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  • Oxford University Press  (22,823)
  • BioMed Central  (8,391)
  • American Physical Society (APS)
  • De Gruyter
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  • 1955-1959  (5,157)
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  • 1
    Publication Date: 2021-01-25
    Description: At Ustica island (Palermo, Italy), in the area of Casa dei Francesi, 119 fragments of obsidian artifacts were collected on the surface of an agricultural field at an altitude of 50 m asl. In the same area, until now, scientific literature reports only the presence of late Roman pottery (4th–6th centuries AD), and no evidence has appeared that it could be the site of a prehistoric settlement. The most important prehistoric settlement, the Faraglioni Village (Middle Bronze Age) is located 700 m further north, overlooking the sea. Obsidian provenance analyses, performed on the 119 samples with absolutely non-destructive techniques WD-XRF and SEM-EDS, indicate two sources areas: Lipari (93 samples, 78%) and Pantelleria (26 samples, 22%). Concerning the obsidians from the island of Pantelleria, it was possible to also establish the sub-source of Salto la Vecchia. The typological and functional analyses of the 119 obsidian fragments point out that 115 are debitages, some of which show evidence of percussion bulbs, and only 4 are tools with micro-retouching. This work focuses on the geochemical and typological characterization of the obsidian assemblage collected, the characteristics of which suggest the existence of a prehistoric settlement in the area of the Casa dei Francesi or nearby
    Description: Published
    Description: 236-247
    Description: 6A. Geochimica per l'ambiente e geologia medica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 2
    Publication Date: 2021-01-25
    Description: The subject of this study consists of 17 ancient glass fragments from the island of Ustica (Palermo, Italy) obtained from local museums. All the 17 glass fragments are stratigraphically decontextualized, as they were collected by archaeological surface surveys. Each fragment was analyzed by Electron Micro Probe Analyzer coupled with an Energy Dispersive X-Ray System (EMPA-EDS) and by Laser Ablation-Inductively Coupled Plasma-Mass Spectrometry (LA-ICP-MS) to obtain the composition of major, minor and trace elements. Surface analyses revealed the presence of corrosion layers in most of the glass fragments which was evident also in the chemical data. Nevertheless, reconstruction of the glassmaking processes and the approximate period of production was possible for almost all the glass fragments. Less than half of the examined fragments are attributable to recognizable typologies as unguentaria, beakers, bottles, and vases; all the other small fragments are typologically undetermined. Out of 17 fragments only one fragment is of HLLA composition possibly being produced in 17th–18th century AD, while all the others can be attributed to soda glass with different periods of production: natron glass from Roman and Early Medieval period, plantash glass from High or Late Medieval period with the exception of possible Byzantine glass from 6th century AD, and synthetic soda glasses typical of modern era. These data confirm the discontinuous habitation of the island from the Roman period as well as the import of glass objects to the island.
    Description: Published
    Description: 124–150
    Description: 6A. Geochimica per l'ambiente e geologia medica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
    Publication Date: 2021-03-15
    Description: In a recent work we computed the relative frequencies with which strong shocks (4.0≤Mw〈5.0), widely felt by the population were followed in the same area by potentially destructive main shocks (Mw≥5.0) in Italy. Assuming the stationarity of the seismic release properties, such frequencies can be tentatively used to estimate the probabilities of potentially destructive shocks after the occurrence of future strong shocks. This allows us to set up an alarm-based forecasting hypothesis related to strong foreshocks occurrence. Such hypothesis is tested retrospectively on the data of a homogenized seismic catalogue of the Italian area against a purely random hypothesis that simply forecasts the target main shocks proportionally to the space-time fraction occupied by the alarms. We compute the latter fraction in two ways a) as the ratio between the average time covered by the alarms in each area and the total duration of the forecasting experiment (60 years) and b) as the same ratio but weighted by the past frequency of occurrence of earthquakes in each area. In both cases the overall retrospective performance of our forecasting algorithm is definitely better than the random case. Considering an alarm duration of three months, the algorithm retrospectively forecasts more than 70% of all shocks with Mw5.5 occurred in Italy from 1960 to 2019 with a total space-time fraction covered by the alarms of the order of 2%. Considering the same space-time coverage, the algorithm is also able to retrospectively forecasts more than 40% of the first main shocks with Mw5.5 of the seismic sequences occurred in the same time interval. Given the good reliability of our results, the forecasting algorithm is set and ready to be tested also prospectively, in parallel to other ongoing procedures operating on the Italian territory.
    Description: This paper benefitted from funding provided by the European Union within the ambit of the H2020 project RISE (No. 821115), which in particular fully financed the PhD grant of one of the authors (E.B.).
    Description: Published
    Description: 1192–1206
    Description: 6T. Studi di pericolosità sismica e da maremoto
    Description: JCR Journal
    Keywords: Earthquake interaction ; Statistical seismology ; forecasting, ; prediction ; 04.06. Seismology
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  • 4
    Publication Date: 2021-01-18
    Description: The horizontal to vertical spectral ratio (HVSR) of seismic noise is often used to investigate site effects, and it is usually assumed to be a stable feature of the site considered. Here we show that such an assumption is not always justified, and may lead to incorrect conclusions. The HVSR analysis was performed on ambient seismic noise recordings lasting from weeks to months at many sites in Calabria, Italy. Results show a variety of site effects, from the resonance of a shallow sedimentary layer to the polarized amplification of horizontal ground motion associated with topographic effects. We describe the results of seven sites whose HVSR is characterized by dual content: one that is persistent, and another appearing only occasionally. Two sites very near the coast of the Tyrrhenian sea and five sites in the Calabrian Arc mountains show the most remarkable results. The shape of the HVSR changes significantly at these sites when the amplitude of background noise increases in a broad frequency band during periods of bad weather. The occasional contribution to the HVSR consists of one or more peaks, depending on the site, that appear only when the amplitude of ambient noise is higher than usual. The seven sites where we observe the HVSR variability are all located in complex geological environments, on mountains, ridges or foothills. A variation of the HVSR correlated with the day–night cycle is also observed at some of these sites.
    Description: Published
    Description: 2162–2171
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 5
    Publication Date: 2021-01-21
    Description: This paper provides new petrochemical and paleomagnetic data from obsidian sub-sources on the island of Pantelleria, exploited since the Neolithic. Data has been obtained from 14 obsidian samples from 4 locations: Fossa della Pernice (2 sites), Salto la Vecchia and Balata dei Turchi. Here, we aim to better characterize these obsidians using a cross-disciplinary and multi-analytical approach, to further understand their archaeological significance. Major element analyses (EMP) have enabled two compositional super-groups to be distinguished: (i) Fossa della Pernice, less peralkaline and (ii) Balata dei Turchi–Salto la Vecchia, distinctly more peralkaline and having almost identical chemical patterns. Trace element analyses (LA-ICP-MS) corroborate major element groupings, with the Balata dei Turchi–Salto la Vecchia super-group being further characterized by a pronounced negative europium anomaly. Glass H2O contents (FT-IR) reveal an overlap among all the sub-sources (H2O = 0.1–0.3 wt. %). Magnetic methods have refined the petrochemical groupings, permitting further distinction between Balata dei Turchi–Salto La Vecchia and the Fossa della Pernice super-groups. The occurrence of sub-microscopic (〈 1 μm) ferromagnetic minerals results in different magnetic susceptibility and Natural Remanent Magnetization values and allows the best distinction among the products from the chosen sites. When compared with obsidian tools excavated from Bronze-age settlements on the island of Ustica (230 km NE of Pantelleria), 12% are distinctly peralkaline, indicating their provenance to be from the Balata dei Turchi sub-source.
    Description: Published
    Description: 434-453
    Description: 1A. Geomagnetismo e Paleomagnetismo
    Description: JCR Journal
    Keywords: Obsidian, Pantelleria, Ustica, Lipari, Bronze age ; 04.05. Geomagnetism
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
    Publication Date: 2021-02-10
    Description: The 2007 caldera-forming eruption of Piton de la Fournaise (PdF) erupted the largest volume of magma (210 Mm3)recorded at this volcano in at least three centuries. Major and trace element and Sr^Nd isotope data for bulk-rocks, groundmasses and olivine phenocrysts have been combined with melt inclusion data (major, trace and volatile elements) to track magma evolution over the whole eruptive sequence. We show that each eruptive phase had a distinctive geochemical and petrological signature and that caldera collapse on 5 April was preceded by a marked shift in bulk magma composition and crystal content and size. Aphyric basalt erupted at the beginning of the sequence (February 2007) had relatively high Sr isotope ratio (87Sr/86Sr ¼ 0·70420^0·704180) and low Nd isotopic ratio(143Nd/144Nd ¼ 0·51285^0·51286). Olivine-basalts extruded on2^5 April just before caldera collapse are less enriched in radiogenic Sr (87Sr/86Sr ¼ 0·70412^0·70416), but characterized by the same Nd isotopic composition. This magma is interpreted as a new deep input, which pressurized the shallow PdF plumbing system and triggered the 2007 activity. Post-collapse oceanite lavas represent the main volume of magma extruded in 2007. Their bulk-rocks and groundmasses have 87Sr/86Sr (0·70418) intermediate between those of February and 5 April, and similar to those of the March 2007 and 2001^2006 lavas.We show that the Steady State Basalts (SSB) commonly erupted at PdF are hybrid melts, which result from multistep mixing between ‘alkaline’and ‘transitional’end-members. Our results lead us to propose a new model of the PdF plumbing system to reconcile the petrological, geochemical and geophysical observations: (1) the shallow portion (above sea level) of the PdF plumbing system hosts several small sills, in which magma experiences variable degrees of degassing, cooling and crystallization; (2) oceanite lavas result from the withdrawal of shallow harrisitic mushes stored at low pressures (548 MPa; 51800^2400 m depth) below both the volcano summit and its eastern flank; (3) water degassing plays a major role in fast magma crystallization at shallow depths. Multistep ascent and periodic extrusion of the shallow magmas is promoted by injections of deeper and hotter basaltic magma, containing up to 1·3 wt % H2O and 1630 ppm S. In 2007, the new deep input was the ultimate source of the large excess in sulfur degassing detected by satellites. Lateral draining and intrusion of magma below the eastern flank of the volcano are the cause of major volcano deformation, flank sliding and summit caldera collapse.
    Description: Published
    Description: 1287-1315
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: 3V. Proprietà chimico-fisiche dei magmi e dei prodotti vulcanici
    Description: 4V. Processi pre-eruttivi
    Description: 6A. Geochimica per l'ambiente e geologia medica
    Description: JCR Journal
    Keywords: Piton de la Fournaise ; plumbing system ; magma reservoir ; caldera collapse ; melt inclusions ; volatile budget ; isotope geochemistry ; basalt
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  • 7
    Publication Date: 2021-02-23
    Description: The preparation, initiation, and occurrence dynamics of earthquakes in Italy are governed by several frequently unknown physical mechanisms and parameters. Understanding these mechanisms is crucial for developing new techniques and approaches for earthquake monitoring and hazard assessments. Here, we develop a first-order numerical model simulating quasi-static crustal interseismic loading, coseismic brittle episodic dislocations, and postseismic relaxation for extensional and compressional earthquakes in Italy based on a common framework of lithostatic and tectonic forces. Our model includes an upper crust, where the fault is locked, and a deep crust, where the fault experiences steady shear.
    Description: Published
    Description: 627–645
    Description: 2T. Deformazione crostale attiva
    Description: JCR Journal
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  • 8
    Publication Date: 2021-03-24
    Description: The 2016–17 central Italy earthquake sequence began with the first mainshock near the town of Amatrice on August 24 (MW 6.0), and was followed by two subsequent large events near Visso on October 26 (MW 5.9) and Norcia on October 30 (MW 6.5), plus a cluster of 4 events with MW 〉 5.0 within few hours on January 18, 2017. The affected area had been monitored before the sequence started by the permanent Italian National Seismic Network (RSNC), and was enhanced during the sequence by temporary stations deployed by the National Institute of Geophysics and Volcanology and the British Geological Survey. By the middle of September, there was a dense network of 155 stations, with a mean separation in the epicentral area of 6–10 km, comparable to the most likely earthquake depth range in the region. This network configuration was kept stable for an entire year, producing 2.5 TB of continuous waveform recordings. Here we describe how this data was used to develop a large and comprehensive earthquake catalogue using the Complete Automatic Seismic Processor (CASP) procedure. This procedure detected more than 450,000 events in the year following the first mainshock, and determined their phase arrival times through an advanced picker engine (RSNI-Picker2), producing a set of about 7 million P- and 10 million S-wave arrival times. These were then used to locate the events using a non-linear location (NLL) algorithm, a 1D velocity model calibrated for the area, and station corrections and then to compute their local magnitudes (ML). The procedure was validated by comparison of the derived data for phase picks and earthquake parameters with a handpicked reference catalogue (hereinafter referred to as ‘RefCat’). The automated procedure takes less than 12 hours on an Intel Core-i7 workstation to analyse the primary waveform data and to detect and locate 3000 events on the most seismically active day of the sequence. This proves the concept that the CASP algorithm can provide effectively real-time data for input into daily operational earthquake forecasts, The results show that there have been significant improvements compared to RefCat obtained in the same period using manual phase picks. The number of detected and located events is higher (from 84,401 to 450,000), the magnitude of completeness is lower (from ML 1.4 to 0.6), and also the number of phase picks is greater with an average number of 72 picked arrival for a ML = 1.4 compared with 30 phases for RefCat using manual phase picking. These propagate into formal uncertainties of ± 0.9km in epicentral location and ± 1.5km in depth for the enhanced catalogue for the vast majority of the events. Together, these provide a significant improvement in the resolution of fine structures such as local planar structures and clusters, in particular the identification of shallow events occurring in parts of the crust previously thought to be inactive. The lower completeness magnitude provides a rich data set for development and testing of analysis techniques of seismic sequences evolution, including real-time, operational monitoring of b-value, time-dependent hazard evaluation and aftershock forecasting.
    Description: Published
    Description: 555–571
    Description: 3T. Fisica dei terremoti e Sorgente Sismica
    Description: JCR Journal
    Keywords: 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 9
    Publication Date: 2021-05-12
    Description: erratum paper
    Description: Published
    Description: 1090-1092
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: Theoretical seismology ; Seismic attenuation ; Seismic noise ; Surface waves ; Free oscillations ; Seismic interferometry ; 04.06. Seismology ; 04.01. Earth Interior
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  • 10
    Publication Date: 2021-05-12
    Description: This article has been accepted for publication inGeophysical Journal International ©The Author(s) 2020. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved.
    Description: Determining the crustal structure of ocean island volcanoes is important to understand the formation and tectonic evolution of the oceanic lithosphere and tectonic swells in marine settings, and to assess seismic hazard in the islands. The Azores Archipelago is located near a triple junction system and is possibly under the influence of a mantle plume, being at the locus of a wide range of geodynamic processes. However, its crustal structure is still poorly constrained and debated due to the limited seismic coverage of the region and the peculiar linear geometry of the islands. To address these limitations, in this study we invert teleseismic Rayleigh wave ellipticity measurements for 1-D shear wave speed (VS) crustal models of the Azores Archipelago. Moreover, we test the reliability of these new models by using them in independent moment tensor inversions of local seismic data and demonstrate that our models improve the waveform fit compared to previous models. We find that data from the westernmost seismic stations used in this study require a shallower Moho depth (∼10 km) than data from stations in the eastern part of the archipelago (∼13–16 km). This apparent increase in the Moho depth with increasing distance from the mid-Atlantic ridge (MAR) is expected. However, the rate at which Moho deepens away from the MAR is greater than that predicted from a half-space cooling model, suggesting that local tectonic perturbations have modified crustal structure. The 1-D VS models obtained beneath the westernmost seismic stations also show higher wave speeds than for the easternmost stations, which correlates well with the ages of the islands except Santa Maria Island. We interpret the relatively low VS profile found beneath Santa Maria Island as resulting from underplating, which agrees with previous geological studies of the island. Compared to a recent receiver function study of the region, the shallow structure (top ∼2 km) in our models shows lower shear wave speed, which may have important implications for future hazard studies of the region. More generally, the new seismic crustal models we present in this study will be useful to better understand the tectonics, seismicity, moment tensors and strong ground motions in the region.
    Description: Published
    Description: 1232–1247
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
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  • 11
    Publication Date: 2021-05-12
    Description: The island of Pantelleria, located in the Sicily Channel Rift Zone (Italy), has been the site of violent peralkaline silicic magmatism alternating with minor effusive to low-intensity Strombolian erup- tions of basaltic composition. The basaltic rock suites exposed on the island were sampled to in- vestigate the plumbing system dynamics through the study of chemical stratigraphy and temporal records of olivine crystals. Our petrographic and geochemical observations, together with the com- positional variability of olivine, suggest different evolutionary histories for basaltic magmas erupted over two major periods divided by the 􏰃45 ka Green Tuff (GT) eruption. Core-to-rim com- positional traverses across olivine crystals document different types of zoning. We recognized oliv- ine zones affected by Fo oscillations at very fine scales in the inner cores, rims and/or in intermedi- ate portions of crystals and used them to reconstruct the residence and passage of crystals through different magmatic environments, with P–T–ƒO2 and compositional characteristics con- strained by thermodynamic modeling. The sequence of magmatic environments evidenced by oliv- ine zoning indicate that the pre-GT volcanic period was dominated by injection at shallow crustal levels (􏰃300–200 MPa) of primitive melts, initially moving from a deep storage zone at the crust- mantle boundary. Supply of this magma significantly decreased after the GT eruption, while the dy- namics of magma transfer within the upper portion of the plumbing system were greatly enhanced. The diffusive relaxation of olivine zoning provided the timing of storage and migration of a crystal through different environments. For magmas feeding the ancient (〉45 ka) basaltic activ- ity we retrieved transfer histories that are much longer (up to 􏰃3 years) if compared with those cal- culated for the post-GT basalts (1–9 months). The compositional and temporal dataset presented in this study supports the idea that the GT eruption and the subsequent collapse of the volcanic edi- fice could have caused major changes to the internal structural setting of Pantelleria, creating more favorable conditions for the migration of magmas in the upper portions of the plumbing system.
    Description: Published
    Description: egaa05
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: JCR Journal
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  • 12
    Publication Date: 2021-05-12
    Description: Ischia, a volcanic island located 18 miles SW of Naples (Southern Italy), is a densely populated active caldera that last erupted in AD 1302. Melt inclusions in phenocrysts of the Vateliero and Cava Nocelle shoshonite^latite eruptive products (6th to 4th centuries BC) constrain the structure and nature of the Ischia deep magmatic feeding system.Their geochemical characteristics make Ischia a natural borehole for probing the physico-chemical conditions of magma generation in mantle contaminated by slab-derived fluids or melts, largely dominated by CO2.Volatile concentrations in olivine-hosted melt inclusions require gas^melt equilibria at between 3 and 18 km depth. In agreement with what has already been demonstrated at the other neighboring Neapolitan volcanoes (Procida, Campi Flegrei caldera and Somma^Vesuvius volcanic complex), a major crystallization depth at 8^10 km has been identified.The analyzed melt inclusions provide clear evidence for CO2-dominated gas fluxing and consequent dehydration of magma batches stagnating at crustal discontinuities. Gas fluxing is further supported by selective enrichment in K owing to fluid-transfer during magma differentiation.This takes place under oxidized conditions (Fe3þ /Fe 0·3) that can be fixed by an equimolar proportion of divalent and trivalent iron in the melt if post-entrapment crystallization of the host olivine is discarded.The melt inclusion data, together with data from the literature for other Neapolitan volcanoes, show that magmatism and volcanism in the Neapolitan area, despite differences in composition and eruption dynamics, are closely linked to supercritical CO2-rich fluids. These fluids are produced by devolatilization of subducting terrigenous^pelagic metasediments and infiltrate the overlying mantle wedge, generate magmas and control their ascent up to eruption. Geochemical characteristics of Ischia and the other Neapolitan volcanoes reveal that the extent of fluid or melt contamination of the pre-subduction asthenospheric mantle wedge was similar among these volcanoes. However, differences in the isotopic compositions of the erupted magmas (more enriched in radiogenic Sr at Ischia, Campi Flegrei and Somma^Vesuvius with respect to Procida) and the amount of H2O in the plumbing system of these volcanoes (almost double at Ischia, Campi Flegrei and Somma^Vesuvius than at Procida) reflect the different flow-rates of deep slab-derived fluids or melts through the mantle wedge, which, in turn, control the amount of generated magma.The high bulk permeability of the lithosphere below Ischia, Campi Flegrei and Somma^Vesuvius, determined by the occurrence of intersecting NW^SE and NE^SW regional fault systems, favours fluid ascent and accumulation at crustal levels, with consequent larger magma production and storage than at Procida, located along the NE^SW system.
    Description: Published
    Description: 951-984
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: 3V. Proprietà chimico-fisiche dei magmi e dei prodotti vulcanici
    Description: 4V. Processi pre-eruttivi
    Description: 6A. Geochimica per l'ambiente e geologia medica
    Description: JCR Journal
    Keywords: CO2-fluxing ; melt inclusions ; redox state ; trachybasalts
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  • 13
    Publication Date: 2021-06-21
    Description: Sulphur behaviour and variations in redox conditions during magma differentiation and degassing in the Mt Etna (Italy) volcanic system have been explored by integrating the study of olivine-hosted melt inclusions (MIs) with an experimental survey of sulphur solubility in hydrous basaltic magmas. Sulphur solubility experiments were performed at conditions relevant to the Etnean plumbing system (1200 C, 200MPa and oxygen fugacity between NNOþ0 2 and NNOþ1 7, with NNO being the nickel–nickel oxide buffer), and their results confirm the important control of oxygen fugacity (fO2) on S abundance in mafic magmas and on S partitioning between fluid and melt phases (DSfluid/melt). The observed DSfluid/melt value increases from 5164 to 14666 when fO2 decreases from NNOþ1 760 5 to NNOþ0 3. Based on the calculated DSfluid/melt and a careful selection of previously published data, an empirical model is proposed for basaltic magmas to predict the variation of DSfluid/melt values with variations in P (25–300 MPa), T (1030–1200 C) and fO2 (between NNO– 0 8 and NNOþ2 4). Olivine-hosted melt inclusions (Fo89-91) from tephra of the prehistoric (4 ka BP) sub-plinian picritic eruption, named FS (‘Fall Stratified’), have been investigated for their major element compositions, volatile contents and iron speciation (expressed as Fe3þ/PFe ratio). These primitive MIs present S content from 235677 to 34456168 ppm, and oxygen fugacity values, estimated from Fe3þ/PFe ratios, range from NNOþ0 760 2 to NNOþ1 660 2. Iron speciation has also been investigated in more evolved and volatile-poorer Etnean MIs. The only primitive melt inclusion from the Mt Spagnolo eruption (4–15 ka BP) presents a S content of 1515649ppm and an estimated fO2 of NNOþ1 460 1. The more evolved MIs (from 2002–2003, 2006, 2008–2009 and 2013 eruptions) have S content lower than 500 ppm, and their Fe3þ/RFe ratios result in fO2 between NNO– 0 960 1 and NNOþ0 460 1. Redox conditions and S behaviour in Etnean magmas during degassing and fractional crystallization were modelled coupling MELTS code with our empirical DSfluid/melt model. Starting from an FS-type magma composition and upon decrease of T and P, fractional crystallization of olivine, clinopyroxene, spinel and plagioclase causes a significant fO2 decrease. The fO2 reduction, in turn, causes a decrease in sulphur solubility and an increase in DSfluid/melt, promoting S exsolution during magma ascent, which further enhances the reduction of fO2. For the evolved MIs of 2002–2013 eruptions, magma differentiation may therefore have played a crucial role in decreasing redox conditions and favouring efficient S degassing. Differently, during the unusual FS eruption, only limited melt evolution is observed and S exsolution seems to have been triggered by a major pressure decrease accompanied by H2O and CO2 exsolution during fast magmatic ascent.
    Description: Published
    Description: egaa095
    Description: 4V. Processi pre-eruttivi
    Description: JCR Journal
    Keywords: melt inclusions ; sulphur solubility experiments ; XANES ; Mt. Etna ; 04.08. Volcanology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 14
    Publication Date: 2021-04-14
    Description: The scaling of earthquake parameters with seismic moment and its interpretation in terms of self- similarity is still debated in the literature. We address this question by examining a worldwide compilation of corner frequency-based and elastic rebound theory (ERT)-based fault slip, area and stress drop values for earthquakes ranging in magnitude from -0.7 to 7.8. We find that corner frequency estimates of slip (and stress drop) scale differently than those inferred from the ERT approach, where the latter deviates from the generally accepted constant stress drop behavior of so- called self-similar scaling models. We also find that average slips from finite-source models are consistent with corner frequency scaling, whereas peak slip values are more consistent with the ERT scaling. The different scaling of corner frequency- and ERT-based estimates of slip and stress drop with earthquake size is interpreted in terms of heterogeneity of the rupture process. ERT-based estimates of stress drop decrease with seismic moment suggesting a self-affine behavior. Despite the inferred heterogeneity at all scales, we do not observe a clear effect on the Brune stress drop scaling with earthquake size.
    Description: Published
    Description: 1771–1781
    Description: 2T. Deformazione crostale attiva
    Description: JCR Journal
    Keywords: Earthquake dynamics ; Earthquake source observations ; Dynamics and mechanics of faulting ; 04.06. Seismology
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  • 15
    Publication Date: 2021-05-12
    Description: We have constructed a 3-D shear wave velocity (Vs) model for the crust and uppermost mantle beneath the Middle East using Rayleigh wave records obtained from ambient-noise cross-correlations and regional earthquakes. We combined one decade of data collected from 852 permanent and temporary broad-band stations in the region to calculate group-velocity dispersion curves. A compilation of 〉54 000 ray paths provides reliable group-velocity measurements for periods between 2 and 150 s. Path-averaged group velocities calculated at different periods were inverted for 2-D group-velocity maps. To overcome the problem of heterogeneous ray coverage, we used an adaptive grid parametrization for the group-velocity tomographic inversion. We then sample the period-dependent group-velocity field at each cell of a predefined grid to generate 1-D group-velocity dispersion curves, which are subsequently inverted for 1-D Vs models beneath each cell and combined to approximate the 3-D Vs structure of the area. The Vs model shows low velocities at shallow depths (5–10 km) beneath the Mesopotamian foredeep, South Caspian Basin, eastern Mediterranean and the Black Sea, in coincidence with deep sedimentary basins. Shallow high-velocity anomalies are observed in regions such as the Arabian Shield, Anatolian Plateau and Central Iran, which are dominated by widespread magmatic exposures. In the 10–20 km depth range, we find evidence for a band of high velocities (〉4.0 km s–1) along the southern Red Sea and Arabian Shield, indicating the presence of upper mantle rocks. Our 3-D velocity model exhibits high velocities in the depth range of 30–50 km beneath western Arabia, eastern Mediterranean, Central Iranian Block, South Caspian Basin and the Black Sea, possibly indicating a relatively thin crust. In contrast, the Zagros mountain range, the Sanandaj-Sirjan metamorphic zone in western central Iran, the easternmost Anatolian plateau and Lesser Caucasus are characterized by low velocities at these depths. Some of these anomalies may be related to thick crustal roots that support the high topography of these regions. In the upper mantle depth range, high-velocity anomalies are obtained beneath the Arabian Platform, southern Zagros, Persian Gulf and the eastern Mediterranean, in contrast to low velocities beneath the Red Sea, Arabian Shield, Afar depression, eastern Turkey and Lut Block in eastern Iran. Our Vs model may be used as a new reference crustal model for the Middle East in a broad range of future studies.
    Description: Published
    Description: 1349-1365
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: 04.01. Earth Interior ; 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 16
    Publication Date: 2021-06-04
    Description: New investigations on Ustica (Palermo, Sicily) originated from the need to improve our knowledge of the island’s archaeological and environmental heritage. Through field surveys, particular attention was paid to human occupation in the Neolithic phases and focused on the less investigated southern side of the island. The systematic survey of the area of Piano dei Cardoni in 2018 brought to light a new Middle/Late Neolithic site, already partially documented in the literature. The island was settled for the first time during these phases, as also testified from the area of Punta Spalmatore. The presence of Serra d’Alto, incised dark burnished, and Diana styles suggests that the site and the archaeological assemblage dates from the mid to late 5th millennium BC, as confirmed by AMS dating. In addition to pottery, obsidian artifacts were also recovered, and a preliminary study of these materials is presented here. Portable XRF analyses on a sample of 41 obsidian artifacts, representing a high percentage of the lithic assemblage compared to chert tools, show that the provenance of the raw material is Gabellotto Gorge (Lipari) and Balata dei Turchi (Pantelleria). These results provide new insight into broader regional debates about obsidian technology and its exchange during the Neolithic and open an important consideration for sites that are far from the raw material sources
    Description: Published
    Description: 273-290
    Description: 3V. Proprietà chimico-fisiche dei magmi e dei prodotti vulcanici
    Description: 6SR VULCANI – Servizi e ricerca per la società
    Description: JCR Journal
    Keywords: obsidian exploitation ; island archaeology ; Middle Neolithic ; pXRF ; Sicily
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 17
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    Unknown
    De Gruyter
    In:  EPIC3Climate Change and Marine and Freshwater Toxins, Climate Change and Marine and Freshwater Toxins, Berlin, De Gruyter, 33 p., pp. 133-166
    Publication Date: 2021-02-20
    Description: The increasingly widespread production of toxins by marine and freshwater microalgae raises serious concerns regarding seafood and drinking water safety. This book compiles studies on the influence of climate change on the spreading of toxin-producing species in aquatic systems. The chemistry and biology of toxin production is revised and an outlook on control and prevention of the toxins' impact on human and animal health is given.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Inbook , peerRev
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  • 18
    Publication Date: 2021-07-23
    Description: Marine aquaculture holds great promise for meeting increasing demand for healthy protein that is sustainably produced, but reaching necessary production levels will be challenging. The ecosystem approach to aquaculture is a framework for sustainable aquaculture development that prioritizes multiple-stakeholder participation and spatial planning. These types of approaches have been increasingly used to help guide sustainable, persistent, and equitable aquaculture planning, but most countries have difficulties in setting or meeting longer-term development goals. Scenario analysis (SA) for future planning uses similar approaches and can complement holistic methods, such as the ecosystem approach to aquaculture framework, by providing a temporal analogue to the spatially robust design. Here we define the SA approach to planning in aquaculture, outline how SA can benefit aquaculture planning, and review how this tool is already being used. We track the use of planning tools in the 20 International Council for the Exploration of the Sea member nations, with particular attention given to Norway’s development goals to 2050. We conclude that employing a combination of an ecosystem framework with scenario analyses may help identify the scale of development aquaculture goals over time, aid in evaluating the feasibility of the desired outcomes, and highlight potential social-ecological conflicts and trade-offs that may otherwise be overlooked.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 19
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    Unknown
    BioMed Central
    In:  http://aquaticcommons.org/id/eprint/25902 | 20794 | 2018-09-26 06:38:40 | 25902 | Department of Biological Sciences, National University of Singapore
    Publication Date: 2021-07-16
    Description: Background. Macroinvertebrates such as non-biting midges (Chironomidae: Diptera) are important components of freshwater ecosystems. However, they are often neglected in biodiversity and conservation research because invertebrate species richness is difficult and expensive to quantify with traditional methods. We here demonstrate that Next Generation Sequencing barcodes (“NGS barcodes”) can provide relief because they allow for fast and large-scale species-level sorting of large samples at low cost. Results. We used NGS barcoding to investigate the midge fauna of Singapore’s swamp forest remnant (Nee Soon Swamp Forest). Based on 〉 14.000 barcoded specimens, we find that the swamp forest maintains an exceptionally rich fauna composed of an observed number of 289 species (estimated 336 species) in a very small area (90 ha). We furthermore barcoded the chironomids from three surrounding reservoirs that are located in close proximity. Although the swamp forest remnant is much smaller than the combined size of the freshwater reservoirs in the study (90 ha vs. 〉 450 ha), the latter only contains 33 (estimated 61) species. We show that the resistance of the swamp forest species assemblage is high because only 8 of the 314 species are shared despite the close proximity. Moreover, shared species are not very abundant (3% of all specimens). A redundancy analysis revealed that ~ 21% of the compositional variance of midge communities within the swamp forest was explained by a range of variables with conductivity, stream order, stream width, temperature, latitude (flow direction), and year being significant factors influencing community structure. An LME analysis demonstrates that the total species richness decreased with increasing conductivity. Conclusion. Our study demonstrates that midge diversity of a swamp forest can be so high that it questions global species diversity estimates for Chironomidae, which are an important component of many freshwater ecosystems. We furthermore demonstrate that small and natural habitat remnants can have high species turnover and can be very resistant to the invasion of species from neighboring reservoirs. Lastly, the study shows how NGS barcodes can be used to integrate specimen- and species-rich invertebrate taxa in biodiversity and conservation research.
    Keywords: Ecology ; Environment ; Limnology
    Repository Name: AquaDocs
    Type: article , TRUE
    Format: application/pdf
    Format: application/pdf
    Format: 31
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  • 20
    facet.materialart.
    Unknown
    De Gruyter
    In:  Life in Extreme Environments
    Publication Date: 2021-02-16
    Description: The cryosphere stands for environments where water appears in a frozen form. It includes permafrost, glaciers, ice sheets, and sea ice and is currently more affected by Global Change than most other regions of the Earth. In the cryosphere, limited water availability and subzero temperatures cause extreme conditions for all kind of life which microorganisms can cope with extremely well. The cryosphere’s microbiota displays an unexpectedly large genetic potential, and taxonomic as well as functional diversity which, however, we still only begin to map. Also, microbial communities influence reaction patterns of the cryosphere towards Global Change. Altered patterns of seasonal temperature fluctuations and precipitation are expected in the Arctic and will affect the microbial turnover of soil organic matter (SOM). Activation of nutrients by thawing and increased active layer thickness as well as erosion renders nutrient stocks accessible to microbial activities. Also, glacier melt and retreat stimulate microbial life in turn influencing albedo and surface temperatures. In this context, the functional resilience of microbial communities in the cryosphere is of major interest. Particularly important is the ability of microorganisms and microbial communities to respond to changes in their surroundings by intracellular regulation and population shifts within functional niches, respectively. Research on microbial life exposed to permanent freeze or seasonal freeze-thaw cycles has led to astonishing findings about microbial versatility, adaptation, and diversity. Microorganisms thrive in cold habitats and new sequencing techniques have produced large amounts of genomic, metagenomic, and metatranscriptomic data that allow insights into the fascinating microbial ecology and physiology at low and subzero temperatures. Moreover, some of the frozen ecosystems such as permafrost constitute major global carbon and nitrogen storages, but can also act as sources of the greenhouse gases methane and nitrous oxide. In this book we summarize state of the art knowledge on whether environmental changes are met by a flexible microbial community retaining its function, or if the altered conditions also render the community in a state of altered properties that affect the Earth’s element cycles and climate. This book brings together research on the cryosphere’s microbiota including permafrost, glaciers, and sea ice in Arctic and Antarctic regions. Different spatial scales and levels of complexity are considered, spanning from ecosystem level to pure culture studies of model microbes in the laboratory. It aims to attract a wide range of parties with interest in the effect of climate change and/or low temperatures on microbial nutrient cycling and physiology.
    Type: info:eu-repo/semantics/book
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  • 21
    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
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  • 22
    Publication Date: 2021-08-20
    Description: Background The results of a previous study verified that umbilical cord mesenchymal stem cells (UCMSCs) have good therapeutic effects for the treatment of HBV-related acute-on-chronic liver failure (ACLF) and liver cirrhosis (LC). Nevertheless, it is still unknown whether the effects of UCMSCs are affected by recipient age. Methods Patients treated with UCMSCs who met the criteria of HBV-related ACLF and liver cirrhosis were identified in this retrospective observational study. Patients were divided into subgroups according to the World Health Organization (WHO) age criteria (
    Electronic ISSN: 1757-6512
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 23
    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
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  • 24
    Publication Date: 2021-08-21
    Description: Objectives To investigate the safety for clinic use and therapeutic effects of basic fibroblast growth factor (bFGF)-overexpressing human umbilical cord-derived mesenchymal stem cells (HUCMSCs) in mice with completely transected spinal cord injury (SCI). Methods Stable bFGF-overexpressing HUCMSCs clones were established by electrotransfection and then subjected to systematic safety evaluations. Then, bFGF-overexpressing and control HUCMSCs were used to treat mice with completely transected SCI by tail intravenous injection. Therapeutic outcomes were then investigated, including functional recovery of locomotion, histological structures, nerve regeneration, and recovery mechanisms. Results Stable bFGF-overexpressing HUCMSCs met the standards and safety of MSCs for clinic use. In the mouse SCI model, stable bFGF-overexpressing HUCMSCs markedly improved therapeutic outcomes such as reducing glial scar formation, improving nerve regeneration and proliferation of endogenous neural stem cells (NSCs), and increasing locomotion functional recovery of posterior limbs compared with the control HUCMSCs group. Furthermore, bFGF-overexpressing HUCMSCs promoted the proliferation and neuronal differentiation of NSCs in vitro through the PI3K-Akt-GSK-3β pathway. Conclusion bFGF-overexpressing HUCMSCs meet the requirements of clinical MSCs and improve evident therapeutic outcomes of mouse SCI treatment, which firmly supports the safety and efficacy of gene-modified MSCs for clinical application.
    Electronic ISSN: 1757-6512
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 25
  • 26
    Publication Date: 2021-08-21
    Description: Background Coronary artery disease (CAD) is considered as a multi-faceted chronic inflammatory disease involving reduced blood supply to the myocardium as a result of accumulating lipids in the atrial walls. Visceral adiposity with disrupted release of adipokines play a key role in its pathogenesis. Asprosin is a newly identified fasting-induced glucogenic adipokine that has been related with metabolic disorders such as type II diabetes mellitus and polycystic ovary syndrome. The preset study sought to assess circulating asprosin in context of CAD. Methods In this study, serum levels of asprosin were determined in 88 CAD patients and 88 non-CAD healthy controls. Serum IL-6, TNF-α, asprosin and adiponectin were assessed using ELISA kits. Results: Serum asprosin was found to be higher in CAD patients when compared to non-CAD subjects (7.84 ± 2.08 versus 5.02 ± 1.29 μg/mL, p 
    Electronic ISSN: 1476-511X
    Topics: Biology
    Published by BioMed Central
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  • 27
    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
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  • 28
    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
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  • 29
    Publication Date: 2021-08-19
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 30
    Publication Date: 2021-06-29
    Description: Background Metabolic stress, as negative energy balance on one hand or obesity on the other hand can lead to increased levels of free fatty acids in the plasma and follicular fluid of animals and humans. In an earlier study, we showed that increased oleic acid (OA) concentrations affected the function of cultured bovine granulosa cells (GCs). Here, we focus on genome wide effects of increased OA concentrations. Results Our data showed that 413 genes were affected, of which 197 were down- and 216 up-regulated. Specifically, the expression of FSH-regulated functional key genes, CCND2, LHCGR, INHA and CYP19A1 and 17-β-estradiol (E2) production were reduced by OA treatment, whereas the expression of the fatty acid transporter CD36 was increased and the morphology of the cells was changed due to lipid droplet accumulation. Bioinformatic analysis revealed that associated pathways of the putative upstream regulators “FSH” and “Cg (choriogonadotropin)” were inhibited and activated, respectively. Down-regulated genes are over-represented in GO terms “reproductive structure/system development”, “ovulation cycle process”, and “(positive) regulation of gonadotropin secretion”, whereas up-regulated genes are involved in “circulatory system development”, “vasculature development”, “angiogenesis” or “extracellular matrix/structure organization”. Conclusions From these data we conclude that besides inhibiting GC functionality, increased OA levels seemingly promote angiogenesis and tissue remodelling, thus suggestively initiating a premature fulliculo-luteal transition. In vivo this may lead to impeded folliculogenesis and ovulation, and cause sub-fertility.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
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  • 31
    Publication Date: 2021-08-20
    Description: Background Left-right (LR) asymmetry is an essential feature of bilateral animals. Studies in vertebrates show that LR asymmetry formation comprises three major steps: symmetry breaking, asymmetric gene expression, and LR morphogenesis. Although much progress has been made in the first two events, mechanisms underlying asymmetric morphogenesis remain largely unknown due to the complex developmental processes deployed by vertebrate organs. Results We here addressed this question by studying Pitx gene function in the basal chordate amphioxus whose asymmetric organogenesis, unlike that in vertebrates, occurs essentially in situ and does not rely on cell migration. Pitx null mutation in amphioxus causes loss of all left-sided organs and incomplete ectopic formation of all right-sided organs on the left side, whereas Pitx partial loss-of-function leads to milder phenotypes with only some LR organs lost or ectopically formed. At the N1 to N3 stages, Pitx expression is gradually expanded from the dorsal anterior domain to surrounding regions. This leads to activation of genes like Lhx3 and/or Prop1 and Pit, which are essential for left-side organs, and downregulation of genes like Hex and/or Nkx2.1 and FoxE4, which are required for right-side organs to form ectopically on the left side. In Pitx mutants, the left-side expressed genes are not activated, while the right-side genes fail to decrease expression on the left side. In contrast, in embryos overexpressing Pitx genes, the left-side genes are induced ectopically on the right side, and the right-side genes are inhibited. Several Pitx binding sites are identified in the upstream sequences of the left-side and right-side genes which are essential for activation of the former and repression of the latter by Pitx. Conclusions Our results demonstrate that (1) Pitx is a major (although not the only) determinant of asymmetric morphogenesis in amphioxus, (2) the development of different LR organs have distinct requirements for Pitx activity, and (3) Pitx controls amphioxus LR morphogenesis probably through inducing left-side organs and inhibiting right-side organs directly. These findings show much more dependence of LR organogenesis on Pitx in amphioxus than in vertebrates. They also provide insight into the molecular developmental mechanism of some vertebrate LR organs like the lungs and atria, since they show a right-isomerism phenotype in Pitx2 knockout mice like right-sided organs in Pitx mutant amphioxus. Our results also explain why some organs like the adenohypophysis are asymmetrically located in amphioxus but symmetrically positioned in vertebrates.
    Electronic ISSN: 1741-7007
    Topics: Biology
    Published by BioMed Central
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  • 32
    Publication Date: 2021-08-20
    Description: Background After repairing double-strand breaks (DSBs) caused by CRISPR-Cas9 cleavage, genomic damage, such as large deletions, may have pathogenic consequences. Results We show that large deletions are ubiquitous but are dependent on editing sites and cell types. Human primary T cells display more significant deletions than hematopoietic stem and progenitor cells (HSPCs), whereas we observe low levels in induced pluripotent stem cells (iPSCs). We find that the homology-directed repair (HDR) with single-stranded oligodeoxynucleotides (ssODNs) carrying short homology reduces the deletion damage by almost half, while adeno-associated virus (AAV) donors with long homology reduce large deletions by approximately 80%. In the absence of HDR, the insertion of a short double-stranded ODN by NHEJ reduces deletion indexes by about 60%. Conclusions Timely bridging of broken ends by HDR and NHEJ vastly decreases the unintended consequences of dsDNA cleavage. These strategies can be harnessed in gene editing applications to attenuate unintended outcomes.
    Print ISSN: 1465-6906
    Electronic ISSN: 1474-760X
    Topics: Biology
    Published by BioMed Central
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  • 33
    Publication Date: 2021-08-20
    Description: Background C. sinensis is an important economic crop with fluoride over-accumulation in its leaves, which poses a serious threat to human health due to its leaf consumption as tea. Recently, our study has indicated that cell wall proteins (CWPs) probably play a vital role in fluoride accumulation/detoxification in C. sinensis. However, there has been a lack in CWP identification and characterization up to now. This study is aimed to characterize cell wall proteome of C. sinensis leaves and to develop more CWPs related to stress response. A strategy of combined cell wall proteomics and N-glycoproteomics was employed to investigate CWPs. CWPs were extracted by sequential salt buffers, while N-glycoproteins were enriched by hydrophilic interaction chromatography method using C. sinensis leaves as a material. Afterwards all the proteins were subjected to UPLC-MS/MS analysis. Results A total of 501 CWPs and 195 CWPs were identified respectively by cell wall proteomics and N-glycoproteomics profiling with 118 CWPs in common. Notably, N-glycoproteomics is a feasible method for CWP identification, and it can enhance CWP coverage. Among identified CWPs, proteins acting on cell wall polysaccharides constitute the largest functional class, most of which might be involved in cell wall structure remodeling. The second largest functional class mainly encompass various proteases related to CWP turnover and maturation. Oxidoreductases represent the third largest functional class, most of which (especially Class III peroxidases) participate in defense response. As expected, identified CWPs are mainly related to plant cell wall formation and defense response. Conclusion This was the first large-scale investigation of CWPs in C. sinensis through cell wall proteomics and N-glycoproteomics. Our results not only provide a database for further research on CWPs, but also an insight into cell wall formation and defense response in C. sinensis.
    Electronic ISSN: 1471-2229
    Topics: Biology
    Published by BioMed Central
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  • 34
    Publication Date: 2021-08-20
    Description: Background Finding meaningful gene-gene interaction and the main Transcription Factors (TFs) in co-expression networks is one of the most important challenges in gene expression data mining. Results Here, we developed the R package “CeTF” that integrates the Partial Correlation with Information Theory (PCIT) and Regulatory Impact Factors (RIF) algorithms applied to gene expression data from microarray, RNA-seq, or single-cell RNA-seq platforms. This approach allows identifying the transcription factors most likely to regulate a given network in different biological systems — for example, regulation of gene pathways in tumor stromal cells and tumor cells of the same tumor. This pipeline can be easily integrated into the high-throughput analysis. To demonstrate the CeTF package application, we analyzed gastric cancer RNA-seq data obtained from TCGA (The Cancer Genome Atlas) and found the HOXB3 gene as the second most relevant TFs with a high regulatory impact (TFs-HRi) regulating gene pathways in the cell cycle. Conclusion This preliminary finding shows the potential of CeTF to list master regulators of gene networks. CeTF was designed as a user-friendly tool that provides many highly automated functions without requiring the user to perform many complicated processes. It is available on Bioconductor (http://bioconductor.org/packages/CeTF) and GitHub (http://github.com/cbiagii/CeTF).
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
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  • 35
    Publication Date: 2021-08-20
    Description: Blueberry (Vaccinium ssp.) is a perennial shrub belonging to the family Ericaceae, which is highly tolerant of acid soils and heavy metal pollution. In the present study, blueberry was subjected to cadmium (Cd) stress in simulated pot culture. The transcriptomics and rhizosphere fungal diversity of blueberry were analyzed, and the iron (Fe), manganese (Mn), copper (Cu), zinc (Zn) and cadmium (Cd) content of blueberry tissues, soil and DGT was determined. A correlation analysis was also performed. A total of 84 374 annotated genes were identified in the root, stem, leaf and fruit tissue of blueberry, of which 3370 were DEGs, and in stem tissue, of which 2521 were DEGs. The annotation data showed that these DEGs were mainly concentrated in a series of metabolic pathways related to signal transduction, defense and the plant–pathogen response. Blueberry transferred excess Cd from the root to the stem for storage, and the highest levels of Cd were found in stem tissue, consistent with the results of transcriptome analysis, while the lowest Cd concentration occurred in the fruit, Cd also inhibited the absorption of other metal elements by blueberry. A series of genes related to Cd regulation were screened by analyzing the correlation between heavy metal content and transcriptome results. The roots of blueberry rely on mycorrhiza to absorb nutrients from the soil. The presence of Cd has a significant effect on the microbial community composition of the blueberry rhizosphere. The fungal family Coniochaetaceae, which is extremely extremelytolerant, has gradually become the dominant population. The results of this study increase our understanding of the plant regulation mechanism for heavy metals, and suggest potential methods of soil remediation using blueberry.
    Electronic ISSN: 1471-2229
    Topics: Biology
    Published by BioMed Central
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  • 36
    Publication Date: 2021-08-20
    Description: Several bioinformatic tools have been developed for genome-wide identification of orthologous and paralogous genes. However, no corresponding tool allows the detection of exon homology relationships. Here, we present ExOrthist, a fully reproducible Nextflow-based software enabling inference of exon homologs and orthogroups, visualization of evolution of exon-intron structures, and assessment of conservation of alternative splicing patterns. ExOrthist evaluates exon sequence conservation and considers the surrounding exon-intron context to derive genome-wide multi-species exon homologies at any evolutionary distance. We demonstrate its use in different evolutionary scenarios: whole genome duplication in frogs and convergence of Nova-regulated splicing networks (https://github.com/biocorecrg/ExOrthist).
    Print ISSN: 1465-6906
    Electronic ISSN: 1474-760X
    Topics: Biology
    Published by BioMed Central
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  • 37
    Publication Date: 2021-08-21
    Description: Objective To compare an objective with a subjective numeracy assessment for association with self-reported health status, where numeracy refers to “the degree to which individuals have the capacity to access, process, interpret, communicate, and act on numerical, quantitative, graphical, biostatistical, and probabilistic health information needed to make effective health decisions” Results We completed a secondary analysis of two population-based surveys, the Empire State Poll (n = 763) and the Program for the International Assessment of Adult Competencies (PIAAC; n = 2609). The first survey assessed numeracy with a 3-item subjective instrument. The second assessed numeracy with more than 20 math problems. Both used the same measure for self-reported health status. Lower numeracy, whether subjectively or objectively assessed, was associated with worse self-reported health, even after controlling for education and other sociodemographic confounders. The odds ratios for the association were very similar (0.91 and 0.90 respectively). A lengthy objective numeracy assessment and a brief self-report assessment had similar associations with health status. A brief self-report measure of numeracy has similar properties to a lengthy objective assessment and is likely to be more feasible to use to screen patients in practice.
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 38
    Publication Date: 2021-08-21
    Description: Background Sorghum yields in sub-Saharan Africa (SSA) are greatly reduced by parasitic plants of the genus Striga (witchweed). Vast global sorghum genetic diversity collections, as well as the availability of modern sequencing technologies, can be potentially harnessed to effectively manage the parasite. Results We used laboratory assays – rhizotrons to screen a global sorghum diversity panel to identify new sources of resistance to Striga; determine mechanisms of resistance, and elucidate genetic loci underlying the resistance using genome-wide association studies (GWAS). New Striga resistant sorghum determined by the number, size and biomass of parasite attachments were identified. Resistance was by; i) mechanical barriers that blocked parasite entry, ii) elicitation of a hypersensitive reaction that interfered with parasite development, and iii) the inability of the parasite to develop vascular connections with hosts. Resistance genes underpinning the resistance corresponded with the resistance mechanisms and included pleiotropic drug resistance proteins that transport resistance molecules; xylanase inhibitors involved in cell wall fortification and hormonal regulators of resistance response, Ethylene Response Factors. Conclusions Our findings are of fundamental importance to developing durable and broad-spectrum resistance against Striga and have far-reaching applications in many SSA countries where Striga threatens the livelihoods of millions of smallholder farmers that rely on sorghum as a food staple.
    Electronic ISSN: 1471-2229
    Topics: Biology
    Published by BioMed Central
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  • 39
    Publication Date: 2021-08-21
    Description: Background Forest carbon models are recognized as suitable tools for the reporting and verification of forest carbon stock and stock change, as well as for evaluating the forest management options to enhance the carbon sink provided by sustainable forestry. However, given their increased complexity and data availability, different models may simulate different estimates. Here, we compare carbon estimates for Romanian forests as simulated by two models (CBM and EFISCEN) that are often used for evaluating the mitigation options given the forest-management choices. Results The models, calibrated and parameterized with identical or harmonized data, derived from two successive national forest inventories, produced similar estimates of carbon accumulation in tree biomass. According to CBM simulations of carbon stocks in Romanian forests, by 2060, the merchantable standing stock volume will reach an average of 377 m3 ha−1, while the carbon stock in tree biomass will reach 76.5 tC ha−1. The EFISCEN simulations produced estimates that are about 5% and 10%, respectively, lower. In addition, 10% stronger biomass sink was simulated by CBM, whereby the difference reduced over time, amounting to only 3% toward 2060. Conclusions This model comparison provided valuable insights on both the conceptual and modelling algorithms, as well as how the quality of the input data may affect calibration and projections of the stock and stock change in the living biomass pool. In our judgement, both models performed well, providing internally consistent results. Therefore, we underline the importance of the input data quality and the need for further data sampling and model improvements, while the preference for one model or the other should be based on the availability and suitability of the required data, on preferred output variables and ease of use.
    Electronic ISSN: 1750-0680
    Topics: Geosciences
    Published by BioMed Central
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  • 40
    Publication Date: 2021-08-21
    Description: Background Significant investments have been made towards the implementation of mHealth applications and eRecord systems globally. However, fragmentation of these technologies remains a big challenge, often unresolved in developing countries. In particular, evidence shows little consideration for linking mHealth applications and eRecord systems. Botswana is a typical developing country in sub-Saharan Africa that has explored mHealth applications, but the solutions are not interoperable with existing eRecord systems. This paper describes Botswana’s eRecord systems interoperability landscape and provides guidance for linking mHealth applications to eRecord systems, both for Botswana and for developing countries using Botswana as an exemplar. Methods A survey and interviews of health ICT workers and a review of the Botswana National eHealth Strategy were completed. Perceived interoperability benefits, opportunities and challenges were charted and analysed, and future guidance derived. Results Survey and interview responses showed the need for interoperable mHealth applications and eRecord systems within the health sector of Botswana and within the context of the National eHealth Strategy. However, the current Strategy does not address linking mHealth applications to eRecord systems. Across Botswana’s health sectors, global interoperability standards and Application Programming Interfaces are widely used, with some level of interoperability within, but not between, public and private facilities. Further, a mix of open source and commercial eRecord systems utilising relational database systems and similar data formats are supported. Challenges for linking mHealth applications and eRecord systems in Botswana were identified and categorised into themes which led to development of guidance to enhance the National eHealth Strategy. Conclusion Interoperability between mHealth applications and eRecord systems is needed and is feasible. Opportunities and challenges for linking mHealth applications to eRecord systems were identified, and future guidance stemming from this insight presented. Findings will aid Botswana, and other developing countries, in resolving the pervasive disconnect between mHealth applications and eRecord systems.
    Electronic ISSN: 1472-6947
    Topics: Computer Science , Medicine
    Published by BioMed Central
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  • 41
    Publication Date: 2021-08-21
    Description: Objective The use of mice as animal models in biomedical research allows the standardization of genetic background and environmental conditions, which both affect phenotypic variability. As the use of both sexes in experiments is strongly recommended, sex-specific phenotypic variability is discussed with regard to putative consequences on the group size which is necessary for achieving valid and reproducible results. In this study, the sex-specific variability of 25 clinical chemical and hematological parameters which represent a comprehensive blood screen of laboratory mice, was analyzed in data sets which have been submitted to the Mouse Phenome Database. Results The overall analysis comprising all 25 clinical chemical and hematological parameters showed no evidence for substantial and robust general sex-specific variability. A large range of the ratio of the female and male coefficient of variation (CV) was found for every parameter among the respective strain data sets. This clearly demonstrated the appearance of unpredictable major interactions between genotype and environment regarding the sex-specific variability of the blood parameters analyzed.
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 42
    Publication Date: 2021-08-21
    Description: Objective Reported rainfall data from multiple rain gauges and its corresponding estimate from Dual-Polarization (Dual-Pol) radar is presented here. The ordered set of data pairs were collected from multiple peer reviewed publications spanning across the last decade. Data description Taken from multiple sources, the data set represents several radar sites and rain gauge sites combined for 12,734 data points. The data is relevant in various applications of hydrometeorology and engineering as well as weather forecasting. Further, the importance of accuracy in radar precipitation estimates continues to increase, necessitating the incorporation of as much data as possible.
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 43
    Publication Date: 2021-08-20
    Description: In the canonical random on-the-job search model with continuous firm heterogeneity, I show that a mean-preserving spread of the firm-productivity distribution raises the returns to mobility, i.e., the inter-firm mobility of workers as measured by the number of outside contacts per employment spell. Both sorting and rent-share mechanisms play a role. In a further contribution, I distinguish frictional and structural impediments to mobility in order to establish a link between mobility and skills via the concept of versatility. Versatility enhances a person’s mobility since a mismatch between job requirements and the person’s skill set is less likely to occur. I provide some statistics in support of the discussed mechanisms. The findings are particularly intriguing in light of the concurrent rise in the productivity dispersion across firms and in the skill premium in many countries.
    Print ISSN: 2194-6124
    Electronic ISSN: 1935-1704
    Topics: Economics
    Published by De Gruyter
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  • 44
    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
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  • 45
    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
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  • 46
    Publication Date: 2021-08-20
    Description: Background The abiotic stress such as soil salinization and heavy metal toxicity has posed a major threat to sustainable crop production worldwide. Previous studies revealed that halophytes were supposed to tolerate other stress including heavy metal toxicity. Though HMAD (heavy-metal-associated domain) was reported to play various important functions in Arabidopsis, little is known in Gossypium. Results A total of 169 G. hirsutum genes were identified belonging to the HMAD gene family with the number of amino acids ranged from 56 to 1011. Additionally, 84, 76 and 159 HMAD genes were identified in each G. arboreum, G. raimondii and G. barbadense, respectively. The phylogenetic tree analysis showed that the HMAD gene family were divided into five classes, and 87 orthologs of HMAD genes were identified in four Gossypium species, such as genes Gh_D08G1950 and Gh_A08G2387 of G. hirsutum are orthologs of the Gorai.004G210800.1 and Cotton_A_25987 gene in G. raimondii and G. arboreum, respectively. In addition, 15 genes were lost during evolution. Furthermore, conserved sequence analysis found the conserved catalytic center containing an anion binding (CXXC) box. The HMAD gene family showed a differential expression levels among different tissues and developmental stages in G. hirsutum with the different cis-elements for abiotic stress. Conclusions Current study provided important information about HMAD family genes under salt-stress in Gossypium genome, which would be useful to understand its putative functions in different species of cotton.
    Electronic ISSN: 1471-2229
    Topics: Biology
    Published by BioMed Central
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  • 47
    Publication Date: 2021-08-20
    Description: Background Soybean is a globally important legume crop that provides a primary source of high-quality vegetable protein and oil. Seed protein content (SPC) is a valuable quality trait controlled by multiple genes in soybean. Results In this study, we performed quantitative trait loci (QTL) mapping, QTL-seq, and RNA sequencing (RNA-seq) to reveal the genes controlling protein content in the soybean by using the high protein content variety Nanxiadou 25. A total of 50 QTL for SPC distributed on 14 chromosomes except chromosomes 4, 12, 14, 17, 18, and 19 were identified by QTL mapping using 178 recombinant inbred lines (RILs). Among these QTL, the major QTL qSPC_20–1 and qSPC_20–2 on chromosome 20 were repeatedly detected across six tested environments, corresponding to the location of the major QTL detected using whole-genome sequencing-based QTL-seq. 329 candidate DEGs were obtained within the QTL region of qSPC_20–1 and qSPC_20–2 via gene expression profile analysis. Nine of which were associated with SPC, potentially representing candidate genes. Clone sequencing results showed that different single nucleotide polymorphisms (SNPs) and indels between high and low protein genotypes in Glyma.20G088000 and Glyma.16G066600 may be the cause of changes in this trait. Conclusions These results provide the basis for research on candidate genes and marker-assisted selection (MAS) in soybean breeding for seed protein content.
    Electronic ISSN: 1471-2229
    Topics: Biology
    Published by BioMed Central
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  • 48
    Publication Date: 2021-08-20
    Description: Functional genomics experiments, like ChIP-Seq or ATAC-Seq, produce results that are summarized as a region set. There is no way to objectively evaluate the effectiveness of region set similarity metrics. We present Bedshift, a tool for perturbing BED files by randomly shifting, adding, and dropping regions from a reference file. The perturbed files can be used to benchmark similarity metrics, as well as for other applications. We highlight differences in behavior between metrics, such as that the Jaccard score is most sensitive to added or dropped regions, while coverage score is most sensitive to shifted regions.
    Print ISSN: 1465-6906
    Electronic ISSN: 1474-760X
    Topics: Biology
    Published by BioMed Central
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  • 49
    Publication Date: 2021-08-21
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
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  • 50
    Publication Date: 2021-08-21
    Description: Background Hypertrophy is a critical process for chondrocyte differentiation and maturation during endochondral ossification, which is responsible for the formation of long bone and postnatal longitudinal growth. Increasing evidence suggests that melatonin, an indole hormone, plays a pivotal role in chondrogenesis. However, little is known about the effects of melatonin on the terminal differentiation of chondrocytes. Methods Mesenchymal stem cell (MSC)-derived chondrocytes generated by a high-density micromass culture system were induced to undergo hypertrophic differentiation. Melatonin-mediated hypertrophic differentiation was examined by reverse transcription polymerase chain reaction analysis (RT-PCR) analysis, histological staining and immunohistochemistry. Activation of the Wnt signaling pathway was evaluated by PCR array, RT-PCR, western blotting and immunofluorescence. XAV-939, a Wnt signaling pathway antagonist, was further used to determine whether the effect of melatonin on chondrocyte hypertrophic differentiation was mediated occurred by activation of Wnt signaling pathway. Results Histological staining showed melatonin increased chondrocyte cell volume and the expression of type X collagen but decreased the expression of type II collagen compared with the control group. RT-PCR showed that melatonin significantly up-regulated the gene expressions of biomarkers of hypertrophic chondrocytes, including type X collagen, alkaline phosphatase, runt-related transcription factor 2, Indian hedgehog and parathyroid hormone-related protein receptor, and melatonin down-regulated the mRNA expression of hallmarks of chondrocytes, including parathyroid hormone-related protein. PCR array showed that the effect of melatonin on chondrocyte hypertrophic differentiation was accompanied by the up-regulation of multiple target genes of the canonical Wnt signaling pathway, and this effect was blocked by XAV-939. Conclusions The current findings demonstrate that melatonin enhances the hypertrophic differentiation of MSC-derived chondrocytes through the Wnt signaling pathway. Our findings add evidence to the role of melatonin in promoting bone development and highlight the positive effects of melatonin on terminal differentiation of chondrocytes.
    Electronic ISSN: 1757-6512
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 51
    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
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  • 53
    Publication Date: 2021-08-21
    Description: Novel coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus-2. The virus causes an exaggerated immune response, resulting in a cytokine storm and acute respiratory distress syndrome, the leading cause of COVID-19-related mortality and morbidity. So far, no therapies have succeeded in circumventing the exacerbated immune response or cytokine storm associated with COVID-19. Mesenchymal stem cells (MSCs), through their immunomodulatory and regenerative activities, mostly mediated by their paracrine effect and extracellular vesicle production, have therapeutic potential in many autoimmune, inflammatory, and degenerative diseases. In this paper, we review clinical studies on the use of MSCs for COVID-19 treatment, including the salutary effects of MSCs on the pathophysiology of COVID-19 and the immunomodulation of the cytokine storm. Ongoing clinical trial designs, cell sources, dose and administration, and populations are summarized, and the paracrine mode of benefit is discussed. We also offer suggestions for optimizing MSC-based therapies, including genetic engineering, strategies for cell surface modification, nanotechnology applications, and combination therapies.
    Electronic ISSN: 1757-6512
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 55
    Publication Date: 2021-08-21
    Description: Quantification of soil organic carbon (SOC) stocks in different land uses holds vital significance because of its implications regarding carbon sequestration as the largest terrestrial carbon pool. The current study was conducted to quantify and compare SOC stocks in forest land, agricultural land, and barren land-use categories in the subtropical ecosystems of the Himalayan foothills in Kashmir. Results showed the highest SOC value in the forest soil (75 ± 11.1 Mg C ha−1) followed by agricultural soil (58 ± 7.0 Mg C ha−1) and barren land (44 ± 6.5 Mg C ha−1). SOC stocks in different land uses showed broad variations with values as high as 106 ± 11.3 Mg C ha−1 (forest soils) and as low as 14.1 ± 7.1 Mg C ha−1 (barren land). The forest SOC values responded significantly to species composition with the highest values in Pinus roxburghii Sarg. pure stands as compared with broad leaved forests. Multivariate ordination analyses revealed that the variations in SOC stocks were significantly correlated with vegetation type, altitude, and soil bulk density. The study has identified anthropogenic disturbances as a major factor deteriorating local SOC stocks and recommends immediate soil restoration efforts to enhance the ecological significance of soils as vital regional carbon sinks. Study Implications The current study was designed to investigate the soil organic carbon (SOC) levels in different land uses of the Kashmir Himalayas, Pakistan. Results revealed forest soils as the major carbon sinks of the region, attributed to diverse species composition having a significant quantity of organic residues, followed by agricultural soils. Barren land-use class exhibited the lowest SOC values due to minimum vegetation cover, erosion, and degradation. Significant correlations of SOC stocks with geographical and edaphic variables were identified by multivariate ordination analysis in the investigated land-use classes. Results validate the significance of forests in enhancing SOC stocks, demanding forest restoration in the area by controlling the forest losses as well as afforestation. This article provides vital information required for better understanding of SOC stocks in different land-use classes in the subtropical ecosystems of the Kashmir region.
    Print ISSN: 0015-749X
    Electronic ISSN: 1938-3738
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 56
    Publication Date: 2021-08-22
    Description: Aims Acid grasslands are threatened both by agricultural intensification with nutrient addition and increased livestock densities as well as by land abandonment. In order to understand and quantify the effect of selected environmental and land-use factors on the observed variation and changes in the vegetation of acid grasslands, large-scale spatial and temporal pin-point plant cover monitoring data are fitted in a structural equation model. Methods The important sources of measurement and sampling uncertainties have been included using a hierarchical model structure. Furthermore, uncertainties associated with the measurement and sampling are separated from the process uncertainty, which is important when generating ecological predictions that may feed into local conservation management decisions. Important Findings Generally, increasing atmospheric nitrogen deposition led to more grass-dominated acid grassland habitats at the expense of the cover of forbs. Sandy soils were relatively more acidic, and the effects of soil type on the vegetation include both direct effects of soil type and indirect effects mediated by the effect of soil type on soil pH. Both soil type and soil pH affected the vegetation of acid grasslands. Even though only a relatively small proportion of the temporal variation in cover was explained by the model, it would still be useful to quantify the uncertainties when using the model for generating local ecological predictions and adaptive management plans.
    Print ISSN: 1752-993X
    Electronic ISSN: 1752-9921
    Topics: Biology
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  • 57
    Publication Date: 2021-08-20
    Description: Acute myeloid leukemia (AML) is a serious, life-threatening, and hardly curable hematological malignancy that affects the myeloid cell progenies and challenges patients of all ages but mostly occurs in adults. Although several therapies are available including chemotherapy, allogeneic hematopoietic stem cell transplantation (alloHSCT), and receptor-antagonist drugs, the 5-year survival of patients is quietly disappointing, less than 30%. alloHSCT is the major curative approach for AML with promising results but the treatment has severe adverse effects such as graft-versus-host disease (GVHD). Therefore, as an alternative, more efficient and less harmful immunotherapy-based approaches such as the adoptive transferring T cell therapy are in development for the treatment of AML. As such, chimeric antigen receptor (CAR) T cells are engineered T cells which have been developed in recent years as a breakthrough in cancer therapy. Interestingly, CAR T cells are effective against both solid tumors and hematological cancers such as AML. Gradually, CAR T cell therapy found its way into cancer therapy and was widely used for the treatment of hematologic malignancies with successful results particularly with somewhat better results in hematological cancer in comparison to solid tumors. The AML is generally fatal, therapy-resistant, and sometimes refractory disease with a disappointing low survival rate and weak prognosis. The 5-year survival rate for AML is only about 30%. However, the survival rate seems to be age-dependent. Novel CAR T cell therapy is a light at the end of the tunnel. The CD19 is an important target antigen in AML and lymphoma and the CAR T cells are engineered to target the CD19. In addition, a lot of research goes on the discovery of novel target antigens with therapeutic efficacy and utilizable for generating CAR T cells against various types of cancers. In recent years, many pieces of research on screening and identification of novel AML antigen targets with the goal of generation of effective anti-cancer CAR T cells have led to new therapies with strong cytotoxicity against cancerous cells and impressive clinical outcomes. Also, more recently, an improved version of CAR T cells which were called modified or smartly reprogrammed CAR T cells has been designed with less unwelcome effects, less toxicity against normal cells, more safety, more specificity, longer persistence, and proliferation capability. The purpose of this review is to discuss and explain the most recent advances in CAR T cell-based therapies targeting AML antigens and review the results of preclinical and clinical trials. Moreover, we will criticize the clinical challenges, side effects, and the different strategies for CAR T cell therapy.
    Electronic ISSN: 1757-6512
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 58
    Publication Date: 2021-08-20
    Description: Background One of the major trends in angiosperm evolution was the shift from woody to herbaceous habit. However, reversals known as derived woodiness have also been reported in numerous, distantly related clades. Among theories evoked to explain the factors promoting the evolution of derived woodiness are moderate climate theory and cavitation theory. The first assumes that woody habit evolves in response to mild climate allowing for prolonged life span, which in turn leads to bigger and woodier bodies. The second sees woodiness as a result of natural selection for higher cavitation resistance in seasonally dry environments. Here, we compare climatic niches of woody and herbaceous, mostly southern African, umbellifers from the Lefebvrea clade to assess whether woody taxa in fact occur in markedly drier habitats. We also calibrate their phylogeny to estimate when derived woodiness evolved. Finally, we describe the wood anatomy of selected woody and herbaceous taxa to see if life forms are linked to any particular wood traits. Results The evolution of derived woodiness in chamaephytes and phanerophytes as well as the shifts to short-lived annual therophytes in the Lefebvrea clade took place at roughly the same time: in the Late Miocene during a trend of global climate aridification. Climatic niches of woody and herbaceous genera from the Cape Floristic Region overlap. There are only two genera with distinctly different climatic preferences: they are herbaceous and occur outside of the Cape Floristic Region. Therefore, studied herbs have an overall climatic niche wider than their woody cousins. Woody and herbaceous species do not differ in qualitative wood anatomy, which is more affected by stem architecture and, probably, reproductive strategy than by habit. Conclusions Palaeodrought was likely a stimulus for the evolution of derived woodiness in the Lefebvrea clade, supporting the cavitation theory. The concurrent evolution of short-lived annuals withering before summer exemplifies an alternative solution to the same problem of drought-induced cavitation. Changes of the life form were most likely neither spurred nor precluded by any qualitative wood traits, which in turn are more affected by internode length and probably also reproductive strategy.
    Electronic ISSN: 1471-2229
    Topics: Biology
    Published by BioMed Central
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  • 59
    Publication Date: 2021-08-20
    Description: Research in the past decade has demonstrated that a single reference genome is not representative of a species’ diversity. MaizeGDB introduces a pan-genomic approach to hosting genomic data, leveraging the large number of diverse maize genomes and their associated datasets to quickly and efficiently connect genomes, gene models, expression, epigenome, sequence variation, structural variation, transposable elements, and diversity data across genomes so that researchers can easily track the structural and functional differences of a locus and its orthologs across maize. We believe our framework is unique and provides a template for any genomic database poised to host large-scale pan-genomic data.
    Electronic ISSN: 1471-2229
    Topics: Biology
    Published by BioMed Central
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  • 60
    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
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  • 61
    Publication Date: 2021-08-21
    Description: Background In most flowering plants, the plastid genome exhibits a quadripartite genome structure, comprising a large and a small single copy as well as two inverted repeat regions. Thousands of plastid genomes have been sequenced and submitted to public sequence repositories in recent years. The quality of sequence annotations in many of these submissions is known to be problematic, especially regarding annotations that specify the length and location of the inverted repeats: such annotations are either missing or portray the length or location of the repeats incorrectly. However, many biological investigations employ publicly available plastid genomes at face value and implicitly assume the correctness of their sequence annotations. Results We introduce , a Python package that automatically assesses the frequency of incomplete or incorrect annotations of the inverted repeats among publicly available plastid genomes. Specifically, the tool automatically retrieves plastid genomes from NCBI Nucleotide under variable search parameters, surveys them for length and location specifications of inverted repeats, and confirms any inverted repeat annotations through self-comparisons of the genome sequences. The package also includes functionality for automatic identification and removal of duplicate genome records and accounts for taxa that genuinely lack inverted repeats. A survey of the presence of inverted repeat annotations among all plastid genomes of flowering plants submitted to NCBI Nucleotide until the end of 2020 using , followed by a statistical analysis of potential associations with record metadata, highlights that release year and publication status of the genome records have a significant effect on the frequency of complete and equal-length inverted repeat annotations. Conclusion The number of plastid genomes on NCBI Nucleotide has increased dramatically in recent years, and many more genomes will likely be submitted over the next decade. enables researchers to automatically access and evaluate the inverted repeats of these plastid genomes as well as their sequence annotations and, thus, contributes to increasing the reliability of publicly available plastid genomes. The software is freely available via the Python package index at http://pypi.python.org/pypi/airpg.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
    Published by BioMed Central
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  • 62
    Publication Date: 2021-08-21
    Description: Objectives Peer support is rapidly being introduced into mental health services internationally, yet peer support interventions are often poorly described, limiting the usefulness of research in informing policy and practice. This paper reports the development of a peer support intervention that aims to improve outcomes of discharge from inpatient to community mental health care. People with experiential knowledge of using mental health services—peer workers and service user researchers—were involved in all stages of developing the intervention: generating intervention components; producing the intervention handbook; piloting the intervention. Results Systematic review and expert panels, including our Lived Experience Advisory Panel, identified 66 candidate intervention components in five domains: Recruitment and Role Description of Peer Workers; Training for Peer Workers; Delivery of Peer Support; Supervision and Support for Peer Workers; Organisation and Team. A series of Local Advisory Groups were used to prioritise components and explore implementation issues using consensus methods, refining an intervention blueprint. A peer support handbook and peer worker training programme were produced by the study team and piloted in two study sites. Feedback workshops were held with peer workers and their supervisors to produce a final handbook and training programme. The ENRICH trial is registered with the ISRCTN clinical trial register, number ISRCTN 10043328, and was overseen by an independent steering committee and a data monitoring committee.
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 63
    Publication Date: 2021-08-21
    Description: Background As effects of global climate change intensify, the interaction of biotic and abiotic stresses increasingly threatens current agricultural practices. The secondary cell wall is a vanguard of resistance to these stresses. Fusarium thapsinum (Fusarium stalk rot) and Macrophomina phaseolina (charcoal rot) cause internal damage to the stalks of the drought tolerant C4 grass, sorghum (Sorghum bicolor (L.) Moench), resulting in reduced transpiration, reduced photosynthesis, and increased lodging, severely reducing yields. Drought can magnify these losses. Two null alleles in monolignol biosynthesis of sorghum (brown midrib 6-ref, bmr6-ref; cinnamyl alcohol dehydrogenase, CAD; and bmr12-ref; caffeic acid O-methyltransferase, COMT) were used to investigate the interaction of water limitation with F. thapsinum or M. phaseolina infection. Results The bmr12 plants inoculated with either of these pathogens had increased levels of salicylic acid (SA) and jasmonic acid (JA) across both watering conditions and significantly reduced lesion sizes under water limitation compared to adequate watering, which suggested that drought may prime induction of pathogen resistance. RNA-Seq analysis revealed coexpressed genes associated with pathogen infection. The defense response included phytohormone signal transduction pathways, primary and secondary cell wall biosynthetic genes, and genes encoding components of the spliceosome and proteasome. Conclusion Alterations in the composition of the secondary cell wall affect immunity by influencing phenolic composition and phytohormone signaling, leading to the action of defense pathways. Some of these pathways appear to be activated or enhanced by drought. Secondary metabolite biosynthesis and modification in SA and JA signal transduction may be involved in priming a stronger defense response in water-limited bmr12 plants.
    Electronic ISSN: 1471-2229
    Topics: Biology
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  • 64
    Publication Date: 2021-08-21
    Description: Background Retinol binding protein 4 (RBP4) has been proposed to play a role in the pathophysiology of coronary artery disease (CAD), but previous findings on the association of RBP4 levels with CAD are inconsistent. Methods A meta-analysis based on observational studies was conducted to evaluate the association between circulating RBP4 levels and CAD. Databases including PubMed, Web of Science, Embase, Google Scholar and ClinicalTrials.gov database were searched for eligible studies published up to 12 July 2021. Standard mean differences (SMDs) with 95% confidence intervals (CIs) were calculated using the inverse variance heterogeneity (IVhet) and random-effects model for data with moderate and high heterogeneity (I2 〉 30%) and data with low heterogeneity were analysed using a fixed-effects model (I2 ≤ 30%). Moreover, a bias-adjusted quality-effects model was generated, and the prediction interval was also calculated under the random-effects model. Results Two nested case-control studies, one cohort study and twelve case–control studies with a total of 7111 participants were included. Circulating RBP4 levels in patients with CAD were comparable to those in the controls under the IVhet model (SMD: 0.25, 95% CI: − 0.29-0.79, I2: 96.00%). The quality-effects model produced consistent results. However, the association turned to be significant under the random-effect model (SMD: 0.46, 95% CI: 0.17–0.75, I2: 96.00%), whereas the 95% predictive interval (PI) included null values (95% PI: − 0.82-1.74). Subgroup analyses illustrated a positive relationship between CAD and RBP4 levels in patients with complications (SMD: 1.34, 95% CI: 0.38–2.29, I2: 96.00%). The meta-regression analysis revealed that the mean BMI of patients (P = 0.03) and complication status (P = 0.01) influenced the variation in SMD. Conclusions There was low-quality evidence that patients with CAD exhibited similar circulating RBP4 levels compared with controls, and high inter-study heterogeneity was also observed. Thus, RBP4 might not be a potential risk factor for CAD. Comparisons among different subtypes of RBP4 with larger sample size are needed in the future.
    Electronic ISSN: 1476-511X
    Topics: Biology
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  • 65
    Publication Date: 2021-08-21
    Description: Background To understand the mechanism of glucosinolates (GSs) accumulation in the specific organs, combined analysis of physiological change and transcriptome sequencing were applied in the current study. Taking Chinese kale as material, seeds and silique walls were divided into different stages based on the development of the embryo in seeds and then subjected to GS analysis and transcriptome sequencing. Results The main GS in seeds of Chinese kale were glucoiberin and gluconapin and their content changed with the development of the seed. During the transition of the embryo from torpedo- to the early cotyledonary-embryo stage, the accumulation of GS in the seed was accompanied by the salient decline of GS in the corresponding silique wall. Thus, the seed and corresponding silique wall at these two stages were subjected to transcriptomic sequencing analysis. 135 genes related to GS metabolism were identified, of which 24 genes were transcription factors, 81 genes were related to biosynthetic pathway, 25 genes encoded catabolic enzymes, and 5 genes matched with transporters. The expression of GS biosynthetic genes was detected both in seeds and silique walls. The high expression of FMOGS-OX and AOP2, which is related to the production of gluconapin by side modification, was noted in seeds at both stages. Interestingly, the expression of GS biosynthetic genes was higher in the silique wall compared with that in the seed albeit lower content of GS existed in the silique wall than in the seed. Combined with the higher expression of transporter genes GTRs in silique walls than in seeds, it was proposed that the transportation of GS from the silique wall to the seed is an important source for seed GS accumulation. In addition, genes related to GS degradation expressed abundantly in the seed at the early cotyledonary-embryo stage indicating its potential role in balancing seed GS content. Conclusions Two stages including the torpedo-embryo and the early cotyledonary-embryo stage were identified as crucial in GS accumulation during seed development. Moreover, we confirmed the transportation of GS from the silique wall to the seed and proposed possible sidechain modification of GS biosynthesis may exist during seed formation.
    Electronic ISSN: 1471-2229
    Topics: Biology
    Published by BioMed Central
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  • 66
    Publication Date: 2021-08-21
    Description: Background Drug–drug interactions (DDIs) refer to processes triggered by the administration of two or more drugs leading to side effects beyond those observed when drugs are administered by themselves. Due to the massive number of possible drug pairs, it is nearly impossible to experimentally test all combinations and discover previously unobserved side effects. Therefore, machine learning based methods are being used to address this issue. Methods We propose a Siamese self-attention multi-modal neural network for DDI prediction that integrates multiple drug similarity measures that have been derived from a comparison of drug characteristics including drug targets, pathways and gene expression profiles. Results Our proposed DDI prediction model provides multiple advantages: (1) It is trained end-to-end, overcoming limitations of models composed of multiple separate steps, (2) it offers model explainability via an Attention mechanism for identifying salient input features and (3) it achieves similar or better prediction performance (AUPR scores ranging from 0.77 to 0.92) compared to state-of-the-art DDI models when tested on various benchmark datasets. Novel DDI predictions are further validated using independent data resources. Conclusions We find that a Siamese multi-modal neural network is able to accurately predict DDIs and that an Attention mechanism, typically used in the Natural Language Processing domain, can be beneficially applied to aid in DDI model explainability.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
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  • 67
    Publication Date: 2021-08-21
    Description: Background Modulating the microbiota is a leading-edge strategy for the restoration and maintenance of a healthy, balanced environment. The use of health-promoting bacteria has demonstrated some potential benefits as an alternative for skin microbiota intervention. Here, we investigate the manipulation of mice skin microbiota using B. subtilis incorporated into a supportive Pluronic F-127 hydrogel formulation. The formula plays an important role in delivering the bacteria to the desired action site. Results The B. subtilis challenge induced a shift in the composition and abundance of the skin microbiota. Containment of B. subtilis in the Pluronic F-127 hydrogel accelerated bacterial modulation compared with free B. subtilis. The abundance of both Staphylococcus and Corynebacterium spp. was altered as a result of the live bacterial intervention: the abundance of Corynebacterium increased while that of Staphylococcus decreased. Four days after last application of the B. subtilis formulation, B. subtilis counts returned to its initial level. Conclusions B. subtilis intervention can induce a shift in the skin microbiota, influencing the abundance of commensal, beneficial, and pathogenic bacteria. Containment of B. subtilis in Pluronic hydrogel accelerates the microbial alteration, probably by facilitating bacterial attachment and supporting continuous growth. Our results reveal the ability of B. subtilis in Pluronic to modulate the skin microbiota composition, suggesting that the formulation holds therapeutic potential for skin disease treatment.
    Electronic ISSN: 1471-2180
    Topics: Biology
    Published by BioMed Central
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  • 68
    Publication Date: 2021-08-21
    Description: Background Mycotoxins are among the environmental stressors whose oxidative action is currently widely studied. The aim of this paper was to investigate the response of seedling leaves to zearalenone (ZEA) applied to the leaves (directly) and to the grains (indirectly) in tolerant and sensitive wheat cultivars. Results Biochemical analyses of antioxidant activity were performed for chloroplasts and showed a similar decrease in this activity irrespective of plant sensitivity and the way of ZEA application. On the other hand, higher amounts of superoxide radical (microscopic observations) were generated in the leaves of plants grown from the grains incubated in ZEA solution and in the sensitive cultivar. Electron paramagnetic resonance (EPR) studies showed that upon ZEA treatment greater numbers of Mn - aqua complexes were formed in the leaves of the tolerant wheat cultivar than in those of the sensitive one, whereas the degradation of Fe-protein complexes occurred independently of the cultivar sensitivity. Conclusion The changes in the quantity of stable, organic radicals formed by stabilizing reactive oxygen species on biochemical macromolecules, indicated greater potential for their generation in leaf tissues subjected to foliar ZEA treatment. This suggested an important role of these radical species in protective mechanisms mainly against direct toxin action. The way the defense mechanisms were activated depended on the method of the toxin application.
    Electronic ISSN: 1471-2229
    Topics: Biology
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  • 69
    Publication Date: 2021-08-21
    Description: Background Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. Results In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. Conclusions Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.
    Electronic ISSN: 1471-2164
    Topics: Biology
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  • 70
    Publication Date: 2021-08-21
    Description: Background Panicle is a harvesting organ of rice, and its morphology and development are closely associated with grain yield. The current study was carried on a mutant screened through an EMS (ethyl-methane sulphonate) mutagenized population of a Japonica cultivar Kitaake (WT). Results A mutant, named as asp-lsl (aberrant spikelet-long sterile lemma), showed a significant decrease in plant height, number of tillers, thousand-grains weight, seed setting rate, spikelet length, kernel length and effective number of grains per panicle as compared to WT. Asp-lsl showed a pleiotropic phenotype coupled with the obvious presence of a long sterile lemma. Cross-sections of lemma showed an increase in the cell volume rather than the number of cells. Genetic segregation analysis revealed its phenotypic trait is controlled by a single recessive nuclear gene. Primary and fine mapping indicated that candidate gene controlling the phenotype of asp-lsl was located in an interval of 212 kb on the short arm of chromosome 8 between RM22445 and RM22453. Further sequencing and indels markers analysis revealed LOC_Os08g06480 harbors a single base substitution (G→A), resulting in a change of 521st amino acid(Gly→Glu. The homology comparison and phylogenetic tree analysis revealed mutation was occurred in a highly conserved domain and had a high degree of similarity in Arabidopsis, corn, and sorghum. The CRISPR/Cas9 mutant line of ASP-LSL produced a similar phenotype as that of asp-lsl. Subcellular localization of ASP-LSL revealed that its protein is localized in the nucleus. Relative expression analysis revealed ASP-LSL was preferentially expressed in panicle, stem, and leaves. The endogenous contents of GA, CTK, and IAA were found significantly decreased in asp-lsl as compared to WT. Conclusions Current study presents the novel phenotype of asp-lsl and also validate the previously reported function of OsREL2 (ROMOSA ENHANCER LOCI2), / ASP1(ABERRANT SPIKELET AND PANICLE 1).
    Electronic ISSN: 1471-2229
    Topics: Biology
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  • 71
    Publication Date: 2021-08-21
    Description: Background Recent advances in sequencing technologies have driven studies identifying the microbiome as a key regulator of overall health and disease in the host. Both 16S amplicon and whole genome shotgun sequencing technologies are currently being used to investigate this relationship, however, the choice of sequencing technology often depends on the nature and experimental design of the study. In principle, the outputs rendered by analysis pipelines are heavily influenced by the data used as input; it is then important to consider that the genomic features produced by different sequencing technologies may emphasize different results. Results In this work, we use public 16S amplicon and whole genome shotgun sequencing (WGS) data from the same dogs to investigate the relationship between sequencing technology and the captured gut metagenomic landscape in dogs. In our analyses, we compare the taxonomic resolution at the species and phyla levels and benchmark 12 classification algorithms in their ability to accurately identify host phenotype using only taxonomic relative abundance information from 16S and WGS datasets with identical study designs. Our best performing model, a random forest trained by the WGS dataset, identified a species (Bacteroides coprocola) that predominantly contributes to the abundance of leuB, a gene involved in branched chain amino acid biosynthesis; a risk factor for glucose intolerance, insulin resistance, and type 2 diabetes. This trend was not conserved when we trained the model using 16S sequencing profiles from the same dogs. Conclusions Our results indicate that WGS sequencing of dog microbiomes detects a greater taxonomic diversity than 16S sequencing of the same dogs at the species level and with respect to four gut-enriched phyla levels. This difference in detection does not significantly impact the performance metrics of machine learning algorithms after down-sampling. Although the important features extracted from our best performing model are not conserved between the two technologies, the important features extracted from either instance indicate the utility of machine learning algorithms in identifying biologically meaningful relationships between the host and microbiome community members. In conclusion, this work provides the first systematic machine learning comparison of dog 16S and WGS microbiomes derived from identical study designs.
    Electronic ISSN: 1756-0381
    Topics: Biology , Computer Science
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  • 72
    Publication Date: 2021-08-21
    Description: Background Aberrant expression of Aldo-Keto reductase family 1 member B10 (AKR1B10) was associated with tumor size and metastasis of breast cancer in our published preliminary studies. However, little is known about the detailed function and underlying molecular mechanism of AKR1B10 in the pathological process of breast cancer. Methods The relationship between elevated AKR1B10 expression and the overall survival and disease-free survival of breast cancer patients was analyzed by Kaplan–Meier Plotter database. Breast cancer cell lines overexpressing AKR1B10 (MCF-7/AKR1B10) and breast cancer cell lines with knockdown of AKR1B10 (BT-20/shAKR1B10) were constructed to analyze the impact of AKR1B10 expression on cell proliferation and migration of breast cancer. The expression levels of AKR1B10 were detected and compared in the breast cancer cell lines and tissues by RT-qPCR, western blot and immunohistochemistry. The proliferation of breast cancer cells was monitored by CCK8 cell proliferation assay, and the migration and invasion of breast cancer cells was observed by cell scratch test and transwell assay. The proliferation- and EMT-related proteins including cyclinD1, c-myc, Survivin, Twist, SNAI1, SLUG, ZEB1, E-cadherin, PI3K, p-PI3K, AKT, p-AKT, IKBα, p-IKBα, NF-κB p65, p-NF-κB p65 were detected by western blot in breast cancer cells. MCF-7/AKR1B10 cells were treated with LY294002, a PI3K inhibitor, to consider the impact of AKR1B10 overexpression on the PI3K/AKT/NF-κB signal cascade and the presence of NF-κB p65 in nuclear. In vivo tumor xenograft experiments were used to observe the role of AKR1B10 in breast cancer growth in mice. Results AKR1B10 expression was significantly greater in breast cancer tissue compared to paired non-cancerous tissue. The expression of AKR1B10 positively correlated with lymph node metastasis, tumor size, Ki67 expression, and p53 expression, but inversely correlated with overall and disease-free survival rates. Gene Ontology analysis showed that AKR1B10 activity contributes to cell proliferation. Overexpression of AKR1B10 facilitated the proliferation of MCF-7 cells, and induced the migration and invasion of MCF-7 cells in vitro in association with induction of epithelial-mesenchymal transition (EMT). Conversely, knockdown of AKR1B10 inhibited these effects in BT-20 cells. Mechanistically, AKR1B10 activated PI3K, AKT, and NF-κB p65, and induced nuclear translocation of NF-κB p65, and expression of proliferation-related proteins including c-myc, cyclinD1, Survivin, and EMT-related proteins including ZEB1, SLUG, Twist, but downregulated E-cadherin expression in MCF-7 cells. AKR1B10 silencing reduced the phosphorylation of PI3K, AKT, and NF-κB p65, the nuclear translocation of NF-κB p65, and the expression of proliferation- and migration-related proteins in BT-20 cells. LY294002, a PI3K inhibitor, attenuated the phosphorylation of PI3K, AKT, and NF-κB p65, and the nuclear translocation of NF-κB p65. In vivo tumor xenograft experiments confirmed that AKR1B10 promoted breast cancer growth in mice. Conclusions AKR1B10 promotes the proliferation, migration and invasion of breast cancer cells via the PI3K/AKT/NF-κB signaling pathway and represents a novel prognostic indicator as well as a potential therapeutic target in breast cancer.
    Electronic ISSN: 2045-3701
    Topics: Biology
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  • 73
    Publication Date: 2021-08-21
    Description: Background To enhance teleconsultation management, demands can be classified into different patterns, and the service of each pattern demand can be improved. Methods For the effective teleconsultation classification, a novel ensemble hierarchical clustering method is proposed in this study. In the proposed method, individual clustering results are first obtained by different hierarchical clustering methods, and then ensembled by one-hot encoding, the calculation and division of cosine similarity, and network graph representation. In the built network graph about the high cosine similarity, the connected demand series can be categorized into one pattern. For verification, 43 teleconsultation demand series are used as sample data, and the efficiency and quality of teleconsultation services are respectively analyzed before and after the demand classification. Results The teleconsultation demands are classified into three categories, erratic, lumpy, and slow. Under the fixed strategies, the service analysis after demand classification reveals the deficiencies of teleconsultation services, but analysis before demand classification can’t. Conclusion The proposed ensemble hierarchical clustering method can effectively category teleconsultation demands, and the effective demand categorization can enhance teleconsultation management.
    Electronic ISSN: 1472-6947
    Topics: Computer Science , Medicine
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  • 74
  • 75
    Publication Date: 2021-08-22
    Description: Aims Moso bamboo expansions into Japanese cedar forests are common. The expansion effects on soil nitrous oxide (N2O) emissions have not been thoroughly understood, and the underlying microbial mechanisms remain unclear. Methods We studied bacterial and fungal contribution to soil N2O emissions under moso bamboo or Japanese cedar by applying bacterial or fungal inhibitors using streptomycin and iprodione, respectively. Soil N2O emissions were measured and the relative contribution of bacteria and fungi to soil N2O emissions was calculated. Important Findings N2O emission from soil with moso bamboo was significantly higher than under Japanese cedar. Compared with control, bacterial or fungal inhibitor or their combination decreased N2O emissions, indicating substantial contribution of microbial activities to N2O emissions. However, the relative contribution of bacteria and fungi to N2O emissions was not affected by plants. Soil organic carbon, total and ammonium nitrogen were lower in soil under moso bamboo than Japanese cedar, suggesting faster microbial decomposition under moso bamboo. Fungal inhibitor and plants interactively affected soil pH, total phosphorus, and ammonium nitrogen, while bacterial inhibitor and plants interactively affected total nitrogen, indicating substantial dependence of effects by microbial communities on plant species. Moso bamboo and Japanese cedar differed in their effects on soil N2O emissions with higher emissions under moso bamboo. Stimulation of N2O emission under moso bamboo might occur due to higher nitrogen mineralization and subsequent denitrification induced by high root exudation. These results highlight the need to consider the effect of species shifts on N2O emissions in forests.
    Print ISSN: 1752-993X
    Electronic ISSN: 1752-9921
    Topics: Biology
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  • 76
    Publication Date: 2021-08-20
    Description: N6-methyladenosine (m6A) is the most abundant form of mRNA modification and controls many aspects of RNA metabolism including gene expression. However, the mechanisms by which m6A regulates cell- and condition-specific gene expression are still poorly understood, partly due to a lack of tools capable of identifying m6A sites that regulate gene expression under different conditions. Here we develop m6A-express, the first algorithm for predicting condition-specific m6A regulation of gene expression (m6A-reg-exp) from limited methylated RNA immunoprecipitation sequencing (MeRIP-seq) data. Comprehensive evaluations of m6A-express using simulated and real data demonstrated its high prediction specificity and sensitivity. When only a few MeRIP-seq samples may be available for the cellular or treatment conditions, m6A-express is particularly more robust than the log-linear model. Using m6A-express, we reported that m6A writers, METTL3 and METTL14, competitively regulate the transcriptional processes by mediating m6A-reg-exp of different genes in Hela cells. In contrast, METTL3 induces different m6A-reg-exp of a distinct group of genes in HepG2 cells to regulate protein functions and stress-related processes. We further uncovered unique m6A-reg-exp patterns in human brain and intestine tissues, which are enriched in organ-specific processes. This study demonstrates the effectiveness of m6A-express in predicting condition-specific m6A-reg-exp and highlights the complex, condition-specific nature of m6A-regulation of gene expression.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 77
    Publication Date: 2021-08-20
    Description: The Internal Linear Combination (ILC) method has been extensively used to extract the cosmic microwave background (CMB) anisotropy map from foreground contaminated multi-frequency maps. However, the performance of simple ILC is limited and can be significantly improved by heavily constraint equations, dubbed constrained ILC (cILC). The standard ILC and cILC works on spin-0 fields. Recently, a generalised version of ILC has been developed, named Polarization ILC (PILC), in which Q ± iU at multiple frequencies are combined using complex coefficients to estimate Stokes Q and U maps. A statistical moment expansion method has recently been developed for high precision modelling of the Galactic foregrounds. This paper develops a semi-blind component separation method combining the moment approach of foreground modelling with a generalised version of the PILC method for heavily constraint equations. The algorithm is developed in pixel space over a spin-2 field. We demonstrate the performance of the method on three sets of absolutely calibrated simulated maps at WMAP and Planck frequencies with varying foreground models. We apply this component separation technique in simultaneous estimation of Stokes Q and U maps of the thermal dust at 353 GHz and synchrotron at 30 GHz. We also recover both dust and synchrotron maps at 100 and 143 GHz, where separating two components is challenging.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 78
    Publication Date: 2021-08-20
    Description: As the robustness for the wave equation-based inversion methods, wave equation migration velocity analysis (WEMVA) is stable for overcoming the multipathing problem and has become popular in recent years. As a rapidly developed method, differential semblance optimisation (DSO) is convenient to implement and can automatically detect the moveout existing in common image gathers (CIGs). However, by implementing in the image domain with the target of minimising moveouts and improving coherence of the CIGs, the DSO method often suffers from imaging artefacts caused by uneven illumination and irregular observation geometry, which may produce poor velocity updates with artefact contamination. To deal with this issue, in this paper, by introducing Wiener-like filters, we modify the conventional image matching-based objective function to a new one by introducing the quadratic Wasserstein metric technique. The new misfit function measures the distance of two distributions obtained by the convolutional filters and target functions. With the new misfit function, the adjoint sources and the corresponding gradients are improved. We apply the new method to two numerical examples and one field dataset. The corresponding results indicate that the new method is robust to compensate low frequency components of velocity models.
    Print ISSN: 1742-2132
    Electronic ISSN: 1742-2140
    Topics: Geosciences
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  • 79
    Publication Date: 2021-08-20
    Description: Background The plant body in duckweed species has undergone reduction and simplification from the ancient Spirodela species towards more derived Wolffia species. Among the five duckweed genera, Wolffia members are rootless and represent the smallest and most reduced species. A better understanding of Wolffia frond architecture is necessary to fully explore duckweed evolution. Results We conducted a comprehensive study of the morphology and anatomy of Wolffia globosa, the only Wolffia species in China. We first used X-ray microtomography imaging to reveal the three-dimensional and internal structure of the W. globosa frond. This showed that new fronds rapidly budded from the hollow reproductive pocket of the mother fronds and that several generations at various developmental stages could coexist in a single W. globosa frond. Using light microscopy, we observed that the meristem area of the W. globosa frond was located at the base of the reproductive pocket and composed of undifferentiated cells that continued to produce new buds. A single epidermal layer surrounded the W. globosa frond, and the mesophyll cells varied from small and dense palisade-like parenchyma cells to large, vacuolated cells from the ventral to the dorsal part. Furthermore, W. globosa fronds contained all the same organelles as other angiosperms; the most prominent organelles were chloroplasts with abundant starch grains. Conclusions Our study revealed that the reproductive strategy of W. globosa plants enables the rapid accumulation of biomass and the wide distribution of this species in various habitats. The reduced body plan and size of Wolffia are consistent with our observation that relatively few cell types are present in these plants. We also propose that W. globosa plants are not only suitable for the study of structural reduction in higher plants, but also an ideal system to explore fundamental developmental processes of higher plants that cannot be addressed using other model plants.
    Electronic ISSN: 1471-2229
    Topics: Biology
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  • 80
    Publication Date: 2021-08-20
    Description: Background Structural variants (SVs) significantly drive genome diversity and environmental adaptation for diverse species. Unlike the prevalent small SVs (〈 kilobase-scale) in higher eukaryotes, large-size SVs rarely exist in the genome, but they function as one of the key evolutionary forces for speciation and adaptation. Results In this study, we discover and characterize several megabase-scale presence-absence variations (PAVs) in the maize genome. Surprisingly, we identify a 3.2 Mb PAV fragment that shows high integrity and is present as complete presence or absence in the natural diversity panel. This PAV is embedded within the nucleolus organizer region (NOR), where the suppressed recombination is found to maintain the PAV against the evolutionary variation. Interestingly, by analyzing the sequence of this PAV, we not only reveal the domestication trace from teosinte to modern maize, but also the footprints of its origin from Tripsacum, shedding light on a previously unknown contribution from Tripsacum to the speciation of Zea species. The functional consequence of the Tripsacum segment migration is also investigated, and environmental fitness conferred by the PAV may explain the whole segment as a selection target during maize domestication and improvement. Conclusions These findings provide a novel perspective that Tripsacum contributes to Zea speciation, and also instantiate a strategy for evolutionary and functional analysis of the “fossil” structure variations during genome evolution and speciation.
    Print ISSN: 1465-6906
    Electronic ISSN: 1474-760X
    Topics: Biology
    Published by BioMed Central
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  • 81
    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.
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    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 82
    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.
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  • 83
    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.
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  • 84
    Publication Date: 2021-08-06
    Description: Motivation The investigation of quantitative trait loci (QTL) is an essential component in our understanding of how organisms vary phenotypically. However, many important crop species are polyploid (carrying more than two copies of each chromosome), requiring specialized tools for such analyses. Moreover, deciphering meiotic processes at higher ploidy levels is not straightforward, but is necessary to understand the reproductive dynamics of these species, or uncover potential barriers to their genetic improvement. Results Here, we present polyqtlR, a novel software tool to facilitate such analyses in (auto)polyploid crops. It performs QTL interval mapping in F1 populations of outcrossing polyploids of any ploidy level using identity-by-descent probabilities. The allelic composition of discovered QTL can be explored, enabling favourable alleles to be identified and tracked in the population. Visualization tools within the package facilitate this process, and options to include genetic co-factors and experimental factors are included. Detailed information on polyploid meiosis including prediction of multivalent pairing structures, detection of preferential chromosomal pairing and location of double reduction events can be performed. Availabilityand implementation polyqtlR is freely available from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/package=polyqtlR. Supplementary information Supplementary data are available at Bioinformatics online.
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  • 85
    Publication Date: 2021-08-20
    Description: Circular RNAs (circRNAs) are widely expressed in highly diverged eukaryotes. Although circRNAs have been known for many years, their function remains unclear. Interaction with RNA-binding protein (RBP) to influence post-transcriptional regulation is considered to be an important pathway for circRNA function, such as acting as an oncogenic RBP sponge to inhibit cancer. In this study, we design a deep learning framework, CRPBsites, to predict the binding sites of RBPs on circRNAs. In this model, the sequences of variable-length binding sites are transformed into embedding vectors by word2vec model. Bidirectional LSTM is used to encode the embedding vectors of binding sites, and then they are fed into another LSTM decoder for decoding and classification tasks. To train and test the model, we construct four datasets that contain sequences of variable-length binding sites on circRNAs, and each set corresponds to an RBP, which is overexpressed in bladder cancer tissues. Experimental results on four datasets and comparison with other existing models show that CRPBsites has superior performance. Afterwards, we found that there were highly similar binding motifs in the four binding site datasets. Finally, we applied well-trained CRPBsites to identify the binding sites of IGF2BP1 on circCDYL, and the results proved the effectiveness of this method. In conclusion, CRPBsites is an effective prediction model for circRNA-RBP interaction site identification. We hope that CRPBsites can provide valuable guidance for experimental studies on the influence of circRNA on post-transcriptional regulation.
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  • 86
    Publication Date: 2021-08-20
    Description: Intratumoral heterogeneity is a well-documented feature of human cancers and is associated with outcome and treatment resistance. However, a heterogeneous tumor transcriptome contributes an unknown level of variability to analyses of differentially expressed genes (DEGs) that may contribute to phenotypes of interest, including treatment response. Although current clinical practice and the vast majority of research studies use a single sample from each patient, decreasing costs of sequencing technologies and computing power have made repeated-measures analyses increasingly economical. Repeatedly sampling the same tumor increases the statistical power of DEG analysis, which is indispensable toward downstream analysis and also increases one’s understanding of within-tumor variance, which may affect conclusions. Here, we compared five different methods for analyzing gene expression profiles derived from repeated sampling of human prostate tumors in two separate cohorts of patients. We also benchmarked the sensitivity of generalized linear models to linear mixed models for identifying DEGs contributing to relevant prostate cancer pathways based on a ground-truth model.
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  • 87
    Publication Date: 2021-08-20
    Description: Single-molecule (particle) tracking is a powerful method to study dynamic processes in cells at highest possible spatial and temporal resolution. We have developed SMTracker, a graphical user interface for automatic quantifying, visualizing and managing of data. Version 2.0 determines distributions of positional displacements in x- and y-direction using multi-state diffusion models, discriminates between Brownian, sub- or superdiffusive behaviour, and locates slow or fast diffusing populations in a standardized cell. Using SMTracker, we show that the Bacillus subtilis RNA degradosome consists of a highly dynamic complex of RNase Y and binding partners. We found similar changes in molecule dynamics for RNase Y, CshA, PNPase and enolase, but not for phosphofructokinase, RNase J1 and J2, to inhibition of transcription. However, the absence of PfkA or of RNase J2 affected molecule dynamics of RNase Y-mVenus, indicating that these two proteins are indeed part of the degradosome. Molecule counting suggests that RNase Y is present as a dimer in cells, at an average copy number of about 500, of which 46% are present in a slow-diffusive state and thus likely engaged within degradosomes. Thus, RNase Y, CshA, PNPase and enolase likely play central roles, and RNase J1, J2 and PfkA more peripheral roles, in degradosome architecture.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 88
    Publication Date: 2021-08-20
    Description: Academic human capital (AHC) is a key element in the explanation of scientific productivity. However, few studies have analysed this topic in the academic context, and their conclusions about composition and measurement remain ambiguous. This study proposes a measurement scale to assess AHC, following a systemic procedure composed of two steps: qualitative and quantitative phases. First, the Delphi technique was applied to reach a consensus on the AHC factors, resulting in a scale of 22 items. Second, exploratory and confirmatory factor analyses were conducted to determine the underlying factorial structure of the scale, using a sample of 2,223 researchers in Spanish universities. The results provided a five-dimensional structure of AHC, measuring the knowledge and abilities required to perform research activities, as well as skills related to the organisation of scientific processes, alertness to research opportunities, and the openness to provide and receive criticism. This study poses interesting challenges for knowledge management in universities.
    Print ISSN: 0302-3427
    Electronic ISSN: 1471-5430
    Topics: Nature of Science, Research, Systems of Higher Education, Museum Science
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  • 89
    Publication Date: 2021-08-20
    Description: Efforts to elucidate protein–DNA interactions at the molecular level rely in part on accurate predictions of DNA-binding residues in protein sequences. While there are over a dozen computational predictors of the DNA-binding residues, they are DNA-type agnostic and significantly cross-predict residues that interact with other ligands as DNA binding. We leverage a custom-designed machine learning architecture to introduce DNAgenie, first-of-its-kind predictor of residues that interact with A-DNA, B-DNA and single-stranded DNA. DNAgenie uses a comprehensive physiochemical profile extracted from an input protein sequence and implements a two-step refinement process to provide accurate predictions and to minimize the cross-predictions. Comparative tests on an independent test dataset demonstrate that DNAgenie outperforms the current methods that we adapt to predict residue-level interactions with the three DNA types. Further analysis finds that the use of the second (refinement) step leads to a substantial reduction in the cross predictions. Empirical tests show that DNAgenie’s outputs that are converted to coarse-grained protein-level predictions compare favorably against recent tools that predict which DNA-binding proteins interact with double-stranded versus single-stranded DNAs. Moreover, predictions from the sequences of the whole human proteome reveal that the results produced by DNAgenie substantially overlap with the known DNA-binding proteins while also including promising leads for several hundred previously unknown putative DNA binders. These results suggest that DNAgenie is a valuable tool for the sequence-based characterization of protein functions. The DNAgenie’s webserver is available at http://biomine.cs.vcu.edu/servers/DNAgenie/.
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  • 90
    Publication Date: 2021-08-20
    Description: Accurate prediction of immunogenic peptide recognized by T cell receptor (TCR) can greatly benefit vaccine development and cancer immunotherapy. However, identifying immunogenic peptides accurately is still a huge challenge. Most of the antigen peptides predicted in silico fail to elicit immune responses in vivo without considering TCR as a key factor. This inevitably causes costly and time-consuming experimental validation test for predicted antigens. Therefore, it is necessary to develop novel computational methods for precisely and effectively predicting immunogenic peptide recognized by TCR. Here, we described DLpTCR, a multimodal ensemble deep learning framework for predicting the likelihood of interaction between single/paired chain(s) of TCR and peptide presented by major histocompatibility complex molecules. To investigate the generality and robustness of the proposed model, COVID-19 data and IEDB data were constructed for independent evaluation. The DLpTCR model exhibited high predictive power with area under the curve up to 0.91 on COVID-19 data while predicting the interaction between peptide and single TCR chain. Additionally, the DLpTCR model achieved the overall accuracy of 81.03% on IEDB data while predicting the interaction between peptide and paired TCR chains. The results demonstrate that DLpTCR has the ability to learn general interaction rules and generalize to antigen peptide recognition by TCR. A user-friendly webserver is available at http://jianglab.org.cn/DLpTCR/. Additionally, a stand-alone software package that can be downloaded from https://github.com/jiangBiolab/DLpTCR.
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  • 91
    Publication Date: 2021-08-21
    Description: Unlike other developed countries, the Fourth Industrial Revolution (4IR) discourse has become the central element within technology governance in Korea. This paper examines the reasons for the discourse’s success and its political and social implications. Based on the analysis of policy documents and the media coverage, I argue that political and economic elites have actively introduced the 4IR discourse to create novel momentum for promoting Information and Communications Technology (ICT) and to justify deregulatory measures while re-enacting the developmentalist imaginary. I also highlight that the 4IR discourse’s promoters have drawn upon the dialectics between the desirable future and the nation’s shared fear to urge the Korean society to accept the measures privileging the industry as the means of making the nation a developed country and avoiding being colonized again.
    Print ISSN: 0302-3427
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    Topics: Nature of Science, Research, Systems of Higher Education, Museum Science
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  • 92
    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
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    Topics: Physics
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  • 93
    Publication Date: 2021-07-10
    Description: Glioblastoma (GB) is the most aggressive and common form of primary brain tumor characterized by fast proliferation, high invasion and resistance to current standard treatment. The average survival rate post-diagnosis is 14.6 months, despite the aggressive standard post-surgery radiotherapy concomitant with chemotherapy with temozolomide (TMZ). Currently, efforts are being endowed to develop new and more efficient therapeutic approaches capable to overcome chemoresistance, inhibit tumor progression and improve overall patient survival rate. Abnormal microRNA (miRNA) expression has been correlated with chemoresistance, proliferation and resistance to apoptosis, which result from their master regulatory role of gene expression. Altered cell metabolism, favoring glycolysis, was identified as an emerging cancer hallmark and has been described in GB, thus offering a new target for innovative GB therapies. In this work, we hypothesized that a gene therapy-based strategy consisting of the overexpression of a miRNA downregulated in GB and predicted to target crucial metabolic enzymes might promote a shift of GB cell metabolism, decreasing the glycolytic dependence of tumor cells and contributing to their sensitization to chemotherapy with TMZ. The increase of miR-200c levels in DBTRG cells resulted in downregulation of messenger RNA of enzymes involved in bioenergetics pathways and impaired cell metabolism and mobility. In addition, miR-200c overexpression prior to DBTRG cell exposure to TMZ resulted in cell cycle arrest. Overall, our results show that miR-200c overexpression could offer a way to overcome chemoresistance developed by GB cells in response to current standard chemotherapy, providing an improvement to current GB standard treatment, with benefit for patient outcome.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 94
    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.
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    Electronic ISSN: 1464-3774
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  • 95
    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.
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  • 96
    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.
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  • 97
    Publication Date: 2021-05-28
    Description: La Réunion Island includes two major volcanic systems. About 0·5 Myr ago, Piton des Neiges volcano declined, while Piton de la Fournaise volcano grew on its flank. Since then the Piton de la Fournaise shield volcano has produced homogeneous lavas with chemical compositions transitional between alkali and tholeiitic basalts. In April 2007, the volcano emitted a very small volume of trachytic pumice during its largest historical eruption. We conducted a comprehensive petrological and geochemical study of the pumice to understand the occurrence of such silicic melt in the feeding system of this highly active basaltic volcano. Isotopes of Sr, Nd, Pb and O, together with trace elements, indicate that the trachyte is genetically related to the La Réunion mantle plume and derives from crystallization of a typical basalt. The trachyte chemistry records a long and complex history of differentiation and outgassing. The extensive depletion of moderately volatile elements (F, Cl, B, Cs, Cu, Li) and less volatile uranium is consistent with exsolution of dense fluids at depths of several kilometres. Lithium isotopes point to closed-system degassing during the very late stages of crystallization. U-series isotopes and radiogenic 208Pb*/206Pb* constrain the age of U loss to between 0·4 and 2·1 Ma. This age is as old as or older than the Piton de la Fournaise shield edifice. The 2007 trachyte could thus be a liquid remnant of an extinct volcano, such as Piton des Neiges or Les Alizés (Piton de la Fournaise proto-volcano). It could also result from partial melting of an old syenite intrusion or remobilization of interstitial melts not fully solidified. Thermal modelling indicates that the sustained heat flux from hot basaltic magmas rising from the mantle can maintain temperatures above 800 °C in the central feeding system, and prevent total solidification of magmas trapped in this hot core.
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  • 98
    Publication Date: 2021-07-11
    Description: Motivation The investigation of the structure of biological systems at the molecular level gives insights about their functions and dynamics. Shape and surface of biomolecules are fundamental to molecular recognition events. Characterizing their geometry can lead to more adequate predictions of their interactions. In the present work, we assess the performance of reference shape retrieval methods from the computer vision community on protein shapes. Results Shape retrieval methods are efficient in identifying orthologous proteins and tracking large conformational changes. This work illustrates the interest for the protein surface shape as a higher-level representation of the protein structure that (i) abstracts the underlying protein sequence, structure or fold, (ii) allows the use of shape retrieval methods to screen large databases of protein structures to identify surficial homologs and possible interacting partners and (iii) opens an extension of the protein structure–function paradigm toward a protein structure-surface(s)-function paradigm. Availabilityand implementation All data are available online at http://datasetmachat.drugdesign.fr. Supplementary information Supplementary data are available at Bioinformatics online.
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  • 99
    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.
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  • 100
    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.
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