ALBERT

All Library Books, journals and Electronic Records Telegrafenberg

X
feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
  • Articles  (77,272)
  • Oxford University Press  (77,272)
  • 2020-2024  (476)
  • 2020-2022  (15,706)
  • 1995-1999  (31,101)
  • 1990-1994  (29,989)
Collection
Source
Keywords
Publisher
Years
Year
Journal
Topic
  • 1
    facet.materialart.
    Unknown
    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)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 2
    facet.materialart.
    Unknown
    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)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 3
    facet.materialart.
    Unknown
    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)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 4
    facet.materialart.
    Unknown
    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)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 5
    facet.materialart.
    Unknown
    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)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 6
    facet.materialart.
    Unknown
    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)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 7
    facet.materialart.
    Unknown
    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)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 8
    facet.materialart.
    Unknown
    Hydrological and volcano-related gravity signals at Mt. Somma–Vesuvius from ∼20 yr of time-lapse gravity monitoring: implications for volcano quiescence (2024)
    Oxford University Press
    Details
    Publication Date: 2024-05-27
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2023. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved.
    Description: We report on about 20 yr of relative gravity measurements, acquired on Mt. Somma–Vesuvius volcano in order to investigate the hydrological and volcano-tectonic processes controlling the present-day activity of the volcano. The retrieved long-term field of time gravity change (2003–2022) shows a pattern essentially related to the subsidence, which have affected the central part of the volcano, as detected by the permanent GNSS network and InSAR data. After reducing the observations for the effect of vertical deformation, no significant residuals are found, indicating no significant mass accumulation or loss within the volcanic system. In the north-western sector of the study area, at the border of the volcano edifice, however, significant residual positive gravity changes are detected which are associated to ground-water rebound after years of intense exploitation of the aquifers. On the seasonal timescale, we find that stations within the caldera rim are affected by the seasonal hydrological effects, while the gravity stations at the base of the Vesuvius show a less clear correlation. Furthermore, within the caldera rim a multiyear gravity transient is detected with an increase phase lasting about 4 yr followed by a slower decrease phase. Analysis of rain data seem to exclude a hydrological origin, hence, we hypothesize a deeper source related to the geothermal activity, which can be present even if the volcano is in a quiescent state. We infer the depth and volume of the source by inverting the spatial pattern of the gravity field at the peak of the transient. A volume of fluids of 9.5 × 107 m3 with density of 1000 kg m−3 at 2.3 km depth is capable to fit reasonably well the observations. To explain the gravity transient, simple synthetic models are produced, that simulate the ascent of fluids from a deep reservoir up to the depth of 2.3 km and a successive diffusion within the carbonate aquifer hosting the geothermal system. The whole process appears to not significantly affect the seismicity rate and the deformation of the volcano. This study demonstrates the importance of a 4-D gravity monitoring of a volcano to understand its complex gravity signals that cover different spatial and temporal scales. Discriminating the different contributions that mix up in the observed gravity changes, in particular those due to hydrologic/anthropogenic activities form those due to the geothermal dynamics, is fundamental for a complete and reliable evaluation of the volcano state.
    Description: Published
    Description: 1565–1580
    Description: OSV2: Complessità dei processi vulcanici: approcci multidisciplinari e multiparametrici
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 9
    facet.materialart.
    Unknown
    Comparison between alarm-based and probability-based earthquake forecasting methods (2024)
    Oxford University Press
    Details
    Publication Date: 2024-05-09
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2023. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved.
    Description: In a recent work, we applied the every earthquake a precursor according to scale (EEPAS) probabilistic model to the pseudo-prospective forecasting of shallow earthquakes with magni- tude M 5.0 in the Italian region. We compared the forecasting performance of EEPAS with that of the epidemic type aftershock sequences (ETAS) forecasting model, using the most recent consistency tests developed within the collaboratory for the study of earthquake predictabil- ity (CSEP). The application of such models for the forecasting of Italian target earthquakes seems to show peculiar characteristics for each of them. In particular, the ETAS model showed higher performance for short-term forecasting, in contrast, the EEPAS model showed higher forecasting performance for the medium/long-term. In this work, we compare the performance of EEPAS and ETAS models with that obtained by a deterministic model based on the occur- rence of strong foreshocks (FORE model) using an alarm-based approach. We apply the two rate-based models (ETAS and EEPAS) estimating the best probability threshold above which we issue an alarm. The model parameters and probability thresholds for issuing the alarms are calibrated on a learning data set from 1990 to 2011 during which 27 target earthquakes have occurred within the analysis region. The pseudo-prospective forecasting performance is as- sessed on a validation data set from 2012 to 2021, which also comprises 27 target earthquakes. Tests to assess the forecasting capability demonstrate that, even if all models outperform a purely random method, which trivially forecast earthquake proportionally to the space–time occupied by alarms, the EEPAS model exhibits lower forecasting performance than ETAS and FORE models. In addition, the relative performance comparison of the three models demonstrates that the forecasting capability of the FORE model appears slightly better than ETAS, but the difference is not statistically significant as it remains within the uncertainty level. However, truly prospective tests are necessary to validate such results, ideally using new testing procedures allowing the analysis of alarm-based models, not yet available within the CSEP.
    Description: Published
    Description: 1541–1551
    Description: OST4 Descrizione in tempo reale del terremoto, del maremoto, loro predicibilità e impatto
    Description: JCR Journal
    Keywords: Computational seismology ; Earthquake interaction, forecasting and prediction ; Statistical seismology ; Comparison betwee earthquake forecasting methods
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 10
    facet.materialart.
    Unknown
    Low-strength shear zone in the western Makran subduction zone, southeastern Iran: insights from a receiver function analysis (2024)
    Oxford University Press
    Details
    Publication Date: 2024-05-09
    Description: To understand the seismic hazard of a subduction zone, it is necessary to know the geometry, location and mechanical characteristics of the interplate boundary below which an oceanic plate is thrust downward. By considering the azimuthal dependence of converted P-to-S (Ps) amplitudes in receiver functions, we have detected the interplate boundary in the Makran subduction zone, revealing significant seismic anisotropy at the base of the accretionary wedge above the slab before it bends down beneath the Jaz Murian basin. This anisotropic feature aligns with a zone of reduced seismic velocity and a high primary/secondary wave velocity ratio (Vp/Vs), as documented in previous studies. The presence of this low-velocity highly anisotropic layer at the base of the accretionary wedge, likely representing a low-strength shear zone, could possibly explain the unusually wide accretionary wedge in Makran. Additionally, it may impact the location and width of the locked zone along the interplate boundary.
    Description: Iranian National Science Foundation (INSF)
    Description: Published
    Description: 64-74
    Description: OST1 Alla ricerca dei Motori Geodinamici
    Description: JCR Journal
    Keywords: Earthquake hazards, Seismic anisotropy, Crustal structure, Subduction zone processes ; 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 11
    facet.materialart.
    Unknown
    Application of the EEPAS earthquake forecasting model to Italy (2024)
    Oxford University Press
    Details
    Publication Date: 2024-05-09
    Description: This article has been accepted for publication in Geophysical Journal International ©:The Author(s) 2023. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.Uploaded in accordance with the publisher's self-archiving policy. All rights reserved.
    Description: The Every Earthquake a Precursor According to Scale (EEPAS) forecasting model is a space– time point-process model based on the precursory scale increase (ψ ) phenomenon and associated predictive scaling relations. It has been previously applied to New Zealand, Cal- ifornia and Japan earthquakes with target magnitude thresholds varying from about 5–7. In all previous application, computations were done using the computer code implemented in Fortran language by the model authors. In this work, we applied it to Italy using a suite of computing codes completely rewritten in Matlab. We first compared the two software codes to ensure the convergence and adequate coincidence between the estimated model parameters for a simple region capable of being analysed by both software codes. Then, using the rewritten codes, we optimized the parameters for a different and more complex polygon of analysis using the Homogenized Instrumental Seismic Catalogue data from 1990 to 2011. We then perform a pseudo-prospective forecasting experiment of Italian earthquakes from 2012 to 2021 with Mw ≥ 5.0 and compare the forecasting skill of EEPAS with those obtained by other time in- dependent (Spatially Uniform Poisson, Spatially Variable Poisson and PPE: Proximity to Past Earthquakes) and time dependent [Epidemic Type Aftershock Sequence (ETAS)] forecasting models using the information gain per active cell. The preference goes to the ETAS model for short time intervals (3 months) and to the EEPAS model for longer time intervals (6 months to 10 yr).
    Description: Published
    Description: 1681–1700
    Description: OST4 Descrizione in tempo reale del terremoto, del maremoto, loro predicibilità e impatto
    Description: JCR Journal
    Keywords: Computational seismology ; Earthquake interaction ; forecasting and prediction ; Statistical seismology ; Earthquake forecasting
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 12
    facet.materialart.
    Unknown
    The Influence of Undercooling and Sector Zoning on Clinopyroxene–Melt Equilibrium and Thermobarometry (2024)
    Oxford University Press
    Details
    Publication Date: 2024-06-17
    Description: Thermobarometry provides a critical means of assessing locations of magma storage and dynamics in the lead-up to volcanic eruptions and crustal growth. A common approach is to utilise minerals that have compositions sensitive to changes in pressure and/or temperature, such as clinopyroxene, which is ubiquitous in mafic to intermediate magmas. However, clinopyroxene thermobarometry may carry significant uncertainty and require an appropriate equilibrium melt composition. In addition, the degree of magma undercooling (ΔT) affects clinopyroxene composition and zoning, with common sector zoning potentially obfuscating thermobarometry results. Here, we use a set of crystallisation experiments on a primitive trachybasalt from Mt. Etna (Italy) at ΔT = 25–233 °C, P = 400–800 MPa, H2O = 0–4 wt % and fO2 = NNO + 2, with clinopyroxene crystals defined by Al-rich zones (prisms and skeletons) and Al-poor zones (hourglass and overgrowths) to assess common equilibrium models and thermobarometric approaches. Under the studied conditions, our data suggest that the commonly applied Fe–Mg exchange (cpx-meltKdFe–Mg) is insensitive to increasing ΔT and may not be a reliable indicator of equilibrium. The combined use of DiHd (CaMgSi2O6 + CaFeSi2O6) and EnFs (Mg2Si2O6 + Fe2Si2O6) models indicate the attainment of equilibrium in both Al-rich and Al-poor zones for almost all investigated ΔT. In contrast, CaTs (CaAl2SiO6) and CaTi (CaTiAl2O6) models reveal substantial deviations from equilibrium with increasing ΔT, particularly in Al-rich zones. We postulate that this reflects slower diffusion of Al and Ti in the melt compared with Ca and Mg and recommend the concurrent application of these four models to evaluate equilibrium between clinopyroxene and melt, particularly for sector-zoned crystals. Thermobarometers calibrated with only isothermal–isobaric experiments closely reproduce experimental P–T at low ΔT, equivalent to natural phenocrysts cores and sector-zoned mantles. Models that also consider decompression experiments are most accurate at high ΔT and are therefore suitable for outermost phenocryst rims and groundmass microlites. Recent machine learning approaches reproduce P–T conditions across all ΔT conditions. Applying our experimental constraints to sector-zoned microphenocrysts and groundmass microlites erupted during the 1974 eccentric eruption at Mt. Etna, we highlight that both hourglass and prism sectors are suitable for thermobarometry, given that equilibrium is sufficiently tested for. The combination of DiHd, EnFs, CaTs and CaTi models identifies compositions closest to equilibrium with the bulk melt composition, and results in smaller differences in P–T calculated for hourglass and prism sectors compared with applying only DiHd and EnFs equilibrium models. This provides a framework to assess crystallisation conditions recorded by sector-zoned clinopyroxene crystals in mafic alkaline settings.
    Description: Published
    Description: egad074
    Description: OSV2: Complessità dei processi vulcanici: approcci multidisciplinari e multiparametrici
    Description: JCR Journal
    Keywords: Experimental Petrology ; Petrology ; Clinopyroxene ; Thermobarometry ; Experimental Petrology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 13
    facet.materialart.
    Unknown
    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)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 14
    facet.materialart.
    Unknown
    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)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 15
    facet.materialart.
    Unknown
    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
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 16
    facet.materialart.
    Unknown
    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
    Type: Article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 17
    facet.materialart.
    Unknown
    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)
    Type: article
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 18
    facet.materialart.
    Unknown
    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
    Format: application/pdf
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 19
    facet.materialart.
    Unknown
    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.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 20
    facet.materialart.
    Unknown
    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
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 21
    facet.materialart.
    Unknown
    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
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 22
    facet.materialart.
    Unknown
    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.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 23
    facet.materialart.
    Unknown
    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.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 24
    facet.materialart.
    Unknown
    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
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 25
    facet.materialart.
    Unknown
    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.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 26
    facet.materialart.
    Unknown
    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
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 27
    facet.materialart.
    Unknown
    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
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 28
    facet.materialart.
    Unknown
    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
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 29
    facet.materialart.
    Unknown
    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
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 30
    facet.materialart.
    Unknown
    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
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 31
    facet.materialart.
    Unknown
    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
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 32
    facet.materialart.
    Unknown
    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
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 33
    facet.materialart.
    Unknown
    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.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 34
    facet.materialart.
    Unknown
    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
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 35
    facet.materialart.
    Unknown
    Moso bamboo and Japanese cedar seedlings differently affected soil N2O emissions (2021)
    Oxford University Press
    Details
    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
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 36
    facet.materialart.
    Unknown
    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
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 37
    facet.materialart.
    Unknown
    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
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 38
    facet.materialart.
    Unknown
    Differential semblance optimisation based on the adaptive quadratic Wasserstein distance (2021)
    Oxford University Press
    Details
    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
    Published by Oxford University Press on behalf of Sinopec Geophysical Research Institute.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 39
    facet.materialart.
    Unknown
    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
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 40
    facet.materialart.
    Unknown
    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
    Published by Oxford University Press on behalf of International Council for the Exploration of the Sea.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 41
    facet.materialart.
    Unknown
    Comparative analysis of molecular fingerprints in prediction of drug combination effects (2021)
    Oxford University Press
    Details
    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
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 42
    facet.materialart.
    Unknown
    Detecting quantitative trait loci and exploring chromosomal pairing in autopolyploids using polyqtlR (2021)
    Oxford University Press
    Details
    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.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 43
    facet.materialart.
    Unknown
    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.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 44
    facet.materialart.
    Unknown
    Comparison of approaches to transcriptomic analysis in multi-sampled tumors (2021)
    Oxford University Press
    Details
    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.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 45
    facet.materialart.
    Unknown
    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
    Details
    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
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 46
    facet.materialart.
    Unknown
    Academic human capital in universities: definition and proposal of a measurement scale (2021)
    Oxford University Press
    Details
    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
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 47
    facet.materialart.
    Unknown
    DNAgenie: accurate prediction of DNA-type-specific binding residues in protein sequences (2021)
    Oxford University Press
    Details
    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/.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 48
    facet.materialart.
    Unknown
    DLpTCR: an ensemble deep learning framework for predicting immunogenic peptide recognized by T cell receptor (2021)
    Oxford University Press
    Details
    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.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 49
    facet.materialart.
    Unknown
    Promoting the ICT Industry for the future with fears from the past (2021)
    Oxford University Press
    Details
    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
    Electronic ISSN: 1471-5430
    Topics: Nature of Science, Research, Systems of Higher Education, Museum Science
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 50
    facet.materialart.
    Unknown
    XMP gas-rich dwarfs in nearby voids: results of BTA spectroscopy (2021)
    Oxford University Press
    Details
    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
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 51
    facet.materialart.
    Unknown
    MiR-200c-based metabolic modulation in glioblastoma cells as a strategy to overcome tumor chemoresistance (2021)
    Oxford University Press
    Details
    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
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 52
    facet.materialart.
    Unknown
    Constraining the sources of nitrogen fueling export production in the Gulf of Mexico using nitrogen isotope budgets (2021)
    Oxford University Press
    Details
    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
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 53
    facet.materialart.
    Unknown
    Optimising sampling frequency for monitoring heterotrophic protists in a marine ecosystem (2021)
    Oxford University Press
    Details
    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
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press on behalf of International Council for the Exploration of the Sea.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 54
    facet.materialart.
    Unknown
    Cordierite-Bearing Orbicules Record Bulk Assimilation and the Pulsating Nature of Magma Ascent: The Lafaye Orbicular Granite (France) (2021)
    Oxford University Press
    Details
    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
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 55
    facet.materialart.
    Unknown
    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
    Details
    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.
    Print ISSN: 0022-3530
    Electronic ISSN: 1460-2415
    Topics: Geosciences
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 56
    facet.materialart.
    Unknown
    Comparative evaluation of shape retrieval methods on macromolecular surfaces: an application of computer vision methods in structural bioinformatics (2021)
    Oxford University Press
    Details
    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.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 57
    facet.materialart.
    Unknown
    Beyond métiers: social factors influence fisher behaviour (2021)
    Oxford University Press
    Details
    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
    Published by Oxford University Press on behalf of International Council for the Exploration of the Sea.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 58
    facet.materialart.
    Unknown
    Using environmental variation to optimize aerial surveys of harbour seals (2021)
    Oxford University Press
    Details
    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
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press on behalf of International Council for the Exploration of the Sea.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 59
    facet.materialart.
    Unknown
    Mapping 3D structure of a Sargassum forest with high-resolution sounding data obtained by multibeam echosounder (2021)
    Oxford University Press
    Details
    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
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press on behalf of International Council for the Exploration of the Sea.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 60
    facet.materialart.
    Unknown
    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
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press on behalf of International Council for the Exploration of the Sea.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 61
    facet.materialart.
    Unknown
    Sverdrup meets Lambert: analytical solution for Sverdrup’s critical depth (2021)
    Oxford University Press
    Details
    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
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press on behalf of International Council for the Exploration of the Sea.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 62
    facet.materialart.
    Unknown
    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
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press on behalf of International Council for the Exploration of the Sea.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 63
    facet.materialart.
    Unknown
    Wrasse fishery on the Swedish West Coast: towards ecosystem-based management (2021)
    Oxford University Press
    Details
    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.
    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.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 64
    facet.materialart.
    Unknown
    The Breeding Information Management System (BIMS): an online resource for crop breeding (2021)
    Oxford University Press
    Details
    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
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 65
    facet.materialart.
    Unknown
    The autism risk gene CNTN4 modulates dendritic spine formation (2021)
    Oxford University Press
    Details
    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
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 66
    facet.materialart.
    Unknown
    Inference of the optical depth to reionization from low multipole temperature and polarization Planck data (2021)
    Oxford University Press
    Details
    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
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 67
    facet.materialart.
    Unknown
    Constraining properties of GRB central engines with X-ray flares (2021)
    Oxford University Press
    Details
    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
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 68
    facet.materialart.
    Unknown
    Generating neutron-star magnetic fields: three dynamo phases (2021)
    Oxford University Press
    Details
    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
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 69
    facet.materialart.
    Unknown
    The magnetic system SMSS J1606−1000 as a period bouncer (2021)
    Oxford University Press
    Details
    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
    Electronic ISSN: 1745-3933
    Topics: Physics
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 70
    facet.materialart.
    Unknown
    AI-assisted superresolution cosmological simulations – II. Halo substructures, velocities, and higher order statistics (2021)
    Oxford University Press
    Details
    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
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 71
    facet.materialart.
    Unknown
    Single-cell Hi-C data analysis: safety in numbers (2021)
    Oxford University Press
    Details
    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
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 72
    facet.materialart.
    Unknown
    APPTEST is a novel protocol for the automatic prediction of peptide tertiary structures (2021)
    Oxford University Press
    Details
    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
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 73
    facet.materialart.
    Unknown
    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
    Details
    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
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 74
    facet.materialart.
    Unknown
    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
    Details
    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 
    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.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 75
    facet.materialart.
    Unknown
    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
    Details
    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.
    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.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 76
    facet.materialart.
    Unknown
    Incorporating spatiotemporal variability in multispecies survey design optimization addresses trade-offs in uncertainty (2021)
    Oxford University Press
    Details
    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.
    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.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 77
    facet.materialart.
    Unknown
    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.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 78
    facet.materialart.
    Unknown
    Multi-scale assessment of distribution and density of procellariiform seabirds within the Northern Antarctic Peninsula marine ecosystem (2021)
    Oxford University Press
    Details
    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.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 79
    facet.materialart.
    Unknown
    Using a genetic algorithm to optimize a data-limited catch rule (2021)
    Oxford University Press
    Details
    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.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 80
    facet.materialart.
    Unknown
    Marine spatial planning and the risk of ocean grabbing in the tropical Atlantic (2021)
    Oxford University Press
    Details
    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.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 81
    facet.materialart.
    Unknown
    Biogeographical patterns of meso- and bathypelagic fish along a Northeastern Atlantic transect (2021)
    Oxford University Press
    Details
    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.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 82
    facet.materialart.
    Unknown
    Six steps to produce stock assessments for the Marine Strategy Framework Directive compliant with Descriptor 3 (2021)
    Oxford University Press
    Details
    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.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 83
    facet.materialart.
    Unknown
    Molecular design in drug discovery: a comprehensive review of deep generative models (2021)
    Oxford University Press
    Details
    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
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 84
    facet.materialart.
    Unknown
    The Genome of the Haptophyte Diacronema lutheri (Pavlova lutheri, Pavlovales): A Model for Lipid Biosynthesis in Eukaryotic Algae (2021)
    Oxford University Press
    Details
    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
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 85
    facet.materialart.
    Unknown
    Detecting methylation quantitative trait loci using a methylation random field method (2021)
    Oxford University Press
    Details
    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
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 86
    facet.materialart.
    Unknown
    Improved nutritional status may promote an “asset protection” reproductive strategy in male rock lizards (2021)
    Oxford University Press
    Details
    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
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 87
    facet.materialart.
    Unknown
    Knowledge transfer profiles of public research organisations: the role of fields of knowledge specialisation (2021)
    Oxford University Press
    Details
    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
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 88
    facet.materialart.
    Unknown
    HCN/HNC chemistry in shocks: a study of L1157-B1 with ASAI (2021)
    Oxford University Press
    Details
    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.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 89
    facet.materialart.
    Unknown
    Genome-wide association study in the Taiwan Biobank identifies four novel genes for human height: NABP2, RASA2, RNF41 and SLC39A5 (2021)
    Oxford University Press
    Details
    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
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 90
    facet.materialart.
    Unknown
    MMpred: a distance-assisted multimodal conformation sampling for de novo protein structure prediction (2021)
    Oxford University Press
    Details
    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
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 91
    facet.materialart.
    Unknown
    CFAP65 is required in the acrosome biogenesis and mitochondrial sheath assembly during spermiogenesis (2021)
    Oxford University Press
    Details
    Publication Date: 2021-07-07
    Description: Asthenoteratospermia is a common cause of male infertility. Recent studies have revealed that CFAP65 mutations lead to severe asthenoteratospermia due to acrosome hypoplasia and flagellum malformations. However, the molecular mechanism underlying CFAP65-associated sperm malformation is largely unclear. Here, we initially examined the role of CFAP65 during spermiogenesis using Cfap65 knockout (Cfap65−/−) mice. The results showed that Cfap65−/− male mice exhibited severe asthenoteratospermia characterized by morphologically defective sperm heads and flagella. In Cfap65−/− mouse testes, hyper-constricted sperm heads were apparent in step 9 spermatids accompanied by abnormal manchette development, and acrosome biogenesis was abnormal in the maturation phase. Moreover, subsequent flagellar elongation was also severely affected and characterized by disrupted assembly of the mitochondrial sheath (MS) in Cfap65−/− male mice. Furthermore, the proteomic analysis revealed that the proteostatic system during acrosome formation, manchette organization and MS assembly was disrupted when CFAP65 was lost. Importantly, endogenous immunoprecipitation and immunostaining experiments revealed that CFAP65 may form a cytoplasmic protein network comprising MNS1, RSPH1, TPPP2, ZPBP1 and SPACA1. Overall, these findings provide insights into the complex molecular mechanisms of spermiogenesis by uncovering the essential roles of CFAP65 during sperm head shaping, acrosome biogenesis and MS assembly.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 92
    facet.materialart.
    Unknown
    Corrigendum to: When phenotypes fail to illuminate underlying genetic processes in fish and fisheries science (2021)
    Oxford University Press
    Details
    Publication Date: 2021-06-14
    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.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 93
    facet.materialart.
    Unknown
    Salmon lice-induced mortality of Atlantic salmon during post-smolt migration in Norway (2021)
    Oxford University Press
    Details
    Publication Date: 2021-06-18
    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.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 94
    facet.materialart.
    Unknown
    Mitochondrial DNA disorders: from pathogenic variants to preventing transmission (2021)
    Oxford University Press
    Details
    Publication Date: 2021-06-24
    Description: Mitochondrial DNA (mtDNA) disorders are recognized as one of the most common causes of inherited metabolic disorders. The mitochondrial genome occurs in multiple copies resulting in both homoplasmic and heteroplasmic pathogenic mtDNA variants. A biochemical defect arises when the pathogenic variant level reaches a threshold, which differs between variants. Moreover, variants can segregate, clonally expand, or be lost from cellular populations resulting in a dynamic and tissue-specific mosaic pattern of oxidative deficiency. MtDNA is maternally inherited but transmission patterns of heteroplasmic pathogenic variants are complex. During oogenesis, a mitochondrial bottleneck results in offspring with widely differing variant levels to their mother, whilst highly deleterious variants, such as deletions, are not transmitted. Complemented by a complex interplay between mitochondrial and nuclear genomes, these peculiar genetics produce marked phenotypic variation, posing challenges to the diagnosis and clinical management of patients. Novel therapeutic compounds and several genetic therapies are currently under investigation, but proven disease-modifying therapies remain elusive. Women who carry pathogenic mtDNA variants require bespoke genetic counselling to determine their reproductive options. Recent advances in in vitro fertilization techniques, have greatly improved reproductive choices, but are not without their challenges. Since the first pathogenic mtDNA variants were identified over 30 years ago, there has been remarkable progress in our understanding of these diseases. However, many questions remain unanswered and future studies are required to investigate the mechanisms of disease progression and to identify new disease-specific therapeutic targets.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 95
    facet.materialart.
    Unknown
    Outflows in the radio-intermediate quasar III Zw 2: a polarization study with the EVLA and uGMRT (2021)
    Oxford University Press
    Details
    Publication Date: 2021-08-20
    Description: We present results from a polarization study of the radio-intermediate quasar, III Zw 2, at a redshift of 0.089, with the upgraded Giant Metrewave Radio Telescope (uGMRT) at 685 MHz and the Karl G. Jansky Very Large Array (VLA) at 5 and 34 GHz. We detect a kpc-scale outflow, exhibiting transverse magnetic (B-) fields. The curved jet terminates in a bow-shock-like radio structure with inferred B-fields aligned with the lobe edges. We suggest that the radio outflow in III Zw 2 is a combination of a collimated jet along with a wind-like component. This ‘wind’ component could be a magnetized accretion disc wind or the outer layers of a broadened jet or a combination of both. The current data cannot differentiate between these possibilities. We also detect kpc-scale lobe emission that is misaligned with the primary lobes in the uGMRT images. The spectral indices and the electron lifetimes in the misaligned lobe are similar to the primary lobe, suggesting that the misaligned lobe is not a relic. We propose that changing spectral states of the accretion disc, and the subsequent intermittent behaviour of the outflow, along with the close interplay between the jet and ‘wind’ could explain the radio-intermediate nature of III Zw 2. Our study shows that radio-intermediate quasars are promising sources for understanding the role of jets and winds in galaxy evolution and demonstrates the power of radio polarization studies towards achieving this.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 96
    facet.materialart.
    Unknown
    Learning by doing: collaborative conceptual modelling as a path forward in ecosystem-based management (2021)
    Oxford University Press
    Details
    Publication Date: 2021-04-01
    Description: Managers, stakeholders, and scientists recognize the need for collaborative, transparent, integrated approaches to complex resource management issues, and frameworks to address these complex issues are developing. Through the course of 2019, the Mid-Atlantic Fishery Management Council developed a conceptual model of ecosystem linkages and risks for summer flounder, a species of recreational and commercial fisheries importance. The proximal aim of the model was to develop a list of integrated management questions that could be refined and addressed through a future quantitative management strategy evaluation. As such, this conceptual model served as a scoping tool. However, the true value of the conceptual model lays elsewhere: familiarizing resource managers historically focused on single-species management with the potential utility of an ecosystem approach to management. This paper details the goals and development of the conceptual model and situates this process in the broader context of best practices for collaborative open science and scientific reproducibility. Further, it highlights a successful path by which the shift towards ecosystem-based management can be actuated.
    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.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 97
    facet.materialart.
    Unknown
    New insight into trophic niche partitioning and diet of mackerel (Scomber scombrus) and herring (Clupea harengus) in Icelandic waters (2021)
    Oxford University Press
    Details
    Publication Date: 2021-03-24
    Description: Understanding the competitive interactions of ecological similar species is essential to determine their role and niche in the ecosystem. Using both conventional dietary methods and stable isotope analysis, we examined the feeding ecology, trophic position and possible niche partitioning of Northeast Atlantic mackerel (Scomber scombrus), Icelandic summer spawning (ISS) herring (Clupea harengus), and Norwegian spring spawning (NSS) herring from Icelandic waters during the spring and summer 2012 and 2014. The stomach analysis showed differences in prey preferences among the species during summer, where mackerel diets were almost exclusively calanoid copepods, while herring ate larger zooplankton, i.e. euphausiids and amphipods. Analysis of isotopic diet contribution of mackerel and herring using Bayesian mixing models, representing mainly the spring consumption, revealed that euphausiids were the main dietary contributor of both mackerel and herring. Fish prey were also an important dietary source for ISS herring, and amphipods were important to the diet of NSS herring. In addition, mackerel encompassed a broad isotopic niche, whereas the two herring stocks had narrower and separated niches from each other. The results from this analysis reveal new and holistic information into the diet of these species, which have various ecological implications.
    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.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 98
    facet.materialart.
    Unknown
    Theoretical size at the onset of maturity and its density-dependent variability as an option in crustacean fisheries management (2021)
    Oxford University Press
    Details
    Publication Date: 2021-03-12
    Description: Theoretical size at the onset of maturity (TSOM) for female Norway lobster was estimated by a new methodology based on the probability distributions of mature individuals built on physiological maturity measures. Onset of maturity using TSOM varied from 18.4- to 33.7-mm carapace length for the Irish functional management units (FUs). These estimates showed a significant negative linear relationship (R2 = 0.60) with population density and a significant positive linear relationship with average size in females (R2 = 0.84). The size class at which 50% of the females are sexually mature (L50) was linked to the new TSOM metric by a significant positive linear relationship (R2 = 0.40). This set of linear relationships ultimately allowed TSOM and L50 to be estimated without a requirement for maturity stages to be distinguished. As well as contributing to the stock assessment and management of Nephrops (e.g. in data-limited FUs) and its potential for the calibration of more routinely used estimates, TSOM might be applied in new species and meta-analyses where size of maturity data are scarce. This new metric also better-defines the maturity process since, taken together, TSOM, L50, and smallest berried female represent sequential maturity events: (i) onset of maturity, (ii) 50% mature (from gonad staging), and (iii) berried females.
    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.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 99
    facet.materialart.
    Unknown
    Interannual variability of gelatinous mesozooplankton in a temperate shelf sea: greater abundance coincides with cooler sea surface temperatures (2021)
    Oxford University Press
    Details
    Publication Date: 2021-03-08
    Description: Although gelatinous zooplankton are an important component of marine ecosystems, gelatinous mesozooplankton that are
    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.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 100
    facet.materialart.
    Unknown
    Dietary Diversification and Specialization in Neotropical Bats Facilitated by Early Molecular Evolution (2021)
    Oxford University Press
    Details
    Publication Date: 2021-03-04
    Description: Dietary adaptation is a major feature of phenotypic and ecological diversification, yet the genetic basis of dietary shifts is poorly understood. Among mammals, Neotropical leaf-nosed bats (family Phyllostomidae) show unmatched diversity in diet; from a putative insectivorous ancestor, phyllostomids have radiated to specialize on diverse food sources including blood, nectar, and fruit. To assess whether dietary diversification in this group was accompanied by molecular adaptations for changing metabolic demands, we sequenced 89 transcriptomes across 58 species and combined these with published data to compare ∼13,000 protein coding genes across 66 species. We tested for positive selection on focal lineages, including those inferred to have undergone dietary shifts. Unexpectedly, we found a broad signature of positive selection in the ancestral phyllostomid branch, spanning genes implicated in the metabolism of all major macronutrients, yet few positively selected genes at the inferred switch to plantivory. Branches corresponding to blood- and nectar-based diets showed selection in loci underpinning nitrogenous waste excretion and glycolysis, respectively. Intriguingly, patterns of selection in metabolism genes were mirrored by those in loci implicated in craniofacial remodeling, a trait previously linked to phyllostomid dietary specialization. Finally, we show that the null model of the widely-used branch-site test is likely to be misspecified, with the implication that the test is too conservative and probably under-reports true cases of positive selection. Our findings point to a complex picture of adaptive radiation, in which the evolution of new dietary specializations has been facilitated by early adaptations combined with the generation of new genetic variation.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...