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  • Articles  (292)
  • Frontiers Media  (285)
  • American Physical Society (APS)
  • Wiley-Blackwell
  • 2020-2024  (292)
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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
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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
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    Wiley-Blackwell
    In:  EPIC3Reviews in Aquaculture, Wiley-Blackwell, ISSN: 1753-5123
    Publication Date: 2024-05-06
    Description: Mass mortality events (MMEs) are defined as the death of large numbers of fish over a short period of time. These events can result in catastrophic losses to the Atlantic salmon aquaculture industry and the local economy. However, they are challenging to understand because of their relative infrequency and the high number of potential factors involved. As a result, the causes and consequences of MMEs in Atlantic salmon aquaculture are not well understood. In this study, we developed a structural network of causal risk factors for MMEs for aquaculture and the communities that depend on Atlantic salmon aquaculture. Using the Interpretive Structural Modeling (ISM) technique, we analysed the causes of Atlantic salmon mass mortalities due to environmental (abiotic), biological (biotic) and nutritional risk factors. The consequences of MMEs were also assessed for the occupational health and safety of aquaculture workers and their implications for the livelihoods of local communities. This structural network deepens our understanding of MMEs and points to management actions and interventions that can help mitigate mass mortalities. MMEs are typically not the result of a single risk factor but are caused by the systematic interaction of risk factors related to the environment, fish diseases, feeding/nutrition and cage-site management. Results also indicate that considerations of health and safety risk, through pre- and post-event risk assessments, may help to minimize workplace injuries and eliminate potential risks of human fatalities. Company and government assisted socio-economic measures could help mitigate post-mass mortality impacts. Appropriate and timely management actions may help reduce MMEs at Atlantic salmon cage sites and minimize the physical and social vulnerabilities of workers and local communities.
    Repository Name: EPIC Alfred Wegener Institut
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  • 11
    Publication Date: 2024-01-31
    Description: The response of permafrost to submergence can vary between ice-rich late Pleistocene deposits and the thermokarst basins that thawed out during the Holocene. We hypothesize that inundated Alases offshore thaw faster than submerged Yedoma. To test this hypothesis, we estimated depths to the top of ice-bearing permafrost offshore of the Bykovsky Peninsula in northeast Siberia using electrical resistivity surveys. The surveys traversed submerged lagoon deposits, drained and refrozen Alas deposits, and undisturbed Yedoma from the coastline to 373 m offshore. While the permafrost degradation rates of the submerged Yedoma were in the range of similar sites, the submerged Alas permafrost degradation rates were up to 170% faster. Given the abundance of thermokarst basins and lakes along parts of the Arctic coastline, its effect on subsea permafrost degradation must be similarly prevalent. Remote sensing analyses suggest that 54% of lagoons wider than 500 m originated in thermokarst basins.
    Repository Name: EPIC Alfred Wegener Institut
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  • 12
    Publication Date: 2024-01-31
    Description: Permafrost thaw leads to thermokarst lake formation and talik growth tens of meters deep, enabling microbial decomposition of formerly frozen organic matter (OM). We analyzed two 17-m-long thermokarst lake sediment cores taken in Central Yakutia, Russia. One core was from an Alas lake in a Holocene thermokarst basin that underwent multiple lake generations, and the second core from a young Yedoma upland lake (formed ca. 70 years ago) whose sediments have thawed for the first time since deposition. This comparison provides a glance into OM fate in thawing Yedoma deposits. We analyzed total organic carbon (TOC) and dissolved organic carbon (DOC) content, n-alkanes concentrations, and bacterial and archaeal membrane markers. Furthermore, we conducted one-year-long incubations (4 °C, dark) and measured anaerobic carbon dioxide (CO2) and methane (CH4) production. The sediments from both cores contained little TOC (0.7±0.4 wt%), but DOC values were relatively high, with highest values in the frozen Yedoma lake sediments (1620 mg L-1). Cumulative GHG production after one year was highest in the Yedoma lake sediments (226±212 μg CO2-C gdw-1, 28±36 μg CH4-C gdw-1) and 3 and 1.5 times lower in the Alas lake sediments, respectively (75±76 μg CO2-C gdw-1, 19±29 μg CH4-C gdw-1). The highest CO2 production in the frozen Yedoma lake sediments likely results from decomposition of readily bioavailable OM, while highest CH4 production in the non-frozen top sediments of this core suggests that methanogenic communities established upon thaw. The lower GHG production in the non-frozen Alas lake sediments resulted from advanced OM decomposition during Holocene talik development. Furthermore, we found that drivers of CO2 and CH4 production differ following thaw. Our results suggest that GHG production from TOC-poor mineral deposits, which are widespread throughout the Arctic, can be substantial. Therefore, our novel data are relevant for vast ice-rich permafrost deposits vulnerable to thermokarst formation.
    Repository Name: EPIC Alfred Wegener Institut
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  • 13
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    Wiley-Blackwell
    In:  EPIC3Permafrost and Periglacial Processes, Wiley-Blackwell, 32(1), pp. 59-75, ISSN: 1045-6740
    Publication Date: 2024-01-31
    Description: Thermal erosion is a major mechanism of permafrost degradation, resulting in characteristic landforms. We inventory thermo-erosional valleys in ice-rich coastal lowlands adjacent to the Siberian Laptev Sea based on remote sensing, Geographic Information System (GIS), and field investigations for a first regional assessment of their spatial distribution and characteristics. Three study areas with similar geological (Yedoma Ice Complex) but diverse geomorphological conditions vary in valley areal extent, incision depth, and branching geometry. The most extensive valley networks are incised deeply (up to 35 m) into the broad inclined lowland around Mamontov Klyk. The flat, low-lying plain forming the Buor Khaya Peninsula is more degraded by thermokarst and characterized by long valleys of lower depth with short tributaries. Small, isolated Yedoma Ice Complex remnants in the Lena River Delta predominantly exhibit shorter but deep valleys. Based on these hydrographical network and topography assessments, we discuss geomorphological and hydrological connections to erosion processes. Relative catchment size along with regional slope interact with other Holocene relief-forming processes such as thermokarst and neotectonics. Our findings suggest that thermo-erosional valleys are prominent, hitherto overlooked permafrost degradation landforms that add to impacts on biogeochemical cycling, sediment transport, and hydrology in the degrading Siberian Yedoma Ice Complex.
    Repository Name: EPIC Alfred Wegener Institut
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  • 14
    Publication Date: 2024-03-22
    Repository Name: EPIC Alfred Wegener Institut
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  • 15
    Publication Date: 2021-10-29
    Description: Steep geochemical gradients surround roots and rhizomes of seagrass and protect the plants against the harsh conditions in anoxic sediment, while enabling nutrient uptake. Imbalance of these gradients, due to e.g., low plant performance and/or changing sediment biogeochemical conditions, can lead to plant stress and large-scale seagrass meadow die-off. Therefore, measuring and mapping the dynamic gradients around seagrass roots and rhizomes is needed to better understand plant responses to human impact and environmental changes. Historically, electrochemical microsensors enabled the first measurements of important chemical species like O2, pH or H2S with high sensitivity and spatial resolution giving important insights to the seagrass rhizosphere microenvironment; however, such measurements only provide information in one dimension at a time. In recent years, the use of reversible optical sensors (in the form of planar optodes or nanoparticles) and accumulative gel sampling methods like Diffusive Gradients in Thin films (DGT) have extended the array of analytes and allowed 2-D mapping of chemical gradients in the seagrass rhizosphere. Here, we review and discuss such microscale methods from a practical angle, discuss their application in seagrass research, and point toward novel experimental approaches to study the (bio)geochemistry around seagrass roots and rhizomes using a combination of available techniques, both in the lab and in situ.
    Electronic ISSN: 2296-7745
    Topics: Biology
    Published by Frontiers Media
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  • 16
    Publication Date: 2021-10-29
    Description: Sweetpotato is an emerging food crop that ensures food and nutrition security in the face of climate change. Alpha-linoleic acid (ALA) is one of the key factors affecting plant stress tolerance and is also an essential nutrient in humans. In plants, fatty acid desaturase 8 (FAD8) synthesizes ALA from linoleic acid (LA). Previously, we identified the cold-induced IbFAD8 gene from RNA-seq of sweetpotato tuberous roots stored at low-temperature. In this study, we investigated the effect of IbFAD8 on the low-temperature storage ability and ALA content of the tuberous roots of sweetpotato. Transgenic sweetpotato plants overexpressing IbFAD8 (TF plants) exhibited increased cold and drought stress tolerance and enhanced heat stress susceptibility compared with non-transgenic (NT) plants. The ALA content of the tuberous roots of TF plants (0.19 g/100 g DW) was ca. 3.8-fold higher than that of NT plants (0.05 g/100 g DW), resulting in 8–9-fold increase in the ALA/LA ratio in TF plants. Furthermore, tuberous roots of TF plants showed better low-temperature storage ability compared with NT plants. These results indicate that IbFAD8 is a valuable candidate gene for increasing the ALA content, environmental stress tolerance, and low-temperature storage ability of sweetpotato tuberous roots via molecular breeding.
    Electronic ISSN: 1664-462X
    Topics: Biology
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  • 17
    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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  • 18
    Publication Date: 2021-11-01
    Description: In this study, we present a tensegrity robot arm that can reproduce the features of complex musculoskeletal structures, and can bend like a continuum manipulator. In particular, we propose a design method for an arm-type tensegrity robot that has a long shape in one direction, and can be deformed like a continuum manipulator. This method is based on the idea of utilizing simple and flexible strict tensegrity modules, and connecting them recursively so that they remain strict tensegrity even after being connected. The tensegrity obtained by this method strongly resists compressive forces in the longitudinal direction, but is flexible in the bending direction. Therefore, the changes in stiffness owing to internal forces, such as in musculoskeletal robots, appear more in the bending direction. First, this study describes this design method, then describes a developed pneumatically driven tensegrity robot arm with 20 actuators. Next, the range of motion and stiffness under various driving patterns are presented as evaluations of the robot performance.
    Electronic ISSN: 2296-9144
    Topics: Computer Science
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  • 19
    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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  • 20
    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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  • 21
    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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  • 23
    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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  • 24
    Publication Date: 2021-11-01
    Description: Autonomy is becoming increasingly important for the robotic exploration of unpredictable environments. One such example is the approach, proximity operation, and surface exploration of small bodies. In this article, we present an overview of an estimation framework to approach and land on small bodies as a key functional capability for an autonomous small-body explorer. We use a multi-phase perception/estimation pipeline with interconnected and overlapping measurements and algorithms to characterize and reach the body, from millions of kilometers down to its surface. We consider a notional spacecraft design that operates across all phases from approach to landing and to maneuvering on the surface of the microgravity body. This SmallSat design makes accommodations to simplify autonomous surface operations. The estimation pipeline combines state-of-the-art techniques with new approaches to estimating the target’s unknown properties across all phases. Centroid and light-curve algorithms estimate the body–spacecraft relative trajectory and rotation, respectively, using a priori knowledge of the initial relative orbit. A new shape-from-silhouette algorithm estimates the pole (i.e., rotation axis) and the initial visual hull that seeds subsequent feature tracking as the body gets more resolved in the narrow field-of-view imager. Feature tracking refines the pole orientation and shape of the body for estimating initial gravity to enable safe close approach. A coarse-shape reconstruction algorithm is used to identify initial landable regions whose hazardous nature would subsequently be assessed by dense 3D reconstruction. Slope stability, thermal, occlusion, and terra-mechanical hazards would be assessed on densely reconstructed regions and continually refined prior to landing. We simulated a mission scenario for approaching a hypothetical small body whose motion and shape were unknown a priori, starting from thousands of kilometers down to 20 km. Results indicate the feasibility of recovering the relative body motion and shape solely relying on onboard measurements and estimates with their associated uncertainties and without human input. Current work continues to mature and characterize the algorithms for the last phases of the estimation framework to land on the surface.
    Electronic ISSN: 2296-9144
    Topics: Computer Science
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  • 25
    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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  • 26
    Publication Date: 2021-11-01
    Description: From the combined perspective of biologists, microscope instrumentation developers, imaging core facility scientists, and high performance computing experts, we discuss the challenges faced when selecting imaging and analysis tools in the field of light-sheet microscopy. Our goal is to provide a contextual framework of basic computing concepts that cell and developmental biologists can refer to when mapping the peculiarities of different light-sheet data to specific existing computing environments and image analysis pipelines. We provide our perspective on efficient processes for tool selection and review current hardware and software commonly used in light-sheet image analysis, as well as discuss what ideal tools for the future may look like.
    Electronic ISSN: 2296-634X
    Topics: Biology
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  • 27
    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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  • 28
    Publication Date: 2021-11-01
    Description: Co-infection of Mycobacterium tuberculosis and Paracoccidioides brasiliensis, present in 20% in Latin America, is a public health problem due to a lack of adequate diagnosis. These microorganisms are capable of forming biofilms, mainly in immunocompromised patients, which can lead to death due to the lack of effective treatment for both diseases. The present research aims to show for the first time the formation of mixed biofilms of M. tuberculosis and P. brasiliensis (Pb18) in vitro, as well as to evaluate the action of 3’hydroxychalcone (3’chalc) -loaded nanoemulsion (NE) (NE3’chalc) against monospecies and mixed biofilms, the formation of mixed biofilms of M. tuberculosis H37Rv (ATCC 27294), 40Rv (clinical strains) and P. brasiliensis (Pb18) (ATCC 32069), and the first condition of formation (H37Rv +Pb18) and (40Rv + Pb18) and second condition of formation (Pb18 + H37Rv) with 45 days of total formation time under both conditions. The results of mixed biofilms (H37Rv + Pb18) and (40Rv + Pb18), showed an organized network of M. tuberculosis bacilli in which P. brasiliensis yeasts are connected with a highly extracellular polysaccharide matrix. The (Pb18 + H37Rv) showed a dense biofilm with an apparent predominance of P. brasiliensis and fragments of M. tuberculosis. PCR assays confirmed the presence of the microorganisms involved in this formation. The characterization of NE and NE3’chalc displayed sizes from 145.00 ± 1.05 and 151.25 ± 0.60, a polydispersity index (PDI) from 0.20± 0.01 to 0.16± 0.01, and zeta potential -58.20 ± 0.92 mV and -56.10 ± 0.71 mV, respectively. The atomic force microscopy (AFM) results showed lamellar structures characteristic of NE. The minimum inhibitory concentration (MIC) values of 3’hidroxychalcone (3’chalc) range from 0.97- 7.8 µg/mL and NE3’chalc from 0.24 - 3.9 µg/mL improved the antibacterial activity when compared with 3’chalc-free, no cytotoxicity. Antibiofilm assays proved the efficacy of 3’chalc-free incorporation in NE. These findings contribute to a greater understanding of the formation of M. tuberculosis and P. brasiliensis in the mixed biofilm. In addition, the findings present a new possible NE3’chalc treatment alternative for the mixed biofilms of these microorganisms, with a high degree of relevance due to the lack of other treatments for these comorbidities.
    Electronic ISSN: 2235-2988
    Topics: Biology , Medicine
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  • 29
    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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  • 30
    Publication Date: 2021-11-01
    Description: The efficacy of a single cell protein (SCP) methanotroph (Methylococcus capsulatus, Bath) bacteria meal (FeedKind®, Calysta, Menlo Park, CA, United States), in Pacific white shrimp (Penaeus vannamei) diets was studied to determine growth performance, survival rate and disease resistance against Vibrio parahaemolyticus causing Acute Hepatopancreatic Necrosis Disease (AHPND). The growth trial was assigned in a completely randomized design (CRD) with four treatments and 5 replicates of each, T1: a fishmeal-based control containing 15% fish meal and 3 diets with graded levels of methanotroph bacteria meal, namely T2: 5% methanotroph bacteria meal, T3: 10% methanotroph bacteria meal, and T4: 15% methanotroph bacteria meal. Shrimp were fed ad libitum for 6 weeks on trial diets to assess growth. Subsequent to the growth trial, three replicates of the same groups were exposed to V. parahaemolyticus by a single bath challenge and held for a further 15 days on the same diets as the growth study to assess survival and resistance. No significant differences (p 〉 0.05) in survival or in growth performance, including final weight, weight gain, specific growth rate, feed consumption or feed conversion ratio of white shrimp fed feeds containing methanotroph bacteria meal or control diets for 6 weeks. Immune markers such as hemocyte counts, phenoloxidase, superoxide dismutase and lysozyme activity were similar across all groups after the 6-week feeding trial. In a V. parahaemolyticus challenge, methanotroph bacteria meal in the diet significantly promoted the survival rate, and the reduction of Vibrio sp. in the hepatopancreas of white shrimp. Hemocyte count and phenoloxidase activity showed no significant differences (p 〉 0.05) between diet treatment groups, but hemolymph protein was significantly higher (p 〈 0.05) in shrimp fed diets containing 15% methanotroph bacteria meal after challenge. The Vibrio colony counts from hepatopancreas in the treatment groups were all significantly lower than the control (p 〈 0.05). The findings show that methanotroph bacteria meal can entirely replace fishmeal in white shrimp diets and the 15% inclusion of methanotroph bacteria meal in shrimp diet shows no adverse effects on growth performance, feed utilization and survival rate. In addition, shrimp fed methanotroph bacteria meal diets exhibited improved survival rates to an AHPND challenge.
    Electronic ISSN: 2296-7745
    Topics: Biology
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  • 31
    Publication Date: 2021-11-01
    Electronic ISSN: 2296-7745
    Topics: Biology
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  • 32
    Publication Date: 2021-11-01
    Description: The coordinated rehabilitation of the upper limb is important for the recovery of the daily living abilities of stroke patients. However, the guidance of the joint coordination model is generally lacking in the current robot-assisted rehabilitation. Modular robots with soft joints can assist patients to perform coordinated training with safety and compliance. In this study, a novel coordinated path planning and impedance control method is proposed for the modular exoskeleton elbow–wrist rehabilitation robot driven by pneumatic artificial muscles (PAMs). A convolutional neural network-long short-term memory (CNN-LSTM) model is established to describe the coordination relationship of the upper limb joints, so as to generate adaptive trajectories conformed to the coordination laws. Guided by the planned trajectory, an impedance adjustment strategy is proposed to realize active training within a virtual coordinated tunnel to achieve the robot-assisted upper limb coordinated training. The experimental results showed that the CNN-LSTM hybrid neural network can effectively quantify the coordinated relationship between the upper limb joints, and the impedance control method ensures that the robotic assistance path is always in the virtual coordination tunnel, which can improve the movement coordination of the patient and enhance the rehabilitation effectiveness.
    Electronic ISSN: 1662-5218
    Topics: Medicine , Technology
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  • 33
    Publication Date: 2021-11-01
    Description: The magnitude and rate of the expansion of the East Asian summer monsoon (EASM) rain belt under future climatic warming are unclear. Appropriate ecological proxy data may provide an improved understanding of the spatial extension of the EASM during past warming intervals. We reconstructed the spatiotemporal pattern of the extension of the EASM since the Last Glacial Maximum (LGM), using six well-dated mollusk fossil sequences from Chinese loess sections located on the modern northern edge of the EASM. The abundance of typical dominant mollusk species indicative of EASM intensity shows a delayed response, from ∼17 ka in the southeastern sections to ∼9 ka in the northwestern sections, during the last deglacial warming. Isoline plots based on a mollusk data synthesis show that the mollusk EASM indicators have a northeast–southwest zonal distribution for both the present-day, the cold LGM, and the warm mid-Holocene, which is consistent with the spatial pattern of modern precipitation. The resulting estimated expansion rate of EASM intensity accelerated during ∼12–9 ka (∼50 km/ka), which corresponds to the early Holocene interval of rapid climatic warming, a northwestward shift of ∼150 km compared to today. This implies that the northern fringe of the EASM in northern China will become wetter in the coming century, under moderate warming scenarios.
    Electronic ISSN: 2296-6463
    Topics: Geosciences
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  • 34
    Publication Date: 2021-11-01
    Description: Endogenous small interfering RNAs (siRNAs) are substantial gene regulators in eukaryotes and play key functions in plant development and stress tolerance. Among environmental factors, heat is serious abiotic stress that severely influences the productivity and quality of flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee). However, how siRNAs are involved in regulating gene expression during heat stress is not fully understood in flowering Chinese cabbage. Combining bioinformatical and next-generation sequencing approaches, we identified heat-responsive siRNAs in four small RNA libraries of flowering Chinese cabbage using leaves collected at 0, 1, 6, and 12 h after a 38°C heat-stress treatment; 536, 816, and 829 siRNAs exhibited substantial differential expression at 1, 6, and 12 h, respectively. Seventy-five upregulated and 69 downregulated differentially expressed siRNAs (DE-siRNAs) were common for the three time points of heat stress. We identified 795 target genes of DE-siRNAs, including serine/threonine-protein kinase SRK2I, CTR1-like, disease resistance protein RML1A-like, and RPP1, which may play a role in regulating heat tolerance. Gene ontology showed that predictive targets of DE-siRNAs may have key roles in the positive regulation of biological processes, organismal processes, responses to temperature stimulus, signaling, and growth and development. These novel results contribute to further understanding how siRNAs modulate the expression of their target genes to control heat tolerance in flowering Chinese cabbage.
    Electronic ISSN: 1664-8021
    Topics: Biology , Medicine
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  • 35
    Publication Date: 2021-11-01
    Description: In the domain of globalization, the global value chain (GVC) is formed across diverse economies. Owing to the expansion of economic globalization and the resultant global trade liberalization, the geographical isolation of production and consumption has resulted in the transfer of polluting emissions from advanced economies to developing states. Developing economies, falling in the middle and low end of the GVC, have to strive hard to expand their production in the GVC, while simultaneously addressing the consequent environmental damage and attending to the core environmental concerns of sustainable growth, energy preservation and drastic cuts in CO2. This paper addresses how manufacturing subsidiaries can improve their low-carbon innovation ability and help to achieve a sustainable competitive advantage through the embedded GVC. Data were gathered employing interview and survey methods, 31 manufacturing companies and 56 enterprise groups across 16 Chinese provinces were selected as the case study. A partial least square structural equation modelling was adopted to analyse the responses. The results indicate that the embedded GVC significantly enhances low-carbon innovation capability and promotes a sustainable competitive advantage. This study proposes that companies should continuously identify high-quality resources from the GVC and discover ways of integrating internal and external carbon innovation resources to form innovation capabilities.
    Electronic ISSN: 2296-665X
    Topics: Energy, Environment Protection, Nuclear Power Engineering
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  • 36
    Publication Date: 2021-10-29
    Description: The suitability of remediation systems using metallic iron (Fe0) has been extensively discussed during the past 3 decades. It has been established that aqueous Fe0 oxidative dissolution is not caused by the presence of any contaminant. Instead, the reductive transformation of contaminants is a consequence of Fe0 oxidation. Yet researchers are still maintaining that electrons from the metal body are involved in the process of contaminant reduction. According to the electron efficiency concept, electrons from Fe0 should be redistributed to: i) contaminants of concern (COCs), ii) natural reducing agents (e.g., H2O, O2), and/or iii) reducible co-contaminants (e.g. NO3-). The electron efficiency is defined as the fraction of electrons from Fe0 oxidation which is utilized for the reductive transformations of COCs. This concept is in frontal contradiction with the view that Fe0 is not directly involved in the process of contaminant reduction. This communication recalls the universality of the concept that reductive processes observed in remediation Fe0/H2O systems are mediated by primary (e.g., FeII, H/H2) and secondary (e.g., Fe3O4, green rusts) products of aqueous iron corrosion. The critical evaluation of the electron efficiency concept suggests that it should be abandoned. Instead, research efforts should be directed towards tackling the real challenges for the design of sustainable Fe0-based water treatment systems based on fundamental mechanisms of iron corrosion.
    Electronic ISSN: 2673-4486
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Chemistry and Pharmacology
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  • 37
    Publication Date: 2021-11-01
    Description: Microorganisms are capable of colonizing extreme environments like deep biosphere and oil reservoirs. The prokaryotes diversity in exploited oil reservoirs is composed of indigenous microbial communities and artificially introduced microbes. In the present work, high throughput sequencing techniques were applied to analyze the microbial community from the injected and produced water in a neotropical hyper-thermophile oil reservoir located in the Orinoquia region of Colombia, South America. Tepidiphilus is the dominant bacteria found in both injection and produced waters. The produced water has a higher microbial richness and exhibits a Tepidiphilus microdiversity. The reservoir injected water is recycled and treated with the biocides glutaraldehyde and tetrakis-hydroxymethyl-phosphonium sulfate (THPS) to reduce microbial load. This process reduces microbial richness and selects a single Tepidiphilus genome (T. sp. UDEAICP_D1) as the dominant isolate. Thermus and Hydrogenobacter were subdominants in both water systems. Phylogenomic analysis of the injection water dominant Tepidiphilus positioned it as an independent branch outside T. succinatimandens and T. thermophilus lineage. Comparative analysis of the Tepidiphilus genomes revealed several genes that might be related to the biocide-resistant phenotype and the tolerance to the stress conditions imposed inside the oil well, like RND efflux pumps and type II toxin-antitoxin systems. Comparing the abundance of Tepidiphilus protein-coding genes in both water systems shows that the biocide selected Tepidiphilus sp. UDEAICP_D1 genome has enriched genes annotated as ABC-2 type transporter, ABC transporter, Methionine biosynthesis protein MetW, Glycosyltransferases, and two-component system NarL.
    Electronic ISSN: 1664-302X
    Topics: Biology
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  • 38
    Publication Date: 2021-11-01
    Description: In recent decades, human activity coupled with climate change has led to a deterioration in the quality of surface freshwater. This has been related to an increase in the appearance of algal blooms, which can produce organic compounds that can be toxic or can affect the organoleptic characteristics of the water, such as its taste and odor. Among these latter compounds is geosmin, a metabolite produced by certain cyanobacteria that confers an earthy taste to water and which can be detected by humans at very low concentrations (nanogram per liter). The difficulty and cost of both monitoring the presence of this compound and its treatment is a problem for drinking water treatment companies, as the appearance of geosmin affects consumer confidence in the quality of the drinking water they supply. In this field study, the evaluation of four sampling sites with different physicochemical conditions located in the upper part of the Ter River basin, a Mediterranean river located in Catalonia (NE Spain), has been carried out, with the aim of identifying the main triggers of geosmin episodes. The results, obtained from 1 year of sampling, have made it possible to find out that: (i) land uses with a higher percentage of agricultural and industrial activity are related to high nutrient conditions in river water, (ii) these higher nutrient concentrations favor the development of benthic cyanobacteria, (iii) in late winter–early spring, when these cyanobacteria are subjected to both an imbalance of the dissolved inorganic nitrogen and soluble reactive phosphorus ratio, guided by a phosphorus concentration increase, and to cold–mild temperatures close to 10°C, they produce and release geosmin, and (iv) 1–2 weeks after cyanobacteria reach a high relative presence in the whole biofilm, an increase in geosmin concentration in water is observed, probably associated with the cyanobacteria detachment from cobbles and consequent cell lysis. These results could serve as a guide for drinking water treatment companies, indicating under what conditions they can expect the appearance of geosmin episodes and implement the appropriate treatment before it reaches consumers’ tap.
    Electronic ISSN: 1664-302X
    Topics: Biology
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  • 39
    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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  • 40
    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
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  • 41
    Publication Date: 2021-11-01
    Description: Genus Ocimum of Labiatae is well known in all traditional medicinal systems like Ayurveda, Unani, Siddha, and Homeopathy. The pharmaceutical activities of different species of Ocimum attributed to all plant parts. Roots are the most significant vital organ of the plant, as they absorb water and nutrients from soil and transport to aerial parts of the plants. Roots of Ocimum were found helpful with free-radical scavenging activity to improve physical and mental strength as well as to treat diabetes, malaria, and liver problems. Antibacterial activity of Ocimum roots and its main component, rosmarinic acid, is very beneficial to protect against several human pathogens, including bacteria and viruses. Being so important in every way, roots of Ocimum need healthy rhizosphere. Bacteria, fungi, nematodes, types of soil, fungicide, pesticides, salt, radioactive elements, as well as heavy metal contaminations, affect roots and overall growth of Ocimum in positive or negative ways. Each component of rhizosphere (natural, treatment or contamination) affects the roots, which highlights current ecological scenario to discover biosafe and more productive approaches. For such prestigious organ of Ocimum, development of in vitro root cultures and hairy root cultures assists to reduce the efforts and timing of the traditional cultivation process along with elimination of negative factors in rhizosphere. Different strains of Agrobacterium rhizogenes, various media compositions, as well as discrete treatments, like elicitors, on nonidentical species or cultivars of Ocimum boost the root induction, biomass, and accumulation of phytoceuticals differently. Hairy roots and in vitro roots of Ocimum accumulate higher quantity of therapeutic metabolites. These metabolites include several phenolics (like rosmarinic acid, 3-hydroxybenzoic acid, m-coumaric acid, p-coumaric acid, caffeic acid, ferulic acid, vanillic acid, chicoric acid, and lithospermic acid), triterpenes (such as betulinic acid, 3-epimaslinic acid, alphitolic acid, euscaphic acids, oleanolic acid, and ursolic acid) as well as flavonoids (flavones, flavonols, and dihydroflavonols). This review highlights pharmaceutical applications of Ocimum roots, a great deal of rhizosphere components and in vitro culturing techniques to enhance biomass as well as chief phytoceuticals.
    Electronic ISSN: 1664-462X
    Topics: Biology
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  • 42
    Publication Date: 2021-11-01
    Description: Diabetic nephropathy (DN) is one of the most common microvascular complications in diabetic patients, and is the main cause of end-stage renal disease. The exact molecular mechanism of DN is not fully understood. The aim of this study was to identify novel biomarkers and mechanisms for DN disease progression by weighted gene co-expression network analysis (WGCNA). From the GSE142153 dataset based on the peripheral blood monouclear cells (PBMC) of DN, we identified 234 genes through WGCNA and differential expression analysis. Gene Ontology (GO) annotations mainly included inflammatory response, leukocyte cell-cell adhesion, and positive regulation of proteolysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways mostly included IL-17 signaling pathway, MAPK signaling pathway, and PPAR signaling pathway in DN. A total of four hub genes (IL6, CXCL8, MMP9 and ATF3) were identified by cytoscape, and the relative expression levels of hub genes were also confirmed by RT-qPCR. ROC curve analysis determined that the expression of the four genes could distinguish DN from controls (the area under the curve is all greater than 0.8), and Pearson correlation coefficient analysis suggested that the expression of the four genes was related to estimated glomerular filtration rate (eGFR) of DN. Finally, through database prediction and literature screening, we constructed lncRNA-miRNA-mRNA network. We propose that NEAT1/XIST/KCNQ1T1-let-7b-5p-IL6, NEAT1/XIST-miR-93-5p-CXCL8 and NEAT1/XIST/KCNQ1T1-miR-27a-3p/miR-16-5p-ATF3 might be potential RNA regulatory pathways to regulate the disease progression of early DN. In conclusion, we identified four hub genes, namely, IL6, CXCL8, MMP9, and ATF3, as markers for early diagnosis of DN, and provided insight into the mechanisms of disease development in DN at the transcriptome level.
    Electronic ISSN: 1664-8021
    Topics: Biology , Medicine
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  • 43
    Publication Date: 2021-11-01
    Description: The development of reliable methods for identification of robust biomarkers for complex diseases is critical for disease diagnosis and prognosis efforts. Integrating multi-omics data with protein-protein interaction (PPI) networks to investigate diseases may help better understand disease characteristics at the molecular level. In this study, we developed and tested a novel network-based method to detect subnetwork markers for patients with colorectal cancer (CRC). We performed an integrated omics analysis using whole-genome gene expression profiling and copy number alterations (CNAs) datasets followed by building a gene interaction network for the significantly altered genes. We then clustered the constructed gene network into subnetworks and assigned a score for each significant subnetwork. We developed a support vector machine (SVM) classifier using these scores as feature values and tested the methodology in independent CRC transcriptomic datasets. The network analysis resulted in 15 subnetwork markers that revealed several hub genes that may play a significant role in colorectal cancer, including PTP4A3, FGFR2, PTX3, AURKA, FEN1, INHBA, and YES1. The 15-subnetwork classifier displayed over 98 percent accuracy in detecting patients with CRC. In comparison to individual gene biomarkers, subnetwork markers based on integrated multi-omics and network analyses may lead to better disease classification, diagnosis, and prognosis.
    Electronic ISSN: 1664-8021
    Topics: Biology , Medicine
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  • 44
    Publication Date: 2021-11-01
    Description: Noble metal nanocrystals enclosed with curved surfaces are of great benefit for applications in electrocatalysis since the atomic steps and kinks on these facets have higher chemical activity. Herein, we report the fabrication of PdAg nanoshells with tunable thickness in the range of 5–13 nm and a unique concave cubic morphology, as well as the exploration of their applications for ethanol oxidation reaction (EOR) in alkaline media. The success of current work relies on the conformal deposition of PdAg on concave Au nanocubes, where the controlled reaction kinetics and proper chosen capping agent are both crucial for the growth mode. When loaded on carbon black and working as electrocatalysts, they exhibited superb electrochemical activity (e.g., 600.21 mA mg−1 in mass activity and 19.57 A m−2 in specific activity), together with improved EOR kinetics and long-term durability, as compared to Au@Pd nanoparticles and commercial Pd/C. The current work offers a feasible strategy to produce PdAg bimetallic nanocrystals with concave surface and validates their promising application as fuel cell catalysts, which could be extended to morphology engineering of other noble-metal nanocrystals for a broad range of applications.
    Electronic ISSN: 2296-8016
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 45
    Publication Date: 2021-11-01
    Description: Temperate species often require or flower most rapidly in the long daylengths, or photoperiods, experienced in summer or after prolonged periods of cold temperatures, referred to as vernalization. Yet, even within species, plants vary in the degree of responsiveness to these cues. In Arabidopsis thaliana, CONSTANS (CO) and FLOWERING LOCUS C (FLC) genes are key to photoperiod and vernalization perception and antagonistically regulate FLOWERING LOCUS T (FT) to influence the flowering time of the plants. However, it is still an open question as to how these genes vary in their interactions among wild accessions with different flowering behaviors and adapted to different microclimates, yet this knowledge could improve our ability to predict plant responses in variable natural conditions. To assess the relationships among these genes and to flowering time, we exposed 10 winter-annual Arabidopsis accessions from throughout Norway, ranging from early to late flowering, along with two summer-annual accessions to 14 weeks of vernalization and either 8- or 19-h photoperiods to mimic Norwegian climate conditions, then assessed gene expression levels 3-, 5-, and 8-days post vernalization. CO and FLC explained both FT levels and flowering time (days) but not rosette leaf number at flowering. The correlation between FT and flowering time increased over time. Although vernalization suppresses FLC, FLC was high in the late-flowering accessions. Across accessions, FT was expressed only at low FLC levels and did not respond to CO in the late-flowering accessions. We proposed that FT may only be expressed below a threshold value of FLC and demonstrated that these three genes correlated to flowering times across genetically distinct accessions of Arabidopsis.
    Electronic ISSN: 1664-462X
    Topics: Biology
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  • 46
    Publication Date: 2021-11-01
    Description: Arctic Treeline is the transition from the boreal forest to the treeless tundra and may be determined by growing season temperatures. The physiological mechanisms involved in determining the relationship between the physical and biological environment and the location of treeline are not fully understood. In Northern Alaska, we studied the relationship between temperature and leaf respiration in 36 white spruce (Picea glauca) trees, sampling both the upper and lower canopy, to test two research hypotheses. The first hypothesis is that upper canopy leaves, which are more directly coupled to the atmosphere, will experience more challenging environmental conditions and thus have higher respiration rates to facilitate metabolic function. The second hypothesis is that saplings [stems that are 5–10cm DBH (diameter at breast height)] will have higher respiration rates than trees (stems ≥10cm DBH) since saplings represent the transition from seedlings growing in the more favorable aerodynamic boundary layer, to trees which are fully coupled to the atmosphere but of sufficient size to persist. Respiration did not change with canopy position, however respiration at 25°C was 42% higher in saplings compared to trees (3.43±0.19 vs. 2.41±0.14μmolm−2 s−1). Furthermore, there were significant differences in the temperature response of respiration, and seedlings reached their maximum respiration rates at 59°C, more than two degrees higher than trees. Our results demonstrate that the respiratory characteristics of white spruce saplings at treeline impose a significant carbon cost that may contribute to their lack of perseverance beyond treeline. In the absence of thermal acclimation, the rate of leaf respiration could increase by 57% by the end of the century, posing further challenges to the ecology of this massive ecotone.
    Electronic ISSN: 1664-462X
    Topics: Biology
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  • 47
    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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  • 48
    Publication Date: 2021-10-29
    Description: Flaxseed (Linum usitatissimum L.) is an oilseed that is used in both industry and food production. Flaxseed contains biologically active compounds including linolenic acid, linoleic acid, and lignans. Flaxseed powder (2.5–10% w/w) and chicken eggs (10–30% v/w) were substituted in cake wheat flour for fried dough (magwinya) production. The physicochemical properties of the fried dough were determined and compared with the control. There was a significant (p 〈 0.05) increase in moisture, protein, ash, and hardness and a decrease in fat content of fried dough enriched with egg (FDE) and flaxseed powder (FDFX). Enrichment with 30% (v/w) egg and/or 7.5–10% flaxseed powder resulted in higher protein, oil reduction, and ash contents compared with the rest of the products. With the current interest in plant-based protein, flaxseed is a good choice of flour-based snacks for consumers without compromise in nutrition.
    Electronic ISSN: 2571-581X
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 49
    Publication Date: 2021-10-29
    Electronic ISSN: 1664-302X
    Topics: Biology
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  • 50
    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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  • 51
    Publication Date: 2021-10-25
    Description: Factor for inversion stimulation (Fis) is a global regulator that is highly expressed during exponential phase growth and undetectable in stationary phase growth. Quorum sensing (QS) is a global regulatory mechanism that controls gene expression in response to changes in cell density and growth phase. In Vibrio parahaemolyticus, a marine species and a significant human pathogen, the QS regulatory sRNAs, Qrr1 to Qrr5, are expressed during exponential growth and negatively regulate the high cell density QS master regulator OpaR. OpaR is a positive regulator of capsule polysaccharide (CPS) formation, which is required for biofilm formation, and is a repressor of lateral flagella required for swarming motility. In V. parahaemolyticus, we show that Fis is a positive regulator of the qrr sRNAs expression. In an in-frame fis deletion mutant, qrr expression was repressed and opaR expression was induced. The Δfis mutant produced CPS and biofilm, but swarming motility was abolished. Also, the fis deletion mutant was more sensitive to polymyxin B. Swarming motility requires expression of both the surface sensing scrABC operon and lateral flagella laf operon. Our data showed that in the Δfis mutant both laf and scrABC genes were repressed. Fis controlled swarming motility indirectly through the QS pathway and directly through the surface sensing pathway. To determine the effects of Fis on cellular metabolism, we performed in vitro growth competition assays, and found that Δfis was outcompeted by wild type in minimal media supplemented with intestinal mucus as a sole nutrient source. The data showed that Fis positively modulated mucus components L-arabinose, D-gluconate and N-acetyl-D-glucosamine catabolism gene expression. In an in vivo colonization competition assay, Δfis was outcompeted by wild type, indicating Fis is required for fitness. Overall, these data demonstrate a global regulatory role for Fis in V. parahaemolyticus that includes QS, motility, and metabolism.
    Electronic ISSN: 1664-302X
    Topics: Biology
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  • 52
    Publication Date: 2021-10-28
    Description: The in trust sweetpotato collection housed by the International Center of Potato (CIP) is one of the largest assemblages of plant material representing the genetic resources of this important staple crop. The collection currently contains almost 6,000 accessions of Ipomoea batatas (cultivated sweetpotato) and over 1,000 accessions of sweetpotato crop wild relatives (CWRs). In this study, the entire cultivated collection (5,979 accessions) was genotyped with a panel of 20 simple sequence repeat (SSR) markers to assess genetic identity, diversity, and population structure. Genotyping and phenotyping of in vitro plantlets and mother plants were conducted simultaneously on 2,711 accessions (45% of the total collection) to identify and correct possible genetic identity errors which could have occurred at any time over the thirty plus years of maintenance in the in vitro collection. Within this group, 533 accessions (19.6%) had errors in identity. Field evaluations of morphological descriptors were carried out to confirm the marker data. A phylogenetic tree was constructed to reveal the intraspecific relationships in the population which uncovered high levels of redundancy in material from Peru and Latin America. These genotypic data were supported by morphological data. Population structure analysis demonstrated support for four ancestral populations with many of the accessions having lower levels of gene flow from the other populations. This was especially true of germplasm derived from Peru, Ecuador, and Africa. The set of 20 SSR markers was subsequently utilized to examine a subset of 189 accessions from the USDA sweetpotato germplasm collection and to identify and reconcile potential errors in the identification of clones shared between these collections. Marker analysis demonstrated that the USDA subset of material had 65 unique accessions that were not found in the larger CIP collection. As far as the authors are aware, this is the first report of genotyping an entire sweetpotato germplasm collection in its entirety.
    Electronic ISSN: 1664-462X
    Topics: Biology
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  • 53
    Publication Date: 2021-10-29
    Description: The United Nations' Development Goals (SDGs) have been criticized but are nonetheless seen by many as an important, if imperfect, international effort to address climate and environmental change, resource depletion and the unsustainability of contemporary life. Many of the Goals need to be implemented at the local level, yet sub-national governments have not been granted any enhanced status at the UN to facilitate this process. As a result, the role and effectiveness of local governments in localizing the SDGs is dependent on multi-level arrangements within respective national contexts. In this paper we present findings on the challenges facing local authorities in England, namely co-dependent ambivalence, partial holism and narrow practices of knowledge governance. We draw on work carried out collaboratively with local authorities and other stakeholders in Greater Manchester and Sheffield, and a UK-wide national workshop. These challenges explain the relatively low uptake and engagement with the SDGs in the context of wider political and economic concerns compared with international comparator cities. Against this background our research found that making the Goals real, relevant, relatable and relational offered a tactical route to localization for English local government.
    Electronic ISSN: 2624-9634
    Topics: Architecture, Civil Engineering, Surveying , Energy, Environment Protection, Nuclear Power Engineering , Medicine
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  • 55
    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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  • 56
    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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  • 57
    Publication Date: 2021-10-29
    Description: Hypokalemic periodic paralysis (HypoPP) is a rare autosomal dominant disorder characterized by episodic flaccid paralysis with concomitant hypokalemia. More than half of patients were associated with mutations in CACNA1S that encodes the alpha-1-subunit of the skeletal muscle L-type voltage-dependent calcium channel. Mutations in CACNA1S may alter the structure of CACNA1S and affect the functions of calcium channels, which damages Ca2+-mediated excitation-contraction coupling. In this research, we identified and described a Chinese HypoPP patient with a novel frameshift mutation in CACNA1S [NM_000069.2: c.1364delA (p.Asn455fs)] by targeted sequencing. This study would expand the spectrum of CACNA1S mutations, further our understanding of HypoPP, and provided a new perspective for selecting effective treatments.
    Electronic ISSN: 1664-8021
    Topics: Biology , Medicine
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  • 58
    Publication Date: 2021-10-29
    Electronic ISSN: 2235-2988
    Topics: Biology , Medicine
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  • 59
    Publication Date: 2021-10-29
    Description: The slow-spreading Mid-Atlantic Ridge (MAR) forms geological heterogeneity throughout the ridge system by deep crustal faults and their resultant tectonic valleys, which results in the existence of different types of hydrothermal vent fields. Therefore, investigating MAR hydrothermal systems opens a gate to understanding the concentration ranges of ecosystem-limiting metals emanating from compositionally distinct fluids for both near-field chemosynthetic ecosystems and far-field transport into the ocean interiors. Here, we present novel data regarding onboard measured, size-fractionated soluble, colloidal, and particulate iron concentrations from the 2018 R/V L’Atalante – ROV Victor research expedition, during which samples were taken from the mixing zone of black smokers using a ROV-assisted plume sampling. Iron size fractionation (200nm) data were obtained from onboard sequential filtering, followed by measurement via ferrozine assay and spectrophotometric detection at 562nm. Our results showed the persistent presence of a nanoparticulate/colloidal phase (retained within 20–200nm filtrates) even in high-temperature samples. A significant fraction of this phase was retrievable only under treatment with HNO3 – a strong acid known to attack and dissolve pyrite nanocrystals. Upon mixing with colder bottom waters and removal of iron in the higher parts of the buoyant plume, the larger size fractions became dominant as the total iron levels decreased, but it was still possible to detect significant (micromolar) levels of nanoparticulate Fe even in samples collected 5m above the orifice in the rising plume. The coolest sample (
    Electronic ISSN: 1664-302X
    Topics: Biology
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  • 60
    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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  • 61
    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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  • 62
    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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  • 63
    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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  • 64
    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
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  • 65
    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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  • 66
    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
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  • 67
    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
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  • 68
    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
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  • 69
    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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  • 70
    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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  • 71
    Publication Date: 2021-10-29
    Description: Locomotor and collision actions that rugby players complete during match-play often lead to substantial fatigue, and in turn, delays in recovery. The methods used to quantify post-match fatigue and recovery can be categorised as subjective and objective, with match-related collision characteristics thought to have a primary role in modulating these recovery measures. The aim of this review was to (1) evaluate how post-match recovery has been quantified in the rugby football codes (i.e., rugby league, rugby union, and rugby sevens), (2) to explore the time-course of commonly used measures of fatigue post-match, and (3) to investigate the relationships between game-related collisions and fatigue metrics. The available evidence suggests that upper-, and lower-body neuromuscular performance are negatively affected, and biomarkers of muscular damage and inflammation increase in the hours and days following match-play, with the largest differences being at 12–36 h post-match. The magnitude of such responses varies within and between neuromuscular performance (Δ ≤ 36%, n = 13 studies) and tissue biomarker (Δ ≤ 585%, n = 18 studies) measures, but nevertheless appears strongly related to collision frequency and intensity. Likewise, the increase in perceived soreness in the hours and days post-match strongly correlate to collision characteristics across the rugby football codes. Within these findings, there are specific differences in positional groups and recovery trajectories between the codes which relate to athlete characteristics, and/or locomotor and collision characteristics. Finally, based on these findings, we offer a conceptual model of fatigue which details the multidimensional latent structure of the load to fatigue relationship contextualised to rugby. Research to date has been limited to univariate associations to explore relationships between collision characteristics and recovery, and multivariate methods are necessary and recommended to account for the latent structures of match-play external load and post-match fatigue constructs. Practitioners should be aware of the typical time windows of fatigue recovery and utilise both subjective and objective metrics to holistically quantify post-match recovery in rugby.
    Electronic ISSN: 1664-042X
    Topics: Biology
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  • 72
    Publication Date: 2021-10-29
    Description: Rice (Oryza sativa) pericarp exhibits various colors due to the accumulation of anthocyanins and/or proanthocyanidins. Previous work revealed that the two basic helix-loop-helix (bHLH) transcription factors OsKala4 and OsRc are key regulators for the black and red pericarp traits, respectively, and their inactivation results in rice with white pericarp. However, their pericarp-specific R2R3 MYB partner remained unknown. Here, we characterized the role of the R2R3 MYB gene OsKala3 in rice pericarp pigmentation through genetic and molecular approaches. A rice protoplast transfection assay showed that OsKala3 is a nuclear-localized protein. Furthermore, OsKala3 physically interacted with OsKala4 in a yeast two-hybrid analysis. Co-transfection assays in rice protoplasts revealed that OsKala3 and OsKala4 mediate the activation of anthocyanin biosynthetic genes. Notably, the OsKala3 promoter region exhibited an insertion polymorphism specifically in rice cultivars with black pericarp, creating two tandem repeats while red and white varieties harbor only one. The number of repeats within the OsKala3 promoter correlated with increased transactivation by OsKala3, thus providing a rationale for the black pericarp characteristic of cultivars with two repeats. These results thus provide evidence for the molecular basis of anthocyanin biosynthesis in rice pericarp and may facilitate the introduction of this beneficial trait to other rice cultivars through marker-assisted breeding.
    Electronic ISSN: 1664-462X
    Topics: Biology
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  • 73
    Publication Date: 2021-10-29
    Electronic ISSN: 2296-598X
    Topics: Energy, Environment Protection, Nuclear Power Engineering
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  • 74
    Publication Date: 2021-10-29
    Description: Liver fibrosis is characterized by a series of events including activation of quiescent hepatic stellate cells (HSCs) into proinflammatory, contractile, and fibrogenic myofibroblasts, which is the primary trigger for the fibrogenesis process. HSC activation involves many signaling pathways such as the TGF-β/smads pathway. Specific microRNAs have been identified to play a crucial role in the activation of HSCs via various signaling pathways. Piperine has recently been studied as a promising anti-fibrotic agent against pancreatic fibrosis through altering the TGF-β1/Smad pathway. Hence, the current study evaluated the beneficial effects of piperine in thioacetamide-induced liver fibrosis in mice through the modulation of miRNA-17 and TGF-β/smads pathways. Mice were allocated into three groups randomly. Thioacetamide was used to induce liver fibrosis for 6 weeks. Starting from the fourth week of the experiment, mice were treated with piperine daily for 21 days. Piperine treatment resulted in a significant downregulation of miRNA-17 expression, leading to the restoration of smad-7 accompanied with marked inhibition of TGF-β/smads signaling with further suppression of the activated HSCs and collagen deposition in the hepatocytes. In conclusion, piperine has the potential to be a promising therapeutic drug for the treatment of liver fibrosis through inhibiting the TGF-β/smads pathway.
    Electronic ISSN: 2296-889X
    Topics: Biology
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  • 75
    Publication Date: 2021-10-29
    Description: The survival of coral reefs largely depends among other factors on the recruitment of a new generation of coral individuals that are more adapted to a rapidly changing climate and other anthropogenic stressors (e.g., pollution, sedimentation). Therefore, a better understanding of the coral settlement process, the molecules involved as well as crucial environmental drivers that control settlement success are needed. In this study, we identified a novel settlement inducer for the brooding scleractinian coral Leptastrea purpurea and highlight the importance of light for the settlement process. Crude extract of the red-pigmented bacterium Pseudoalteromonas rubra reliably triggered attachment and metamorphosis in L. purpurea larvae in less than 24 h. Prodigiosin (II) and the two derivatives, cycloprodigiosin (I) and 2-methyl-3-hexyl prodiginine (III) were isolated and structurally elucidated from the crude extract of P. rubra. We demonstrated that the photosensitive pigment cycloprodigiosin (I) was the responsible compound for attachment and metamorphosis in L. purpurea larvae. Under the tested light regimes (i.e., darkness, constant light and a dark-light alternation), cycloprodigiosin (I) triggered approximately 90% settlement at a concentration of 0.2 μg mL–1 under a 12 h alternating dark-light cycle, mimicking the light-flooded coral reef environment. Our findings enable for the first time a mechanistic understanding of the light-dependent larva to polyp transformation by discovering the novel bacterial settlement cue cycloprodigiosin and its photosensitivity as a determining factor for coral settlement.
    Electronic ISSN: 2296-7745
    Topics: Biology
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  • 76
    Publication Date: 2021-11-01
    Description: High-gradient headwater streams are major participants in the carbon (C) cycle because of their capabilities of emitting a significant amount of carbon dioxide (CO2). Notwithstanding, their CO2 emissions have been largely overlooked in previous studies owing to their small water surface area and are sometimes strenuous to be measured because of their narrow channel widths and strong turbulence. This study examined the spatial and seasonal variabilities of CO2 dynamics of a subtropical steep headwater stream fed by groundwater. Our study found that the pH and dissolved oxygen exhibited a general increasing trend away from the source of the headwater whereas the partial pressure of carbon dioxide (pCO2) showed a downward trend. The stream water pCO2 in the upper reach was found to be higher than the ambient level by 19–114 times, with an average drop of 〉70% at just 9.2 m from the groundwater source, demonstrating the potentially large emission of CO2 into the atmosphere within this short distance. Additionally, the sampling works conducted further downstream revealed that the CO2 derived from groundwater could almost completely dissipate within approximately half a kilometer downstream of the source. The concentrations of dissolved organic carbon and pCO2 were also lower during the period with lower air temperatures in the headwater stream, indicating temperature-dependent metabolism and decomposition of organic matter in soil might modulate the C dynamics in the headwater stream, although the rapid gas exchange along the stream remained the determinative factor. Our findings reassert that headwater streams are an essential source of CO2 and disregarding them from the studies of greenhouse gas emissions of inland waters would underestimate their potency to influence the global C cycle.
    Electronic ISSN: 2296-6463
    Topics: Geosciences
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  • 77
    Publication Date: 2021-11-01
    Electronic ISSN: 1664-302X
    Topics: Biology
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  • 78
    Publication Date: 2021-11-01
    Description: This paper introduces Deep4D a compact generative representation of shape and appearance from captured 4D volumetric video sequences of people. 4D volumetric video achieves highly realistic reproduction, replay and free-viewpoint rendering of actor performance from multiple view video acquisition systems. A deep generative network is trained on 4D video sequences of an actor performing multiple motions to learn a generative model of the dynamic shape and appearance. We demonstrate the proposed generative model can provide a compact encoded representation capable of high-quality synthesis of 4D volumetric video with two orders of magnitude compression. A variational encoder-decoder network is employed to learn an encoded latent space that maps from 3D skeletal pose to 4D shape and appearance. This enables high-quality 4D volumetric video synthesis to be driven by skeletal motion, including skeletal motion capture data. This encoded latent space supports the representation of multiple sequences with dynamic interpolation to transition between motions. Therefore we introduce Deep4D motion graphs, a direct application of the proposed generative representation. Deep4D motion graphs allow real-tiome interactive character animation whilst preserving the plausible realism of movement and appearance from the captured volumetric video. Deep4D motion graphs implicitly combine multiple captured motions from a unified representation for character animation from volumetric video, allowing novel character movements to be generated with dynamic shape and appearance detail.
    Electronic ISSN: 2673-4192
    Topics: Computer Science
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  • 79
    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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  • 80
    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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  • 81
    Publication Date: 2021-11-01
    Description: Citizen science and informed citizens have become fundamental in providing the first records and accounts about the expansion of numerous non-indigenous species. However, implementing a successful citizen science campaign can be expensive and particularly difficult for aquatic species. Here, we demonstrate how a low-cost citizen science campaign and its outreach plan in social and traditional media enabled to track the expansion of the Atlantic blue crab Callinectes sapidus Rathbun, 1896 along the coast of Algarve (southern Portugal, Europe). We describe the outreach strategy and a cost-benefit analysis of the first year of the citizen science campaign. Social media platforms allowed us to reach a significant number of citizens (over 31,500 clicks in Facebook publications), while traditional media gave national visibility to the citizen science campaign and biological invasions. In only 1 year, we documented the spread of the invasive Atlantic blue crab across the entire 140 km of the Algarve coast with 166 valid observations referring to 1747 specimens, submitted by 62 citizen scientists. We spent 0 € on the citizen science campaign, but considering the time invested in the campaign the cost would have summed up to 3,751 €, while the total minimum cost for one scientist to go to the field and retrieve the equivalent information would have exceeded 11,000 €. We used free online tools of communication to obtain the records about the Atlantic blue crab, instead of a dedicated web platform or mobile app, and handled social media accounts ourselves, which saved us at least 18,815 €. The citizen science campaign revealed that the Atlantic blue crab is unequivocally established in southern Portugal and that females appear to exhibit summer migrations to coastal areas to spawn as in the native area. Overall, our low-cost citizen science campaign effectively documented the rapid spread of a marine invasive species while providing some insights into its ecology. Our strategy can be easily replicated and implemented elsewhere in the world to tackle the ever-growing problem of biological invasions while increasing the scientific literacy of local populations.
    Electronic ISSN: 2296-665X
    Topics: Energy, Environment Protection, Nuclear Power Engineering
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  • 82
    Publication Date: 2021-11-01
    Description: Organoids are three-dimensional structures fabricated in vitro from pluripotent stem cells or adult tissue stem cells via a process of self-organization that results in the formation of organ-specific cell types. Human organoids are expected to mimic complex microenvironments and many of the in vivo physiological functions of relevant tissues, thus filling the translational gap between animals and humans and increasing our understanding of the mechanisms underlying disease and developmental processes. In the last decade, organoid research has attracted increasing attention in areas such as disease modeling, drug development, regenerative medicine, toxicology research, and personalized medicine. In particular, in the field of toxicology, where there are various traditional models, human organoids are expected to blaze a new path in future research by overcoming the current limitations, such as those related to differences in drug responses among species. Here, we discuss the potential usefulness, limitations, and future prospects of human liver, heart, kidney, gut, and brain organoids from the viewpoints of predictive toxicology research and drug development, providing cutting edge information on their fabrication methods and functional characteristics.
    Electronic ISSN: 1664-8021
    Topics: Biology , Medicine
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  • 83
    Publication Date: 2021-11-01
    Electronic ISSN: 2296-861X
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 84
    Publication Date: 2021-10-29
    Description: This experiment aims to explore the effects of compound enzyme preparation substituting chlortetracycline on growth performance, serum immune markers, and antioxidant capacity and intestinal health in weaned piglets. A total of twenty-four 28-day-old “Duroc × Landrace × Yorkshire” weaned piglets with an average initial weight of 7.25 ± 0.25 kg were randomly divided into three groups according to their body weight, with eight replicates in each group and one pig in each replicate. The three dietary treatments were basal diet (CON), basal diet + 1,000 mg/kg compound enzyme preparation (cellulase 4,000 IU/g, α-amylase 1,000 IU/g, β-glucanase 150 IU/g, and neutral protease 3,000 IU/g, CE), and basal diet + 75 mg/kg chlortetracycline (CTC). The animal experiment lasted for 28 days and was divided into two stages: the early stage (0–14 days) and the late stage (15–28 days). The results showed that (1) compared with the CON, the CE and CTC significantly increased the ADG of weaned piglets during the early and whole period of experiment (p 〈 0.05), decreased the F:G in the whole experiment period (p 〈 0.05), and diarrhea rate in the early stage (p 〈 0.01). (2) Compared with the CON, the apparent total tract digestibility of ADF and NDF was significantly increased in pigs fed the CE diet in the early and late stages of experiment (p 〈 0.05) with no significant difference compared with the CTC. (3) Compared with the CON, the concentrations of serum IgA and SOD in weaned piglets were significantly increased in the CE group in the early stage of the experiment (p 〈 0.05). (4) Compared with the CON group, the acetic acid, propionic acid, and total VFA contents in cecum and colon segments were elevated in the CE group (p 〈 0.05) with no significant difference compared with the CTC. (5) Compared with the CON group, the villus height of duodenum and jejunum and the ratio of villus height to recess depth of ileum were increased in the CE and CTC group (p 〈 0.05). (6) Compared with the CON group, the abundance of Lactobacillus significantly increased (p 〈 0.01) while the abundance of Escherichia coli decreased in the CE group and CTC group (p 〈 0.01). In conclusion, CE preparation instead of CTC can significantly improve the nutrient digestibility, the immunity, antioxidant capacity, and intestinal health of pigs, which may contribute to the improved growth performance of piglets.
    Electronic ISSN: 1664-302X
    Topics: Biology
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  • 85
    Publication Date: 2021-10-29
    Description: As a cold tumor, malignant glioma has strong immunosuppression and immune escape characteristics. The tumor microenvironment (TME) provides the “soil” for the survival of malignant tumors, and cancer-associated fibroblasts (CAFs) are the architects of matrix remodeling in TME. Therefore, CAFs have potent regulatory effects on the recruitment and functional differentiation of immune cells, whereby they synthesize and secrete numerous collagens, cytokines, chemokines, and other soluble factors whose interaction with tumor cells creates an immunosuppressive TME. This consequently facilitates the immune escape of tumor cells. Targeting CAFs would improve the TME and enhance the efficacy of immunotherapy. Thus, regulation of CAFs and CAFs-related genes holds promise as effective immunotherapies for gliomas. Here, by analyzing the Chinese Glioma Genome Atlas and the Cancer Genome Atlas database, the proportion of CAFs in the tumor was revealed to be associated with clinical and immune characteristics of gliomas. Moreover, a risk model based on the expression of CAFs-related six-gene for the assessment of glioma patients was constructed using the least absolute shrinkage and selection operator and the results showed that a high-risk group had a higher expression of the CAFs-related six-genes and lower overall survival rates compared with those in the low-risk group. Additionally, patients in the high-risk group exhibited older age, high tumor grade, isocitrate dehydrogenase wildtype, 1p/19q non-codeletion, O-6-methylguanine-DNA methyltransferase promoter unmethylation and poor prognosis. The high-risk subtype had a high proportion CAFs in the TME of glioma, and a high expression of immune checkpoint genes. Analysis of the Submap algorithm indicated that the high-risk patients could show potent response to anti-PD-1 therapy. The established risk prediction model based on the expression of six CAFs-related genes has application prospects as an independent prognostic indicator and a predictor of the response of patients to immunotherapy.
    Electronic ISSN: 2296-634X
    Topics: Biology
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  • 86
    Publication Date: 2021-10-27
    Description: Correlated, spontaneous neural activity is known to play a necessary role in visual development, but the higher-order statistical structure of these coherent, amorphous patterns has only begun to emerge in the past decade. Several computational studies have demonstrated how this endogenous activity can be used to train a developing visual system. Models that generate spontaneous activity analogous to retinal waves have shown that these waves can serve as stimuli for efficient coding models of V1. This general strategy in development has one clear advantage: The same learning algorithm can be used both before and after eye-opening. This same insight can be applied to understanding LGN/V1 spontaneous activity. Although lateral geniculate nucleus (LGN) activity has been less discussed in the literature than retinal waves, here we argue that the waves found in the LGN have a number of properties that fill the role of a training pattern. We make the case that the role of “innate learning” with spontaneous activity is not only possible, but likely in later stages of visual development, and worth pursuing further using an efficient coding paradigm.
    Electronic ISSN: 1664-042X
    Topics: Biology
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  • 87
    Publication Date: 2021-10-29
    Description: The objective of this study was to elucidate the impacts of irregular eating patterns on gut microbiota and transcriptomic responses in a pig model with different feeding regimens. The experiment involved 24 growing pigs (Duroc × Landrace × Large White, 48 days of age) which were randomly allocated to one of three feeding patterns: one-meal (M1), three-meals (M3), or five-meals (M5) per day with the same daily feed intake. The results showed that different feeding frequencies had no significant effects on the microbial composition of ileal digesta, colonic digesta, colon mucosa, as well as the concentration of SCFAs in colonic digesta. Mucosa transcriptomic profiling data showed the pathways related to vitamin metabolism were enriched in the ileum and colon of pigs in the pairwise comparison between M3 and M1 groups. On the other hand, the pathways related to lipid metabolism were enriched in the ileum and colon of pigs in the pairwise comparison between M5 and M1 groups. Lastly, the pathways related to protein metabolism were enriched in the colon in the pairwise comparison between M3 and M1 groups, M5 and M1 groups, M5 and M3 groups, while the ileum was not enriched. Differentially expressed genes (DEG) related to metabolism showed that carbohydrate transport was suppressed in the ileum and enhanced in the colon in M5 and M3 groups compared with the M1 group. Compared with the M3 group, carbohydrate transport in the ileum was enhanced in the M5 group, while in the colon was inhibited. With the increase of feeding frequency, the catabolism, biosynthesis, and transport of lipid in the ileum were suppressed, while those in the colon were enhanced. Compared with the M1 group, amino acid transport in the ileum and colon in the M3 group was enhanced. Amino acid catabolism in the ileum in the M5 group was enhanced compared with M1 and M3 groups. In summary, different feeding frequencies affected the transport of carbohydrate, lipid, and amino acid in the ileum and colon, and affected the catabolism and biosynthesis of lipid in the ileum and colon with a low impact on intestinal microbiota.
    Electronic ISSN: 2296-861X
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 88
    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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  • 89
    Publication Date: 2021-10-29
    Description: Gonad-inhibiting hormone (GIH) belongs to a family of neuropeptides that are released from the eyestalks of male crustaceans and plays key roles in gonadal maturity, reproduction, and molting. However, the detailed mechanisms underlying the effects of GIH on sexual regulation have yet to be elucidated. In the present study, we aimed to demonstrate how GIH mediate the activity of the androgenic gland (AG) to affect sexual regulation. To do this, we cloned and characterized a GIH sequence from Macrobrachium rosenbergii (MrGIH). The open reading frame (ORF) of MrGIH was 360 bp and codes for a polypeptide of 119 amino acids and a putative protein of 13.56 KDa. Tissue analysis showed that MrGIH is widely expressed in a range of tissues but particularly, the eyestalk, intestine, and nerve cord. Following the dsRNA silencing of MrGIH for 24 h, the expression levels of MrGIH were down-regulated in both the eyestalk and AG when compared with the negative control, but significantly increased the expression of Macrobrachium rosenbergii insulin-like androgenic gland hormone-binding protein (MrIAGBP) in AG, thus suggesting that MrGIH is an inhibitory factor for MrIAGBP. In addition, we found that eyestalk removal on certain days led to increased expression levels of MrIAGBP expression. The expression levels of MrIAGBP peaked at 2 d in the AG after unilateral and bilateral eyestalk ablation, exhibiting a 7.27- and 6.03-fold increase, respectively. Afterward, the expression of GIH protein levels were down-regulated and IAGBP protein levels were up-regulated after GIH silencing using immunohistochemistry method, combined with the increase of IAGBP protein levels after eyestalk ablation, confirming that MrGIH is an inhibitory factor that can moderately regulate AG development and IAGBP expression. Collectively, our findings enriched the mechanisms that control the sexual regulation pathway of male M. rosenbergii, and provided significant information for further explorations of the mechanism underlying sex regulation in other decapod crustaceans.
    Electronic ISSN: 2296-7745
    Topics: Biology
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  • 90
    Publication Date: 2021-10-29
    Description: Different models of community dynamics, such as the MacArthur–Wilson theory of island biogeography and Hubbell’s neutral theory, have given us useful insights into the workings of ecological communities. Here, we develop the niche-hypervolume concept of the community into a powerful model of community dynamics. We describe the community’s size through the volume of the hypercube and the dynamics of the populations in it through the fluctuations of the axes of the niche hypercube on different timescales. While the community’s size remains constant, the relative volumes of the niches within it change continuously, thus allowing the populations of different species to rise and fall in a zero-sum fashion. This dynamic hypercube model reproduces several key patterns in communities: lognormal species abundance distributions, 1/f-noise population abundance, multiscale patterns of extinction debt and logarithmic species-time curves. It also provides a powerful framework to explore significant ideas in ecology, such as the drift of ecological communities into evolutionary time.
    Electronic ISSN: 2296-701X
    Topics: Biology
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  • 91
    Publication Date: 2021-10-29
    Description: Introduction: Divers with a patent Foramen Ovale (PFO) have an increased risk for decompression sickness (DCS) when diving with compressed breathing gas. The relative risk increase, however, is difficult to establish as the PFO status of divers is usually only determined after a DCS occurrence.Methods: This prospective, single-blinded, observational study was designed to collect DCS data from volunteer divers after screening for right-to-left shunt (RLS) using a Carotid Doppler test. Divers were blinded to the result of the test, but all received a standardized briefing on current scientific knowledge of diving physiology and “low-bubble” diving techniques; they were then allowed to dive without restrictions. After a mean interval of 8 years, a questionnaire was sent collecting data on their dives and cases of DCS (if any occurred).Results: Data was collected on 148 divers totaling 66,859 dives. There was no significant difference in diving data between divers with or without RLS. Divers with RLS had a 3.02 times higher incidence of (confirmed) DCS than divers without RLS (p = 0.04). When all cases of (confirmed or possible DCS) were considered, the Relative Risk was 1.42 (p = 0.46). DCS occurred mainly in divers who did not dive according to “low-bubble” diving techniques, in both groups.Conclusion: This prospective study confirms that DCS is more frequent in divers with RLS (such as a PFO), with a Relative Risk of 1.42 (all DCS) to 3.02 (confirmed DCS). It appears this risk is linked to diving behavior, more specifically diving to the limits of the adopted decompression procedures.
    Electronic ISSN: 1664-042X
    Topics: Biology
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  • 92
  • 93
    Publication Date: 2021-10-29
    Description: The glycine-rich domain proteins (GRDP) have been functionally implicated in the cell wall structure, biotic, and abiotic stress responses. However, little is known about GRDP genes in female gametophyte development of Arabidopsis. This study shows that GRDP2, a GRDP, plays a crucial role in female gametophyte development. In GRDP2 overexpression lines, grdp2-3, the embryo sacs were arrested at FG1 and no nucleus stages. Furthermore, callose staining shows that cell plate formation during megasporogenesis is disturbed in grdp2-3. In contrast, the pollen development is not affected in grdp2-3. The expression patterns of auxin-specific marker lines in female gametophytes showed that the auxin distribution and transport were significantly changed during megagametogenesis in grdp2-3. In addition, compared with the membrane-localized pattern of PIN1, PIN2, and PIN7 in WT, the signals were detected in the cytoplasm in grdp2-3. Together, our data suggest that GRDP2 plays an essential role in auxin-mediated female gametophyte development.
    Electronic ISSN: 1664-462X
    Topics: Biology
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  • 94
    Publication Date: 2021-10-29
    Description: Heat stress affects oocyte developmental competence and is a major cause of reduced fertility in heat stressed cattle. Negative effects of heat stress on the oocyte have been observed at morphological, biochemical and developmental levels. However, the mechanisms by which heat stress affects the oocyte at the transcriptional and epigenetic levels remain to be further elucidated. Here we aimed to investigate the effect of heat stress on oocyte quality, transcriptomic profiles and DNA methylation of oocytes collected through the transition from spring to summer under Louisiana conditions. Summer season resulted in a lower number of high quality oocytes obtained compared to the spring season. There was no difference in in vitro maturation rates of oocytes collected during spring as compared to summer. RNA sequencing analysis showed that a total of 211 and 92 genes were differentially expressed as a result of heat stress in GV and MII oocytes, respectively. Five common genes (E2F8, GATAD2B, BHLHE41, FBXO44, and RAB39B) were significantly affected by heat in both GV and MII oocytes. A number of pathways were also influenced by heat stress including glucocorticoid biosynthesis, apoptosis signaling, and HIPPO signaling in GV oocytes, and Oct4 pluripotency, Wnt/beta-catenin signaling, and melatonin degradation I in MII oocytes. In addition, fluorescent immunocytochemistry analysis showed no difference in global levels of DNA methylation and DNA hydroxymethylation at either the GV or MII stage between spring and summer oocytes. The results of this study contribute to a better understanding of the effect of heat stress on the molecular mechanisms altered in bovine oocytes.
    Electronic ISSN: 1664-8021
    Topics: Biology , Medicine
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  • 95
    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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  • 96
    Publication Date: 2021-10-29
    Description: During plant embryogenesis, regardless of whether it begins with a fertilized egg cell (zygotic embryogenesis) or an induced somatic cell (somatic embryogenesis), significant epigenetic reprogramming occurs with the purpose of parental or vegetative transcript silencing and establishment of a next-generation epigenetic patterning. To ensure genome stability of a developing embryo, large-scale transposon silencing occurs by an RNA-directed DNA methylation (RdDM) pathway, which introduces methylation patterns de novo and as such potentially serves as a global mechanism of transcription control during developmental transitions. RdDM is controlled by a two-armed mechanism based around the activity of two RNA polymerases. While PolIV produces siRNAs accompanied by protein complexes comprising the methylation machinery, PolV produces lncRNA which guides the methylation machinery toward specific genomic locations. Recently, RdDM has been proposed as a dominant methylation mechanism during gamete formation and early embryo development in Arabidopsis thaliana, overshadowing all other methylation mechanisms. Here, we bring an overview of current knowledge about different roles of DNA methylation with emphasis on RdDM during plant zygotic and somatic embryogenesis. Based on published chromatin immunoprecipitation data on PolV binding sites within the A. thaliana genome, we uncover groups of auxin metabolism, reproductive development and embryogenesis-related genes, and discuss possible roles of RdDM at the onset of early embryonic development via targeted methylation at sites involved in different embryogenesis-related developmental mechanisms.
    Electronic ISSN: 1664-462X
    Topics: Biology
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  • 97
    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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  • 98
    Publication Date: 2021-10-29
    Description: The control architecture guiding simple movements such as reaching toward a visual target remains an open problem. The nervous system needs to integrate different sensory modalities and coordinate multiple degrees of freedom in the human arm to achieve that goal. The challenge increases due to noise and transport delays in neural signals, non-linear and fatigable muscles as actuators, and unpredictable environmental disturbances. Here we examined the capabilities of hierarchical feedback control models proposed by W. T. Powers, so far only tested in silico. We built a robot arm system with four degrees of freedom, including a visual system for locating the planar position of the hand, joint angle proprioception, and pressure sensing in one point of contact. We subjected the robot to various human-inspired reaching and tracking tasks and found features of biological movement, such as isochrony and bell-shaped velocity profiles in straight-line movements, and the speed-curvature power law in curved movements. These behavioral properties emerge without trajectory planning or explicit optimization algorithms. We then applied static structural perturbations to the robot: we blocked the wrist joint, tilted the writing surface, extended the hand with a tool, and rotated the visual system. For all of them, we found that the arm in machina adapts its behavior without being reprogrammed. In sum, while limited in speed and precision (by the nature of the do-it-yourself inexpensive components we used to build the robot from scratch), when faced with the noise, delays, non-linearities, and unpredictable disturbances of the real world, the embodied control architecture shown here balances biological realism with design simplicity.
    Electronic ISSN: 1662-5218
    Topics: Medicine , Technology
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  • 99
    Publication Date: 2021-10-29
    Description: Background: Acute Myeloid Leukemia (AML) is a complex and heterogeneous hematologic malignancy. However, the function of prognosis-related signature genes in AML remains unclear.Methods: In the current study, transcriptome sequencing was performed on 15 clinical samples, differentially expressed RNAs were identified using R software. The potential interactions network was constructed by using the common genes between target genes of differentially expressed miRNAs with transcriptome sequencing results. Functional and pathway enrichment analysis was performed to identify candidate gene-mediated aberrant signaling pathways. Hub genes were identified by the cytohubba plugin in Cytoscape software, which then expanded the potential interactions regulatory module for hub genes. TCGA-LAML clinical data were used for the prognostic analysis of the hub genes in the regulatory network, and GVSA analysis was used to identify the immune signature of prognosis-related hub genes. qRT-PCR was used to verify the expression of hub genes in independent clinical samples.Results: We obtained 1,610 differentially expressed lncRNAs, 233 differentially expressed miRNAs, and 2,217 differentially expressed mRNAs from transcriptome sequencing. The potential interactions network is constructed by 12 lncRNAs, 25 miRNAs, and 692 mRNAs. Subsequently, a sub-network including 15 miRNAs as well as 12 lncRNAs was created based on the expanded regulatory modules of 25 key genes. The prognostic analysis results show that CCL5 and lncRNA UCA1 was a significant impact on the prognosis of AML. Besides, we found three potential interactions networks such as lncRNA UCA1/hsa-miR-16-5p/COL4A5, lncRNA UCA1/hsa-miR-16-5p/SPARC, and lncRNA SNORA27/hsa-miR-17-5p/CCL5 may play an important role in AML. Furthermore, the evaluation of the immune infiltration shows that CCL5 is positively correlated with various immune signatures, and lncRNA UCA1 is negatively correlated with the immune signatures. Finally, the result of qRT-PCR showed that CCL5 is down-regulated and lncRNA UCA1 is up-regulated in AML samples separately.Conclusions: In conclusion, we propose that CCL5 and lncRNA UCA1 could be recognized biomarkers for predicting survival prognosis based on constructing competing endogenous RNAs in AML, which will provide us novel insight into developing novel prognostic, diagnostic, and therapeutic for AML.
    Electronic ISSN: 1664-8021
    Topics: Biology , Medicine
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  • 100
    Publication Date: 2021-10-29
    Description: The tuberous sclerosis protein complex (TSC complex) is a key integrator of metabolic signals and cellular stress. In response to nutrient shortage and stresses, the TSC complex inhibits the mechanistic target of rapamycin complex 1 (mTORC1) at the lysosomes. mTORC1 is also inhibited by stress granules (SGs), RNA-protein assemblies that dissociate mTORC1. The mechanisms of lysosome and SG recruitment of mTORC1 are well studied. In contrast, molecular details on lysosomal recruitment of the TSC complex have emerged only recently. The TSC complex subunit 1 (TSC1) binds lysosomes via phosphatidylinositol-3,5-bisphosphate [PI(3,5)P2]. The SG assembly factors 1 and 2 (G3BP1/2) have an unexpected lysosomal function in recruiting TSC2 when SGs are absent. In addition, high density lipoprotein binding protein (HDLBP, also named Vigilin) recruits TSC2 to SGs under stress. In this mini-review, we integrate the molecular mechanisms of lysosome and SG recruitment of the TSC complex. We discuss their interplay in the context of cell proliferation and migration in cancer and in the clinical manifestations of tuberous sclerosis complex disease (TSC) and lymphangioleiomyomatosis (LAM).
    Electronic ISSN: 2296-634X
    Topics: Biology
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