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  • 2020-2023  (8)
  • 1
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    The Ah receptor: adaptive metabolism, ligand diversity, and the xenokine model (2020)
    American Chemical Society
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Chemical Society, 2020. This is an open access article published under an ACS AuthorChoice License. The definitive version was published in Chemical Research in Toxicology, 33(4), (2020): 860-879, doi:10.1021/acs.chemrestox.9b00476.
    Description: The Ah receptor (AHR) has been studied for almost five decades. Yet, we still have many important questions about its role in normal physiology and development. Moreover, we still do not fully understand how this protein mediates the adverse effects of a variety of environmental pollutants, such as the polycyclic aromatic hydrocarbons (PAHs), the chlorinated dibenzo-p-dioxins (“dioxins”), and many polyhalogenated biphenyls. To provide a platform for future research, we provide the historical underpinnings of our current state of knowledge about AHR signal transduction, identify a few areas of needed research, and then develop concepts such as adaptive metabolism, ligand structural diversity, and the importance of proligands in receptor activation. We finish with a discussion of the cognate physiological role of the AHR, our perspective on why this receptor is so highly conserved, and how we might think about its cognate ligands in the future.
    Description: This review is dedicated in memory of the career of Alan Poland, one of the truly great minds in pharmacology and toxicology. This work was supported by the National Institutes of Health Grants R35-ES028377, T32-ES007015, P30-CA014520, P42-ES007381, and U01-ES1026127, The UW SciMed GRS Program, and The Morgridge Foundation. The authors would like to thank Catherine Stanley of UW Media Solutions for her artwork.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 2
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    A standardisation framework for bio-logging data to advance ecological research and conservation (2021)
    Wiley
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sequeira, A. M. M., O'Toole, M., Keates, T. R., McDonnell, L. H., Braun, C. D., Hoenner, X., Jaine, F. R. A., Jonsen, I. D., Newman, P., Pye, J., Bograd, S. J., Hays, G. C., Hazen, E. L., Holland, M., Tsontos, V. M., Blight, C., Cagnacci, F., Davidson, S. C., Dettki, H., Duarte, C. M., Dunn, D. C., Eguiluz, V. M., Fedak, M., Gleiss, A. C., Hammerschlag, N., Hindell, M. A., Holland, K., Janekovic, I., McKinzie, M. K., Muelbert, M. M. C., Pattiaratchi, C., Rutz, C., Sims, D. W., Simmons, S. E., Townsend, B., Whoriskey, F., Woodward, B., Costa, D. P., Heupel, M. R., McMahon, C. R., Harcourt, R., & Weise, M. A standardisation framework for bio-logging data to advance ecological research and conservation. Methods in Ecology and Evolution, 12, (2021): 996–1007, https://doi.org/10.1111/2041-210X.13593.
    Description: 1. Bio-logging data obtained by tagging animals are key to addressing global conservation challenges. However, the many thousands of existing bio-logging datasets are not easily discoverable, universally comparable, nor readily accessible through existing repositories and across platforms, slowing down ecological research and effective management. A set of universal standards is needed to ensure discoverability, interoperability and effective translation of bio-logging data into research and management recommendations. 2. We propose a standardisation framework adhering to existing data principles (FAIR: Findable, Accessible, Interoperable and Reusable; and TRUST: Transparency, Responsibility, User focus, Sustainability and Technology) and involving the use of simple templates to create a data flow from manufacturers and researchers to compliant repositories, where automated procedures should be in place to prepare data availability into four standardised levels: (a) decoded raw data, (b) curated data, (c) interpolated data and (d) gridded data. Our framework allows for integration of simple tabular arrays (e.g. csv files) and creation of sharable and interoperable network Common Data Form (netCDF) files containing all the needed information for accuracy-of-use, rightful attribution (ensuring data providers keep ownership through the entire process) and data preservation security. 3. We show the standardisation benefits for all stakeholders involved, and illustrate the application of our framework by focusing on marine animals and by providing examples of the workflow across all data levels, including filled templates and code to process data between levels, as well as templates to prepare netCDF files ready for sharing. 4. Adoption of our framework will facilitate collection of Essential Ocean Variables (EOVs) in support of the Global Ocean Observing System (GOOS) and inter-governmental assessments (e.g. the World Ocean Assessment), and will provide a starting point for broader efforts to establish interoperable bio-logging data formats across all fields in animal ecology.
    Description: We are thankful to ONR and UWA OI for funding the workshop, and to ARC for DP210103091. A.M.M.S. was funded by a 2020 Pew Fellowship in Marine Conservation, and also supported by AIMS. C.R. was the recipient of a Radcliffe Fellowship at the Radcliffe Institute for Advanced Study, Harvard University.
    Keywords: bio-logging template ; data accessibility and interoperability ; data standards ; metadata templates ; movement ecology ; sensors ; telemetry ; tracking
    Repository Name: Woods Hole Open Access Server
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  • 3
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    Iron Acquisition Systems of Gram-negative Bacterial Pathogens Define TonB-Dependent Pathways to Novel Antibiotics (2021)
    American Chemical Society
    In:  Chemical Reviews, 121 (9). pp. 5193-5239.
    Details
    Publication Date: 2022-01-07
    Description: Iron is an indispensable metabolic cofactor in both pro- and eukaryotes, which engenders a natural competition for the metal between bacterial pathogens and their human or animal hosts. Bacteria secrete siderophores that extract Fe3+ from tissues, fluids, cells, and proteins; the ligand gated porins of the Gram-negative bacterial outer membrane actively acquire the resulting ferric siderophores, as well as other iron-containing molecules like heme. Conversely, eukaryotic hosts combat bacterial iron scavenging by sequestering Fe3+ in binding proteins and ferritin. The variety of iron uptake systems in Gram-negative bacterial pathogens illustrates a range of chemical and biochemical mechanisms that facilitate microbial pathogenesis. This document attempts to summarize and understand these processes, to guide discovery of immunological or chemical interventions that may thwart infectious disease.
    Type: Article , PeerReviewed
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  • 4
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    Contrasting Biophysical Controls on Carbon Dioxide and Methane Outgassing From Streams (2021)
    Details
    Publication Date: 2022-04-06
    Description: Small headwater streams are recognized for intense outgassing to the atmosphere of climate‐relevant carbon dioxide (CO2) and methane (CH4). Though these headwaters are markedly oversaturated for both CO2 and CH4, the origins and controls over the fate of these two carbon‐gases are still poorly constrained, especially for the stronger greenhouse gas CH4. Here, by measuring stream‐based production of CO2 and CH4, concurrently with their rates of outgassing to the atmosphere, we identify distinct biophysical control mechanisms for each gas. We show that while CO2 is largely imported from the catchment in proportion to discharge, CO2 outgassing can be modulated by in‐stream metabolism to offset outgassing by up to 30% in spring and summer. In contrast, CH4 shows a non‐linear response to seasonal changes in discharge and is predominantly produced in the streambed in relation to sediment type. Further, once released from the streambed, outgassing of CH4 at the surface and flow‐driven dilution occur far more rapidly than biological methane oxidation and CH4 leaves the water largely unaltered by biology. Incorporating the intense carbon cycling of headwater streams into the global carbon cycle will require distinct parameterizations for each carbon gas in Earth system models.
    Description: Plain Language Summary: There is growing interest in the global carbon cycle and how carbon is transformed in the landscape into the greenhouse gases carbon dioxide (CO2) and methane–with methane being by far the more potent than CO2. Streams and rivers are recognized hotspots of carbon cycling in the landscape, commonly harboring large amounts of CO2 and methane–yet what controls either gas in streams is not fully understood. Without that understanding, we cannot predict how carbon cycling will respond to climate change or to other human alteration of the landscape. Here we researched different components of the carbon cycle in streams to show that each gas is influenced by quite distinct “biophysical” control mechanisms. While CO2 in streams results largely from physical run‐off from the land, once in a stream it can be changed by the stream biology that ebbs and flows with the seasons. Contrastingly, methane is largely created by biology within the streambed itself but once released into the wider stream that methane is then dispersed by the physical forces of stream flow. Put more simply, CO2 is physically carried to the stream to then be altered by biology, whereas as methane is borne from biology in the stream, to then be physically carried away.
    Description: Key Points: There are different controls on the outgassing of the greenhouse gases carbon dioxide and methane in streams. Carbon dioxide results largely from physical run‐off from the land and is then altered in stream by biology depending on season. In contrast, methane is created in the streambed but once released to the stream is then dispersed by the physical forces of stream flow.
    Description: Natural Environment Research Council (NERC) http://dx.doi.org/10.13039/501100000270
    Description: Deutsche Forschungsgemeinschaft (DFG) http://dx.doi.org/10.13039/501100001659
    Description: EC | H2020 | H2020 Priority Excellent Science | H2020 European Research Council (ERC) http://dx.doi.org/10.13039/100010663
    Description: FNU
    Description: Danish National Research Foundation
    Keywords: ddc:551.48
    Language: English
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  • 5
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    Ionospheric disturbances in a large area of the terrestrial globe by two strong solar flares of September 6, 2017, the strongest space weather events in the last decade (2020)
    Elsevier
    Details
    Publication Date: 2022-02-16
    Description: On September 6, 2017, the solar active region AR 2673 emitted two solar flares: the first at 08:57 UT (X2.2) and the second at 11:53 UT (X9.3); both were powerful enough to black-out high and low frequency radio waves (where UT is universal time). The X9.3 was the strongest solar flare event in the past decade. In this study, we took the advantage of these two extreme flare events to investigate corresponding effects on the ionosphere using multi-instrument observations from magnetometers, Global Positioning System – Total Electron content (GPS-TEC) receivers, ionosondes and Swarm satellites over a large geographical extent covering South American, African and European sectors. During the X2.2 flare, European and African sectors were sunlit and during X9.3 European, African, and South American sectors were sunlit and exposed to the solar flare radiation. During the X2.2 flare, there was an ionosonde blackout for a duration of about 45 min, while during the X9.3 flare this blackout lasted for 1 h and 30 min. The blackout are seen over a large global extent which demonstrates the severity of solar flare events in disrupting the radio communication. The horizontal component of Earth’s geomagnetic field has shown ripples and enhancements during these flare events. The ionospheric Vertical Total Electron Content (VTEC) showed a positive phase along with an intensification of the Equatorial Ionization Anomaly (EIA) over the South American and African sectors. The dynamical and physical processes associated with the TEC and EIA variabilities due to solar flare are discussed.
    Description: Published
    Description: 1775-1791
    Description: 1A. Geomagnetismo e Paleomagnetismo
    Description: 2A. Fisica dell'alta atmosfera
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
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    The Birth of a Hawaiian Fissure Eruption (2022)
    Wiley-AGU
    Details
    Publication Date: 2022-02-25
    Description: Most basaltic explosive eruptions intensify abruptly, allowing little time to document processes at the start of eruption. One opportunity came with the initiation of activity from fissure 8 (F8) during the 2018 eruption on the lower East Rift Zone of Kīlauea, Hawaii. F8 erupted in four episodes. We recorded 28 min of high-definition video during a 51-min period, capturing the onset of the second episode on 5 May. From the videos, we were able to analyze the following in-flight parameters: frequency and duration of explosions; ejecta heights; pyroclast exit velocities; in-flight total mass and estimated mass eruption rates; and the in-flight total grain size distributions. The videos record a transition from initial pulsating outgassing, via spaced, but increasingly rapid, discrete explosions, to quasisustained, unsteady fountaining. This transition accompanied waxing intensity (mass flux) of the F8 eruption. We infer that all activity was driven by a combination of the ascent of a coupled mixture of small bubbles and melt, and the buoyant rise of decoupled gas slugs and/or pockets. The balance between these two types of concurrent flow determined the exact form of the eruptive activity at any point in time, and changes to their relative contributions drove the transition we observed at early F8. Qualitative observations of other Hawaiian fountains at Kīlauea suggest that this physical model may apply more generally. This study demonstrates the value of in-flight parameters derived from high-resolution videos, which offer a rapid and highly timesensitive alternative to measurements based on sampling of deposits posteruption.
    Description: Published
    Description: e2020JB020903
    Description: 5V. Processi eruttivi e post-eruttivi
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 7
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    Thickness of Fluvial Deposits Records Climate Oscillations (2022)
    Details
    Publication Date: 2022-08-04
    Description: Fluvial deposits offer Earth’s best‐preserved geomorphic record of past climate change over geological timescales. However, quantitatively extracting this information remains challenging in part due to the complexity of erosion, sediment transport and deposition processes and how each of them responds to climate. Furthermore, sedimentary basins have the potential to temporarily store sediments, and rivers subsequently rework those sediments. This may introduce time lags into sedimentary signals and obscure any direct correlation with climate forcing. Here, using a numerical model that combines all three processes—and a new analytical solution—we show that the thickness of fluvial deposits at the outlet of a mountain river can be linked to the amplitude and period of rainfall oscillations but is modulated by the mountain uplift rate. For typical uplift rates of a few mm/yr, climate oscillations at Milankovitch periods lead to alluvial sediment thickness of tens of meters as observed in nature. We also explain the time lag of the order of 20%–25% of the forcing period that is commonly observed between the timing of maximum rainfall and erosion. By comparing to field datasets, our predictions for the thickness and time lag of fluvial deposits are broadly consistent with observations despite the simplicity of our modeling approach. These findings provide a new theoretical framework for quantitatively extracting information on past rainfall variations from fluvial deposits.
    Description: Plain Language Summary: Climate influences the evolution of terrestrial landscapes through the amount of precipitation, which provides water to erode rocks and transport sediment in rivers. At the outlets of mountain ranges, rivers can deposit part of their sediment load; the shape of the deposits is influenced by the amount of flow in the rivers. If the climate changes such that the precipitation rate increases, rivers can cut into their own previous deposits. The remaining deposits are then abandoned above the riverbed. On the contrary, if precipitation decreases, rivers tend to deposit more sediment, leading to increases in the thickness of sediments at the outlets of mountain rivers. Thus, there is a relationship between the amount of precipitations and the thickness of sediments deposited at river outlets. We study this with a computer model that allows us to relate the variations in precipitation rates to variations in thickness of fluvial terrace deposits. This work can be used to better understand how rivers respond to climatic changes, and also to reconstruct climatic variations of the past from observed river deposits.
    Description: Key Points: We use a numerical model and a new analytical solution to quantify a physical link between fluvial deposits and climate oscillations. Our method provides a theoretical framework for extracting information on past climate variations from fluvial terrace deposits. Our results explain time lag of 20%–25% of forcing period commonly observed between the timing of maximum rainfall and erosion.
    Description: TOTAL
    Description: Marie Sklodowska‐Curie grant
    Description: https://doi.org/10.5281/zenodo.3833983
    Keywords: ddc:550.724
    Language: English
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  • 8
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    Multiple Angle Observations Would Benefit Visible Band Remote Sensing Using Night Lights (2022)
    Details
    Publication Date: 2022-10-05
    Description: The spatial and angular emission patterns of artificial and natural light emitted, scattered, and reflected from the Earth at night are far more complex than those for scattered and reflected solar radiation during daytime. In this commentary, we use examples to show that there is additional information contained in the angular distribution of emitted light. We argue that this information could be used to improve existing remote sensing retrievals based on night lights, and in some cases could make entirely new remote sensing analyses possible. This work will be challenging, so we hope this article will encourage researchers and funding agencies to pursue further study of how multi‐angle views can be analyzed or acquired.
    Description: Plain Language Summary: When satellites take images of Earth, they usually do so from directly above (or as close to it as is reasonably possible). In this comment, we show that for studies that use imagery of Earth at night, it may be beneficial to take several images of the same area at different angles within a short period of time. For example, different types of lights shine in different directions (street lights usually shine down, while video advertisements shine sideways), and tall buildings can block the view of a street from some viewing angles. Additionally, since views from different directions pass through different amounts of air, imagery at multiple angles could be used to obtain information about Earth's atmosphere, and measure artificial and natural night sky brightness. The main point of the paper is to encourage researchers, funding agencies, and space agencies to think about what new possibilities could be achieved in the future with views of night lights at different angles.
    Description: Key Points: Remote sensing using the visible band at night is more complex than during the daytime, especially due to the variety of artificial lights. Views of night lights intentionally taken from multiple angles provide several advantages over near‐nadir or circumstantial view geometries. Night lights remote sensing would benefit from greater consideration of the role viewing geometry plays in the observed radiance.
    Description: EC H2020 H2020 Societal Challenges http://dx.doi.org/10.13039/100010676
    Description: Helmholtz Association http://dx.doi.org/10.13039/501100009318
    Description: Slovak Research and Development Agency
    Description: Xunta de Galicia (Regional Government of Galicia) http://dx.doi.org/10.13039/501100010801
    Description: National Aeronautics and Space Administration http://dx.doi.org/10.13039/100000104
    Description: University of Hong Kong http://dx.doi.org/10.13039/501100003803
    Description: Fonds de recherche du Québec
    Description: EC Emprego, Assuntos Sociais e Inclusão European Social Fund http://dx.doi.org/10.13039/501100004895
    Description: Natural Environment Research Council http://dx.doi.org/10.13039/501100000270
    Description: City of Cologne, Germany
    Keywords: ddc:551.5
    Language: English
    Type: doc-type:article
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