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  • Frontiers Media  (285)
  • Institute of Physics  (219)
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  • 1
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    American Physical Society (APS)
    In:  EPIC3Physical Review Letters, American Physical Society (APS), 130(18), pp. 188401-188401, ISSN: 0031-9007
    Publication Date: 2023-12-05
    Description: It has been postulated that the brain operates in a self-organized critical state that brings multiple benefits, such as optimal sensitivity to input. Thus far, self-organized criticality has typically been depicted as a one-dimensional process, where one parameter is tuned to a critical value. However, the number of adjustable parameters in the brain is vast, and hence critical states can be expected to occupy a high-dimensional manifold inside a high-dimensional parameter space. Here, we show that adaptation rules inspired by homeostatic plasticity drive a neuro-inspired network to drift on a critical manifold, where the system is poised between inactivity and persistent activity. During the drift, global network parameters continue to change while the system remains at criticality.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 2
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    American Physical Society (APS)
    In:  EPIC3Physical Review E, American Physical Society (APS), 105(4), pp. 044310-044310, ISSN: 2470-0045
    Publication Date: 2023-12-05
    Description: Current questions in ecology revolve around instabilities in the dynamics on spatial networks and particularly the effect of node heterogeneity. We extend the master stability function formalism to inhomogeneous biregular networks having two types of spatial nodes. Notably, this class of systems also allows the investigation of certain types of dynamics on higher-order networks. Combined with the generalized modeling approach to study the linear stability of steady states, this is a powerful tool to numerically asses the stability of large ensembles of systems. We analyze the stability of ecological metacommunities with two distinct types of habitats analytically and numerically in order to identify several sets of conditions under which the dynamics can become stabilized by dispersal. Our analytical approach allows general insights into stabilizing and destabilizing effects in metapopulations. Specifically, we identify self-regulation and negative feedback loops between source and sink populations as stabilizing mechanisms and we show that maladaptive dispersal may be stable under certain conditions.
    Repository Name: EPIC Alfred Wegener Institut
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  • 3
    Publication Date: 2023-02-21
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Fairall, C. W. W., Yang, M., Brumer, S. E. E., Blomquist, B. W. W., Edson, J. B. B., Zappa, C. J. J., Bariteau, L., Pezoa, S., Bell, T. G. G., & Saltzman, E. S. S. Air-Sea trace gas fluxes: direct and indirect measurements. Frontiers in Marine Science, 9, (2022): 826606, https://doi.org/10.3389/fmars.2022.826606.
    Description: The past decade has seen significant technological advance in the observation of trace gas fluxes over the open ocean, most notably CO2, but also an impressive list of other gases. Here we will emphasize flux observations from the air-side of the interface including both turbulent covariance (direct) and surface-layer similarity-based (indirect) bulk transfer velocity methods. Most applications of direct covariance observations have been from ships but recently work has intensified on buoy-based implementation. The principal use of direct methods is to quantify empirical coefficients in bulk estimates of the gas transfer velocity. Advances in direct measurements and some recent field programs that capture a considerable range of conditions with wind speeds exceeding 20 ms-1 are discussed. We use coincident direct flux measurements of CO2 and dimethylsulfide (DMS) to infer the scaling of interfacial viscous and bubble-mediated (whitecap driven) gas transfer mechanisms. This analysis suggests modest chemical enhancement of CO2 flux at low wind speed. We include some updates to the theoretical structure of bulk parameterizations (including chemical enhancement) as framed in the COAREG gas transfer algorithm.
    Description: This work, and the contributions of MY and TB, is supported by the UK Natural Environment Research Council’s ORCHESTRA (Grant No. NE/N018095/1) and PICCOLO (Grant No. NE/P021409/1) projects, and by the European Space Agency’s AMT4OceanSatFlux project (Grant No. 4000125730/18/NL/FF/gp). CF and BB are funded by the National Oceanic and Atmospheric Administration’s Global Ocean Monitoring and Observing program (http://data.crossref.org/fundingdata/funder/10.13039/100018302). CZ was funded by the National Science Foundation (CJZ: OCE-2049579, Grants OCE-1537890 and OCE-1923935). Funding for HiWinGS was provided by the US National Science Foundation grant AGS-1036062. The Knorr-11 and SOAP campaigns were supported by the NSF Atmospheric Chemistry Program (Grant No. ATM-0426314, AGS-08568, -0851472, -0851407 and -1143709).
    Keywords: Gas transfer velocity ; Chemical enhancement ; Bubble mediated transfer ; COARE gas flux parameterization ; Dimethylsufide (DMS) ; Cardon dioxide (CO2) ; Bulk algorithm ; Direct observation
    Repository Name: Woods Hole Open Access Server
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  • 4
    Publication Date: 2023-02-16
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sayigh, L., Janik, V., Jensen, F., Scott, M., Tyack, P., & Wells, R. The Sarasota Dolphin whistle database: a unique long-term resource for understanding dolphin communication. Frontiers in Marine Science, 9, (2022): 923046, https://doi.org/10.3389/fmars.2022.923046.
    Description: Common bottlenose dolphins (Tursiops truncatus) produce individually distinctive signature whistles that are learned early in life and that help animals recognize and maintain contact with conspecifics. Signature whistles are the predominant whistle type produced when animals are isolated from conspecifics. Health assessments of dolphins in Sarasota, Florida (USA) provide a unique opportunity to record signature whistles, as dolphins are briefly separated from conspecifics. Recordings were first made in the mid 1970’s, and then nearly annually since 1984. The Sarasota Dolphin Whistle Database (SDWD) now contains 926 recording sessions of 293 individual dolphins, most of known age, sex, and matrilineal relatedness. The longest time span over which an individual has been recorded is 43 years, and 85 individuals have been recorded over a decade or more. Here we describe insights about signature whistle structure revealed by this unique and expansive dataset. Signature whistles of different dolphins show great variety in their fundamental frequency contours. Signature whistle types (with ‘whistle type’ defined as all whistles visually categorized as sharing a particular frequency modulation pattern) can consist of a single stereotyped element, or loop (single-loop whistles), or of multiple stereotyped loops with or without gaps (multi-loop whistles). Multi-loop signature whistle types can also show extensive variation in both number and contour of loops. In addition, fundamental frequency contours of all signature whistle types can be truncated (deletions) or embellished (additions), and other features are also occasionally incorporated. However, even with these variable features, signature whistle types tend to be highly stereotyped and easily distinguishable due to the extensive variability in contours among individuals. In an effort to quantify this individual distinctiveness, and to compare it to other species, we calculated Beecher’s Information Statistic and found it to be higher than for any other animal signal studied so far. Thus, signature whistles have an unusually high capacity to convey information on individual identity. We briefly review the large range of research projects that the SDWD has enabled thus far, and look ahead to its potential to answer a broad suite of questions about dolphin communication.
    Description: Funding for data collection and analysis over the years has been provided by the National Science Foundation, The Royal Society of London, Dolphin Quest, Adelaide M. and Charles B. Link Foundation, Marine Mammal Commission, National Oceanic and Atmospheric Administration, Earthwatch Institute, Protect Wild Dolphins Fund of the Harbor Branch Oceanographic Institute, Grossman Family Foundation, WHOI Ocean Life Institute, Vulcan Machine Learning Center for Impact, and the Allen Institute for Artificial Intelligence. Current support for PT’s involvement is provided by the Office of Naval Research Grants N00014-18-1-2062 and N00014-20-1-2709 through a subaward from Carnegie Mellon University. Current support for LS’s involvement is provided by the Adelaide M. & Charles B. Link Foundation and Dolphin Quest.
    Keywords: Signature whistle ; Communication ; Cognition ; Database ; Individual identity
    Repository Name: Woods Hole Open Access Server
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  • 5
    Publication Date: 2023-02-28
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lillis, A., & Mooney, T. Sounds of a changing sea: temperature drives acoustic output by dominant biological sound-producers in shallow water habitats. Frontiers in Marine Science, 9, (2022): 960881, https://doi.org/10.3389/fmars.2022.960881.
    Description: The ocean’s soundscape is fundamental to marine ecosystems, not only as a source of sensory information critical to many ecological processes but also as an indicator of biodiversity and habitat health. Yet, little is known about how ecoacoustic activity in marine habitats is altered by environmental changes such as temperature. The sounds produced by dense colonies of snapping shrimp dominate temperate and tropical coastal soundscapes worldwide and are a major driver broadband sound pressure level (SPL) patterns. Field recordings of soundscape patterns from the range limit of a snapping shrimp distribution showed that rates of snap production and associated SPL were closely positively correlated to water temperature. Snap rates changed by 15-60% per °C change in regional temperature, accompanied by fluctuations in SPL between 1-2 dB per °C. To test if this relationship was due to a direct effect of temperature, we measured snap rates in controlled experiments using two snapping shrimp species dominant in the Western Atlantic Ocean and Gulf of Mexico (Alpheus heterochaelis and A. angulosus). Snap rates were measured for shrimp held at different temperatures (across 10-30 °C range, with upper limit 2°C above current summer mean temperatures) and under different social groupings. Temperature had a significant effect on shrimp snap rates for all social contexts tested (individuals, pairs, and groups). For individuals and shrimp groups, snap production more than doubled between mid-range (20°C) and high (30°C) temperature treatments. Given that snapping shrimp sounds dominate the soundscapes of diverse habitats, including coral reefs, rocky bottoms, seagrass, and oyster beds, the strong influence of temperature on their activity will potentially alter soundscape patterns broadly. Increases in ambient sound levels driven by elevated water temperatures has ecological implications for signal detection, communication, and navigation in key coastal ecosystems for a wide range of organisms, including humans.
    Description: Financial support was provided by NSF Biological Oceanography Grant #1536782, Woods Hole Oceanographic Institution’s Interdisciplinary Award and Postdoctoral Scholar Programs.
    Keywords: Soundscape ; Underwater noise ; Acoustic ecology ; Acoustic monitoring ; Crustacean ; Ecoacoustics
    Repository Name: Woods Hole Open Access Server
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  • 6
    Publication Date: 2023-03-02
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Koguchi, Y., Tokuhiro, K., Ashjian, C., Campbell, R., & Yamaguchi, A. Inter-species comparison of the copepodite stage morphology, vertical distribution, and seasonal population structure of five sympatric mesopelagic aetideid copepods in the western Arctic Ocean. Frontiers in Marine Science, 9, (2022): 943100, https://doi.org/10.3389/fmars.2022.943100.
    Description: Aetideidae is a calanoid copepod family dominant in the mesopelagic layer of the Arctic Ocean for which little ecological information is available because species identification, especially of early copepodite stages, is difficult. In this study, we developed a species identification flow for the whole copepodite stages of five sympatric aetideid copepods (Chiridius obtusifrons, Gaetanus tenuispinus, G. brevispinus, Aetideopsis multiserrata, and A. rostrata). Vertical distributions and seasonal population structures of these species were evaluated using a year-round sample time-series collected at the drifting ice station (SHEBA) in the western Arctic Ocean. Combinations of morphological characteristics (prosome length, cephalosome, and prosome widths) were used to identify the early copepodite stages to species. Aetideopsis rostrata was distributed in deep waters (1,032–1,065 m) throughout the year. The other species all were found at 600–700 m during the midnight sun. However, during the polar night, the vertical distributions of each species were distinct, resulting from ascent, descent, or depth maintenance, indicating seasonal vertical migration which may function to reduce inter-specific competition during the polar night when food resources are scarce. Reproduction timing varied among four aetideid copepods: C.obtusifrons and G. tenuispinus showed polar night ascent and reproduction at the end of the polar night, whereas G. brevispinus and A. multiserrata showed descent or depth maintenance during the polar night and reproduction at the beginning of the polar night. There was not sufficient data to examine reproduction timing of A. rostrata. Common for all aetideid species, δ15N values of the adult females indicate more carnivorous feeding modes during the polar night than those in the midnight sun. Such vertical distribution and timing of reproduction variation among these five aetideid copepods may function to reduce species competition in the mesopelagic layer of the Arctic Ocean.
    Description: Collection of the samples was supported in part by grants #OCE9707184 to CA and #OCE9707182 to RC from the US National Science Foundation. This work was partially supported by the Arctic Challenge for Sustainability II (ArCS II), Program Grant Number JPMXD1420318865. This research was also supported by the Environment Research and Technology Development Fund (JPMEERF20214002) of the Environmental Restoration and Conservation Agency of Japan. In addition, this work was partly supported by a Grant-in-Aid for Challenging Research (Pioneering) JP20K20573, and Scientific Research JP20H03054 (B), JP19H03037 (B), JP21H02263 (B), and JP17H01483 (A) from the Japanese Society for the Promotion of Science (JSPS).
    Keywords: Aetideidae ; Sympatric mesopelagic copepods ; Vertical distribution ; Population structure ; Reproduction ; The Arctic Ocean
    Repository Name: Woods Hole Open Access Server
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  • 7
    Publication Date: 2023-03-08
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Visser, A.-N., Wankel, S., Frey, C., Kappler, A., & Lehmann, M. Unchanged nitrate and nitrite isotope fractionation during heterotrophic and Fe(II)-mixotrophic denitrification suggest a non-enzymatic link between denitrification and Fe(II) oxidation. Frontiers in Microbiology, 13, (2022): 927475, https://doi.org/10.3389/fmicb.2022.927475.
    Description: Natural-abundance measurements of nitrate and nitrite (NOx) isotope ratios (δ15N and δ18O) can be a valuable tool to study the biogeochemical fate of NOx species in the environment. A prerequisite for using NOx isotopes in this regard is an understanding of the mechanistic details of isotope fractionation (15ε, 18ε) associated with the biotic and abiotic NOx transformation processes involved (e.g., denitrification). However, possible impacts on isotope fractionation resulting from changing growth conditions during denitrification, different carbon substrates, or simply the presence of compounds that may be involved in NOx reduction as co-substrates [e.g., Fe(II)] remain uncertain. Here we investigated whether the type of organic substrate, i.e., short-chained organic acids, and the presence/absence of Fe(II) (mixotrophic vs. heterotrophic growth conditions) affect N and O isotope fractionation dynamics during nitrate (NO3–) and nitrite (NO2–) reduction in laboratory experiments with three strains of putative nitrate-dependent Fe(II)-oxidizing bacteria and one canonical denitrifier. Our results revealed that 15ε and 18ε values obtained for heterotrophic (15ε-NO3–: 17.6 ± 2.8‰, 18ε-NO3–:18.1 ± 2.5‰; 15ε-NO2–: 14.4 ± 3.2‰) vs. mixotrophic (15ε-NO3–: 20.2 ± 1.4‰, 18ε-NO3–: 19.5 ± 1.5‰; 15ε-NO2–: 16.1 ± 1.4‰) growth conditions are very similar and fall within the range previously reported for classical heterotrophic denitrification. Moreover, availability of different short-chain organic acids (succinate vs. acetate), while slightly affecting the NOx reduction dynamics, did not produce distinct differences in N and O isotope effects. N isotope fractionation in abiotic controls, although exhibiting fluctuating results, even expressed transient inverse isotope dynamics (15ε-NO2–: –12.4 ± 1.3 ‰). These findings imply that neither the mechanisms ordaining cellular uptake of short-chain organic acids nor the presence of Fe(II) seem to systematically impact the overall N and O isotope effect during NOx reduction. The similar isotope effects detected during mixotrophic and heterotrophic NOx reduction, as well as the results obtained from the abiotic controls, may not only imply that the enzymatic control of NOx reduction in putative NDFeOx bacteria is decoupled from Fe(II) oxidation, but also that Fe(II) oxidation is indirectly driven by biologically (i.e., via organic compounds) or abiotically (catalysis via reactive surfaces) mediated processes co-occurring during heterotrophic denitrification.
    Description: This study was supported by the German Research Foundation (DFG)-funded RTG 1708 “Molecular Principles of Bacterial Survival Strategies.” Work performed under the supervision of ML was supported by the University of Basel funds.
    Keywords: Denitrification ; Nitrate/nitrite isotopes ; Iron oxidation ; Isotope fractionation ; Carbon substrate
    Repository Name: Woods Hole Open Access Server
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  • 8
    Publication Date: 2023-03-08
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Franks, B. R., Tyminski, J. P., Hussey, N. E., Braun, C. D., Newton, A. L., Thorrold, S. R., Fischer, G. C., McBride, B., & Hueter, R. E. Spatio-temporal variability in white shark (Carcharodon carcharias) movement ecology during residency and migration phases in the western North Atlantic. Frontiers in Marine Science, 8, (2021): 744202, https://doi.org/10.3389/fmars.2021.744202.
    Description: Understanding how mobile, marine predators use three-dimensional space over time is central to inform management and conservation actions. Combining tracking technologies can yield powerful datasets over multiple spatio-temporal scales to provide critical information for these purposes. For the white shark (Carcharodon carcharias), detailed movement and migration information over ontogeny, including inter- and intra-annual variation in timing of movement phases, is largely unknown in the western North Atlantic (WNA), a relatively understudied area for this species. To address this need, we tracked 48 large juvenile to adult white sharks between 2012 and 2020, using a combination of satellite-linked and acoustic telemetry. Overall, WNA white sharks showed repeatable and predictable patterns in horizontal movements, although there was variation in these movements related to sex and size. While most sharks undertook an annual migratory cycle with the majority of time spent over the continental shelf, some individuals, particularly adult females, made extensive forays into the open ocean as far east as beyond the Mid-Atlantic Ridge. Moreover, increased off-shelf use occurred with body size even though migration and residency phases were conserved. Summer residency areas included coastal Massachusetts and portions of Atlantic Canada, with individuals showing fidelity to specific regions over multiple years. An autumn/winter migration occurred with sharks moving rapidly south to overwintering residency areas in the southeastern United States Atlantic and Gulf of Mexico, where they remained until the following spring/summer. While broad residency and migration periods were consistent, migratory timing varied among years and among individuals within years. White sharks monitored with pop-up satellite-linked archival tags made extensive use of the water column (0–872 m) and experienced a broad range of temperatures (−0.9 – 30.5°C), with evidence for differential vertical use based on migration and residency phases. Overall, results show dynamic inter- and intra-annual three-dimensional patterns of movements conserved within discrete phases. These results demonstrate the value of using multiple tag types to track long-term movements of large mobile species. Our findings expand knowledge of the movements and migration of the WNA white shark population and comprise critically important information to inform sound management strategies for the species.
    Description: Primary funding for this work, including research shiptime, fishing operations, and acoustic and SPOT tags, was provided by OCEARCH and its sponsors. Funding for PSATs was provided by the Shark Foundation (Hai Siftung) and the Disney Conservation Fund. PSAT data analysis was supported by a grant from NOAA/National Sea Grant to RH. Support for RH’s contributions was provided by the Perry W. Gilbert Chair in Shark Research at Mote Marine Laboratory, NOAA, and OCEARCH.
    Keywords: White shark ; Western North Atlantic ; Telemetry ; Migration ; Fidelity
    Repository Name: Woods Hole Open Access Server
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  • 9
    Publication Date: 2023-03-11
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Conte, M., Pàmies, R., Honda, M., & Herndl, G. Editorial: the oceanic particle flux and its cycling within the deep water column. Frontiers in Earth Science, 10, (2022): 1020065, https://doi.org/10.3389/feart.2022.1020065.
    Description: The oceanic particle flux transfers energy and material from the surface through the water column to the seafloor. (See review by Conte (2019) and references therein). The particle flux fuels life below the sunlit photic zone, exerts a major control on the global cycling of carbon and particle-associated elements, and also plays a major role in long-term carbon sequestration. In this Research Topic we present a collection of articles that provide a broad overview of current research on the interlinked processes controlling the magnitude and composition of the oceanic particle flux, and its cycling and depth attenuation within the deep water column.
    Keywords: Particle flux ; Deep ocean ; Marine particles ; Ocean biogeochemistry ; Carbon cycling ; Marine chemistry
    Repository Name: Woods Hole Open Access Server
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  • 10
    Publication Date: 2021-10-29
    Description: The aim of the present work is to introduce a lens whose faces are a conical surface and a spherical surface. We illuminate this lens by a plane wavefront and its associated refracted wavefronts, light rays and caustic are computed. We find that the caustic region has two branches and can be virtual, real or one part virtual and the other real, depending on the values of the parameters characterizing the lens. Furthermore, we present a particular example where one of the branches of the caustic region is constituted by two segments of a line, one part is real and the other one virtual. The second branch is a two-dimensional surface with a singularity of the cusp ridge type such that its Gaussian curvature is different from zero. It is important to remark that for this example, the two branches of the caustic are disconnected. Because of this property and the result obtained by Berry and Balazs on the relationship between the acceleration of an Airy beam and the curvature of its corresponding caustic, we believe that using this optical element one could generate a scalar optical accelerating beam in the region where the caustic is a two-dimensional surface of revolution, and at the same time a scalar optical beam with similar properties to the Bessel beam of zero order in the region were the real caustic is a segment of a line along the optical axis.
    Print ISSN: 2040-8978
    Electronic ISSN: 2040-8986
    Topics: Physics
    Published by Institute of Physics
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  • 11
    Publication Date: 2021-10-29
    Description: Purpose The aim of this study was to assess the feasibility of the development and training of a deep learning object detection model for automating the assessment of fiducial marker migration and tracking of the prostate in radiotherapy patients. Methods and Materials A fiducial marker detection model was trained on the YOLO v2 detection framework using approximately 20,000 pelvis kV projection images with fiducial markers labelled. The ability of the trained model to detect marker positions was validated by tracking the motion of markers in a respiratory phantom and comparing detection data with the expected displacement from a reference position. Marker migration was then assessed in 14 prostate radiotherapy patients using the detector for comparison with previously conducted studies. This was done by determining variations in intermarker distance between the first and subsequent fractions in each patient. Results On completion of training, a detection model was developed that operated at a 96% detection efficacy and with a root mean square error of 0.3 pixels. By determining the displacement from a reference position in a respiratory phantom, experimentally and with the detector it was found that the detector was able to compute displacements with a mean accuracy of 97.8% when compared to the actual values. Interfraction marker migration was measured in 14 patients and the average and maximum ± standard deviation marker migration were found to be 2.0±0.9 mm and 2.3±0.9 mm, respectively. Conclusion This study demonstrates the benefits of pairing deep learning object detection, and image-guided radiotherapy and how a workflow to automate the assessment of organ motion and seed migration during prostate radiotherapy can be developed. The high detection efficacy and low error make the advantages of using a pre-trained model to automate the assessment of the target volume positional variation and the migration of fiducial markers between fractions.
    Electronic ISSN: 2057-1976
    Topics: Biology , Medicine , Physics , Technology
    Published by Institute of Physics
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  • 12
    Publication Date: 2021-10-29
    Description: Electron removal in collisions of alpha particles with neon dimers is studied using an independent-atom-independent-electron model based on the semiclassical approximation of heavy-particle collision physics. The dimer is assumed to be frozen at its equilibrium bond length and collision events for the two ion-atom subsystems are combined in an impact parameter by impact parameter fashion for three mutually perpendicular orientations. Both frozen atomic target and dynamic response model calculations are carried out using the coupled-channel two-center basis generator method. We pay particular attention to inner-valence Ne(2s) electron removal, which is associated with interatomic Coulombic decay (ICD), resulting in low-energy electron emission and dimer fragmentation. Our calculations confirm a previous experimental result at 150 keV/amu impact energy regarding the relative strength of ICD compared to direct electron emission. They further indicate that ICD is the dominant Ne+ + Ne+ fragmentation process below 10 keV/amu, suggesting that a strong low-energy electron yield will be observed in the ion-dimer system in a regime in which the creation of continuum electrons is a rare event in the ion-atom problem.
    Print ISSN: 0953-4075
    Electronic ISSN: 1361-6455
    Topics: Physics
    Published by Institute of Physics
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  • 13
    Publication Date: 2021-10-29
    Description: In general, superconducting tokamaks require low loop voltage current start up for the safety purpose of its poloidal field coils. The loop voltage inside the vacuum vessel of Steady-state Superconducting Tokamak (SST-1) is low in nature since its central solenoid is located outside the cryostat. The low loop voltage current start up of the SST-1 is routinely performed by Electron Cyclotron Resonance (ECR) method at the toroidal magnetic field Bt=1.5T(first harmonic) and 0.75T(second harmonic). Recently, an alternative RF based plasma current start up system had been planned for operating the machine specially for higher toroidal magnetic field regime 1.5T ≤ Bt ≤3T. The system is already developed based on an antenna system, made of series combinations of two at spiral antenna, to assist plasma current start up at lower inductive electric field. It is already tested and installed in SST-1 chamber. The system testing had been performed without background magnetic field within frequency regime 35-60MHz at present. The test results show that it can produce electron density ne ≈1016m-3 measured by the Langmuir probe in expense of 500W RF power. The spectroscopy results indicate that its capability to produce plasma density higher than 1013 m-3 and electron temperature Te = 2 -6eV. In addition, it also shows that the presence of turbulent electric field of the order of 106V/m at antenna center and finite anomalous temperature of neutral particles. Calculations show that the obtained density is enough for SST-1 low loop voltage plasma breakdown. The antenna system is also capable to produce plasma at higher frequencies. This article will discuss the development of the prototype and the installed antenna system along with their test results in detail.
    Print ISSN: 0741-3335
    Electronic ISSN: 1361-6587
    Topics: Physics
    Published by Institute of Physics
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  • 14
    Publication Date: 2021-10-29
    Description: Alport syndrome with intellectual disability (ATS-ID, AMME complex; OMIM #300194) is an X-linked contiguous gene deletion syndrome associated with an Xq22.3 locus mainly characterized by hematuria, renal failure, hearing loss/deafness, neurodevelopmental disorder (NDD), midface retrusion, and elliptocytosis. It is thought that ATS-ID is caused by the loss of function of COL4A5 (ATS) and FACL4 (ACSL4) genes through the interstitial (micro)deletion of chromosomal band Xq22.3. We report detailed phenotypic description and results from genome-wide screening of a Czech family with diagnosis ATS-ID (proband, maternal uncle, and two female carriers). Female carriers showed mild clinical features of microscopic hematuria only, while affected males displayed several novel clinical features associated with ATS-ID. Utilization of whole-exome sequencing discovered the presence of approximately 3 Mb of deletion in the Xq23 area, which affected 19 genes from TSC22D3 to CHRDL1. We compared the clinical phenotype with previously reported three ATS-ID families worldwide and correlated their clinical manifestations with the incidence of genes in both telomeric and centromeric regions of the deleted chromosomal area. In addition to previously described phenotypes associated with aberrations in AMMECR1 and FACL4, we identified two genes, members of tripartite motif family MID2 and subunit of the proteasome PA700/19S complex (PSMD10), respectively, as prime candidate genes responsible for additional clinical features observed in our patients with ATS-ID. Overall, our findings further improve the knowledge about the clinical impact of Xq23 deletions and bring novel information about phenotype/genotype association of this chromosomal aberration.
    Electronic ISSN: 1664-8021
    Topics: Biology , Medicine
    Published by Frontiers Media
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  • 15
    Publication Date: 2021-10-29
    Description: Quantum metrology requires a stable single-photon emission and a high single-photon purity. Since nitrogen-vacancy (NV-) centers provide both features at room temperature, they are promising candidates for the application in this field [1, 2]. The knowledge about a suitable sample preparation technique is crucial, because the quality of the single-photon emission strongly depends on the sample purity and on the spatial resolvability of the emitters. This work presents the comparison and optimization of various sample fabrication techniques of nitrogen vacancy center doped nanodiamonds on standard cover glasses. The preparation is followed by a comparative characterization of the centers of the various samples. The sample fabrication includes the removal of contaminants on the cover glass surface. This was carried out by using peroxymonosulfuric acid (piranha solution, H2SO5) in comparison to the commercially available lye Hellmanex III (by Hellma Analytics). After cleaning the cover glasses, volumes of various nanodiamond dilutions were applied via spin coating. In subsequent steps, the nanodiamonds themselves were cleaned with peroxymonosulfuric acid, too, to remove contaminants resulting from the manufacturing process, e.g. graphite. The samples were analyzed by using a confocal laser scanning microscope with an oil immersion objective. Single-photon purity was determined by measuring the second order correlation function with a Hanbury Brown and Twiss setup. Spectral analysis revealed the presence of NV-- and NV0-centers. It was shown that a suitable cleansing method has an immense impact on single-photon emission, as was proven by a comparative characterization of differently manufactured nanodiamonds.
    Electronic ISSN: 2631-8695
    Topics: Technology
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  • 16
    Publication Date: 2021-10-29
    Description: Akebia trifoliata is an important multiuse perennial plant that often suffers attacks from various pathogens due to its long growth cycle, seriously affecting its commercial value. The absence of research on the resistance (R) genes of A. trifoliata has greatly limited progress in the breeding of resistant varieties. Genes encoding proteins containing nucleotide binding sites (NBSs) and C-terminal leucine-rich repeats (LRRs), the largest family of plant resistance (R) genes, are vital for plant disease resistance. A comprehensive genome-wide analysis showed that there were only 73 NBS genes in the A. trifoliata genome, including three main subfamilies (50 coiled coil (CC)-NBS-LRR (CNL), 19 Toll/interleukin-1 receptor (TIR)-NBS-LRR (TNL) and four resistance to powdery mildew8 (RPW8)-NBS-LRR (RNL) genes). Additionally, 64 mapped NBS candidates were unevenly distributed on 14 chromosomes, most of which were assigned to the chromosome ends; 41 of these genes were located in clusters, and the remaining 23 genes were singletons. Both the CNLs and TNLs were further divided into four subgroups, and the CNLs had fewer exons than the TNLs. Structurally, all eight previously reported conserved motifs were identified in the NBS domains, and both their order and their amino acid sequences exhibited high conservation. Evolutionarily, tandem and dispersed duplications were shown to be the two main forces responsible for NBS expansion, producing 33 and 29 genes, respectively. A transcriptome analysis of three fruit tissues at four developmental stages showed that NBS genes were generally expressed at low levels, while a few of these genes showed relatively high expression during later development in rind tissues. Overall, this research is the first to identify and characterize A. trifoliata NBS genes and is valuable for both the development of new resistant cultivars and the study of molecular mechanisms of resistance.
    Electronic ISSN: 1664-462X
    Topics: Biology
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  • 17
    Publication Date: 2021-10-29
    Description: Data providers holding sensitive medical data often need to exchange data pertaining to patients for whom they hold particular data. This involves requesting information from other providers to augment the data they hold. However, revealing the superset of identifiers for which a provider requires information can, in itself, leak sensitive private data. Data linkage services exist to facilitate the exchange of anonymized identifiers between data providers. Reliance on third parties to provide these services still raises issues around the trust, privacy and security of such implementations. The rise and use of blockchain and distributed ledger technologies over the last decade has, alongside innovation and disruption in the financial sphere, also brought to the fore and refined the use of associated privacy-preserving cryptographic protocols and techniques. These techniques are now being adopted and used in fields removed from the original financial use cases. In this paper we present a combination of a blockchain-native auditing and trust-enabling environment alongside a query exchange protocol. This allows the exchange of sets of patient identifiers between data providers in such a way that only identifiers lying in the intersection of sets of identifiers are revealed and shared, allowing further secure and privacy-preserving exchange of medical information to be carried out between the two parties. We present the design and implementation of a system demonstrating the effectiveness of these exchange protocols giving a reference architecture for the implementation of such a system.
    Electronic ISSN: 2624-7852
    Topics: Computer Science
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  • 18
    Publication Date: 2021-10-29
    Description: Measurements of frequency dependent ferromagnetic resonance (FMR) and spin pumping driven dc voltage (Vdc) are reported for amorphous films of Fe78Ga13B9 (FeGaB) alloy to address the phenomenon of self-induced inverse spin Hall effect (ISHE) in plain films of metallic ferromagnets. The Vdc signal, which is antisymmetric on field reversal, comprises of symmetric and asymmetric Lorentzians centered around the resonance field. Dominant role of thin film size effects is seen in setting the magnitude of static magnetization, Vdc and dynamics of magnetization precession in thinner films (≤ 8 nm). The film thickness dependence of magnetization parameters indicates the presence of a magnetically disordered region at the film – substrate interface, which may promote preferential flow of spins generated by the precessing magnetization towards the substrate. However, the Vdc signal also draws contributions from rectification effects of a ≈ 0.4 % anisotropic magnetoresistance and a large (≈ 54 nΩ.m) anomalous Hall resistivity (AHR) of these films which ride over the effect of spin – orbit coupling driven spin-to-charge conversion near the film – substrate interface. We have addressed these data in the framework of the existing theories of electrodynamics of a ferromagnetic film subjected to radio-frequency field in a coplanar waveguide geometry. Our estimation of the self-induced ISHE for the sample with 54 nΩ.m AHR shows that it may contribute significantly (≈ 90%) to the measured symmetric voltage. This study is expected to be very useful for fully understanding the spin pumping induced dc voltages in metallic ferromagnets with disordered interfaces and large anomalous Hall effect.
    Print ISSN: 0022-3727
    Electronic ISSN: 1361-6463
    Topics: Physics
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  • 19
    Publication Date: 2021-10-29
    Description: Surface integrity of micro components is a major concern particularly in manufacturing industries as most geometry of the products must meet out necessary surface quality requirements. Advanced machining process like electrochemical micro machining possess the capabilities to machine micro parts with best surface properties exempting them from secondary operations. In this research work, different electrolytes have been employed for producing micro holes in A286 super alloy material to achieve the best surface quality and the measurement of surface roughness and surface integrity to evaluate the machined surface is carried out. The machined micro hole provides detailed information on the geometrical features. A study of parametric analysis meant for controlling surface roughness and improvement of surface integrity has been made to find out the suitable parameters for machining. The suitability of various electrolytes with their dissolution mechanism and the influence of various electrolytes have been thoroughly studied. Among the utilized electrolytes, EG + NaNO3 electrolyte provided the best results in terms of overcut and average surface roughness.
    Electronic ISSN: 2051-672X
    Topics: Physics
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  • 20
    Publication Date: 2021-10-29
    Description: We calculate Bardeen-Cooper-Schrieffer (BCS) state of a unitary Fermi gas of atoms interacting with the finite-ranged Jost-Kohn potential which has been recently shown to account for the resonant interactions [2019 { m J. Phys. B: At. Mol. Opt. Phys.} { f 52}, 165004]. Using exact scattering solution of the potential, we derive two-body ${mathbf T}$-matrix element which is employed to construct the BCS Hamiltonian in momentum space. We present results on the energy- and range-dependence of the pairing gap and superfluid density and the range-dependence of the chemical potential for a wide variation of the scattering length including the extcolor{red}{unitary} regime. In the zero range limit our calculated gap at the Fermi energy is found to be nearly equal to that calculated extcolor{red}{in mean-field theory with contact potential}. The mean gap averaged over the full width at half maximum of the gap function in the zero range and unitary limits is found to be $0.42 E_F$ which is quite close to the recent result of the quantum Monte Carlo simulation [2018 { m Phys. Rev.A} { f 97}, 013601]. The chemical potential in the zero range limit also agrees well with that for the contact potential.
    Print ISSN: 0953-4075
    Electronic ISSN: 1361-6455
    Topics: Physics
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  • 21
    Publication Date: 2021-10-29
    Description: We address the stability issue in Calderón’s problem for a special class of anisotropic conductivities of the form σ=γA in a Lipschitz domain Ω⊆R, n≧3, when A is a known Lipschitz continuous matrix-valued function and γ is the unknown piecewise affine scalar function on a given partition of Ω. We define an ad-hoc misfit functional encoding our data and establish estimates for this class of anisotropic conductivities in terms of both the misfit functional and the more commonly used local Dirichlet-to-Neumann map.
    Print ISSN: 0266-5611
    Electronic ISSN: 1361-6420
    Topics: Mathematics , Physics
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  • 22
    Publication Date: 2021-10-29
    Description: As AA 7075 T651 comprehensively is used in the marine naval vessels, the factor of corrosion performance always plays a significant role. In this work, an investigation is carried out to study the effect of corrosion behaviour of shot peened AA 7075 T651 in 3.5% solution. From the potentiodynamic polarization study, a 27.72% decrease is ascertained in the Icorr in shot peened specimen in correlation to unpeened aluminium alloy. A drop in Icorr from 1.883 to 1.480 mA/cm2 in shot peened specimen, indicates enhanced pitting corrosion resistance. An electrochemical impedance spectroscopy reveals a surge in the oxide layer formation on the peened surface aiding the drop in corrosion rate. Resistance to pit formations and improvement in oxygen deposition in the peened specimen is observed availing a Scanning Electron Microscopy (SEM) and Energy Dispersive X-Ray analysis (EDX). The micro structures of the peened and unpeened specimen are captured using optical microscopy and Transmission electron microscopy (TEM). Micro-strain, dislocation density is also calculated from the X- ray diffraction analysis (XRD), in which grain size reduces by 28.07%, dislocation density surges by 38.65% and micro strain increases by 21.95% in peened specimen in correlation to unpeened AA 7075 T651, resulting in a surge in corrosion resistance by 27.92% in the peened specimen in correlation to unpeened aluminium alloy.
    Electronic ISSN: 2051-672X
    Topics: Physics
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  • 23
    Publication Date: 2021-10-29
    Description: Cities are at the front line of combating environmental pollution and climate change, thus support from cities is crucial for successful enforcement of environmental policy. To mitigate environmental problems, China introduced at provincial level the Environmental Protection Tax Law in 2018. Yet the resulting economic burden on households in different cities with significantly different affluence levels remains unknown. The extent of the economic impacts is likely to affect cities’ support and public acceptability. This study quantifies the economic burden of urban households from taxation of fine particle pollution (PM2.5) for 200 cities nationwide from a “consumer” perspective, accounting for PM2.5 and precursor emissions along the national supply chain. Calculations are based on a Multi-Regional Input-Output (MRIO) analysis, the official tax calculation method and urban household consumption data from China’s statistical yearbooks. We find that the current taxation method intensifies economic inequality between cities nationally and within each province, with some of the richest cities having lower tax intensities than some of the poorest. This is due to the fact that taxes are collected based on tax rates of producing regions rather than consuming regions, that cities with very different affluence levels within a province bear the same tax rate, and that emission intensities in several less affluent cities are relatively high. If the tax could be levied based on tax rates of each city where the consumer lives, with tax rates determined based on cities’ affluence levels and with tax revenues used to support emission control, inter-city economic inequality could be reduced. Our work provides quantitative evidence to improve the environmental tax and can serve as the knowledge base for coordinated inter-city policy.
    Print ISSN: 1748-9318
    Electronic ISSN: 1748-9326
    Topics: Energy, Environment Protection, Nuclear Power Engineering
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  • 24
    Publication Date: 2021-10-29
    Description: While drinking water is known to create significant health risk in arsenic hazard areas, the role of exposure to arsenic through food intake is less well understood, including the impact of food trade. Using the best available datasets on crop production, irrigation, groundwater arsenic hazard, and international crop trade flows, we estimate that globally 17.2% of irrigated harvested area (or 45.2 million hectares) of 42 main crops are grown in arsenic hazard areas, contributing 19.7% of total irrigated crop production, or 418 million metric tons (MMT) per year of these crops by mass. Two-thirds of this area is dedicated to the major staple crops of rice, wheat, and maize (RWM) and produces 158 MMT per year of RWM, which is 8.0% of the total RWM production and 18% of irrigated production. More than 25% of RWM consumed in the South Asian countries of India, Pakistan, and Bangladesh, where both arsenic hazard and degree of groundwater irrigation are high, originate from arsenic hazard areas. Exposure to arsenic risk from crops also comes from international trade, with 10.6% of rice, 2.4% of wheat, and 4.1% of maize trade flows coming from production in hazard areas. Trade plays a critical role in redistributing risk, with the greatest exposure risk borne by countries with a high dependence on food imports, particularly in the Middle East and small island nations for which all arsenic risk in crops is imported. Intensifying climate variability and population growth may increase reliance on groundwater irrigation, including in arsenic hazard areas. Results show that RWM harvested area could increase by 54.1 million hectares (179% increase over current risk area), predominantly in South and Southeast Asia. This calls for the need to better understand the relative risk of arsenic exposure through food intake, considering the influence of growing trade and increased groundwater reliance for crop production.
    Print ISSN: 1748-9318
    Electronic ISSN: 1748-9326
    Topics: Energy, Environment Protection, Nuclear Power Engineering
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  • 25
    Publication Date: 2021-10-29
    Electronic ISSN: 2296-861X
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 26
    Publication Date: 2021-10-29
    Description: This article discusses the fabrication and performance of a multi-channel fibre switch, consisting of 19 single-mode fibres, with enhanced coupling efficiency due to micro-optics, directly printed via two-photon-polymerization on the end-face of each fibre. The use of high-resolution two-photon-polymerization not only allows the enhancement of the coupling efficiency with respect to the coupling device in use but likewise offers great freedom in the arrangement of the used fibres. This letter gives a thorough explanation of the fabrication method as well as the optical simulations for the lenses on the fibre assembly.
    Electronic ISSN: 2631-8695
    Topics: Technology
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  • 27
    Publication Date: 2021-10-29
    Description: In the warm, oligotrophic oceans, phytoplankton frequently experience high light exposure and must compete for a potentially limited nutrient supply. Additionally, the light regimes are dynamic in view of the diel solar cycle, weather conditions, and depth. Dealing with these challenges is critical to their survival. Here, we explored, using active chlorophyll a fluorescence, the photophysiological responses of cyanobacteria-dominated phytoplankton assemblages to intra-day variations in the light regime in the oligotrophic South China Sea (SCS). Experiments were conducted at three stations (SEATS, DC2, and DC6) where phytoplankton communities were dominated by Prochlorococcus and Synechococcus, and environmental conditions were similar except for daytime light conditions. We found that, at each station, the maximum quantum yield of PSII (Fv/Fm) at dawn was as high as ∼0.5, although concentrations of both dissolved inorganic nitrogen and soluble reactive phosphate were below the detection limits. Subsequently, diurnal patterns of Fv/Fm diverged between stations. At stations DC2 and DC6, we observed significant drops (25–48%) of Fv/Fm around midday, coinciding with the incident solar photosynthetically active radiation (PAR) reaching over 2,000 μmol quanta m–2 s–1, but Fv/Fm was nearly stable at SEATS where the daily maximal PAR was less than 1,000 μmol quanta m–2 s–1. Further analysis suggests that the midday drops in Fv/Fm at DC2 and DC6 were a consequence of high light-induced PSII photoinactivation. On the other hand, we found that the patterns of diurnal variation in maximum relative electron transport rate (rETRmax) presented as being unimodal with a peak around midday at all three stations. Furthermore, we found that the diurnal pattern of rETRmax was mainly controlled by the extent of photochemical quenching (qP) which reflects the redox status of electron carriers downstream of PSII. In conclusion, our results indicate that, in the oligotrophic SCS, through increasing the activity of the electron-consuming mechanisms (high qP), the phytoplankton communities are able to maintain their midday photosynthetic potential (high rETRmax) even with a degree of PSII photoinactivation (low Fv/Fm).
    Electronic ISSN: 2296-7745
    Topics: Biology
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  • 28
    Publication Date: 2021-11-01
    Description: High mortality during grow out in the sea is a challenge for farmed Atlantic salmon production in Norway and globally, which is partly attributed to suboptimal smolt quality. In this study, two groups of pre-smolts were put on a standard light smoltification regime with alternating 12L:12D per day for 6 weeks (Phase I), followed by 24L:0D per day for 6 weeks (Phase II); one group was 0 + smolt (EXP1) and the other 1 + smolt (EXP2). To monitor the smoltification status of the fish, 100 (EXP1) and 60 (EXP2) fish were randomly sampled per week during Phase II. The following phenotypes for smoltification status were studied: RT-qPCR relative mRNA expression of values of two alpha catalytic subunits of the variants of the Na+K+ATPase (NKA) expressed in the sampled gill tissues of each fish. The first variant, alpha1a with increased expression in freshwater (FW) and the second variant alpha1b with increased expression in seawater variant (SW), as well as their ratio SW/FW. At the optimal time for seawater transfer based on the SW/FW trait, 1,000 (at sixth sampling of EXP1) and 1,500 (at fifth sampling of EXP2) fish were sampled for genetic parameter estimation. The individual variation in FW, SW, and SW/FW was very large at each of the seven samplings indicating a large variation among individuals in the optimum time of transfer to seawater. SW/FW showed significant genetic variation in both 0+ and 1+ smolts, which indicates the possibility for selection for improved synchronization of smoltification status of Atlantic salmon at the time where the largest proportion of the fish is considered to be smolt. However, the genetic correlation between SW/FW of 0+ and 1+ was not significantly different from zero indicating very little shared genetic variation in SW/FW in 0+ and 1+ fish. Smoltification phenotypes showed temporal progression over the smoltification period, and this progression varied between 0+ and 1+ smolt highlighting the importance of correctly timing the major sampling point, and when cohorts are transferred to seawater. This also highlighted the need for further research into noninvasive methods of objectively measuring individual smoltification through time and subsequent smolt survival and growth rate at sea.
    Electronic ISSN: 1664-8021
    Topics: Biology , Medicine
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  • 29
    Publication Date: 2021-11-01
    Electronic ISSN: 2504-284X
    Topics: Education , Nature of Science, Research, Systems of Higher Education, Museum Science
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  • 30
    Publication Date: 2021-11-01
    Description: The use of glycosylphosphatidylinositol (GPI) to anchor proteins to the cell surface is widespread among eukaryotes. The GPI-anchor is covalently attached to the C-terminus of a protein and mediates the protein’s attachment to the outer leaflet of the lipid bilayer. GPI-anchored proteins have a wide range of functions, including acting as receptors, transporters, and adhesion molecules. In unicellular eukaryotic parasites, abundantly expressed GPI-anchored proteins are major virulence factors, which support infection and survival within distinct host environments. While, for example, the variant surface glycoprotein (VSG) is the major component of the cell surface of the bloodstream form of African trypanosomes, procyclin is the most abundant protein of the procyclic form which is found in the invertebrate host, the tsetse fly vector. Trypanosoma cruzi, on the other hand, expresses a variety of GPI-anchored molecules on their cell surface, such as mucins, that interact with their hosts. The latter is also true for Leishmania, which use GPI anchors to display, amongst others, lipophosphoglycans on their surface. Clearly, GPI-anchoring is a common feature in trypanosomatids and the fact that it has been maintained throughout eukaryote evolution indicates its adaptive value. Here, we explore and discuss GPI anchors as universal evolutionary building blocks that support the great variety of surface molecules of trypanosomatids.
    Electronic ISSN: 2296-634X
    Topics: Biology
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  • 31
    Publication Date: 2021-11-01
    Print ISSN: 1674-1056
    Electronic ISSN: 2058-3834
    Topics: Physics
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  • 32
  • 33
    Publication Date: 2021-11-01
    Description: This study develops an implementation framework for asset management strategic planning of water distribution networks to meet sustainable infrastructure, socio-political, and financial targets over the life cycle of the infrastructure. The proposed framework is comprised of three decision-making layers: (1) Visions and Values, (2) Function, and (3) Performance. The asset management strategy framework is implemented and validated by demonstrating functionality and value by using data from three water utilities in Canada. The Visions and Values layer is set to meet the needs of the water utilities' stakeholders. The Function layer uses an advanced system dynamics model to simulate and forecast the system's future behavior. The Performance layer benchmarks, compares, and graphically illustrates the situation and performance of water utilities against each other regardless of their size. Benchmarking results indicate that all three water utilities can sustainably meet the strategic targets established in the Visions and Values layer of the asset management strategy over the benchmarking period. The impact of the desired cash reserve on infrastructure and financial benchmarking performance indicators is also investigated to explore the “optimal” combination of allowable fee-hike and rehabilitation rates using the contour plots developed over the benchmarking period. The results indicate that the optimal combinations of allowable fee-hike of ~8% per year and rehabilitation rate of 1.3% per year along with a 1–4% cash reserve, depends on the network condition, will allow water utilities to have sufficient funds to meet their strategic targets. The performance modeling and simulation approach presented in this study represents a powerful tool for other utilities to develop optimal strategic and operational plans for their networks and thus better service to their stakeholders.
    Electronic ISSN: 2624-9375
    Topics: Architecture, Civil Engineering, Surveying , Energy, Environment Protection, Nuclear Power Engineering
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  • 34
    Publication Date: 2021-11-01
    Description: Ferroptosis, a distinct type of regulated cell death, has been reported to be involved in the tumorigenesis of liver hepatocellular carcinoma (LIHC). However, the precise functions and potential mechanisms of ferroptosis in LIHC were still poorly understood. Herein, we investigated the biological roles of ferroptosis-related gene STEAP3 in LIHC. STEAP3 was previously proved to serve a key regulator in ferroptosis via mediating the iron metabolism. Comprehensive bioinformatics from several databases revealed that STEAP3 was significantly downregulated in LIHC tissues and exhibited the favorable prognostic significance in LIHC patients. The downregulated STEAP3 was further confirmed in two LIHC cells Huh7 and MHCC97H using real-time PCR and western blot. And STEAP3 overexpression significantly inhibited the cell proliferation in Huh7 and MHCC97H cells. In addition, clinical data identified the relationship between STEAP3 expression and several clinicopathological parameters of LIHC patients, including histologic grade, alpha fetal protein (AFP) concentration, etc. Receiver operation characteristic (ROC) curve revealed STEAP3 as a potential diagnostic biomarker for LIHC patients. Moreover, the co-expression network of STEAP3 was explored to gain a better insight into its underlying signaling pathways. Finally, aberrant STEAP3 might participate in varieties of immune-associated signatures in LIHC pathogenesis, including immunostimulators, immunoinhibitors, chemokines, and chemokine receptors. Taken together, these findings could enhance our knowledge regarding the inhibitory roles and underlying biological significance of STEAP3 in LIHC tumorigenesis.
    Electronic ISSN: 2296-634X
    Topics: Biology
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  • 35
    Publication Date: 2021-11-01
    Description: ObjectivesRecently, KPC-producing P. aeruginosa has rapidly emerged and expanded in East China. Here we described the clinical impact and characteristics of bloodstream infections (BSIs) from the dominant KPC-producing CRPA belonging to Sequence Type (ST) 463.MethodsRetrospective cohort study was performed with CRPA BSI cases from 2019 to 2020 in a hospital in East China. Clinical characteristics, risk factors, and all-course mortality were evaluated. All CRPA isolates had whole-genome sequencing, antimicrobial susceptibility testing, and serum resistance assay. Representative isolates were tested for virulence in a Galleria mellonella infection model.ResultsAmong the 50 CRPA BSI cases, ST463 predominated (48.0%). In multivariate analysis, we found three independent risk factors for fatal outcome: KPC carriage (OR 4.8; CI95% 1.0-23.7; P = 0.05), Pitt bacteremia score (OR 1.3; CI95% 1.0-1.6; P = 0.02), and underlying hematological disease (OR 8.5; CI95% 1.6-46.4; P = 0.01). The baseline clinical variables were not statistically different across STs, however the 28-day mortality was significantly higher in ST463 cases than that in non-ST463 cases (66.7% vs 33.3%, P = 0.03). ExoU and exoS virulence genes coexisted in all ST463 isolates, and the carbapenem resistant gene blaKPC were produced in almost all ST463 isolates, significantly higher than in the non-ST463 group(95.8% vs 7.7%, P
    Electronic ISSN: 2235-2988
    Topics: Biology , Medicine
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  • 36
    Publication Date: 2021-11-01
    Electronic ISSN: 2296-2646
    Topics: Chemistry and Pharmacology
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  • 37
    Publication Date: 2021-11-01
    Description: It has been recognized that rebalancing the abnormal proliferation and migration of vascular smooth muscle cells (VSMCs) helps relieve vascular injury. Presently, we aim to investigate whether long non-coding RNA (lncRNA) maternally expressed 8 (MEG8) plays a role in affecting the excessive proliferation and migration of VSMCs following hypoxia stimulation. A percutaneous transluminal angioplasty balloon dilatation catheter was adopted to establish vascular intimal injury, the levels of MEG8 and miR-195-5p in the carotid artery were tested by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Hypoxia was used to stimulate VSMCs, then the cell counting kit-8 (CCK-8) assay, Transnwell assay, and wound healing assay were conducted to evaluate the proliferation, and migration of VSMCs. The protein levels of RECK (reversion inducing cysteine rich protein with kazal motifs), MMP (matrix metalloproteinase) 3/9/13, COX2 (cytochrome c oxidase subunit II), macrophage inflammatory protein (MIP)-1beta, VCAM-1 (vascular cell adhesion molecule 1), ICAM-1 (intercellular adhesion molecule 1), and HIF-1α (hypoxia inducible factor 1 subunit alpha) were determined by western blot or cellular immunofluorescence. As the data showed, MEG8 was down-regulated in the carotid artery after balloon injury in rats and hypoxia-treated VSMCs, and miR-195-5p was overexpressed. Forced MEG8 overexpression or inhibiting miR-195-5p attenuated hypoxia-promoted cell proliferation and migration of VSMCs. In addition, miR-195-5p up-regulation reversed MEG8-mediated effects. Hypoxia hindered the RECK expression while boosted MMP3/9/13 levels, and the effect was markedly reversed with MEG8 up-regulation or miR-195-5p down-regulation. Mechanistically, MEG8 functioned as a competitive endogenous (ceRNA) by sponging miR-195-5p which targeted RECK. Moreover, the HIF-1α inhibitor PX478 prevented hypoxia-induced proliferation, and migration of VSMCs, upregulated MEG8, and restrained miR-195-5p expression. Overall, lncRNA MEG8 participated in hypoxia-induced excessive proliferation, inflammation and migration of VSMCs through the miR-195-5p/RECK axis.
    Electronic ISSN: 2296-889X
    Topics: Biology
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  • 38
    Publication Date: 2021-11-01
    Description: We report the different nonlinear optical mechanisms and defect-related carrier dynamics in Sn-doped β-Ga2O3 crystal by utilizing time-resolved pump-probe technique based on phase object under UV excitation. The obtained nonlinear optical parameters arise from bound electron can be well explained by the theoretical calculation of two-band model and Kramers-Kronig transformation. By tuning the probe wavelength, the carrier nonlinearity can be modulated greatly due to additional absorption of defects within the bandgap. The results reveal that by choosing a proper probe wavelength that matches the defect state to the valence band, the nonlinear absorption and refraction of the carriers can be greatly enhanced, which provides an important reference for the design of gallium oxide-based waveguide materials and all-optical switching materials in the future.
    Electronic ISSN: 2296-8016
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 39
    Publication Date: 2021-11-01
    Description: Light is a ubiquitous source of both energy and information in surface environments, and regulates gene expression not only in photosynthetic microorganisms, but in a broad range of photoheterotrophic and heterotrophic microbes as well. Actinobacteria are keystone species in surface freshwater environments, where the ability to sense light could allow them to coordinate periods of nutrient uptake and metabolic activity with primary production. The model freshwater Actinobacteria Rhodoluna (R.) lacicola strain MWH-Ta8 and Aurantimicrobium (A.) photophilum strain MWH-Mo1 grow faster in the light than in the dark, but do not use light energy to support growth. Here, we characterize transcription throughout a light-dark cycle in R. lacicola and A. photophilum. In both species, some genes encoding carbohydrate metabolism and storage are upregulated in the light. However, expression of genes of the TCA cycle is only coordinated with light availability in R. lacicola. In fact, the majority of genes that respond to light and darkness in these two species are different, even though their light-responsive phenotypes are similar. The ability to respond to light and darkness may be widespread in freshwater Actinobacteria, but the genetic networks controlled by these two stimuli may vary significantly.
    Electronic ISSN: 1664-302X
    Topics: Biology
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  • 40
    Publication Date: 2021-11-01
    Description: Phytoplankton functional groups and their influence on water quality have been studied in various types of water bodies but have yet to be studied in agricultural irrigation ponds. Freshwater sources (e.g., lakes, rivers, and reservoirs) have been previously shown to exhibit high spatial and temporal variability in phytoplankton populations. Improvements in the monitoring of phytoplankton populations may be achieved if patterns of stable spatial variability can be found in the phytoplankton populations through time. The objective of this work was to determine if temporally stable spatial patterns in phytoplankton communities could be detected in agricultural irrigation ponds using a functional group approach. The study was performed at two working agricultural irrigation ponds located in Maryland, USA over two summer sampling campaigns in 2017 and 2018. Concentrations of four phytoplankton groups, along with sensor-based and fluorometer based water quality parameters were measured. Temporal stability was assessed using mean relative differences between measurements in each location and averaged measurements across ponds on each sampling date. Temporally stable spatial patterns of three phytoplankton functional groups were found for both ponds over the two sampling seasons. Both ponds had locations where specific phytoplankton functional group concentrations were consistently higher or lower than the pond's average concentration for each sampling date. Zones of consistently higher or lower than average concentrations were associated with flow conditions, pond morphology, and human activities. The existence of temporally stable patterns of phytoplankton functional group concentrations can affect the outcome of a water quality assessment and should be considered in water quality monitoring designs.
    Electronic ISSN: 2624-9375
    Topics: Architecture, Civil Engineering, Surveying , Energy, Environment Protection, Nuclear Power Engineering
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  • 41
    Publication Date: 2021-11-01
    Description: Nutrition plays an important role in the development and progress of several health conditions, but the exact mechanism is often still unclear. Blood metabolites are likely candidates to be mediating these relationships, as their levels are strongly dependent on the frequency of consumption of several foods/drinks. Understanding the causal effect of food on metabolites is thus of extreme importance. To establish these effects, we utilized two-sample Mendelian randomization using the genetic variants associated with dietary traits as instrumental variables. The estimates of single-nucleotide polymorphisms’ effects on exposures were obtained from a recent genome-wide association study (GWAS) of 25 individual and 15 principal-component dietary traits, whereas the ones for outcomes were obtained from a GWAS of 123 blood metabolites measured by nuclear magnetic resonance spectroscopy. We identified 413 potentially causal links between food and metabolites, replicating previous findings, such as the association between increased oily fish consumption and higher DHA, and highlighting several novel associations. Most of the associations were related to very-low-density, intermediate-density (IDL), and low-density lipoproteins (LDL). For example, we found that constituents of IDL particles and large LDL particles were raised by coffee and alcohol while lowered by an overall healthier diet and fruit consumption. Our findings provide a strong base of evidence for planning future RCTs aimed at understanding the role of diet in determining blood metabolite levels.
    Electronic ISSN: 1664-8021
    Topics: Biology , Medicine
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  • 42
    Publication Date: 2021-11-01
    Description: The damage of Riptortus pedestris is exceptional by leading soybean plants to keep green in late autumn. Identification of the salivary proteins is essential to understand how the pest-plant interaction occurs. Here, we have tried to identify them by a combination of proteomic and transcriptomic analyses. The transcriptomes of salivary glands from R. pedestris males, females and nymphs showed about 28,000 unigenes, in which about 40% had open reading frames (ORFs). Therefore, the predicted proteins in the transcriptomes with secretion signals were obtained. Many of the top 1,000 expressed transcripts were involved in protein biosynthesis and transport, suggesting that the salivary glands produce a rich repertoire of proteins. In addition, saliva of R. pedestris males, females and nymphs was collected and proteins inside were identified. In total, 155, 20, and 11 proteins were, respectively, found in their saliva. We have tested the tissue-specific expression of 68 genes that are likely to be effectors, either because they are homologs of reported effectors of other sap-feeding arthropods, or because they are within the top 1,000 expressed genes or found in the salivary proteomes. Their potential functions in regulating plant defenses were discussed. The datasets reported here represent the first step in identifying effectors of R. pedestris.
    Electronic ISSN: 2296-701X
    Topics: Biology
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  • 43
    Publication Date: 2021-11-01
    Description: Maastrichtian–Danian sediments of the Navesink and Hornerstown formations at the Jean and Ric Edelman Fossil Park of Rowan University in Mantua Township, New Jersey, have long intrigued paleontologists. Within the basal Hornerstown Formation occurs the Main Fossiliferous Layer (MFL), a regionally well-known and diverse bonebed. The lithostratigraphic and chronostratigraphic position of this fossil layer have been debated for more than 50 years, fueling debate over its origin. Herein, we present the results of a microstratigraphic analysis of the fossil composition and distribution of the MFL undertaken to rectify these discrepancies. Through methodical top-down excavation, we recorded the three-dimensional position of every fossil encountered. Three-dimensional visualization and analyses of these data in ArcGIS Pro yielded an unprecedented view of this bonebed. Most reported discrepancies about the stratigraphic placement and thickness of the MFL can be explained by the presence of two distinct fossil assemblages within this interval that are occasionally combined into a single bonebed. The stratigraphically-lower assemblage, herein termed an “oyster layer”, is geometrically-tabular and exhibits low taxonomic diversity, high abundance of the oyster Pycnodonte, and moderate taxonomic richness. The stratigraphically-higher assemblage, the MFL, occurs approximately 9 cm higher in section and exhibits high values of taxonomic diversity, fossil abundance, and taxonomic richness. Sedimentological homogeneity throughout this interval suggests that these faunal contrasts arise from the two assemblages having formed via independent taphonomic pathways. Specifically, prevalence of Pycnodonte in the oyster layer implies formation by a selective mortality event, whereas the diversity of the MFL appears to reflect a more universal agent of mortality. Spatial variations in the stratigraphic distribution of fossils within the MFL in our excavation area indicate this assemblage does not form a simple, tabular layer as previously thought and may, in part, record original bathymetry. Importantly, our definition of the MFL and detailed characterization of its stratigraphic placement are essential for future studies on the taphonomic origin and chronostratigraphy of this bonebed. Universal use of this definition would allow researchers to confidently elucidate the exact lithostratigraphic positions of precise chronostratigraphic indicators within the MFL and accurately estimate the degree of time averaging of its fossils.
    Electronic ISSN: 2296-6463
    Topics: Geosciences
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  • 44
    Publication Date: 2021-11-01
    Description: Wilt disease of roselle (Hibiscus sabdariffa L.) is common in Taiwan; however, the causative agent remains unknown. The stems of wilted roselle are browned, slightly constricted, and covered by white aerial hyphae, suggesting that potential pathogens may originate from soil. To identify the potential pathogens, we conducted a rhizosphere microbiota survey in phenotypically healthy and diseased plants through fungal internal transcribed spacer (ITS) and bacterial 16S rRNA amplicon sequencing for uncovering the microbial compositions in the roselle rhizosphere. The fungal family Nectriaceae exhibited significantly higher abundance in diseased rhizospheres than in healthy rhizospheres, and this bacterial community was more specific to geography (i.e., plot-dependent) than to rhizosphere disease status. However, a few bacterial groups such as Bacilli were associated with the healthy rhizosphere. Fusarium species were the most dominant species of Nectriaceae in the survey and became the main target for potential pathogen isolation. We successfully isolated 119 strains from diseased plants in roselle fields. Koch’s postulates were used to evaluate the pathogenicity of these strains; our results indicated that Fusarium solani K1 (FsK1) can cause wilting and a rotted pith in roselles, which was consistent with observations in the fields. This is the first demonstration that F. solani can cause roselle wilt in Taiwan. Furthermore, these newly isolated strains are the most dominant operational taxonomic units detected in ITS amplicon sequencing in diseased rhizospheres, which serves as further evidence that F. solani is the main pathogen causing the roselle wilt disease. Administration of Bacillus velezensis SOI-3374, a strain isolated from a healthy roselle rhizosphere, caused considerable anti-FsK1 activity, and it can serve as a potential biocontrol agent against roselle wilt disease.
    Electronic ISSN: 1664-302X
    Topics: Biology
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  • 45
    Publication Date: 2021-11-01
    Description: Reefs are the richest marine ecosystems. Their benthic communities generate structural complexity and participate in nutrient cycles, providing habitat and food for many marine species. These ecosystems have been threatened by local and global anthropogenic impacts and changes in community structure have led to loss of biodiversity, ecosystem function and services worldwide. Most studies about these structural changes have been conducted in Caribbean and Indo-Pacific coral reefs. In the Southwestern Atlantic, where reefs are naturally algae-dominated, these efforts are incipient, especially at oceanic islands where local anthropic impacts tend to be lower, and natural and climate-induced fluctuations might be easily detected. We conducted the first temporal assessment of benthic communities and the influence of oceanographic parameters between 2013 and 2019 in Fernando de Noronha (FNA), the largest Brazilian oceanic archipelago. We annually sampled benthic communities in FNA’s shallow reefs (2–21 m) using photoquadrats, quantified and gathered organisms in major groups according to their functional roles. We also characterized and tested “sea surface temperature,” “marine heatwaves,” “diffuse attenuation coefficient,” and “wave energy” influence for the same period. The most abundant groups were epilithic algal matrix (EAM; mean annual coverage: 23–60%), macroalgae (15–35%) and calcifiers (15–29%), followed by cyanobacteria (1–37%), suspension/filter-feeders (
    Electronic ISSN: 2296-7745
    Topics: Biology
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  • 46
    Publication Date: 2021-11-01
    Description: BackgroundAutism spectrum disorder (ASD) are complex behavioral changes manifesting early in childhood, which impacts how an individual perceives and socializes with others. The study aims to assess the disparities in gut microbiota (GM) amongst healthy controls and children with ASD.MethodsThe study was performed on 25 children with ASD and 20 healthy children. Autistic symptoms were diagnosed and assessed with the Diagnostic and Statistical Manual for Mental Disorders and the Autism Treatment Evaluation Checklist (ATEC). Gastrointestinal (GI) symptoms were assessed with a GI Severity Index (GSI) questionnaire. The fecal bacteria composition was investigated by the high−throughput sequencing of the V3–V4 region of the 16S rRNA gene. The alpha diversity was estimated using the Shannon, Chao, and ACE indexes. The unweighted UniFrac analysis and the PCA plots were used to represent the beta diversity. LDA and LEfSe were used to assess the effect sizes of each abundant differential taxon.ResultsChildren with high GSI scores had much higher ATEC Total scores than those with lower GSI-scores. GI symptoms were strongly associated with symptoms of ASD. There was no difference in Chao, ACE, and Shannon indexes between ASD patients and healthy controls. Both groups showed a significant microbiota structure clustering in the plotted PCAs and significant differences in its composition at the family, order, genus, and phyla levels. There were also noteworthy overall relative differences in Actinobacteria and Firmicutes between both groups.ConclusionsThis study shows the relationship between the clinical manifestations of Autistic symptoms and GI symptoms. ASD patients have dysbiosis of gut microbiota, which may be related to the onset of ASD. These findings may be beneficial for developing ASD symptoms by changing gut microbiota.
    Electronic ISSN: 2235-2988
    Topics: Biology , Medicine
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  • 47
    Publication Date: 2021-11-01
    Description: Millions of college students in the United States lack access to adequate food, housing, and other basic human needs. These insecurities have only been exacerbated in recent decades by the country's neoliberal approach to higher education, with disproportionately negative consequences for historically underserved populations (e.g., racial/ethnic minorities, low-income students, and first-generation college students). For each of these reasons, this study explores the organizational paradoxes faced by students attending a public, 4-year Hispanic-Serving Institution (HSI) in southern California. Drawing upon 30 semi-structured interviews with undergraduates who self-identified as historically underserved, our three-stage conceptualization of data analysis revealed three specific paradoxes: (1) provision vs. dependence, (2) sympathy vs. distancing, and (3) bootstrapping vs. unattainability. We conclude with practical and theoretical implications for alleviating the repercussions of neoliberal policies on today's college students.
    Electronic ISSN: 2571-581X
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Frontiers Media
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  • 48
    Publication Date: 2021-11-01
    Description: The aggregation of the human islet amyloid polypeptide (IAPP) is associated with diabetes type II. A quantitative understanding of this connection at the molecular level requires that the aggregation mechanism of IAPP is resolved in terms of the underlying microscopic steps. Here we have systematically studied recombinant IAPP, with amidated C-terminus in oxidised form with a disulphide bond between residues 3 and 7, using thioflavin T fluorescence to monitor the formation of amyloid fibrils as a function of time and IAPP concentration. We used global kinetic analyses to connect the macroscopic measurements of aggregation to the microscopic mechanisms, and show that the generation of new aggregates is dominated by the secondary nucleation of monomers on the fibril surface. We then exposed insulinoma cells to aliquots extracted from different time points of the aggregation process, finding the highest toxicity at the midpoint of the reaction, when the secondary nucleation rate reaches its maximum. These results identify IAPP oligomers as the most cytotoxic species generated during IAPP aggregation, and suggest that compounds that target secondary nucleation of IAPP could be most effective as therapeutic candidates for diabetes type II.
    Electronic ISSN: 2296-889X
    Topics: Biology
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  • 49
    Publication Date: 2021-11-01
    Description: During geomagnetically active periods ions are transported from the magnetotail into the inner magnetosphere and accelerated to energies of tens to hundreds of keV. These energetic ions, of mixed composition with the most important species being H+ and O+, become the dominant source of plasma pressure in the inner magnetosphere. Ion transport and acceleration can occur at different spatial and temporal scales ranging from global quasi-steady convection to localized impulsive injection events and may depend on the ion gyroradius. In this study we ascertain the relative importance of mesoscale flow structures and the effects of ion non-adiabaticity on the produced ring current. For this we use: global magnetohydrodynamic (MHD) simulations to generate self-consistent electromagnetic fields under typical driving conditions which exhibit bursty bulk flows (BBFs); and injected test particles, initialized to match the plasma moments of the MHD simulation, and subsequently evolved according to the kinetic equations of motion. We show that the BBFs produced by our simulation reproduce thermodynamic and magnetic statistics from in situ measurements and are numerically robust. Mining the simulation data we create a data set, over a billion points, connecting particle transport to characteristics of the MHD flow. From this we show that mesoscale bubbles, localized depleted entropy regions, and particle gradient drifts are critical for ion transport. Finally we show, using identical particle ensembles with varying mass, that O+ non-adiabaticity creates qualitative differences in energization and spatial distribution while H+ non-adiabaticity has non-negligible implications for loss timescales.
    Electronic ISSN: 2296-987X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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  • 50
    Publication Date: 2021-11-01
    Description: Background: Endometrial cancer (EC) is one of the most common gynecological malignancies in women. Cholesterol metabolism has been confirmed to be closely related to tumor proliferation, invasion and metastasis. However, the correlation between cholesterol homeostasis-related genes and prognosis of EC remains unclear.Methods: EC patients from the Cancer Genome Atlas (TCGA) database were randomly divided into training cohort and test cohort. Transcriptome analysis, univariate survival analysis and LASSO Cox regression analysis were adopted to construct a cholesterol homeostasis-related gene signature from the training cohort. Subsequently, Kaplan-Meier (KM) plot, receiver operating characteristic (ROC) curve and principal component analysis (PCA) were utilized to verify the predictive performance of the gene signature in two cohorts. Additionally, enrichment analysis and immune infiltration analysis were performed on differentially expressed genes (DEGs) between two risk groups.Results: Seven cholesterol homeostasis-related genes were selected to establish a gene signature. KM plot, ROC curve and PCA in two cohorts demonstrated that the gene signature was an efficient independent prognostic indicator. The enrichment analysis and immune infiltration analysis indicated that the high-risk group generally had lower immune infiltrating cells and immune function.Conclusion: We constructed and validated a cholesterol homeostasis-related gene signature to predict the prognosis of EC, which correlated to immune infiltration and expected to help the diagnosis and precision treatment of EC.
    Electronic ISSN: 1664-8021
    Topics: Biology , Medicine
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  • 51
    Publication Date: 2021-11-01
    Description: Luteolin is a natural flavone with neurotrophic effects observed on different neuronal cell lines. In the present study, we aimed to assess the effect of luteolin on hNSCs fate determination and the LPS-induced neuroinflammation in a mouse model of depression with astrocytogenesis defect. hNSCs were cultured in basal cell culture medium (control) or medium supplemented with luteolin or AICAR, a known inducer of astrogenesis. A whole-genome transcriptomic analysis showed that luteolin upregulated the expressions of genes related to neurotrophin, dopaminergic, hippo, and Wnt signaling pathways, and downregulated the genes involved in p53, TNF, FOXO, and Notch signaling pathways. We also found that astrocyte-specific gene GFAP, as well as other genes of the key signaling pathways involved in astrogenesis such as Wnt, BMP, and JAK-STAT pathways were upregulated in luteolin-treated hNSCs. On the other hand, neurogenesis and oligodendrogenesis-related genes, TUBB3, NEUROD 1 and 6, and MBP, were downregulated in luteolin-treated hNSCs. Furthermore, immunostaining showed that percentages of GFAP+ cells were significantly higher in luteolin- and AICAR-treated hNSCs compared to control hNSCs. Additionally, RT-qPCR results showed that luteolin upregulated the expressions of GFAP, BMP2, and STAT3, whereas the expression of TUBB3 remained unchanged. Next, we evaluated the effects of luteolin in LPS-induced mice model of depression that represents defects in astrocytogenesis. We found that oral administration of luteolin (10 mg/Kg) for eight consecutive days could decrease the immobility time on tail suspension test, a mouse behavioral test measuring depression-like behavior, and attenuate LPS-induced inflammatory responses by significantly decreasing IL-6 production in mice brain-derived astrocytes and serum, and TNFα and corticosterone levels in serum. Luteolin treatment also significantly increased mature BDNF, dopamine, and noradrenaline levels in the hypothalamus of LPS-induced depression mice. Though the behavioral effects of luteolin did not reach statistical significance, global gene expression analyses of mice hippocampus and brain-derived NSCs highlighted the modulatory effects of luteolin on different signaling pathways involved in the pathophysiology of depression. Altogether, our findings suggest an astrocytogenic potential of luteolin and its possible therapeutic benefits in neuroinflammatory and neurodegenerative diseases. However, further studies are required to identify the specific mechanism of action of luteolin.
    Electronic ISSN: 2296-634X
    Topics: Biology
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  • 52
    Publication Date: 2021-11-01
    Description: Anti-VEGF drugs are first-line treatments for retinal neovascular diseases, but these anti-angiogenic agents may also aggravate retinal damage by inducing hypoxia. Mitophagy can protect against hypoxia by maintaining mitochondrial quality, thereby sustaining metabolic homeostasis and reducing reactive oxygen species (ROS) generation. Here we report that the anti-VEGF agent bevacizumab upregulated the hypoxic cell marker HIF-1α in photoreceptors, Müller cells, and vascular endothelial cells of oxygen-induced retinopathy (OIR) model mice, as well as in hypoxic cultured 661W photoreceptors, MIO-MI Müller cells, and human vascular endothelial cells. Bevacizumab also increased expression of mitophagy-related proteins, and mitophagosome formation both in vivo and in vitro, but did not influence cellular ROS production or apoptosis rate. The HIF-1α inhibitor LW6 blocked mitophagy, augmented ROS production, and triggered apoptosis. Induction of HIF-1α and mitophagy were associated with upregulation of BCL2/adenovirus E1B 19-kDa protein-interacting protein 3 (BNIP3) and FUN14 domain containing 1 (FUNDC1), and overexpression of these proteins in culture reversed the effects of HIF-1α inhibition. These findings suggest that bevacizumab does induce retinal hypoxia, but that concomitant activation of the HIF-1α-BNIP3/FUNDC1 signaling pathway also induces mitophagy, which can mitigate the deleterious effects by reducing oxidative stress secondary. Promoting HIF-1α-BNIP3/FUNDC1-mediated mitophagy may enhance the safety of anti-VEGF therapy for retinal neovascular diseases and indicate new explanation and possible new target of the anti-VEGF therapy with suboptimal effect.
    Electronic ISSN: 2296-634X
    Topics: Biology
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  • 53
    Publication Date: 2021-11-01
    Description: The pathobiont Streptococcus pneumoniae causes life-threatening diseases, including pneumonia, sepsis, meningitis, or non-invasive infections such as otitis media. Serine proteases are enzymes that have been emerged during evolution as one of the most abundant and functionally diverse group of proteins in eukaryotic and prokaryotic organisms. S. pneumoniae expresses up to four extracellular serine proteases belonging to the category of trypsin-like or subtilisin-like family proteins: HtrA, SFP, PrtA, and CbpG. These serine proteases have recently received increasing attention because of their immunogenicity and pivotal role in the interaction with host proteins. This review is summarizing and focusing on the molecular and functional analysis of pneumococcal serine proteases, thereby discussing their contribution to pathogenesis.
    Electronic ISSN: 2235-2988
    Topics: Biology , Medicine
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  • 54
    Publication Date: 2021-11-01
    Description: Birds are our best models to understand vocal learning – a vocal production ability guided by auditory feedback, which includes human language. Among all vocal learners, songbirds have the most diverse life histories, and some aspects of their vocal learning ability are well-known, such as the neural substrates and vocal control centers, through vocal development studies. Currently, species are classified as either vocal learners or non-learners, and a key difference between the two is the development period, extended in learners, but short in non-learners. But this clear dichotomy has been challenged by the vocal learning continuum hypothesis. One way to address this challenge is to examine both learners and canonical non-learners and determine whether their vocal development is dichotomous or falls along a continuum. However, when we examined the existing empirical data we found that surprisingly few species have their vocal development periods documented. Furthermore, we identified multiple biases within previous vocal development studies in birds, including an extremely narrow focus on (1) a few model species, (2) oscines, (3) males, and (4) songs. Consequently, these biases may have led to an incomplete and possibly erroneous conclusions regarding the nature of the relationships between vocal development patterns and vocal learning ability. Diversifying vocal development studies to include a broader range of taxa is urgently needed to advance the field of vocal learning and examine how vocal development patterns might inform our understanding of vocal learning.
    Electronic ISSN: 2296-701X
    Topics: Biology
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  • 55
    Publication Date: 2021-11-01
    Description: Animals exploring a new environment develop cognitive maps using diverse sensory input and, thereby, gain information needed to establish home ranges. Experiencing, and learning information about, resources should be advantageous to the resident of a home range while lack of such information should put invaders into the home range at a disadvantage. Conspecifics, especially, should avoid the home ranges of one another to ensure that they do not experience reduced resource availability caused by resource depression or depletion. Yet, encountering conspecific competitors of different sexes may elicit responses that can lead to spacing on a landscape that has different costs and benefits on males and females. We tested the hypothesis that female fishers (Pekania pennanti) avoid competition from both males and female conspecifics whereas male fishers avoid competition only from other males. We reintroduced fishers onto our study site in the presence or absence of competitors’ home ranges during late 2009 through 2011. Using satellite transmitters (Argos) and land-based (VHF) telemetry, we monitored fishers and estimated their locations, movements and use of the surrounding landscape during their first 500 days after release. All fishers settled in relatively high-quality habitat but females that encountered the home ranges of conspecifics moved farther, explored larger areas, and settled farther from their release locations than did females that did not encounter a conspecific’s home range. Male fishers exhibited diverse responses upon encountering the home ranges of conspecifics. Thus, female fishers avoid conspecific competition from all fishers, but males tolerate, or impose, competition with females, apparently to increase mating opportunities. These observations are consistent with the movements and strategies of other solitary carnivores.
    Electronic ISSN: 2296-701X
    Topics: Biology
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  • 56
    Publication Date: 2021-11-01
    Description: Cadmium (Cd) ranks seventh on the list of most significant potential threats to human health based on its suspected toxicity and the possibility of exposure to it. It has been reported that some bacterial exopolysaccharides (EPSs) have the ability to bind heavy metal ions. We therefore investigated the capacity of eight EPS-producing lactobacilli to adsorb Cd in the present study, and Lactiplantibacillus plantarum BGAN8 was chosen as the best candidate. In addition, we demonstrate that an EPS derived from BGAN8 (EPS-AN8) exhibits a high Cd-binding capacity and prevents Cd-mediated toxicity in intestinal epithelial Caco-2 cells. Simultaneous use of EPS-AN8 with Cd treatment prevents inflammation, disruption of tight-junction proteins, and oxidative stress. Our results indicate that the EPS in question has a strong potential to be used as a postbiotic in combatting the adverse effects of Cd. Moreover, we show that higher concentrations of EPS-AN8 can alleviate Cd-induced cell damage.
    Electronic ISSN: 1664-302X
    Topics: Biology
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  • 57
    Publication Date: 2021-11-01
    Description: Background: Ferroptosis is an iron-dependent programmed cell death (PCD) form that plays a crucial role in tumorigenesis and might affect the antitumor effect of radiotherapy and immunotherapy. This study aimed to investigate distinct ferroptosis-related genes, their prognostic value and their relationship with immunotherapy in patients with head and neck squamous cell carcinoma (HNSCC).Methods: The differentially expressed ferroptosis-related genes in HNSCC were filtered based on multiple public databases. To avoid overfitting and improve clinical practicability, univariable, least absolute shrinkage and selection operator (LASSO) and multivariable Cox algorithms were performed to construct a prognostic risk model. Moreover, a nomogram was constructed to forecast individual prognosis. The differences in tumor mutational burden (TMB), immune infiltration and immune checkpoint genes in HNSCC patients with different prognoses were investigated. The correlation between drug sensitivity and the model was firstly analyzed by the Pearson method.Results: Ten genes related to ferroptosis were screened to construct the prognostic risk model. Kaplan-Meier (K-M) analysis showed that the prognosis of HNSCC patients in the high-risk group was significantly lower than that in the low-risk group (P 〈 0.001), and the area under the curve (AUC) of the 1-, 3- and 5-year receiver operating characteristic (ROC) curve increased year by year (0.665, 0.743, and 0.755). The internal and external validation further verified the accuracy of the model. Then, a nomogram was build based on the reliable model. The C-index of the nomogram was superior to a previous study (0.752 vs. 0.640), and the AUC (0.729 vs. 0.597 at 1 year, 0.828 vs. 0.706 at 3 years and 0.853 vs. 0.645 at 5 years), calibration plot and decision curve analysis (DCA) also shown the satisfactory predictive capacity. Furthermore, the TMB was revealed to be positively correlated with the risk score in HNSCC patients (R = 0.14; P 〈 0.01). The differences in immune infiltration and immune checkpoint genes were significant (P 〈 0.05). Pearson analysis showed that the relationship between the model and the sensitivity to antitumor drugs was significant (P 〈 0.05).Conclusion: Our findings identified potential novel therapeutic targets, providing further potential improvement in the individualized treatment of patients with HNSCC.
    Electronic ISSN: 2296-634X
    Topics: Biology
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  • 58
    Publication Date: 2021-11-01
    Print ISSN: 1674-1056
    Electronic ISSN: 2058-3834
    Topics: Physics
    Published by Institute of Physics
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  • 59
    Publication Date: 2021-08-01
    Print ISSN: 0036-0279
    Electronic ISSN: 1468-4829
    Topics: Mathematics
    Published by Institute of Physics
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  • 60
    Publication Date: 2021-10-29
    Description: Sustainable development remains unattainable unless we move to reduce the negative impact of economic factors on environmental quality. It is noteworthy to provide new evidence on whether and how the empirical association between export diversification, agricultural value-addition, renewable energy, and regulatory quality with greenhouse gas (GHG) emissions evolved in Asian countries from 1996 to 2014. The study examines the relationships between these variables using current panel data techniques. The econometric procedure includes second-generation cointegration and unit root tests together with a novel Method of Movements Quantile Regression (MMQR). This approach offers an asymmetric relationship between the variables and is very robust to outliers compared to traditional quantile regression. The empirical outcomes show that export diversification, renewable energy, and regulatory quality are significantly and negatively associated with GHG emissions. In contrast, agricultural value-added in Asia has become a source of increased GHG emissions. Our findings are also robust with alternate specifications, including fully modified, dynamic and fixed effect regressions. This study will help policymakers for diversifying their export portfolio while ensuring a sustainable environment in Asia.
    Electronic ISSN: 2296-665X
    Topics: Energy, Environment Protection, Nuclear Power Engineering
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  • 61
    Publication Date: 2021-10-29
    Description: Otitis media (OM) encompasses a spectrum of clinical presentations ranging from the readily identifiable Acute OM (AOM), which is characterised by otalgia and fever, to chronic otitis media with effusion (COME) where impaired hearing due to middle ear effusion may be the only clinical symptom. Chronic suppurative OM (CSOM) presents as a more severe form of OM, involving perforation of the tympanic membrane. The pathogenesis of OM in these varied clinical presentations is unclear but activation of the innate inflammatory responses to viral and/or bacterial infection of the upper respiratory tract performs an integral role. This localised inflammatory response can persist even after pathogens are cleared from the middle ear, eustachian tubes and, in the case of respiratory viruses, even the nasal compartment. Children prone to OM may experience an over exuberant inflammatory response that underlies the development of chronic forms of OM and their sequelae, including hearing impairment. Treatments for chronic effusive forms of OM are limited, with current therapeutic guidelines recommending a “watch and wait” strategy rather than active treatment with antibiotics, corticosteroids or other anti-inflammatory drugs. Overall, there is a clear need for more targeted and effective treatments that either prevent or reduce the hyper-inflammatory response associated with chronic forms of OM. Improved treatment options rely upon an in-depth understanding of OM pathogenesis, particularly the role of the host innate immune response during acute OM. In this paper, we review the current literature regarding the innate immune response within the middle ear to bacterial and viral otopathogens alone, and as co-infections. This is an important consideration, as the role of respiratory viruses as primary pathogens in OM is not yet fully understood. Furthermore, increased reporting from PCR-based diagnostics, indicates that viral/bacterial co-infections in the middle ear are more common than bacterial infections alone. Increasingly, the mechanisms by which viral/bacterial co-infections may drive or maintain complex innate immune responses and inflammation during OM as a chronic response require investigation. Improved understanding of the pathogenesis of chronic OM, including host innate immune response within the middle ear is vital for development of improved diagnostic and treatment options for our children.
    Electronic ISSN: 2235-2988
    Topics: Biology , Medicine
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  • 62
    Publication Date: 2021-10-29
    Description: Ferroptosis induced by lipid peroxidation is closely related to cancer biology. Prostate cancer (PCa) is not only a malignant tumor but also a lipid metabolic disease. Previous studies have identified ferroptosis as an important pathophysiological pathway in PCa development and treatment, but its role in the prognosis of PCa is less well known. In this study, we constructed a nine-ferroptosis-related gene risk model that demonstrated strong prognostic and therapeutic predictive power. The higher risk score calculated by the model was significantly associated with a higher ferroptosis potential index, higher Ki67 expression, higher immune infiltration, higher probability of biochemical recurrence, worse clinicopathological characteristics, and worse response to chemotherapy and antiandrogen therapy in PCa. The mechanisms identified by the gene set enrichment analysis suggested that this signature can accurately distinguish high- and low-risk populations, which is possibly closely related to variations in steroid hormone secretion, regulation of endocrine processes, positive regulation of humoral immune response, and androgen response. Results of this study were confirmed in two independent PCa cohorts, namely, The Cancer Genome Atlas cohort and the MSK-IMPACT Clinical Sequencing Cohort, which contributed to the body of scientific evidence for the prediction of biochemical recurrence in patients with PCa. In addition, as the main components of this signature, the effects of the AIFM2 and NFS1 genes on ferroptosis were evaluated and verified by in vivo and in vitro experiments, respectively. The above findings provided new insights and presented potential clinical applications of ferroptosis in PCa.
    Electronic ISSN: 2296-634X
    Topics: Biology
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  • 63
    Publication Date: 2021-10-29
    Description: In recent decades, degradation and loss of the world’s forest ecosystems have been key contributors to biodiversity loss and future climate change. This article analyzes plant diversity, biomass, carbon sequestration potential (CSP), and the net primary productivity (NPP) of four vegetation types viz., Dense mixed forest (DMF); Open mixed forest (OMF); Teak plantation (TP), and Sal mixed forest (SMF) in the dry tropical forest ecosystem of central India through remote sensing techniques together with physical ground observations during 2013–2018. The total C storage in trees varied from 16.02 to 47.15 Mg ha−1 in studied vegetation types with the highest in DMF and lowest in OMF. The total C storage in stem wood, branches, and foliage falls in the range of 52.93–78.30%, 9.49–22.99%, and 3.31–12.89% respectively. The total standing biomass varied from 83.77 to 111.21 Mg ha−1 and these variations are due to different vegetation types, with the highest in DMF followed by TP, SMF while the lowest was estimated in OMF. The net primary productivity (NPP) [aboveground (AG) + belowground (BG)] varied from 7.61 to 9.94 Mg ha−1 yr−1 with mean values of 8.74 Mg ha−1 yr−1 where AG shares a maximum contribution of 77.66%. The total biomass production was distributed from 64.09 to 82.91% in AG and 17.08–35.91% in BG components. The present study outlines that the studied forest ecosystem has the substantial potential of carbon sequestration and a great possibility of mitigating local and global climate change.
    Electronic ISSN: 2296-665X
    Topics: Energy, Environment Protection, Nuclear Power Engineering
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  • 64
    Publication Date: 2021-10-29
    Electronic ISSN: 1664-302X
    Topics: Biology
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  • 65
    Publication Date: 2021-10-29
    Description: The challenge of effectively regenerating bone tissue through tissue engineering technology is that most tissue engineering scaffolds cannot imitate the three-dimensional structure and function of the natural extracellular matrix. Herein, we have prepared the poly(L-lactic acid)–based dual bioactive component reinforced nanofiber mats which were named as poly(L-lactic acid)/bovine serum albumin/nanohydroxyapatite (PLLA/BSA/nHAp) with dual bioactive components by combining homogeneous blending and electrospinning technology. The results showed that these nanofiber mats had sufficient mechanical properties and a porous structure suitable for cell growth and migration. Furthermore, the results of cell experiments in vitro showed that PLLA/BSA/nHAp composite nanofiber mat could preferably stimulate the proliferation of mouse osteoblastic cells (MC3T3 cells) compared with pure PLLA nanofiber mats. Based on these results, the scaffolds developed in this study are considered to have a great potential to be adhibited as bone repair materials.
    Electronic ISSN: 2296-2646
    Topics: Chemistry and Pharmacology
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  • 66
    Publication Date: 2021-10-29
    Description: Commercial table salt is a condiment with food preservative properties by decreasing water activity and increasing osmotic pressure. Salt is also a source of halophilic bacteria and archaea. In the present research, the diversity of halotolerant and halophilic microorganisms was studied in six commercial table salts by culture-dependent and culture-independent techniques. Three table salts were obtained from marine origins: Atlantic Ocean, Mediterranean (Ibiza Island), and Odiel marshes (supermarket marine salt). Other salts supplemented with mineral and nutritional ingredients were also used: Himalayan pink, Hawaiian black, and one with dried vegetables known as Viking salt. The results of 16S rRNA gene sequencing reveal that the salts from marine origins display a similar archaeal taxonomy, but with significant variations among genera. Archaeal taxa Halorubrum, Halobacterium, Hallobellus, Natronomonas, Haloplanus, Halonotius, Halomarina, and Haloarcula were prevalent in those three marine salts. Furthermore, the most abundant archaeal genera present in all salts were Natronomonas, Halolamina, Halonotius, Halapricum, Halobacterium, Haloarcula, and uncultured Halobacterales. Sulfitobacter sp. was the most frequent bacteria, represented almost in all salts. Other genera such as Bacillus, Enterococcus, and Flavobacterium were the most frequent taxa in the Viking, Himalayan pink, and black salts, respectively. Interestingly, the genus Salinibacter was detected only in marine-originated salts. A collection of 76 halotolerant and halophilic bacterial and haloarchaeal species was set by culturing on different media with a broad range of salinity and nutrient composition. Comparing the results of 16S rRNA gene metataxonomic and culturomics revealed that culturable bacteria Acinetobacter, Aquibacillus, Bacillus, Brevundimonas, Fictibacillus, Gracilibacillus, Halobacillus, Micrococcus, Oceanobacillus, Salibacterium, Salinibacter, Terribacillus, Thalassobacillus, and also Archaea Haloarcula, Halobacterium, and Halorubrum were identified at least in one sample by both methods. Our results show that salts from marine origins are dominated by Archaea, whereas salts from other sources or salt supplemented with ingredients are dominated by bacteria.
    Electronic ISSN: 1664-302X
    Topics: Biology
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  • 67
    Publication Date: 2021-10-29
    Description: Urbanization and seasonality strongly influence the bacterial composition of the soil. However, aquatic environments such as rivers are understudied owing to their high dynamics and therefore rules relating to more static habitats such as lentic or terrestrial environments may be limited. Here, we compared the spatiotemporal patterns of bacterioplankton communities in the Zhangxi river along a gradient of urbanization using 16S ribosomal DNA identification. The alpha and beta diversity of bacterioplankton showed no significant response to watershed urbanization. A significant difference in predicted functional profiles of the bacterioplankton community was also revealed between the wet and dry seasons. The bacterioplankton community assembly was driven by both deterministic and stochastic processes. Stochasticity was one of the most vital processes affecting the bacterioplankton communities in both wet and dry seasons, explaining over 50% variation in the community by the null model analysis. Bacterioplankton co-occurrence patterns in the river changed with the seasons. More notably, the composition of bacterioplankton communities was inconsistent with alternations of the spatial distance offering meaningful implications for interactions between zero-radius operational taxonomic units and the dynamics of the bacterioplankton communities in surface water. In summary, we found clear patterns of seasonal variations in the bacterioplankton community structures.
    Electronic ISSN: 2296-665X
    Topics: Energy, Environment Protection, Nuclear Power Engineering
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  • 68
    Publication Date: 2021-10-29
    Description: The properties of the solar wind fraction that exhibits an Interplanetary Magnetic Field (IMF) orientation orthogonal to the classical Parker spiral (so-called ortho-Parker) are investigated. We make use of a solar wind plasma categorization scheme, using 10 years of OMNI data, and show that the fractions of the different plasma origins (streamer-belt-origin plasma, coronal-hole-origin plasma, sector-reversal-region plasma and ejecta) identified by this scheme are rather constant when expressed as a function of the IMF orientation whereas the Alfvén Mach number significantly depends on this orientation. This has direct implication on the magnetosheath dynamics and, as an example, the stability of the mirror mode in this compressed plasma is studied thanks to Rankine-Hugoniot anisotropic relations. This study sheds light on previously reported, yet unexplained, observations of a larger occurrence of mirror mode in the magnetosheath downstream of ortho-Parker IMF.
    Electronic ISSN: 2296-987X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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  • 69
    Publication Date: 2021-10-29
    Description: Atherosclerotic plaque rupture in carotid arteries can lead to stroke which is one of the leading causes of death or disability worldwide. The accumulation of atherosclerotic plaque in an artery changes the mechanical properties of the vessel. Whilst healthy arteries can continuously adapt to mechanical loads by remodelling their internal structure, particularly the load-bearing collagen fibres, diseased vessels may have limited remodelling capabilities. In this study, a local stress modulated remodelling algorithm is proposed to explore the mechanical response of arterial tissue to the remodelling of collagen fibres. This stress driven remodelling algorithm is used to predict the optimum distribution of fibres in healthy and diseased human carotid bifurcations obtained using Magnetic Resonance Imaging (MRI). In the models, healthy geometries were segmented into two layers: media and adventitia and diseased into four components: adventitia, media, plaque atheroma and lipid pool (when present in the MRI images). A novel meshing technique for hexahedral meshing of these geometries is also demonstrated. Using the remodelling algorithm, the optimum fibre patterns in various patient specific plaques are identified and the role that deviations from these fibre configurations in plaque vulnerability is shown. This study provides critical insights into the collagen fibre patterns required in carotid artery and plaque tissue to maintain plaque stability.
    Electronic ISSN: 1664-042X
    Topics: Biology
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  • 70
    Publication Date: 2021-10-29
    Description: Flow boiling is one of the most effective mechanisms in heat transfer thanks to the latent heat of vaporization. Surface modifications such as mixed-wettability have a considerable effect on the boiling heat transfer performance in terms of enhancement in boiling heat transfer as well as critical heat flux. This study introduces a new method of fabrication of biphilic surfaces, where C4F8 (Octafluorocyclobutane) islands are surrounded by silicon. Two different biphilic surfaces were fabricated and compared with the entirely uniform hydrophobic surface taken as a reference,. Each of the biphilic surfaces has three different sections, namely inlet, middle and outlet regions. The first region is mainly hydrophobic (inlet), while the third region is mainly hydrophilic (outlet). The heat transfer coefficients were obtained at different heat fluxes. Compared to the entirely uniform hydrophobic surface, the results show that biphilic surfaces enhance the boiling heat transfer performance by up to 50%. The visualization results revealed that the biphilic surfaces lead to more nucleation sites in the bubbly flow regime and break up the elongated bubbles in the slug flow regime.
    Electronic ISSN: 2297-3079
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 71
    Publication Date: 2021-10-29
    Description: Benthic quadrat surveys using 2-D images are one of the most common methods of quantifying the composition of coral reef communities, but they and other methods fail to assess changes in species composition as a 3-dimensional system, arguably one of the most important attributes in foundational systems. Structure-from-motion (SfM) algorithms that utilize images collected from various viewpoints to form an accurate 3-D model have become more common among ecologists in recent years. However, there exist few efficient methods that can classify portions of the 3-D model to specific ecological functional groups. This lack of granularity makes it more difficult to identify the class category responsible for changes in the structure of coral reef communities. We present a novel method that can efficiently provide semantic labels of functional groups to 3-D reconstructed models created from commonly used SfM software (i.e., Agisoft Metashape) using fully convolutional networks (FCNs). Unlike other methods, ours involves creating dense labels for each of the images used in the 3-D reconstruction and then reusing the projection matrices created during the SfM process to project semantic labels onto either the point cloud or mesh to create fully classified versions. When quantitatively validating the classification results we found that this method is capable of accurately projecting semantic labels from image-space to model-space with scores as high as 91% pixel accuracy. Furthermore, because each image only needs to be provided with a single set of dense labels this method scales linearly making it useful for large areas or high resolution-models. Although SfM has become widely adopted by ecologists, deep learning presents a steep learning curve for many. To ensure repeatability and ease-of-use, we provide a comprehensive workflow with detailed instructions and open-sourced the programming code to assist others in replicating our methodology. Our method will allow researchers to assess precise changes in 3-D community composition of reef habitats in an entirely novel way, providing more insight into changes in ecological paradigms, such as those that occur during coral-algae shifts.
    Electronic ISSN: 2296-7745
    Topics: Biology
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  • 72
    Publication Date: 2021-10-29
    Description: Antibiotics resistance genes (ARGs) are mainly caused by the extensive use and abuse of antibiotics and have become a global public health concern. Owing to the development of high-throughput sequencing, metagenomic sequencing has been widely applied to profile the composition of ARGs, investigate their distribution pattern, and track their sources in diverse environments. However, the lack of a detailed transmission mechanism of ARGs limits the management of its pollution. Hence, it’s essential to introduce how to utilize the metagenomic data to obtain an in-depth understanding of the distribution pattern and transmission of ARGs. This review provides an assessment of metagenomic data utilization in ARG studies and summarizes current bioinformatic tools and databases, including ARGs-OAP, ARG analyzer, DeepARG, CARD, and SARG, for profiling the composition of ARGs and tracking the source of ARGs. Several bioinformatic tools and databases were then benchmarked. Our results showed that although SARG is a good database, the application of two or more bioinformatic tools and databases could provide a comprehensive view of ARG profiles in diverse environmental samples. Finally, several perspectives were proposed for future studies to obtain an in-depth understanding of ARGs based on metagenomic data. Our review of the utilization of metagenomic data together with bioinformatic tools and databases in ARG studies could provide insights on exploring the profiles and transmission mechanism of ARG in different environments that mitigate the spread of ARGs and manage the ARGs pollution.
    Electronic ISSN: 2296-665X
    Topics: Energy, Environment Protection, Nuclear Power Engineering
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  • 73
    Publication Date: 2021-10-28
    Description: The spatiotemporal distribution of terahertz (THz) radiation from plasma has been demonstrated with the technology of THz focal-plane imaging. It has been found that the spatiotemporal distribution will vary with the frequency, as well as the length of plasma. A doughnut-shaped distribution appears in the lower frequency range, while the bell-shaped distribution corresponds to the higher frequency range. For plasmas with different lengths, their generated THz images in the time domain are similar, the THz images in the frequency domain as well. The spatiotemporal distributions are simulated with the off-axis-phase matching theory. All the findings will renew the understanding of the THz generation from plasma induced by two-color pulses.
    Electronic ISSN: 2296-424X
    Topics: Physics
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  • 74
    Publication Date: 2021-10-29
    Description: Rice remains a major staple food source for the rapidly growing world population. However, regular occurrences of carcinogenic arsenic (As) minerals in waterlogged paddy topsoil pose a great threat to rice production and consumers across the globe. Although As contamination in rice has been well recognized over the past two decades, no suitable rice germplasm had been identified to exploit in adaptive breeding programs. Therefore, this current study identified suitable rice germplasm for As tolerance and exclusion based on a variety of traits and investigated the interlinkages of favorable traits during different growth stages. Fifty-three different genotypes were systematically evaluated for As tolerance and accumulation. A germination screening assay was carried out to identify the ability of individual germplasm to germinate under varying As stress. Seedling-stage screening was conducted in hydroponics under varying As stress to identify tolerant and excluder genotypes, and a field experiment was carried out to identify genotypes accumulating less As in grain. Irrespective of the rice genotypes, plant health declined significantly with increasing As in the treatment. However, genotype-dependent variation in germination, tolerance, and As accumulation was observed among the genotypes. Some genotypes (WTR1-BRRI dhan69, NPT-IR68552-55-3-2, OM997, and GSR IR1-5-Y4-S1-Y1) showed high tolerance by excluding As in the shoot system. Arsenic content in grain ranged from 0.12 mg kg−1 in Huang-Hua-Zhan (indica) from China to 0.48 mg kg−1 in IRAT 109 (japonica) from Brazil. This current study provides novel insights into the performance of rice genotypes under varying As stress during different growth stages for further use in ongoing breeding programs for the development of As-excluding rice varieties for As-polluted environments.
    Electronic ISSN: 1664-462X
    Topics: Biology
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  • 75
    Publication Date: 2021-10-29
    Description: Plant growth-promoting bacteria (PGPB) and humic substances (HSs) are promising options for reducing the use of pesticides and mineral fertilizers. Although many studies have shown the effects of PGPB and HSs separately, little information is available on plant responses to the combined application of these biostimulants despite the great potential for the simultaneous action of these biological inputs. Thus, the objective of this review is to present an overview of scientific studies that addressed the application of PGPB and HSs to different crops. First, we discuss the effect of these biostimulants on biological nitrogen fixation, the various effects of the inoculation of beneficial bacteria combined with the application of HSs on promoting the growth of nonleguminous plants and how this combination can increase bacterial colonization of plant hosts. We also address the effect of PGPB and HSs on plant responses to abiotic stresses, in addition to discussing the role of HSs in protecting plants against pathogens. There is a lack of studies that address the role of PGPB + HSs in biocontrol. Understanding the factors involved in the promotion of plant growth through the application of PGPB and HSs can assist in the development of efficient biostimulants for agricultural management. This approach has the potential to accelerate the transition from conventional cultivation to sustainable agrosystems.
    Electronic ISSN: 1664-302X
    Topics: Biology
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  • 76
    Publication Date: 2021-10-29
    Description: Hypertension is regulated by immunological components. Spontaneously hypertensive rats (SHR) display a large population of proinflammatory CD161 + immune cells. We investigated the effect of early post-natal gut microbiota on the development of the immune system and resulting hypertension in the SHR. We first examined the microbial populations in the fecal samples of SHR and normotensive control WKY using 16S rDNA sequencing. We found that in the newborn SHR (1-week old) the gut microbiota was qualitatively and quantitatively different from the newborns of normotensive WKY. The representation of the predominant bacterial phylum Proteobacteria was significantly less in 1-week old SHR pups than in WKY (94.5% Proteobacteria in WKY vs. 65.2% in SHR neonates). Even within the phylum Proteobacteria, the colonizing genera in WKY and SHR differed dramatically. Whereas WKY microbiota was predominantly comprised of Escherichia-Shigella, SHR microbiota was represented by other taxa of Enterobacteriaceae and Pasteurellaceae. In contrast, the representation of phylum Firmicutes in the neonatal SHR gut was greater than WKY. Cross-fostering newborn SHR pups by lactating WKY dams caused a dramatic shift in 1-week old cross-fostered SHR gut microbiota. The two major bacterial taxa of phylum Proteobacteria, Enterobacteriaceae and Pasteurellaceae as well as Lactobacillus intestinalis, Proteus, Romboustia and Rothia were depleted after cross-fostering and were replaced by the predominant genera of WKY (Escherichia-Shigella). A proinflammatory IL-17F producing CD161 + immune cell population in the spleen and aorta of cross-fostered SHR was also reduced (30.7% in self-fostered SHR vs. 12.6% in cross-fostered SHR at 30 weeks of age) as was the systolic blood pressure in adult cross-fostered SHR at 10 weeks of age. Thus, altered composition of gut microbiota of SHR toward WKY at early neonatal age had a long-lasting effect on immune system by reducing proinflammatory immune cells and lowering systolic blood pressure.
    Electronic ISSN: 1664-042X
    Topics: Biology
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  • 77
    Publication Date: 2021-10-29
    Description: Peptide-appended Pillar[5]arene (PAP) is an artificial water channel that can be incorporated into lipid and polymeric membranes to achieve high permeability and enhanced selectivity for angstrom-scale separations [Shen et al. Nat. Commun.9:2294 (2018)]. In comparison to commonly studied rigid carbon nanotubes, PAP channels are conformationally flexible, yet these channels allow a high water permeability [Y. Liu and H. Vashisth Phys. Chem. Chem. Phys.21:22711 (2019)]. Using molecular dynamics (MD) simulations, we study water dynamics in PAP channels embedded in biological (lipid) and biomimetic (block-copolymer) membranes to probe the effect of the membrane environment on water transport characteristics of PAP channels. We have resolved the free energy surface and local minima for water diffusion within the channel in each type of membrane. We find that water follows single file transport with low free-energy barriers in regions surroundings the central ring of the PAP channel and the single file diffusivity of water correlates with the number of hydrogen bonding sites within the channel, as is known for other sub-nm pore-size synthetic and biological water channels [Horner et al. Sci. Adv.1:e1400083 (2015)].
    Electronic ISSN: 2296-2646
    Topics: Chemistry and Pharmacology
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  • 78
    Publication Date: 2021-10-29
    Description: The GeneLEAD VIII (Diagenode, Belgium) is a new, fully automated, sample-to-result precision instrument for the extraction of DNA and PCR detection of Mycobacterium tuberculosis complex (MTBC) directly from clinical samples. The Deeplex Myc-TB® assay (Genoscreen, France) is a diagnostic kit based on the deep sequencing of a 24-plexed amplicon mix allowing simultaneously the detection of resistance to 13 antituberculous (antiTB) drugs and the determination of spoligotype. We evaluated the performance of a strategy combining the both mentioned tools to detect directly from clinical samples, in 8 days, MTBC and its resistance to 13 antiTB drugs, and identify potential transmission of strains from patient-to-patient. Using this approach, we screened 112 clinical samples (65 smear-negative) and 94 MTBC cultured strains. The sensitivity and the specificity of the GeneLEAD/Deeplex Myc-TB approach for MTBC detection were 79.3% and 100%, respectively. One hundred forty successful Deeplex Myc-TB results were obtained for 46 clinical samples and 94 strains, a total of 85.4% of which had a Deeplex Myc-TB susceptibility and resistance prediction consistent with phenotypic drug susceptibility testing (DST). Importantly, the Deeplex Myc-TB assay was able to detect 100% of the multidrug-resistant (MDR) MTBC tested. The lowest concordance rates were for pyrazinamide, ethambutol, streptomycin, and ethionamide (84.5%, 81.5%, 73%, and 55%, respectively) for which the determination of susceptibility or resistance is generally difficult with current tools. One of the main difficulties of Deeplex Myc-TB is to interpret the non-synonymous uncharacterized variants that can represent up to 30% of the detected single nucleotide variants. We observed a good level of concordance between Deeplex Myc-TB-spoligotyping and MIRU-VNTR despite a lower discriminatory power for spoligotyping. The median time to obtain complete results from clinical samples was 8 days (IQR 7–13) provided a high-throughput NGS sequencing platform was available. Our results highlight that the GeneLEAD/Deeplex Myc-TB approach could be a breakthrough in rapid diagnosis of MDR TB in routine practice.
    Electronic ISSN: 2235-2988
    Topics: Biology , Medicine
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  • 79
    Publication Date: 2021-10-29
    Description: c-Jun N-terminal kinase (JNK) is a multi-functional protein involved in a diverse array of context-dependent processes, including apoptosis, cell cycle regulation, adhesion, and differentiation. It is integral to several signalling cascades, notably downstream of non-canonical Wnt and mitogen activated protein kinase (MAPK) signalling pathways. As such, it is a key regulator of cellular behaviour and patterning during embryonic development across the animal kingdom. The cephalochordate amphioxus is an invertebrate chordate model system straddling the invertebrate to vertebrate transition and is thus ideally suited for comparative studies of morphogenesis. However, next to nothing is known about JNK signalling or cellular processes in this lineage. Pharmacological inhibition of JNK signalling using SP600125 during embryonic development arrests gastrula invagination and causes convergence extension-like defects in axial elongation, particularly of the notochord. Pharynx formation and anterior oral mesoderm derivatives like the preoral pit are also affected. This is accompanied by tissue-specific transcriptional changes, including reduced expression of six3/6 and wnt2 in the notochord, and ectopic wnt11 in neurulating embryos treated at late gastrula stages. Cellular delamination results in accumulation of cells in the gut cavity and a dorsal fin-like protrusion, followed by secondary Caspase-3-mediated apoptosis of polarity-deficient cells, a phenotype only partly rescued by co-culture with the pan-Caspase inhibitor Z-VAD-fmk. Ectopic activation of extracellular signal regulated kinase (ERK) signalling in the neighbours of extruded notochord and neural cells, possibly due to altered adhesive and tensile properties, as well as defects in cellular migration, may explain some phenotypes caused by JNK inhibition. Overall, this study supports conserved functions of JNK signalling in mediating the complex balance between cell survival, apoptosis, differentiation, and cell fate specification during cephalochordate morphogenesis.
    Electronic ISSN: 2296-634X
    Topics: Biology
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  • 80
    Publication Date: 2021-10-29
    Description: Nitrapyrin, a nitrification inhibitor, produces liver tumors in B6C3F1 mice. In a 2-year oncogenicity study, increased incidence of mice with hepatocellular tumors was observed following exposure to 125 (females only) or 250 mg/kg/day (males and females) nitrapyrin in the diet. Previous data was generated in male mice to support a mode-of-action (MoA) characterized by constitutive androstane receptor (CAR) nuclear receptor (NR) activation, increased hepatocellular proliferation, and subsequent hepatocellular foci and tumor formation. Uncertainty as to the relevance of this MoA for females remained given the increased sensitivity to tumor formation in female mice. A targeted MoA study was conducted to evaluate CAR activation and hepatic responses in female mice treated with the female carcinogenic dose of nitrapyrin for 4 days. Nitrapyrin induced a treatment-related increase in hepatocellular hypertrophy and hepatocellular proliferation. Nitrapyrin also induced a dose-related increase in the Cyp2b10/CAR-associated transcript and liver weights. Nitrapyrin-induced liver weights and Cyp2b10 gene expression for both males and females were compared to data generated from three other established CAR activators; methyl isobutyl ketone, phenobarbital, and sulfoxaflor. The response observed in female mice following exposure to nitrapyrin was within range of the degree of change observed in mice following exposure to tumorigenic doses of other CAR activators. Consistent with the liver MoA in male mice, these data support a CAR-mediated mode of action for nitrapyrin-induced liver tumors in female mice, with the understanding that a focused approach minimizing animal use can bridge male and female datasets when sex-specific carcinogenic differences are observed.
    Electronic ISSN: 2673-3080
    Topics: Chemistry and Pharmacology
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  • 81
    Publication Date: 2021-10-29
    Description: Choosing an appropriate GCM (Global Climate Model, GCM) is of great significance for the simulation of the hydrological cycle over a basin under future climate scenarios. In this study, the Rank Score Method (RS) with eight indicators were applied to comprehensively evaluate the suitability of 19 GCMs issued in the Sixth Global Atmosphere and Coupled Model Intercomparison Project (CMIP6) to the Yellow River Basin (YRB). The results indicated that: 1) The GCMs perform differently in simulating precipitation over the YRB with the top six GCMs ranking from MRI-ESM2-0, ACCESS-CM2, CNRM-CM6-1, CNRM-ESM2-1, FGOALS-f3-L, to MPI-ESM1-2-HR. 2) Most GCMs overestimated the precipitation, and poorly simulated the phase distribution of extremes mainly due to overstimulation of wet season span and precipitation amount in the season, although all GCMs could capture decadal feature of annual precipitation. Meanwhile, it is also found that most GCMs underestimated summer precipitation and overestimated spring precipitation. 3) The GCMs well simulated the spatial distribution of annual precipitation, with an overestimation in the source area, and an underestimation in the northern part of the middle reaches of YRB.
    Electronic ISSN: 2296-6463
    Topics: Geosciences
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  • 82
    Publication Date: 2021-10-29
    Description: Being able to reproduce and survive is fundamental to all forms of life. In primitive unicellular organisms, the emergence of quiescence as a reversible proliferation arrest has most likely improved cell survival under unfavorable environmental conditions. During evolution, with the repeated appearances of multicellularity, several aspects of unicellular quiescence were conserved while new quiescent cell intrinsic abilities arose. We propose that the formation of a microenvironment by neighboring cells has allowed disconnecting quiescence from nutritional cues. In this new context, non-proliferative cells can stay metabolically active, potentially authorizing the emergence of new quiescent cell properties, and thereby favoring cell specialization. Through its co-evolution with cell specialization, quiescence may have been a key motor of the fascinating diversity of multicellular complexity.
    Electronic ISSN: 2296-634X
    Topics: Biology
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  • 83
    Publication Date: 2021-10-29
    Description: The organization of biomolecules and bioassemblies is highly governed by the nature and extent of their interactions with water. These interactions are of high intricacy and a broad range of methods based on various principles have been introduced to characterize them. As these methods view the hydration phenomena differently (e.g., in terms of time and length scales), a detailed insight in each particular technique is to promote the overall understanding of the stunning “hydration world.” In this prospective mini-review we therefore critically examine time-dependent fluorescence shift (TDFS)—an experimental method with a high potential for studying the hydration in the biological systems. We demonstrate that TDFS is very useful especially for phospholipid bilayers for mapping the interfacial region formed by the hydrated lipid headgroups. TDFS, when properly applied, reports on the degree of hydration and mobility of the hydrated phospholipid segments in the close vicinity of the fluorophore embedded in the bilayer. Here, the interpretation of the recorded TDFS parameters are thoroughly discussed, also in the context of the findings obtained by other experimental techniques addressing the hydration phenomena (e.g., molecular dynamics simulations, NMR spectroscopy, scattering techniques, etc.). The differences in the interpretations of TDFS outputs between phospholipid biomembranes and proteins are also addressed. Additionally, prerequisites for the successful TDFS application are presented (i.e., the proper choice of fluorescence dye for TDFS studies, and TDFS instrumentation). Finally, the effects of ions and oxidized phospholipids on the bilayer organization and headgroup packing viewed from TDFS perspective are presented as application examples.
    Electronic ISSN: 2296-2646
    Topics: Chemistry and Pharmacology
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  • 84
    Publication Date: 2021-10-29
    Description: Ocean aerobiology is defined here as the study of biological particles of marine origin, including living organisms, present in the atmosphere and their role in ecological, biogeochemical, and climate processes. Hundreds of trillions of microorganisms are exchanged between ocean and atmosphere daily. Within a few days, tropospheric transport potentially disperses microorganisms over continents and between oceans. There is a need to better identify and quantify marine aerobiota, characterize the time spans and distances of marine microorganisms’ atmospheric transport, and determine whether microorganisms acclimate to atmospheric conditions and remain viable, or even grow. Exploring the atmosphere as a microbial habitat is fundamental for understanding the consequences of dispersal and will expand our knowledge of biodiversity, biogeography, and ecosystem connectivity across different marine environments. Marine organic matter is chemically transformed in the atmosphere, including remineralization back to CO2. The magnitude of these transformations is insignificant in the context of the annual marine carbon cycle, but may be a significant sink for marine recalcitrant organic matter over long (∼104 years) timescales. In addition, organic matter in sea spray aerosol plays a significant role in the Earth’s radiative budget by scattering solar radiation, and indirectly by affecting cloud properties. Marine organic matter is generally a poor source of cloud condensation nuclei (CCN), but a significant source of ice nucleating particles (INPs), affecting the formation of mixed-phase and ice clouds. This review will show that marine biogenic aerosol plays an impactful, but poorly constrained, role in marine ecosystems, biogeochemical processes, and the Earth’s climate system. Further work is needed to characterize the connectivity and feedbacks between the atmosphere and ocean ecosystems in order to integrate this complexity into Earth System models, facilitating future climate and biogeochemical predictions.
    Electronic ISSN: 1664-302X
    Topics: Biology
    Published by Frontiers Media
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  • 85
    Publication Date: 2021-10-29
    Description: A high-quality genome is of significant value when seeking to control forest pests such as Dendrolimus kikuchii, a destructive member of the order Lepidoptera that is widespread in China. Herein, a high quality, chromosome-level reference genome for D. kikuchii based on Nanopore, Pacbio HiFi sequencing and the Hi-C capture system is presented. Overall, a final genome assembly of 705.51 Mb with contig and scaffold N50 values of 20.89 and 24.73 Mb, respectively, was obtained. Of these contigs, 95.89% had unique locations on 29 chromosomes. In silico analysis revealed that the genome contained 15,323 protein-coding genes and 63.44% repetitive sequences. Phylogenetic analyses indicated that D. kikuchii may diverged from the common ancestor of Thaumetopoea. Pityocampa, Thaumetopoea ni, Heliothis virescens, Hyphantria armigera, Spodoptera frugiperda, and Spodoptera litura approximately 122.05 million years ago. Many gene families were expanded in the D. kikuchii genome, particularly those of the Toll and IMD signaling pathway, which included 10 genes in peptidoglycan recognition protein, 19 genes in MODSP, and 11 genes in Toll. The findings from this study will help to elucidate the mechanisms involved in protection of D. kikuchii against foreign substances and pathogens, and may highlight a potential channel to control this pest.
    Electronic ISSN: 1664-8021
    Topics: Biology , Medicine
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  • 86
    Publication Date: 2021-10-29
    Description: Every year, billions of birds undertake extensive migrations between breeding and non-breeding areas, facing challenges that require behavioural adjustments, particularly to flight timing and duration. Such adjustments in daily activity patterns and the influence of extrinsic factors (e.g., environmental conditions, moonlight) have received much more research attention in terrestrial than marine migrants. Taking advantage of the widespread deployment in recent decades of combined light-level geolocator-immersion loggers, we investigated diel organisation and influence of the moon on flight activities during the non-breeding season of 21 migrant seabird species from a wide taxonomic range (6 families, 3 orders). Migrant seabirds regularly stopped (to either feed or rest) during migration, unlike some terrestrial and wetland birds which fly non-stop. We found an overall increase for most seabird species in time in flight and, for several species, also in flight bout duration, during migration compared to when resident at the non-breeding grounds. Additionally, several nocturnal species spent more of the day in flight during migration than at non-breeding areas, and vice versa for diurnal species. Nocturnal time in flight tended to increase during full moon, both during migration and at the non-breeding grounds, depending on species. Our study provides an extensive overview of activity patterns of migrant seabirds, paving the way for further research on the underlying mechanisms and drivers.
    Electronic ISSN: 2296-7745
    Topics: Biology
    Published by Frontiers Media
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  • 87
    Publication Date: 2021-10-29
    Description: Gait phase classification is important for rehabilitation training in patients with lower extremity motor dysfunction. Classification accuracy of the gait phase also directly affects the effect and rehabilitation training cycle. In this article, a multiple information (multi-information) fusion method for gait phase classification in lower limb rehabilitation exoskeleton is proposed to improve the classification accuracy. The advantage of this method is that a multi-information acquisition system is constructed, and a variety of information directly related to gait movement is synchronously collected. Multi-information includes the surface electromyography (sEMG) signals of the human lower limb during the gait movement, the angle information of the knee joints, and the plantar pressure information. The acquired multi-information is processed and input into a modified convolutional neural network (CNN) model to classify the gait phase. The experiment of gait phase classification with multi-information is carried out under different speed conditions, and the experiment is analyzed to obtain higher accuracy. At the same time, the gait phase classification results of multi-information and single information are compared. The experimental results verify the effectiveness of the multi-information fusion method. In addition, the delay time of each sensor and model classification time is measured, which shows that the system has tremendous real-time performance.
    Electronic ISSN: 1662-5218
    Topics: Medicine , Technology
    Published by Frontiers Media
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  • 88
    Publication Date: 2021-10-29
    Description: Background: Acute myeloid leukemia (AML) is a clinically heterogeneous group of cancers. While some patients respond well to chemotherapy, we describe here a subgroup with distinct molecular features that has very poor prognosis under chemotherapy. The classification of AML relies substantially on cytogenetics, but most cytogenetic abnormalities do not offer targets for development of targeted therapeutics. Therefore, it is important to create a detailed molecular characterization of the subgroup most in need of new targeted therapeutics.Methods: We used a multi-omics approach to identify a molecular subgroup with the worst response to chemotherapy, and to identify promising drug targets specifically for this AML subgroup.Results: Multi-omics clustering analysis resulted in three primary clusters among 166 AML adult cancer cases in TCGA data. One of these clusters, which we label as the high-risk molecular subgroup (HRMS), consisted of cases that responded very poorly to standard chemotherapy, with only about 10% survival to 2 years. The gene TP53 was mutated in most cases in this subgroup but not in all of them. The top six genes over-expressed in the HRMS subgroup included E2F4, CD34, CD109, MN1, MMLT3, and CD200. Multi-omics pathway analysis using RNA and CNA expression data identified in the HRMS subgroup over-activated pathways related to immune function, cell proliferation, and DNA damage.Conclusion: A distinct subgroup of AML patients are not successfully treated with chemotherapy, and urgently need targeted therapeutics based on the molecular features of this subgroup. Potential drug targets include over-expressed genes E2F4, and MN1, as well as mutations in TP53, and several over-activated molecular pathways.
    Electronic ISSN: 1664-8021
    Topics: Biology , Medicine
    Published by Frontiers Media
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  • 89
    Publication Date: 2021-10-29
    Description: Given the importance of wood in many industrial applications, much research has focused on wood formation, especially lignin biosynthesis. However, the mechanisms governing the regulation of lignin biosynthesis in the rubber tree (Hevea brasiliensis) remain to be elucidated. Here, we gained insight into the mechanisms of rubber tree lignin biosynthesis using reaction wood (wood with abnormal tissue structure induced by gravity or artificial mechanical treatment) as an experimental model. We performed transcriptome analysis of rubber tree mature xylem from tension wood (TW), opposite wood (OW), and normal wood (NW) using RNA sequencing (RNA-seq). A total of 214, 1,280, and 32 differentially expressed genes (DEGs) were identified in TW vs. NW, OW vs. NW, and TW vs. OW, respectively. GO and KEGG enrichment analysis of DEGs from different comparison groups showed that zeatin biosynthesis, plant hormone signal transduction, phenylpropanoid biosynthesis, and plant–pathogen interaction pathways may play important roles in reaction wood formation. Sixteen transcripts involved in phenylpropanoid biosynthesis and 129 transcripts encoding transcription factors (TFs) were used to construct a TF–gene regulatory network for rubber tree lignin biosynthesis. Among them, MYB, C2H2, and NAC TFs could regulate all the DEGs involved in phenylpropanoid biosynthesis. Overall, this study identified candidate genes and TFs likely involved in phenylpropanoid biosynthesis and provides novel insights into the mechanisms regulating rubber tree lignin biosynthesis.
    Electronic ISSN: 1664-8021
    Topics: Biology , Medicine
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  • 90
    Publication Date: 2021-10-29
    Description: Rye is the only cross-pollinating Triticeae crop species. Knowledge of rye genes controlling complex-inherited traits is scarce, which, currently, largely disables the genomics assisted introgression of untapped genetic variation from self-incompatible germplasm collections in elite inbred lines for hybrid breeding. We report on the first genome-wide association study (GWAS) in rye based on the phenotypic evaluation of 526 experimental hybrids for plant height, heading date, grain quality, and yield in 2 years and up to 19 environments. We established a cross-validated NIRS calibration model as a fast, effective, and robust analytical method to determine grain quality parameters. We observed phenotypic plasticity in plant height and tiller number as a resource use strategy of rye under drought and identified increased grain arabinoxylan content as a striking phenotype in osmotically stressed rye. We used DArTseq™ as a genotyping-by-sequencing technology to reduce the complexity of the rye genome. We established a novel high-density genetic linkage map that describes the position of almost 19k markers and that allowed us to estimate a low genome-wide LD based on the assessed genetic diversity in elite germplasm. We analyzed the relationship between plant height, heading date, agronomic, as well as grain quality traits, and genotype based on 20k novel single-nucleotide polymorphism markers. In addition, we integrated the DArTseq™ markers in the recently established ‘Lo7' reference genome assembly. We identified cross-validated SNPs in ‘Lo7' protein-coding genes associated with all traits studied. These include associations of the WUSCHEL-related homeobox transcription factor DWT1 and grain yield, the DELLA protein gene SLR1 and heading date, the Ethylene overproducer 1-like protein gene ETOL1 and thousand-grain weight, protein and starch content, as well as the Lectin receptor kinase SIT2 and plant height. A Leucine-rich repeat receptor protein kinase and a Xyloglucan alpha-1,6-xylosyltransferase count among the cross-validated genes associated with water-extractable arabinoxylan content. This study demonstrates the power of GWAS, hybrid breeding, and the reference genome sequence in rye genetics research to dissect and identify the function of genes shaping genetic diversity in agronomic and grain quality traits of rye. The described links between genetic causes and phenotypic variation will accelerate genomics-enabled rye improvement.
    Electronic ISSN: 1664-462X
    Topics: Biology
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  • 91
    Publication Date: 2021-10-29
    Description: Background: Hypertensive patients are sensitive to the amount of dietary cholesterol intake, especially cholesterol from the whole eggs. Whether whole egg and dietary cholesterol consumption are suitable for hypertensive patients is still controversial.Aim: The objective of the study was to examine the associations of intake of eggs as well as the dietary cholesterol with total mortality in a Chinese nationwide cohort.Methods: We utilized data from the China Health and Nutrition Survey (CHNS) from the year of 1991 to 2015. Cumulative averages of egg and cholesterol intake were calculated to represent the consumption of the long-term diet of the participants in each available round of the survey. Cox regression models were employed to estimate the effects of eggs and dietary cholesterol from the different sources on mortality among hypertensive patients.Results: A total of 8,095 participants were included in the final analysis and followed up for a mean of 11.4 years. Finally, 927 cases of death were detected. After adjustment for the multivariate factors, consuming more than seven eggs per week was related to 29% lower mortality among the hypertensive patients compared with the consumers with not more than two eggs per week [hazard ratio (HR): 0.71; 95% CI: 0.59–0.85; P 〈 0.001]. Similarly, the egg-sourced cholesterol intake was inversely associated with mortality (P = 0.002) whereas intake of the dietary cholesterol from the non-egg sources was significantly related to the higher mortality (P 〈 0.001). However, total cholesterol intake was not related to mortality among hypertensive patients. Substituting eggs for an equivalent amount of non-egg-sourced protein-abundant foods was also associated with lower mortality.Conclusion: Higher consumption of eggs and egg-sourced dietary cholesterol was associated with lower mortality among the enrolled Chinese hypertensive patients but non-egg-sourced cholesterol intake was related to higher mortality. Therefore, our findings do not support the view that hypertensive patients should avoid whole egg consumption for the purpose of restricting dietary cholesterol intake.
    Electronic ISSN: 2296-861X
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 92
    Publication Date: 2021-10-29
    Description: We present a method for communicating personalized genetic risk information to citizens and their physicians using a secure web portal. We apply the method for 3,177 Finnish individuals in the P5 Study where estimates of genetic and absolute risk, based on genetic and clinical risk factors, of future disease are reported to study participants, allowing individuals to participate in managing their own health. Our method facilitates using polygenic risk score as a personalized tool to estimate a person’s future disease risk while offering a way for health care professionals to utilize the polygenic risk scores as a preventive tool in patient care.
    Electronic ISSN: 1664-8021
    Topics: Biology , Medicine
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  • 93
    Publication Date: 2021-10-29
    Description: Head smut, caused by Sporisorium reilianum [(Kuhn) Langdon and Fullerton], is a major disease of sorghum. Seed treatment is considered to be the most effective way to control the disease; however, the pathogen can infect at the seedling stage and the infected plant will not display symptoms until the reproductive stage is reached. The evaluation of the efficacy of seed treatments is time consuming and is dependent upon visible symptoms. Polymerase chain reaction (PCR) methods have the ability to identify pathogens and diagnose their presence at an early stage of infection. In this study, the S. reilianum-specific primer SR3 was used for PCR detection pathogen. We optimized temperature, humidity, and spore quantity test conditions and were able to achieve 〉88% infection incidence in sorghum seedlings. Sorghum seeds were soaked in various concentrations of tebuconazole and planted for 7 days in soil containing 0.2% teliospores. The efficacy of tebuconazole against S. reilianum was evaluated by PCR and recorded as disease incidence. Results indicated that the reduction in disease incidence after exposure to 0.15, 0.30, 0.45, 0.60, and 0.75 μg/mL tebuconazole was 6.24, 37.48, 67.74, 81.24, and 93.74%, respectively. Significant differences between the concentrations of tebuconazole were observed. The PCR assay represents a valuable tool for evaluating the efficacy of fungicide seed treatments for the control of S. reilianum in sorghum under laboratory conditions.
    Electronic ISSN: 1664-302X
    Topics: Biology
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  • 94
    Publication Date: 2021-10-29
    Description: Diutina catenulata (Candida catenulata) is an ascomycete yeast species widely used in environmental and industrial research and capable of causing infections in humans and animals. At present, there are only a few studies on D. catenulata, and further research is required for its more in-depth characterization and analysis. Eleven strains of D. catenulata collected from China Hospital Invasive Fungal Surveillance Net (CHIF-NET) and the CHIF-NET North China Program were identified using matrix-assisted laser desorption ionization–time of flight mass spectrometry and internal transcribed spacer sequencing. The antifungal susceptibility of the Diutina catenulata strains was tested using the Clinical and Laboratory Standards Institute broth microdilution method and Sensititre YeastOne™. Furthermore, ERG11 and FKS1 were sequenced to determine any mutations related to azole and echinocandin resistance in D. catenulata. All isolates exhibited low minimum inhibitory concentration (MIC) values for itraconazole (0.06–0.12 μg/ml), posaconazole (0.06–0.12 μg/ml), amphotericin B (0.25–1 μg/ml), and 5-flucytosine (range,
    Electronic ISSN: 2235-2988
    Topics: Biology , Medicine
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  • 95
    Publication Date: 2021-10-29
    Description: The Okhotsk Sea, which connects the high latitude Asian continent and the North Pacific, plays an important role in modern and past climate changes due to seasonal sea ice coverage and as a precursor of the North Pacific Intermediate Water. The long-term glacial-interglacial changes of sea ice coverage and its impacts on terrigenous transport and surface primary productivity in the Okhotsk Sea remain, however, not well constrained. Base on the paleomagnetic, rock magnetic, micropaleontological (diatom), and geochemical studies of the marine sediment core MD01-2414 (53°11.77′N, 149°34.80′E, water depth: 1,123 m) taken in the central Okhotsk Sea, we reconstruct the terrigenous sediment transport and paleoceanographic variations during the past 1550 thousand years (kyr). Seventeen geomagnetic excursions are identified from the paleomagnetic directional record. Close to the bottom of the core, an excursion was observed, which is proposed to be the Gilsa event ∼1550 thousand years ago (ka). During glacial intervals, our records reveal a wide extension of sea ice coverage and low marine productivity. We observed ice-rafted debris from mountain icebergs composed of coarse and high magnetic terrigenous detritus which were derived from the Kamchatka Peninsula to the central Okhotsk basin. Still during glacial intervals, the initiation (i.e., at ∼900 ka) of the Mid-Pleistocene Transition marks the changes to even lower marine productivity, suggesting that sea-ice coverage became larger during the last 900 ka. During interglacial intervals, the central Okhotsk Sea was either devoid of sea-ice or the ice was at best seasonal; resulting in high marine productivity. The weaker formation of Okhotsk Sea Intermediate Water, lower ventilation, and microbial degradation of organic matter depleted the oxygen concentration in the bottom water and created a reduced environment condition in the sea basin. The freshwater supplied by snow or glacier melting from Siberia and Kamchatka delivered fine grain sediments to the Okhotsk Sea. During the stronger interglacial intervals after the Mid-Brunhes Transition (i.e., Marine Isotope Stages 1, 5e, 9, and 11), strong freshwater discharges from Amur River drainage area are in association with intensified East Asian Summer Monsoon. This process may have enhanced the input of fine-grained terrigenous sediments to the central Okhotsk Sea.
    Electronic ISSN: 2296-6463
    Topics: Geosciences
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  • 96
    Publication Date: 2021-10-29
    Description: The present paper discusses families of Interior Penalty Discontinuous Galerkin (IP) methods for solving heterogeneous and anisotropic diffusion problems. Specifically, we focus on distinctive schemes, namely the Hybridized-, Embedded-, and Weighted-IP schemes, leading to final matrixes of different sizes and sparsities. Both the Hybridized- and Embedded-IP schemes are eligible for static condensation, and their degrees of freedom are distributed on the mesh skeleton. In contrast, the unknowns are located inside the mesh elements for the Weighted-IP variant. For a given mesh, it is well-known that the number of degrees of freedom related to the standard Discontinuous Galerkin methods increases more rapidly than those of the skeletal approaches (Hybridized- and Embedded-IP). We then quantify the impact of the static condensation procedure on the computational performances of the different IP classes in terms of robustness, accuracy, and CPU time. To this aim, numerical experiments are investigated by considering strong heterogeneities and anisotropies. We analyze the fixed error tolerance versus the run time and mesh size to guide our performance criterion. We also outlined some relationships between these Interior Penalty schemes. Eventually, we confirm the superiority of the Hybridized- and Embedded-IP schemes, regardless of the mesh, the polynomial degree, and the physical properties (homogeneous, heterogeneous, and/or anisotropic).
    Electronic ISSN: 2624-9375
    Topics: Architecture, Civil Engineering, Surveying , Energy, Environment Protection, Nuclear Power Engineering
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  • 97
    Publication Date: 2021-10-29
    Description: The compression behavior of osmium metal was investigated up to 280 GPa (volume compression V/Vo =0.725) under nonhydrostatic conditions at ambient temperature using angle dispersive axial x-ray diffraction (A-XRD) with a diamond anvil cell (DAC). In addition, shear strength of osmium was measured to 170 GPa using radial x-ray diffraction (R-XRD) technique in DAC. Both diffraction techniques in DAC employed platinum as an internal pressure standard. Density functional theory (DFT) calculations were also performed, and the computed lattice parameters and volumes under compression are in good agreement with the experiments. DFT predicts a monotonous increase in axial ratio (c/a) with pressure and the structural anomalies of less than 1 % in (c/a) ratio below 150 GPa were not reproduced in theoretical calculations and hydrostatic measurements. The measured value of shear strength of osmium (τ) approaches a limiting value of 6 GPa above a pressure of 50 GPa in contrast to theoretical predictions of 24 GPa and is likely due to imperfections in polycrystalline samples. DFT calculations also enable the studies of shear and tensile deformations. The theoretical ideal shear stress is found along the (001)[1-10] shear direction with the maximal shear stress ~24 GPa at critical strain ~0.13.
    Electronic ISSN: 2631-8695
    Topics: Technology
    Published by Institute of Physics
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  • 98
    Publication Date: 2021-10-29
    Description: In order to tune the magnetic properties of the cleavable high-Curie temperature ferromagnet Fe5-xGeTe2, the effect of increasing the electron count through arsenic substitution has been investigated. Small additions of arsenic (2.5 and 5%) seemingly enhance ferromagnetic order in polycrystalline samples by quenching fluctuations on one of the three magnetic sublattices, whereas larger As concentrations decrease the ferromagnetic Curie temperature (TC) and saturation magnetization. This work also describes the growth and characterization of Fe4.8AsTe2 single crystals that are structurally analogous to Fe5-xGeTe2 but with some phase stability complications. Magnetization measurements reveal dominant antiferromagnetic behavior in Fe4.8AsTe2 with a Neel temperature of TN ≈42K. A field-induced spin-flop below TN results in a switch from negative to positive magnetoresistance, with significant hysteresis causing butterfly-shaped resistance loops. In addition to reporting the properties of Fe4.8GeTe2, this work shows the importance of manipulating the individual magnetic sublattices in Fe5-xGeTe2 and motivates further efforts to control the magnetic properties in related materials by fine tuning of the Fermi energy or crystal chemistry.
    Electronic ISSN: 2053-1583
    Topics: Physics
    Published by Institute of Physics
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  • 99
    Publication Date: 2021-10-29
    Description: Thickness-shear (TSh) vibration of a rectangular piezoelectric crystal plate is studied with the consideration of flexoelectric effect in this paper. The developed theoretical model is based on the assumed displacement function which includes the anti-symmetric mode through thickness and symmetric mode in length. The constitutive equation with flexoelectricity, governing equations and boundary conditions are derived from the Gibbs energy density function and variational principle. For the effect of flexoelectricity, we only consider the shear strain gradient in the thickness direction so as to simply the mathematical model. Thus, two flexoelectric coefficients are used in the present model. The electric potential functions are also obtained for different electric boundary conditions. The present results clearly show that the flexoelectric effect has significant effect on vibration frequencies of thickness-shear modes of thin piezoelectric crystal plate. It is also found that the flexoelectric coefficients and length to thickness ratio have influence on the thickness-shear modes. The results tell that flexoelectricity cannot be neglected for design of small size piezoelectric resonators.
    Electronic ISSN: 2053-1591
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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  • 100
    Publication Date: 2021-10-29
    Description: Active NPA measurements of the fast ion distribution using the neutral beam as an additional charge exchange target are discussed. Expressions for the calculation of the NPA signal based on the fast ion distribution and for the reconstruction of the fast ion distribution from the NPA signal are provided. Demonstration of the described approach is carried out on the Globus-M2 spherical tokamak, where a scanning system for the NPAs was recently installed. Main features of the active NPA application on Globus-M2 are considered. The energy and spatial distributions of fast deuterium ions at dedicated pitch angles are obtained and compared with the calculated ones. Key traits of the obtained distributions are considered and explained.
    Print ISSN: 0741-3335
    Electronic ISSN: 1361-6587
    Topics: Physics
    Published by Institute of Physics
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