaturation. However, the final polyhedral shapes and primary zoning of many individual plagioclase crystals, as well as evidence of partial recrystallization, imply significant textural maturation. Whole-rock major and trace element data (A/CNK = 1.12–1.46) and Sr and Nd isotopic compositions (εNd(355 Ma)  = −8.6 to −7.4; 87Sr/86Sr(355 Ma) = 0.7110–0.7147) suggest that the parental magma of the orbicules resulted from bulk assimilation of aluminous metasediments by a Villatange-type granodioritic magma. Heterogeneous nucleation and growth of plagioclase and cordierite around xenoliths/autoliths are interpreted in terms of (1) adiabatic decompression of magma pulses ascending in dykes leading to superheating and resorption of early solids, and (2) volatile exsolution, inducing undercooling, supersaturation, and rim crystallization. The variability of layers (number, thickness, mineral distribution, and texture) is considered to result from oscillatory crystallization combined with variable plagioclase growth rates linked to changes in the degree of supersaturation as a function of the extent of melt degassing, itself linked to magma transfer dynamics.
    Print ISSN: 0022-3530
    Electronic ISSN: 1460-2415
    Topics: Geosciences
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    Prolonged Trachyte Storage and Unusual Remobilization at Piton de la Fournaise, La Réunion Island, Indian Ocean: Li, O, Sr, Nd, Pb and Th Isotope Study (2021)
    Oxford University Press
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    Publication Date: 2021-05-28
    Description: La Réunion Island includes two major volcanic systems. About 0·5 Myr ago, Piton des Neiges volcano declined, while Piton de la Fournaise volcano grew on its flank. Since then the Piton de la Fournaise shield volcano has produced homogeneous lavas with chemical compositions transitional between alkali and tholeiitic basalts. In April 2007, the volcano emitted a very small volume of trachytic pumice during its largest historical eruption. We conducted a comprehensive petrological and geochemical study of the pumice to understand the occurrence of such silicic melt in the feeding system of this highly active basaltic volcano. Isotopes of Sr, Nd, Pb and O, together with trace elements, indicate that the trachyte is genetically related to the La Réunion mantle plume and derives from crystallization of a typical basalt. The trachyte chemistry records a long and complex history of differentiation and outgassing. The extensive depletion of moderately volatile elements (F, Cl, B, Cs, Cu, Li) and less volatile uranium is consistent with exsolution of dense fluids at depths of several kilometres. Lithium isotopes point to closed-system degassing during the very late stages of crystallization. U-series isotopes and radiogenic 208Pb*/206Pb* constrain the age of U loss to between 0·4 and 2·1 Ma. This age is as old as or older than the Piton de la Fournaise shield edifice. The 2007 trachyte could thus be a liquid remnant of an extinct volcano, such as Piton des Neiges or Les Alizés (Piton de la Fournaise proto-volcano). It could also result from partial melting of an old syenite intrusion or remobilization of interstitial melts not fully solidified. Thermal modelling indicates that the sustained heat flux from hot basaltic magmas rising from the mantle can maintain temperatures above 800 °C in the central feeding system, and prevent total solidification of magmas trapped in this hot core.
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    Comparative evaluation of shape retrieval methods on macromolecular surfaces: an application of computer vision methods in structural bioinformatics (2021)
    Oxford University Press
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    Publication Date: 2021-07-11
    Description: Motivation The investigation of the structure of biological systems at the molecular level gives insights about their functions and dynamics. Shape and surface of biomolecules are fundamental to molecular recognition events. Characterizing their geometry can lead to more adequate predictions of their interactions. In the present work, we assess the performance of reference shape retrieval methods from the computer vision community on protein shapes. Results Shape retrieval methods are efficient in identifying orthologous proteins and tracking large conformational changes. This work illustrates the interest for the protein surface shape as a higher-level representation of the protein structure that (i) abstracts the underlying protein sequence, structure or fold, (ii) allows the use of shape retrieval methods to screen large databases of protein structures to identify surficial homologs and possible interacting partners and (iii) opens an extension of the protein structure–function paradigm toward a protein structure-surface(s)-function paradigm. Availabilityand implementation All data are available online at http://datasetmachat.drugdesign.fr. Supplementary information Supplementary data are available at Bioinformatics online.
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    Topics: Biology , Computer Science , Medicine
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    Beyond métiers: social factors influence fisher behaviour (2021)
    Oxford University Press
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    Publication Date: 2021-04-01
    Description: Fisheries management is usually supported by technical and financial measurements (i.e. logbooks and market data), which are helpful for ecological or economic assessments. Yet this information is not able to address social heterogeneity and fisher motivations, which are key to understanding fisher behaviour. This case study of the demersal segment in the Netherlands shows that combining quantitative analysis of logbooks with qualitative data collected by engaging with fishers can capture both fishing activity and its motivations, generating a more social understanding of fisher behaviour. A métier analysis of logbook data describes five dominant fishing practices among the selected segment. Twenty-five in-depth interviews with fishers along with focus groups including other experts identify three social factors that influence fisher behaviour in the Dutch demersal fleet: business structure, working rhythm, and polyvalence. The results show that motivations for fisher behaviour are more complex than complying with regulations or seeking profit: social factors also influence fishing activity. Furthermore, these social factors have real implications for the impacts of management measures on both the fishing communities and the environment, especially in times of change. These results are useful for management strategy development or evaluation because they are feasibly observable through existing data collection protocols.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
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    Using environmental variation to optimize aerial surveys of harbour seals (2021)
    Oxford University Press
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    Publication Date: 2021-03-25
    Description: Harbour seals are surveyed aerially when they haul-out to moult in August. The proportion of the population hauled out throughout the year is related to temporal, environmental, and meteorological variables. Thus, monitoring is conducted under predefined ranges of conditions. Effects of variation within these ranges are rarely reviewed. We used linear models to assess effects of time, date and weather on the difference between counts predicted by a population growth model and observed counts, based on a 30-year time-series. Our top-ranked model explained 34.4% of the variance. Survey date and its interaction with survey year were the most important variables, with higher counts earlier in August, particularly early in the time series, where surveys may not have been timed optimally to capture the peak in the moult. Cloud cover, wind speed, temperature, and interactions between these were of lesser importance; there were fewer seals on land during cloudy, windy days and on clear, warm days. These effects of weather are likely related to temperature regulation. Power analyses suggested that correction for survey conditions would allow detection of a one percentage point annual change in population growth rate with 80% power 4 years sooner than without taking survey conditions into account.
    Print ISSN: 1054-3139
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    Topics: Biology , Geosciences , Physics
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    Mapping 3D structure of a Sargassum forest with high-resolution sounding data obtained by multibeam echosounder (2021)
    Oxford University Press
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    Publication Date: 2021-03-13
    Description: Sargassum forests play an important role in coastal waters as habitats for marine organisms, including commercial species. However, human activities have negatively affected their distribution causing a worldwide decline of Sargassum forests. Mapping and monitoring the distribution and biomass of these habitats using acoustic remote sensing techniques is key for their conservation. Nonetheless, most researches based on acoustic remote sensing methods focus on estimations of macrophyte area and its canopy height, and less researches reporting 3D visualization of these habitats. This study demonstrates the use of high-resolution multibeam echosounder (MBES) bathymetric data to visualize the 3D structure of Sargassum forests. Comparing acoustic data and underwater camera photos collected in field surveys, we identified Sargassum individuals as vertical clusters of contiguous sounding points with a base close to the sea bottom in the sounding data of the MBES. Using this criterion, we could distinguish Sargassum echoes, visualize the 3D structure of Sargassum forests and estimate the number of Sargassum individuals in the survey area. Using the relation between thallus length and dry weight of sampled Sargassum plants, standing stock and biomass could be estimated assuming the thallus length was the height of Sargassum plants identified with the MBES.
    Print ISSN: 1054-3139
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    Topics: Biology , Geosciences , Physics
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    Increasing the precision of the daily egg production method; 2020’s remix of a 1980’s classic (2021)
    Oxford University Press
    Details
    Publication Date: 2021-03-29
    Description: This paper reviews application of the Daily Egg Production Method (DEPM) to sardine (Sardinops sagax) off southern Australia between 1995 and 2019. Coefficients of variation (CVs) of estimates of spawning biomass (SB) were reduced from 23–59% to 8–12% by: (i) estimating mean daily egg production (P0), spawning fraction (S), and sex ratio (R) from all historical data rather than annually; and (ii) combining batch fecundity (F) and female weight (W) into a single parameter, relative fecundity (F′ = F^/W). Total daily egg production was estimated most precisely from annual estimates of spawning area (A) and estimates of P0 obtained from historical data. Both S and R were estimated most precisely from historical data. Estimating W and F from historical data did not increase precision. F′ had lower CVs than both W and F, and was stable across years and a wide range of W. Findings demonstrate that A can be converted into a precise estimates of SB using estimates of P0, S, R, and F′ obtained from historical data. However, the possibility that DEPM parameters may change in the future cannot be discounted. Future monitoring should include annual estimation of P0 and periodic (e.g. 3–5 years) re-estimation of adult parameters.
    Print ISSN: 1054-3139
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    Sverdrup meets Lambert: analytical solution for Sverdrup’s critical depth (2021)
    Oxford University Press
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    Publication Date: 2021-03-10
    Description: In his 1953 paper, Harald Sverdrup argued that the development of a spring bloom in the ocean depends on the juxtaposition of two depth horizons: the mixed-layer depth and the critical depth. Mixed-layer depth shallower than the critical depth favours phytoplankton growth in the layer and vice versa. However, mathematically, Sverdrup left the problem unsolved in the form of a transcendental equation. In spite of the high number of citations that this paper has garnered, the solution to this equation has not been found, until now. In this work, we present an analytical solution for the critical depth, as originally defined by Sverdrup. The paper opens with the definition of the critical depth and the description of the Lambert W function. The analytical solution for critical depth follows. Sverdrup’s original model is extended to include the effect of light attenuation by phytoplankton and the analytical solution for steady-state biomass in the mixed layer is derived. The expression for mixed-layer production at steady state is also presented. Two novel variants of the critical depth are defined: the optically uncoupled critical depth and the optically coupled critical depth. It is demonstrated that at steady state the optically coupled critical depth equals the mixed-layer depth and that the irradiance at the base of the mixed layer equals the irradiance at the optically uncoupled critical depth. Competitive exclusion is demonstrated to hold and the optically uncoupled critical depth is linked to the critical light intensity in multi-species competition. Finally, a conservation principle for the critical depth is found.
    Print ISSN: 1054-3139
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    Topics: Biology , Geosciences , Physics
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    Interaction frequency of seabirds with longline fisheries: risk factors and implications for management (2021)
    Oxford University Press
    Details
    Publication Date: 2021-03-01
    Description: Fishery bycatch poses a serious threat to seabird populations globally. Traditional haul-only post-capture observations are inadequate and inefficient to document seabird bycatch due to the substantial bycatch loss known to occur. Pre-capture observations offer an alternative by documenting seabird interactions leading up to captures. Based on the long-term large-scale dedicated field observations, this study revealed significant risk factors for the pre-capture stages of the seabird bycatch process in pelagic longline fisheries using Bayesian methods. Rough sea conditions were found to correlate with more seabirds following fishing vessels. Species identity, density effect, inter-species effect, and sea condition were found to significantly affect how frequently seabirds aggregated around a fishing vessel engage in bait-taking interactions. Intra-species competition was found to be the dominant type of density effect. Moreover, a web of inter-species interactions was identified to facilitate the bait-taking of superior competitors at the expense of inferior ones. The findings of this study are relevant to fishery managers in updating current data collection protocols to alleviate data issues caused by bycatch loss, to conservation biologists in quantifying bycatch risks for susceptible seabird populations, and in aiding the design and evaluation of bycatch mitigation measures.
    Print ISSN: 1054-3139
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    Topics: Biology , Geosciences , Physics
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    Wrasse fishery on the Swedish West Coast: towards ecosystem-based management (2021)
    Oxford University Press
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    Publication Date: 2021-03-10
    Description: Fishing and translocation of marine species for use in aquaculture is widespread. Corkwing, goldsinny, and ballan wrasse (Symphodus melops, Ctenolabrus rupestris, and Labrus bergylta) are fished on the Swedish west coast for use as cleaner-fish in Norwegian salmon farms. Here, we aim to provide knowledge and recommendations to support ecosystem-based management for wrasse fisheries in Sweden. We compared fished and non-fished areas to test if current fishery levels have led to stock depletion. To gain insight on the role of wrasse in the algal belt trophic chain, we analysed the gut contents of goldsinny and corkwing using metabarcoding. Finally, we analysed the trophic interactions of wrasse and potential prey in a mesocosm study. We could not detect any signs of stock depletion or altered size structure in fished areas compared to the protected control area. Gut analyses confirmed both goldsinny and corkwing as non-specialized, omnivorous opportunists and revealed, with 189 prey taxa detected, a broader spectrum of prey than previously known. Common prey items included mesoherbivores such as small gastropods and crustaceans, but also insects and algae. We conclude that there are no visible signs of stock depletion at the current removal level of wrasses by the fishery. However, this emerging fishery should be closely monitored for potential cascading effects on the algal belt ecosystem, and our study could provide a baseline for future monitoring.
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    The Breeding Information Management System (BIMS): an online resource for crop breeding (2021)
    Oxford University Press
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    Publication Date: 2021-01-01
    Description: In this era of big data, breeding programs are producing ever larger amounts of data. This necessitates access to efficient management systems to keep track of cross, performance, pedigree, geographical and image-based data, as well as genotyping data. In this article, we report the progress on the Breeding Information Management System (BIMS), a free, secure and online breeding management system that allows breeders to store, manage, archive and analyze their private breeding data. BIMS is the first publicly available database system that enables individual breeders to integrate their private phenotypic and genotypic data with public data and, at the same time, have complete control of their own breeding data along with access to tools such as data import/export, data analysis and data archiving. The integration of breeding data with publicly available genomic and genetic data enhances genetic understanding of important traits and maximizes the marker-assisted breeding utility for breeders and allied scientists. BIMS incorporates the use of the Android App Field Book, open-source phenotype data collection software for phones and tablets that allows breeders to replace hard copy field books, thus alleviating the possibility of transcription errors while providing faster access to the collected data. BIMS comes with training materials and support for individual or small group training and is currently implemented in the Genome Database for Rosaceae, CottonGEN, the Citrus Genome Database, the Pulse Crop Database, and the Genome Database for Vaccinium. Database URLs: (https://www.rosaceae.org/), (https://www.cottongen.org/), (https://www.citrusgenomedb.org/), (https://www.pulsedb.org/) and (https://www.vaccinium.org/)
    Electronic ISSN: 1758-0463
    Topics: Biology
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    The autism risk gene CNTN4 modulates dendritic spine formation (2021)
    Oxford University Press
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    Publication Date: 2021-08-20
    Description: Contactin 4 (CNTN4) is a crucial synaptic adhesion protein that belongs to the contactin superfamily. Evidence from both human genetics and mouse models suggests that synapse formation and structural deficits strongly correlate with neurodevelopmental disorders, including autism. In addition, several lines of evidence suggest that CNTN4 is associated with the risk of autism. However, the biological functions of CNTN4 in neural development and disease pathogenesis are poorly understood. In this study, we investigated whether and how CNTN4 is autonomously involved in the development of dendrites and dendritic spines in cortical neurons. Disruption of Cntn4 decreased the number of excitatory synapses, which led to a reduction in neural activity. Truncated proteins lacking the signal peptide, FnIII domains, or GPI domain lacked the ability to regulate dendritic spine formation, indicating that CNTN4 regulates dendritic spine density through a mechanism dependent on FnIII domains. Importantly, we revealed that autism-related variants lacked the ability to regulate spine density and neural activity. In conclusion, our study suggests that CNTN4 is essential for promoting dendrite growth and dendritic spine formation and that disruptive variants of CNTN4 interfere with abnormal synapse formation and may increase the risk of autism.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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    Inference of the optical depth to reionization from low multipole temperature and polarization Planck data (2021)
    Oxford University Press
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    Publication Date: 2021-08-11
    Description: This paper explores methods for constructing low multipole temperature and polarization likelihoods from maps of the cosmic microwave background anisotropies that have complex noise properties and partial sky coverage. We use Planck 2018 High Frequency Instrument (HFI) and updated SRoll2 temperature and polarization maps to test our methods. We present three likelihood approximations based on quadratic cross spectrum estimators: (i) a variant of the simulation-based likelihood (SimBaL) techniques used in the Planck legacy papers to produce a low multipole EE likelihood; (ii) a semi-analytical likelihood approximation (momento) based on the principle of maximum entropy; (iii) a density-estimation ‘likelihood-free’ scheme (delfi). Approaches (ii) and (iii) can be generalized to produce low multipole joint temperature-polarization (TTTEEE) likelihoods. We present extensive tests of these methods on simulations with realistic correlated noise. We then analyse the Planck data and confirm the robustness of our method and likelihoods on multiple inter- and intra-frequency detector set combinations of SRoll2 maps. The three likelihood techniques give consistent results and support a low value of the optical depth to reoinization, τ, from the HFI. Our best estimate of τ comes from combining the low multipole SRoll2momento (TTTEEE) likelihood with the CamSpec high multipole likelihood and is $au = 0.0627^{+0.0050}_{-0.0058}$. This is consistent with the SRoll2 team’s determination of τ, though slightly higher by ∼0.5σ, mainly because of our joint treatment of temperature and polarization.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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    Constraining properties of GRB central engines with X-ray flares (2021)
    Oxford University Press
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    Publication Date: 2021-07-31
    Description: X-ray flares in gamma-ray bursts (GRBs) are believed to be generated by the late activities of central engine, and thus provide an useful tool to diagnose the properties of central objects. In this paper, we work on a GRB X-ray flare sample whose bulk Lorentz factors are constrained by two different methods and the jet opening angles are determined by the jet breaks in afterglow light curves. Considering a hyperaccreting stellar-mass black hole (BH) as the central engine of GRBs and the Blandford & Znajek process (BZ) as the jet production mechanism, we constrain the parameters of central engine by using the X-ray flare data. We find that the BZ mechanism is so powerful making it possible to interpret both GRB prompt emissions and bright X-ray flares. The wind parameter (p) and accreted mass (Md) fall into reasonable ranges. Our result is also applied to GRB 170817A. The late X-ray flare in GRB 170817A, if it is true, might not be a BH origin.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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    Generating neutron-star magnetic fields: three dynamo phases (2021)
    Oxford University Press
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    Publication Date: 2021-07-26
    Description: Young neutron stars (NSs) have magnetic fields in the range 1012–1015 G, believed to be generated by dynamo action at birth. We argue that such a dynamo is actually too inefficient to explain the strongest of these fields. Dynamo action in the mature star is also unlikely. Instead we propose a promising new precession-driven dynamo and examine its basic properties, as well as arguing for a revised mean-field approach to NS dynamos. The precession-driven dynamo could also play a role in field generation in main-sequence stars.
    Print ISSN: 1745-3925
    Electronic ISSN: 1745-3933
    Topics: Physics
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    The magnetic system SMSS J1606−1000 as a period bouncer (2021)
    Oxford University Press
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    Publication Date: 2021-07-27
    Description: We report the discovery of a rare close binary system, SMSS J160639.78−100010.7, comprising a magnetic white dwarf with a field of about 30 MG and a brown dwarf. We measured an orbital period of 92 min which is consistent with the photometric period. Minimum and maximum light occur at the orbital quadratures Φ = 0.25 and 0.75, respectively, and cannot be caused by reflection on the brown dwarf, but, instead, by a spot on the synchronously rotating magnetic white dwarf. The brown dwarf does not fill its Roche lobe and the system may be in a low-accretion state or, more likely, in a detached state following episodes of mass transfer. SMSS J160639.78−100010.7 is the nearest known magnetic white dwarf plus brown dwarf system.
    Print ISSN: 1745-3925
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    AI-assisted superresolution cosmological simulations – II. Halo substructures, velocities, and higher order statistics (2021)
    Oxford University Press
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    Publication Date: 2021-07-24
    Description: In this work, we expand and test the capabilities of our recently developed superresolution (SR) model to generate high-resolution (HR) realizations of the full phase-space matter distribution, including both displacement and velocity, from computationally cheap low-resolution (LR) cosmological N-body simulations. The SR model enhances the simulation resolution by generating 512 times more tracer particles, extending into the deeply nonlinear regime where complex structure formation processes take place. We validate the SR model by deploying the model in 10 test simulations of box size 100 h−1 Mpc, and examine the matter power spectra, bispectra, and two-dimensional power spectra in redshift space. We find the generated SR field matches the true HR result at per cent level down to scales of k ∼ 10 h  Mpc−1. We also identify and inspect dark matter haloes and their substructures. Our SR model generates visually authentic small-scale structures that cannot be resolved by the LR input, and are in good statistical agreement with the real HR results. The SR model performs satisfactorily on the halo occupation distribution, halo correlations in both real and redshift space, and the pairwise velocity distribution, matching the HR results with comparable scatter, thus demonstrating its potential in making mock halo catalogues. The SR technique can be a powerful and promising tool for modelling small-scale galaxy formation physics in large cosmological volumes.
    Print ISSN: 0035-8711
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    Single-cell Hi-C data analysis: safety in numbers (2021)
    Oxford University Press
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    Publication Date: 2021-08-18
    Description: Over the past decade, genome-wide assays for chromatin interactions in single cells have enabled the study of individual nuclei at unprecedented resolution and throughput. Current chromosome conformation capture techniques survey contacts for up to tens of thousands of individual cells, improving our understanding of genome function in 3D. However, these methods recover a small fraction of all contacts in single cells, requiring specialised processing of sparse interactome data. In this review, we highlight recent advances in methods for the interpretation of single-cell genomic contacts. After discussing the strengths and limitations of these methods, we outline frontiers for future development in this rapidly moving field.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
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    APPTEST is a novel protocol for the automatic prediction of peptide tertiary structures (2021)
    Oxford University Press
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    Publication Date: 2021-08-14
    Description: Good knowledge of a peptide’s tertiary structure is important for understanding its function and its interactions with its biological targets. APPTEST is a novel computational protocol that employs a neural network architecture and simulated annealing methods for the prediction of peptide tertiary structure from the primary sequence. APPTEST works for both linear and cyclic peptides of 5–40 natural amino acids. APPTEST is computationally efficient, returning predicted structures within a number of minutes. APPTEST performance was evaluated on a set of 356 test peptides; the best structure predicted for each peptide deviated by an average of 1.9Å from its experimentally determined backbone conformation, and a native or near-native structure was predicted for 97% of the target sequences. A comparison of APPTEST performance with PEP-FOLD, PEPstrMOD and PepLook across benchmark datasets of short, long and cyclic peptides shows that on average APPTEST produces structures more native than the existing methods in all three categories. This innovative, cutting-edge peptide structure prediction method is available as an online web server at https://research.timmons.eu/apptest, facilitating in silico study and design of peptides by the wider research community.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
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    Positive Selection of Transcription Factors Is a Prominent Feature of the Evolution of a Plant Pathogenic Genus Originating in the Miocene (2021)
    Oxford University Press
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    Publication Date: 2021-07-20
    Description: Tests based on the dN/dS statistic are used to identify positive selection of nonsynonymous polymorphisms. Using these tests on alignments of all orthologs from related species can provide insights into which gene categories have been most frequently positively selected. However, longer alignments have more power to detect positive selection, creating a detection bias that could create misleading results from functional enrichment tests. Most studies of positive selection in plant pathogens focus on genes with specific virulence functions, with little emphasis on broader molecular processes. Furthermore, no studies in plant pathogens have accounted for detection bias due to alignment length when performing functional enrichment tests. To address these research gaps, we analyze 12 genomes of the phytopathogenic fungal genus Botrytis, including two sequenced in this study. To establish a temporal context, we estimated fossil-calibrated divergence times for the genus. We find that Botrytis likely originated 16–18 Ma in the Miocene and underwent continuous radiation ending in the Pliocene. An untargeted scan of Botrytis single-copy orthologs for positive selection with three different statistical tests uncovered evidence for positive selection among proteases, signaling proteins, CAZymes, and secreted proteins. There was also a strong overrepresentation of transcription factors among positively selected genes. This overrepresentation was still apparent after two complementary controls for detection bias due to sequence length. Positively selected sites were depleted within DNA-binding domains, suggesting changes in transcriptional responses to internal and external cues or protein–protein interactions have undergone positive selection more frequently than changes in promoter fidelity.
    Electronic ISSN: 1759-6653
    Topics: Biology
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    Individual variability in sub-Arctic krill material properties, lipid composition, and other scattering model inputs affect acoustic estimates of their population (2021)
    Oxford University Press
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    Publication Date: 2021-03-22
    Description: Target strength model inputs including morphometry, material properties, lipid composition, and in situ orientations were measured for sub-Arctic krill (Euphausia pacifica, Thysanoessa spinifera, T. inermis, and T. raschii) in the eastern Bering Sea (EBS, 2016) and Gulf of Alaska (GOA, 2017). Inter-species and -regional animal lengths were significantly different (F1,680 = 114.10, p 
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    Exploring the role of temperature in observed inter-population differences of Atlantic cod (Gadus morhua) growth with a 4-dimensional modelling approach (2021)
    Oxford University Press
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    Publication Date: 2021-04-01
    Description: Atlantic cod (Gadus morhua) is one of the most commercially important fish species in the North Atlantic. Environmental factors, such as water temperatures, influence growth of individuals over time, thus forming population-specific growth patterns across climatic regions. Here we develop an integrative approach to investigate the role of temperature in shaping geographic differences of cod growth in the Celtic Sea, North Sea, Iceland, and Barents Sea. We combine a physiology-based growth model and 50-years observational temperature data of 0.5 × 0.5° spatial resolution to simulate continuous growth of cod. The model generated weight-at-age data for the period 1959–2007 which we compared to observational data from fishery-independent scientific surveys. In the Celtic and the northern North Sea, simulated growth matches well observational data. We also show that relatively warm temperatures in the Celtic Sea facilitate maximum growth rates; future warming is likely to have a negative impact on growth of these cod stocks. Growth simulations in Icelandic waters and the Barents Sea are less consistent with local observational data. More complex growth patterns in these regions are probably shaped by ontogenetic shifts in temperature regimes, feeding conditions and physiological adaptations. These findings should stimulate further research on critical processes to be considered in population-specific projections of growth of cod and productivity.
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    Incorporating spatiotemporal variability in multispecies survey design optimization addresses trade-offs in uncertainty (2021)
    Oxford University Press
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    Publication Date: 2021-03-03
    Description: In designing and performing surveys of animal abundance, monitoring programs often struggle to determine the sampling intensity and design required to achieve their objectives, and this problem greatly increases in complexity for multispecies surveys with inherent trade-offs among species. To address these issues, we conducted a multispecies stratified random survey design optimization using a spatiotemporal operating model and a genetic algorithm that optimizes both the stratification (defined by depth and longitude) and the minimum optimal allocation of samples across strata subject to prespecified precision limits. Surveys were then simulated under those optimized designs and performance was evaluated by calculating the precision and accuracy of a resulting design-based abundance index. We applied this framework to a multispecies fishery-independent bottom trawl survey in the Gulf of Alaska, USA. Incorporating only spatial variation in the optimization failed to produce population estimates within the prespecified precision constraints, whereas including additional spatiotemporal variation ensured that estimates were both unbiased and within prespecified precision constraints. In general, results were not sensitive to the number of strata in the optimized solutions. This optimization approach provides an objective quantitative framework for designing new, or improving existing, survey designs for many different ecosystems.
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    Application of a multibeam echosounder to document changes in animal movement and behaviour around a tidal turbine structure (2021)
    Oxford University Press
    Details
    Publication Date: 2021-02-28
    Description: Changes in animal movement and behaviour at fine scales (tens of metres) in immediate proximity to tidal stream turbine structures are largely unknown and have implications for risks of animal collision with turbine blades. This study used upward-facing multibeam echosounder data to detect and track animal movement comprising fish, diving seabirds, and marine mammals. Measurements over spring-neap tidal cycles at a turbine structure (no blades present) are compared to a neighbouring reference area with no structure and comparable conditions, with measurements consecutive in time to maximize comparability. The majority of tracked animals (93.4% around turbine structure and 99.1% without turbine structure) were observed swimming against the flow, with 87.5% and 97.8%, respectively, making ground and showing capability of manoeuvring in tidal stream flow speeds. Track tortuosity increased around the turbine structure compared to the reference site, particularly in the wake and at low flow speeds, indicating animal station-holding or milling behaviour. These data also evidence the benefits of multibeam echosounders to measure animal movement through larger measurement volumes rather than relying on single-beam echosounders to measure animal presence alone, including to avoid large biases overestimating the size of schools swimming against the flow measured by time-in-beam.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press on behalf of International Council for the Exploration of the Sea.
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    Multi-scale assessment of distribution and density of procellariiform seabirds within the Northern Antarctic Peninsula marine ecosystem (2021)
    Oxford University Press
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    Publication Date: 2021-03-07
    Description: The Antarctic Peninsula is one of the most rapidly warming regions on earth, and it is likely that the abundance and distribution of marine predators will change as a result.Procellariiform seabirds are highly mobile predators, which target specific habitat characteristics associated with underlying distributions of prey and areas of increased prey availability. We use ship surveys and hurdle models, to estimate the summer distribution and relative density of 11 seabird species within the northern Antarctic Peninsula marine ecosystem. Models differed among species; however, sea surface temperature and depth were frequently associated with seabird occurrence and had the greatest explanatory power across many species. Null models based on observation data were better at predicting seabird density than models that included environmental covariates. This suggests that the main driver of distribution patterns is the broad-scale habitat features, and fine-scale aggregations within these ranges are harder to predict. Our seabird distribution models reflect known habitat associations, species hotspots, and community organization relative to oceanic and coastal marine processes. Application of species distribution models will benefit the assessments of critical habitat and potential responses to climate change and anthropogenic disturbance, which will provide insight into how species may change in polar ecosystems.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press on behalf of International Council for the Exploration of the Sea.
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    Using a genetic algorithm to optimize a data-limited catch rule (2021)
    Oxford University Press
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    Publication Date: 2021-03-06
    Description: Many data-limited fish stocks worldwide require management advice. Simple empirical management procedures have been used to manage data-limited fisheries but do not necessarily ensure compliance with maximum sustainable yield objectives and precautionary principles. Genetic algorithms are efficient optimization procedures for which the objectives are formalized as a fitness function. This optimization can be included when testing management procedures in a management strategy evaluation. This study explored the application of a genetic algorithm to an empirical catch rule and found that this approach could substantially improve the performance of the catch rule. The optimized parameterization and the magnitude of the improvement were dependent on the specific stock, stock status, and definition of the fitness function. The genetic algorithm proved to be an efficient and automated method for tuning the catch rule and removed the need for manual intervention during the optimization process. Therefore, we conclude that the approach could also be applied to other management procedures, case-specific tuning, and even data-rich stocks. Finally, we recommend the phasing out of the current generic ICES “2 over 3” advice rule in favour of case-specific catch rules of the form tested here, although we caution that neither works well for fast-growing stocks.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press on behalf of International Council for the Exploration of the Sea.
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    Marine spatial planning and the risk of ocean grabbing in the tropical Atlantic (2021)
    Oxford University Press
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    Publication Date: 2021-02-28
    Description: Ocean grabbing occurs when traditional users, such as small-scale fishers, are pushed aside by new development activities. This grabbing must be prevented to avoid sea uses that maintain or increase social inequity. In this paper, we show that in tropical Atlantic countries, such as Brazil and Senegal, examples of ocean grabbing already occur. In this context, we analyse if Maritime Spatial Planning (MSP) may be an opportunity to limit ocean grabbing or, to the contrary, poses a risk to increase it. MSP calls for an ecosystem approach that requires integrated coastal and marine management and involves stakeholders in developing a shared vision of the future, where society and environment are preserved. However, recent studies have shown that MSP is a process to be used cautiously to ensure equitable decisions. Meanwhile, the concept is spreading worldwide including in tropical Atlantic countries. We highlight that context matters and the specificities of the tropical Atlantic must be taken into account when deploying MSP processes. In the tropical Atlantic context, there is increased imbalances of stakeholder power, traps from decision support tools, and a need for adaptive management. These specific features must be addressed when deploying MSP in a way to avoid ocean grabbing.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press on behalf of International Council for the Exploration of the Sea.
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    Biogeographical patterns of meso- and bathypelagic fish along a Northeastern Atlantic transect (2021)
    Oxford University Press
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    Publication Date: 2021-03-13
    Description: The influence of oceanographic variables on assemblages of meso- and bathypelagic fish was investigated along a Northeastern Atlantic Ocean transect (Cape Verde to the Bay of Biscay) during May 2019. Fish were collected using a mrozooplankton trawl during daylight hours at ten stations. Along the transect, 17 hydrographic stations were also performed with a CTD (Conductivity, Temperature, and Depth). A total of 130 fish taxa were identified. The dominant family was Gonostomatidae, with four species (Cyclothone braueri, Cyclothone microdon, Cyclothone pseudopallida, and Cyclothone pallida) being responsible of more than 78% of the total density. The most frequent species that appeared to be ubiquitous were C. braueri and C. pseudopallida, while Myctophidae was the most diverse family. Multivariate analyses revealed two clusters related with the latitudinal gradient. The fish community in the southern stations (25–37°N) was more diverse than in the northern stations (42–48°N). Temperature from 300 to 700 m depth explained 65% of variation in terms of density and 58% in terms of biomass, both statistically significant. The investigated variation in the deep-pelagic ecosystems on a large spatial scale gives essential information to ecosystem management approhes and marine spatial planning.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press on behalf of International Council for the Exploration of the Sea.
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    Six steps to produce stock assessments for the Marine Strategy Framework Directive compliant with Descriptor 3 (2021)
    Oxford University Press
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    Publication Date: 2021-02-26
    Description: In the European Union (EU), the ecosystem approach to fisheries is implemented through several directives and polices, which are overarched by the Marine Strategy Framework Directive (MSFD). The MSFD requires the assessment of the environmental status of exploited fish and shellfish stocks, among others, to advise the EU Common Fisheries Policy (CFP) on sustainable catch options. The stock assessments for the CFP and the MSFD are supposed to be congruent, yet they differ in several substantial subjects. While the annual CFP assessment is based on two indicators, fishing mortality (F) and spawning stock biomass (SSB), in its Descriptor 3 (D3) the MSFD requires the assessment of three criteria (F, SSB, and age or size structure) within a six year period. Assessing exploited fish and shellfish stocks under the MSFD by using existing CFP assessments has therefore been a half-completed task, which had to be fulfilled by the member states of the EU. This paper suggests six easy steps, referred to as “quick wins” (QW), which are based on existing information from CFP stock assessments. The implementation of these six QW would allow for assessments of exploited fish and shellfish stocks that are compliant to D3. These QW are to (i) assess length/age structure within a stock, (ii) analyse and assess selectivity by fisheries, (iii) use all available information to assess a stock, (iv) use response indicators to assess environmental targets, (v) provide integrated stock-specific advice, and (vi) provide assessments with a mid-term perspective over a-period of six years. International Council for the Exploration of the Sea (ICES) combines the infrastructure and expertise to produce stock-specific assessment products tailored to the requirements of MSFD D3. Thereby, ICES could provide a valuable service to EU member states in the north-east Atlantic region by providing scientifically validated, quality-assured, and MSFD-compliant single-stock assessment products. This would be a big advancement towards implementing the ecosystem approach to fisheries management within Europe.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press on behalf of International Council for the Exploration of the Sea.
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    Molecular design in drug discovery: a comprehensive review of deep generative models (2021)
    Oxford University Press
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    Publication Date: 2021-08-20
    Description: Deep generative models have been an upsurge in the deep learning community since they were proposed. These models are designed for generating new synthetic data including images, videos and texts by fitting the data approximate distributions. In the last few years, deep generative models have shown superior performance in drug discovery especially de novo molecular design. In this study, deep generative models are reviewed to witness the recent advances of de novo molecular design for drug discovery. In addition, we divide those models into two categories based on molecular representations in silico. Then these two classical types of models are reported in detail and discussed about both pros and cons. We also indicate the current challenges in deep generative models for de novo molecular design. De novo molecular design automatically is promising but a long road to be explored.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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    The Genome of the Haptophyte Diacronema lutheri (Pavlova lutheri, Pavlovales): A Model for Lipid Biosynthesis in Eukaryotic Algae (2021)
    Oxford University Press
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    Publication Date: 2021-08-01
    Description: Haptophytes are biogeochemically and industrially important protists with underexplored genomic diversity. We present a nuclear genome assembly for the class Pavlovales, which was assembled with PacBio long-read data into highly contiguous sequences. We sequenced strain Diacronema lutheri NIVA-4/92, formerly known as Pavlova lutheri, because it has established roles in aquaculture and has been a key organism for studying microalgal lipid biosynthesis. Our data show that D. lutheri has the smallest and most streamlined haptophycean genome assembled to date, with an assembly size of 43.503 Mb and 14,446 protein-coding genes. Together with its high nuclear GC content, Diacronema is an important genus for investigating selective pressures on haptophyte genome evolution, contrasting with the much larger and more repetitive genome of the coccolithophore Emiliania huxleyi. The D. lutheri genome will be a valuable resource for resolving the genetic basis of algal lipid biosynthesis and metabolic remodeling that takes place during adaptation and stress response in natural and engineered environments.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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    Detecting methylation quantitative trait loci using a methylation random field method (2021)
    Oxford University Press
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    Publication Date: 2021-08-19
    Description: DNA methylation may be regulated by genetic variants within a genomic region, referred to as methylation quantitative trait loci (mQTLs). The changes of methylation levels can further lead to alterations of gene expression, and influence the risk of various complex human diseases. Detecting mQTLs may provide insights into the underlying mechanism of how genotypic variations may influence the disease risk. In this article, we propose a methylation random field (MRF) method to detect mQTLs by testing the association between the methylation level of a CpG site and a set of genetic variants within a genomic region. The proposed MRF has two major advantages over existing approaches. First, it uses a beta distribution to characterize the bimodal and interval properties of the methylation trait at a CpG site. Second, it considers multiple common and rare genetic variants within a genomic region to identify mQTLs. Through simulations, we demonstrated that the MRF had improved power over other existing methods in detecting rare variants of relatively large effect, especially when the sample size is small. We further applied our method to a study of congenital heart defects with 83 cardiac tissue samples and identified two mQTL regions, MRPS10 and PSORS1C1, which were colocalized with expression QTL in cardiac tissue. In conclusion, the proposed MRF is a useful tool to identify novel mQTLs, especially for studies with limited sample sizes.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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    Improved nutritional status may promote an “asset protection” reproductive strategy in male rock lizards (2021)
    Oxford University Press
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    Publication Date: 2021-08-20
    Description: Investing in the current reproduction requires diverting energy resources from other metabolic functions, which may compromise future reproduction and lifespan. To solve this trade-off, an individual may consider its labile state to decide how much to invest in current reproduction. We tested experimentally whether the “state quality” of male rock lizards influences their reproductive strategies. To improve the nutritional status of males before the mating season, we captured and supplemented experimental males (N = 20) with dietary vitamin D3 (an essential nutrient for lizards) and had a control group of males (N = 20). Then, we released all these males and females (N = 31) in a large semi-natural outdoor enclosure where lizards could interact and mate freely during the mating period. Activity levels of males did not vary between treatments, but supplemented males started fewer intrasexual agonistic interactions and made fewer mating advances to females. When the mating season ended, we incubated eggs laid by females to obtain the offspring and estimated the paternity of males using DNA microsatellites. Supplemented males sired fewer offspring than control males. These results suggest that vitamin D3 supplemented males used a low risk/less costly mating strategy to protect their assets (i.e., vitamin D reserves), but that still resulted in “some” current reproductive success, while likely increasing longevity and the expected future total reproductive success.
    Print ISSN: 1045-2249
    Electronic ISSN: 1465-7279
    Topics: Biology
    Published by Oxford University Press
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    Knowledge transfer profiles of public research organisations: the role of fields of knowledge specialisation (2021)
    Oxford University Press
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    Publication Date: 2021-08-20
    Description: While public research organisations (PROs) are increasingly expected to transfer knowledge to businesses and other stakeholders, their engagement in knowledge transfer (KT) activities is still under-researched. Better understanding of PROs’ KT engagement, including how it is shaped by PROs’ organisational characteristics, could lead to better tailored policies in support to PROs’ effort to transfer knowledge. We develop a conceptual framework linking PROs’ specialisation in different fields of knowledge to their profiles of KT engagement and validate it empirically using a six-year panel data set of 33 PROs in the UK. We use multidimensional scaling and cluster analysis techniques to identify three distinct KT profiles, which are stable over time, and strongly associated with the PROs’ knowledge field specialisation. We argue that these profiles may depend on the different market readiness and user specificity of knowledge outputs arising from different fields of knowledge and derive implications for theory, policy, and practice.
    Print ISSN: 0302-3427
    Electronic ISSN: 1471-5430
    Topics: Nature of Science, Research, Systems of Higher Education, Museum Science
    Published by Oxford University Press
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    HCN/HNC chemistry in shocks: a study of L1157-B1 with ASAI (2021)
    Oxford University Press
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    Publication Date: 2021-07-24
    Description: Hydrogen cyanide (HCN) and its isomer hydrogen isocyanide (HNC) play an important role in molecular cloud chemistry and the formation of more complex molecules. We investigate here the impact of protostellar shocks on the HCN and HNC abundances from high-sensitivity IRAM 30 m observations of the prototypical shock region L1157-B1 and the envelope of the associated Class 0 protostar, as a proxy for the pre-shock gas. The isotopologues H12CN, HN12C, H13CN, HN13C, HC15N, H15NC, DCN, and DNC were all detected towards both regions. Abundances and excitation conditions were obtained from radiative transfer analysis of molecular line emission under the assumption of local thermodynamical equilibrium. In the pre-shock gas, the abundances of the HCN and HNC isotopologues are similar to those encountered in dark clouds, with an HCN/HNC abundance ratio ≈1 for all isotopologues. A strong D-enrichment (D/H ≈ 0.06) is measured in the pre-shock gas. There is no evidence of 15N fractionation neither in the quiescent nor in the shocked gas. At the passage of the shock, the HCN and HNC abundances increase in the gas phase in different manners so that the HCN/HNC relative abundance ratio increases by a factor 20. The gas-grain chemical and shock model uclchem allows us to reproduce the observed trends for a C-type shock with pre-shock density n(H) = $10^5hbox{cm$^{-3}$}$ and shock velocity $V_mathrm{ s}= 40hbox{kms$^{-1}$}$. We conclude that the HCN/HNC variations across the shock are mainly caused by the sputtering of the grain mantle material in relation with the history of the grain ices.
    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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    Genome-wide association study in the Taiwan Biobank identifies four novel genes for human height: NABP2, RASA2, RNF41 and SLC39A5 (2021)
    Oxford University Press
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    Publication Date: 2021-07-16
    Description: Numerous genome-wide association studies (GWASs) have been conducted for the identification of genetic variants involved with human height. The vast majority of these studies, however, have been conducted in populations of European ancestry. Here, we report the first GWAS of adult height in the Taiwan Biobank using a discovery sample of 14 571 individuals and an independent replication sample of 20 506 individuals. From our analysis, we generalize to the Taiwanese population genome-wide significant associations with height and 18 previously identified genes in European and non-Taiwanese East Asian populations. We also identify and replicate, at the genome-wide significance level, associated variants for height in four novel genes at two loci that have not previously been reported: RASA2 on chromosome 3 and NABP2, RNF41 and SLC39A5 at 12q13.3 on chromosome 12. RASA2 and RNF41 are strong candidates for having a role in height with copy number and loss of function variants in RASA2 previously found to be associated with short stature disorders, and decreased expression of the RNF41 gene resulting in insulin resistance in skeletal muscle. The results from our analysis of the Taiwan Biobank underscore the potential for the identification of novel genetic discoveries in underrepresented worldwide populations, even for traits, such as height, that have been extensively investigated in large-scale studies of European ancestry populations.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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    MMpred: a distance-assisted multimodal conformation sampling for de novo protein structure prediction (2021)
    Oxford University Press
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    Publication Date: 2021-06-29
    Description: Motivation The mathematically optimal solution in computational protein folding simulations does not always correspond to the native structure, due to the imperfection of the energy force fields. There is therefore a need to search for more diverse suboptimal solutions in order to identify the states close to the native. We propose a novel multimodal optimization protocol to improve the conformation sampling efficiency and modeling accuracy of de novo protein structure folding simulations. Results A distance-assisted multimodal optimization sampling algorithm, MMpred, is proposed for de novo protein structure prediction. The protocol consists of three stages: The first is a modal exploration stage, in which a structural similarity evaluation model DMscore is designed to control the diversity of conformations, generating a population of diverse structures in different low-energy basins. The second is a modal maintaining stage, where an adaptive clustering algorithm MNDcluster is proposed to divide the populations and merge the modal by adjusting the annealing temperature to locate the promising basins. In the last stage of modal exploitation, a greedy search strategy is used to accelerate the convergence of the modal. Distance constraint information is used to construct the conformation scoring model to guide sampling. MMpred is tested on a large set of 320 non-redundant proteins, where MMpred obtains models with TM-score≥0.5 on 291 cases, which is 28% higher than that of Rosetta guided with the same set of distance constraints. In addition, on 320 benchmark proteins, the enhanced version of MMpred (E-MMpred) has 167 targets better than trRosetta when the best of five models are evaluated. The average TM-score of the best model of E-MMpred is 0.732, which is comparable to trRosetta (0.730). Availability and implementation The source code and executable are freely available at https://github.com/iobio-zjut/MMpred. 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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