Showing papers by "University of Maine published in 2019"
Ohio State University1, Rega Institute for Medical Research2, University of Exeter3, Université Paris-Saclay4, University of Paris5, Utrecht University6, École Normale Supérieure7, Laval University8, University of Bremen9, Shirshov Institute of Oceanology10, University of Maine11, Wellcome Trust12, Massachusetts Institute of Technology13, Stazione Zoologica Anton Dohrn14, Bigelow Laboratory For Ocean Sciences15, Université catholique de Louvain16, University of Arizona17, Swiss Institute of Bioinformatics18, Radboud University Nijmegen19
TL;DR: An ∼12-fold expanded global ocean DNA virome dataset is established of 195,728 viral populations, now including the Arctic Ocean, and it is validated that these populations form discrete genotypic clusters.
441 citations
University of Maine1, Charles University in Prague2, Polytechnic University of Catalonia3, Microsoft4, University of Tartu5, Dublin City University6, University of Edinburgh7, Johns Hopkins University8, Harvard University9, University of Amsterdam10, University of Zurich11, Saarland University12, University of Wolverhampton13
TL;DR: This paper presents the results of the premier shared task organized alongside the Conference on Machine Translation (WMT) 2019, asked to build machine translation systems for any of 18 language pairs, to be evaluated on a test set of news stories.
Abstract: This paper presents the results of the premier shared task organized alongside the Conference on Machine Translation (WMT) 2019. Participants were asked to build machine translation systems for any of 18 language pairs, to be evaluated on a test set of news stories. The main metric for this task is human judgment of translation quality. The task was also opened up to additional test suites to probe specific aspects of translation.
433 citations
Martin Luther University of Halle-Wittenberg1, Denison University2, University of St Andrews3, University of Helsinki4, University of Aveiro5, Memorial University of Newfoundland6, University of Maine7, University of Edinburgh8, University of Massachusetts Boston9, McGill University10, Leipzig University11, University of Minnesota12, Northern Illinois University13, University of British Columbia14, Université de Sherbrooke15, National Oceanography Centre16
TL;DR: Examining spatial variation in species richness and composition change using more than 50,000 biodiversity time series from 239 studies found clear geographic variation in biodiversity change, suggesting that biodiversity change may be spatially structured.
Abstract: Human activities are fundamentally altering biodiversity. Projections of declines at the global scale are contrasted by highly variable trends at local scales, suggesting that biodiversity change may be spatially structured. Here, we examined spatial variation in species richness and composition change using more than 50,000 biodiversity time series from 239 studies and found clear geographic variation in biodiversity change. Rapid compositional change is prevalent, with marine biomes exceeding and terrestrial biomes trailing the overall trend. Assemblage richness is not changing on average, although locations exhibiting increasing and decreasing trends of up to about 20% per year were found in some marine studies. At local scales, widespread compositional reorganization is most often decoupled from richness change, and biodiversity change is strongest and most variable in the oceans.
318 citations
Swiss Institute of Bioinformatics1, French Alternative Energies and Atomic Energy Commission2, Technical University of Madrid3, Fudan University4, Ohio State University5, Laval University6, IFREMER7, Spanish National Research Council8, Hewlett-Packard9, University of Paris10, École Normale Supérieure11, Shirshov Institute of Oceanology12, University of Maine13, European Bioinformatics Institute14, Massachusetts Institute of Technology15, Bigelow Laboratory For Ocean Sciences16
TL;DR: The relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and it is hypothesized that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms.
217 citations
École Normale Supérieure1, University of Paris2, Stazione Zoologica Anton Dohrn3, Harvard University4, Fudan University5, Kyoto University6, Edith Cowan University7, Ohio State University8, University of Montpellier9, French Alternative Energies and Atomic Energy Commission10, Spanish National Research Council11, Swiss Institute of Bioinformatics12, Laval University13, Shirshov Institute of Oceanology14, University of Bremen15, University of Maine16, PSL Research University17
TL;DR: This work investigates the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans to show a decline of diversity for most planktonic groups toward the poles.
217 citations
Institut Universitaire de France1, University of Paris2, University of Maine3, Dalhousie University4, Woods Hole Oceanographic Institution5, University of Oldenburg6, IFREMER7, Alfred Wegener Institute for Polar and Marine Research8, Simón Bolívar University9, University of Tasmania10, University of California, Santa Cruz11, University of São Paulo12, Leibniz Institute of Marine Sciences13, Scripps Institution of Oceanography14, University of Bremen15, National Oceanography Centre16, Johns Hopkins University Applied Physics Laboratory17, Oregon State University18, Aix-Marseille University19, Monterey Bay Aquarium Research Institute20, Commonwealth Scientific and Industrial Research Organisation21, University of the French West Indies and Guiana22
TL;DR: A review on the technologies available to make globally quantitative observations of particles, in general, and plankton, in particular, in the world oceans, and for sizes varying from sub-micron to centimeters is presented in this article.
Abstract: In this paper we review on the technologies available to make globally quantitative observations of particles, in general, and plankton, in particular, in the world oceans, and for sizes varying from sub-micron to centimeters. Some of these technologies have been available for years while others have only recently emerged. Use of these technologies is critical to improve understanding of the processes that control abundances, distributions and composition of plankton, provide data necessary to constrain and improve ecosystem and biogeochemical models, and forecast changes in marine ecosystems in light of climate change. In this paper we begin by providing the motivation for plankton observations, quantification and diversity qualification on a global scale. We then expand on the state-of-the-art, detailing a variety of relevant and (mostly) mature technologies and measurements, including bulk measurements of plankton, pigment composition, uses of genomic, optical, acoustical methods and analysis using particles counters, flow cytometers and quantitative imaging devices. We follow by highlighting the requirements necessary for a plankton observing system, the approach to achieve it and associated challenges. We conclude with ranked action-item recommendations for the next ten years to move towards our vision of a holistic ocean-wide plankton observing system. Particularly, we suggest to begin with a demonstration project on a GO-SHIP line and/or a long-term observation site and expand from there ensuring that issues associated with methods, observation tools, data analysis, quality assessment and curation are addressed early in the implementation. Global coordination is key for the success of this vision and will bring new insights on processes associated with nutrient regeneration, ocean production, fisheries, and carbon sequestration.
210 citations
Santa Fe Institute1, University of Arizona2, Missouri Botanical Garden3, Conservation International4, New York Botanical Garden5, Xishuangbanna Tropical Botanical Garden6, University of Montpellier7, South African National Parks8, University of Leeds9, Royal Botanic Gardens10, Pontifical Catholic University of Chile11, University of Connecticut12, Stellenbosch University13, University of Copenhagen14, Universidade Federal de Minas Gerais15, University of California, Los Angeles16, Harvard University17, University of North Carolina at Chapel Hill18, University of Lorraine19, Santa Clara University20, University of California, Santa Barbara21, Charles University in Prague22, Paul Valéry University, Montpellier III23, Naturalis24, Landcare Research25, Aarhus University26, University of Maine27
TL;DR: The results indicate that (i) climatically more stable regions have harbored rare species and hence a large fraction of Earth’s plant species via reduced extinction risk but that (ii) climate change and human land use are now disproportionately impacting rare species.
Abstract: A key feature of life’s diversity is that some species are common but many more are rare. Nonetheless, at global scales, we do not know what fraction of biodiversity consists of rare species. Here, we present the largest compilation of global plant diversity to quantify the fraction of Earth’s plant biodiversity that are rare. A large fraction, ~36.5% of Earth’s ~435,000 plant species, are exceedingly rare. Sampling biases and prominent models, such as neutral theory and the k-niche model, cannot account for the observed prevalence of rarity. Our results indicate that (i) climatically more stable regions have harbored rare species and hence a large fraction of Earth’s plant species via reduced extinction risk but that (ii) climate change and human land use are now disproportionately impacting rare species. Estimates of global species abundance distributions have important implications for risk assessments and conservation planning in this era of rapid global change.
170 citations
TL;DR: The Plankton, Aerosol, Cloud, Ocean Ecosystem (PACE) mission represents the National Aeronautics and Space Administration's (NASA) next investment in satellite ocean color and the study of...
Abstract: The Plankton, Aerosol, Cloud, Ocean Ecosystem (PACE) mission represents the National Aeronautics and Space Administration’s (NASA) next investment in satellite ocean color and the study of ...
159 citations
University of Western Ontario1, Colorado State University2, Utah State University3, University of Maine4, University of California, Davis5, Academy of Sciences of the Czech Republic6, University of Innsbruck7, Portland State University8, University of Nevada, Reno9, United States Geological Survey10, University of Wisconsin-Madison11, Queen's University12, SUPSI13, University of California, Santa Barbara14
TL;DR: A review and update of the growing body of research that shows that sediments in remote mountain lakes archive regional and global environmental changes, including those linked to climate change, altered biogeochemical cycles, and changes in dust composition and deposition, atmospheric fertilization, and biological manipulations can be found in this paper.
Abstract: Mountain lakes are often situated in protected natural areas, a feature that leads to their role as sentinels of global environmental change. Despite variations in latitude, mountain lakes share many features, including their location in catchments with steep topographic gradients, cold temperatures, high incident solar and ultraviolet radiation (UVR), and prolonged ice and snow cover. These characteristics, in turn, affect mountain lake ecosystem structure, diversity, and productivity. The lakes themselves are mostly small, and up until recently, have been characterized as oligotrophic. This paper provides a review and update of the growing body of research that shows that sediments in remote mountain lakes archive regional and global environmental changes, including those linked to climate change, altered biogeochemical cycles, and changes in dust composition and deposition, atmospheric fertilization, and biological manipulations. These archives provide an important record of global environmental change that pre-dates typical monitoring windows. Paleolimnological research at strategically selected lakes has increased our knowledge of interactions among multiple stressors and their synergistic effects on lake systems. Lakes from transects across steep climate (i.e., temperature and effective moisture) gradients in mountain regions show how environmental change alters lakes in close proximity, but at differing climate starting points. Such research in particular highlights the impacts of melting glaciers on mountain lakes. The addition of new proxies, including DNA-based techniques and advanced stable isotopic analyses, provides a gateway to addressing novel research questions about global environmental change. Recent advances in remote sensing and continuous, high-frequency, limnological measurements will improve spatial and temporal resolution and help to add records to spatial gaps including tropical and southern latitudes. Mountain lake records provide a unique opportunity for global scale assessments that provide knowledge necessary to protect the Earth system.
159 citations
TL;DR: The roles of IL-6 in the progression of MM are discussed, including roles in bone homing, cancer-associated bone loss, disease progression and drug resistance, and current and potential therapeutic interventions involving IL- 6 and connected signaling molecules are discussed in this review.
Abstract: The immune system is strongly linked to the maintenance of healthy bone. Inflammatory cytokines, specifically, are crucial to skeletal homeostasis and any dysregulation can result in detrimental health complications. Interleukins, such as interleukin 6 (IL-6), act as osteoclast differentiation modulators and as such, must be carefully monitored and regulated. IL-6 encourages osteoclastogenesis when bound to progenitors and can cause excessive osteoclastic activity and osteolysis when overly abundant. Numerous bone diseases are tied to IL-6 overexpression, including rheumatoid arthritis, osteoporosis, and bone-metastatic cancers. In the latter, IL-6 can be released with growth factors into the bone marrow microenvironment (BMM) during osteolysis from bone matrix or from cancer cells and osteoblasts in an inflammatory response to cancer cells. Thus, IL-6 helps create an ideal microenvironment for oncogenesis and metastasis. Multiple myeloma (MM) is a blood cancer that homes to the BMM and is strongly tied to overexpression of IL-6 and bone loss. The roles of IL-6 in the progression of MM are discussed in this review, including roles in bone homing, cancer-associated bone loss, disease progression and drug resistance. MM disease progression often includes the development of drug-resistant clones, and patients commonly struggle with reoccurrence. As such, therapeutics that specifically target the microenvironment, rather than the cancer itself, are ideal and IL-6, and its myriad of downstream signalling partners, are model targets. Lastly, current and potential therapeutic interventions involving IL-6 and connected signalling molecules are discussed in this review.
145 citations
TL;DR: In this paper, annealing was identified as a suitable post-processing method to improve the interlayer tensile strength of extrusion-based 3D printed composites, and two different thermoplastic polymers, which are common in 3D printing, were selected to study the enhancement of interlayer strength of composites by additive manufacturing: an amorphous polyethylene terephthalate-glycol (PETG), and a semi-crystalline poly (lactic acid) (PLA).
Abstract: Previous studies have shown that 3D printed composites exhibit an orthotropic nature with inherently lower interlayer mechanical properties. This research work is an attempt to improve the interlayer tensile strength of extrusion-based 3D printed composites. Annealing was identified as a suitable post-processing method and was the focus of this study. Two distinct thermoplastic polymers, which are common in 3D printing, were selected to study the enhancement of interlayer tensile strength of composites by additive manufacturing: a) an amorphous polyethylene terephthalate-glycol (PETG), and b) a semi-crystalline poly (lactic acid) (PLA). It was determined that short carbon fiber reinforced composites have lower interlayer tensile strength than the corresponding neat polymers in 3D printed parts. This reduction in mechanical performance was attributable to an increase in melt viscosity and the consequential slower interlayer diffusion bonding. However, the reduction in interlayer tensile strength could be recovered by post-processing when the annealing temperature was higher than the glass transition temperature of the amorphous polymer. In the case of the semi-crystalline polymer, the recovery of the interlayer tensile strength was only observed when the annealing temperature was higher than the glass transition temperature but lower than the cold-crystallization temperature. This study utilized rheological and thermal analysis of 3D printed composites to provide a better understanding of the interlayer strength response and, therefore, overcome a mechanical performance limitation of these materials.
TL;DR: For a set of 23 241 populations, 16 009 species, in 158 assemblages, significantly accelerating extinction and colonisation rates were detected, with both rates being approximately balanced.
Abstract: Scientists disagree about the nature of biodiversity change. While there is evidence for widespread declines from population surveys, assemblage surveys reveal a mix of declines and increases. These conflicting conclusions may be caused by the use of different metrics: assemblage metrics may average out drastic changes in individual populations. Alternatively, differences may arise from data sources: populations monitored individually, versus whole assemblage monitoring. To test these hypotheses, we estimated population change metrics using assemblage data. For a set of 23,241 populations, 16,009 species, in 158 assemblages, we detected significantly accelerating extinction and colonisation rates, with both rates being approximately balanced. Most populations (85%) did not show significant trends in abundance, and those that did were balanced between winners (8%) and losers (7%). Thus, population metrics estimated with assemblage data are commensurate with assemblage metrics and reveal sustained and increasing species turnover.
Martin Luther University of Halle-Wittenberg1, University of Maine2, University of British Columbia3, University of St Andrews4, Memorial University of Newfoundland5, McGill University6, Denison University7, Aarhus University8, University of Massachusetts Boston9, University of Würzburg10, Stanford University11, Smithsonian Tropical Research Institute12, University of Minnesota13, University of Edinburgh14, Northern Illinois University15, National Oceanography Centre, Southampton16
TL;DR: A novel method for constructing IATs using online survey software (Qualtrics) is introduced and its validity is empirically assessed; it appears to be reliable and valid, offer numerous advantages, and make I ATs accessible for researchers who use survey software to conduct online research.
Abstract: The implicit association test (IAT) is widely used in psychology Unfortunately, the IAT cannot be run within online surveys, requiring researchers who conduct online surveys to rely on third-party tools We introduce a novel method for constructing IATs using online survey software (Qualtrics); we then empirically assess its validity Study 1 (student n = 239) revealed good psychometric properties, expected IAT effects, and expected correlations with explicit measures for survey-software IATs Study 2 (MTurk n = 818) showed predicted IAT effects across four survey-software IATs (ds = 082 [Black-White IAT] to 213 [insect-flower IAT]) Study 3 (MTurk n = 270) compared survey-software IATs and IATs run via Inquisit, yielding nearly identical results and intercorrelations that would be expected for identical IATs Survey-software IATs appear to be reliable and valid, offer numerous advantages, and make IATs accessible for researchers who use survey software to conduct online research We present all the materials, links to tutorials, and an open-source tool that rapidly automates survey-software IAT construction and analysis
TL;DR: In this paper, an ambidextrous strategy where exploration and exploitation capabilities are combined simultaneously is presented. But, the strategy is not suitable for large organizations that are competing in dynamic global markets.
Abstract: Organizations that are competing in dynamic global markets are increasingly adopting ambidextrous strategies where exploration and exploitation capabilities are combined simultaneously. However, am...
TL;DR: In this Perspective article, R. Dean Astumian shows that in addition to disequilibrium of the catalyzed reaction, kinetic asymmetry is the essential feature required to drive non-equilibrium response by an information ratchet mechanism.
Abstract: Molecular machines carry out their function by equilibrium mechanical motions in environments that are far from thermodynamic equilibrium. The mechanically equilibrated character of the trajectories of the macromolecule has allowed development of a powerful theoretical description, reminiscent of Onsager’s trajectory thermodynamics, that is based on the principle of microscopic reversibility. Unlike the situation at thermodynamic equilibrium, kinetic parameters play a dominant role in determining steady-state concentrations away from thermodynamic equilibrium, and kinetic asymmetry provides a mechanism by which chemical free-energy released by catalysis can drive directed motion, molecular adaptation, and self-assembly. Several examples drawn from the recent literature, including a catenane-based chemically driven molecular rotor and a synthetic molecular assembler or pump, are discussed. The mechanism by which macromolecular catalysts use energy from exergonic reactions to move, adapt, and assemble has been unclear. In this Perspective article, R. Dean Astumian shows that in addition to disequilibrium of the catalyzed reaction, kinetic asymmetry is the essential feature required to drive non-equilibrium response by an information ratchet mechanism.
Oregon State University1, Langley Research Center2, Johns Hopkins University Applied Physics Laboratory3, Scripps Institution of Oceanography4, University of Virginia5, National Institute of Aerospace6, Goddard Space Flight Center7, University of California, Santa Barbara8, Pacific Marine Environmental Laboratory9, Joint Institute for the Study of the Atmosphere and Ocean10, Plymouth Marine Laboratory11, Rutgers University12, University of Maine13, Texas A&M University14, Skidaway Institute of Oceanography15, University of South Florida16, University of Rhode Island17, University of Oklahoma18, University of California, Irvine19, University of Oslo20, University of Innsbruck21
TL;DR: The North Atlantic Aerosols and Marine Ecosystems Study (NAAMES) as discussed by the authors is an interdisciplinary investigation to improve understanding of Earth's ocean ecosystem-aerosol-cloud system.
Abstract: The North Atlantic Aerosols and Marine Ecosystems Study (NAAMES) is an interdisciplinary investigation to improve understanding of Earth's ocean ecosystem-aerosol-cloud system. Specific overarching science objectives for NAAMES are to (1) characterize plankton ecosystem properties during primary phases of the annual cycle and their dependence on environmental forcings, (2)determine how these phases interact to recreate each year the conditions for an annual plankton bloom, and (3) resolve how remote marine aerosols and boundary layer clouds are influenced by plankton ecosystems. Four NAAMES field campaigns were conducted in the western subarctic Atlantic between November 2015 and April 2018, with each campaign targeting specific seasonal events in the annual plankton cycle. A broad diversity of measurements were collected during each campaign, including ship, aircraft, autonomous float and drifter, and satellite observations. Here, we present an overview of NAAMES science motives, experimental design, and measurements. We then briefly describe conditions and accomplishments during each of the four field campaigns and provide information on how to access NAAMES data. The intent of this manuscript is to familiarize the broad scientific community with NAAMES and to provide a common reference overview of the project for upcoming publications.
University of California, San Diego1, Goddard Space Flight Center2, Business International Corporation3, Goddard Institute for Space Studies4, Columbia University5, University of Connecticut6, Lille University of Science and Technology7, California Institute of Technology8, University of Maryland, Baltimore County9, University of Maine10, University of Colorado Boulder11, United States Naval Research Laboratory12, Netherlands Institute for Space Research13, Langley Research Center14, University of Rennes15
TL;DR: A strategy for atmospheric correction is presented that ensures continuity and consistency with past and present ocean-color missions while enabling full exploitation of the new dimensions and possibilities of the EOS era.
Abstract: The Plankton, Aerosol, Cloud, ocean Ecosystem (PACE) mission will carry into space the Ocean Color Instrument (OCI), a spectrometer measuring at 5nm spectral resolution in the ultraviolet (UV) to near infrared (NIR) with additional spectral bands in the shortwave infrared (SWIR), and two multi-angle polarimeters that will overlap the OCI spectral range and spatial coverage, i. e., the Spectrometer for Planetary Exploration (SPEXone) and the Hyper-Angular Rainbow Polarimeter (HARP2). These instruments, especially when used in synergy, have great potential for improving estimates of water reflectance in the post Earth Observing System (EOS) era. Extending the top-of-atmosphere (TOA) observations to the UV, where aerosol absorption is effective, adding spectral bands in the SWIR, where even the most turbid waters are black and sensitivity to the aerosol coarse mode is higher than at shorter wavelengths, and measuring in the oxygen A-band to estimate aerosol altitude will enable greater accuracy in atmospheric correction for ocean color science. The multi-angular and polarized measurements, sensitive to aerosol properties (e.g., size distribution, index of refraction), can further help to identify or constrain the aerosol model, or to retrieve directly water reflectance. Algorithms that exploit the new capabilities are presented, and their ability to improve accuracy is discussed. They embrace a modern, adapted heritage two-step algorithm and alternative schemes (deterministic, statistical) that aim at inverting the TOA signal in a single step. These schemes, by the nature of their construction, their robustness, their generalization properties, and their ability to associate uncertainties, are expected to become the new standard in the future. A strategy for atmospheric correction is presented that ensures continuity and consistency with past and present ocean-color missions while enabling full exploitation of the new dimensions and possibilities. Despite the major improvements anticipated with the PACE instruments, gaps/issues remain to be filled/tackled. They include dealing properly with whitecaps, taking into account Earth-curvature effects, correcting for adjacency effects, accounting for the coupling between scattering and absorption, modeling accurately water reflectance, and acquiring a sufficiently representative dataset of water reflectance in the UV to SWIR. Dedicated efforts, experimental and theoretical, are in order to gather the necessary information and rectify inadequacies. Ideas and solutions are put forward to address the unresolved issues. Thanks to its design and characteristics, the PACE mission will mark the beginning of a new era of unprecedented accuracy in ocean-color radiometry from space.
TL;DR: Direct detection of sequential molecular assembly of organic matter at the mineral interface is presented, an important yet abstruse regulator of carbon stabilization and composition across temporal and spatial scales.
Abstract: While the importance of organic matter adsorption onto reactive iron-bearing mineral surfaces to carbon stabilization in soils and sediments has been well-established, fundamental understanding of how compounds assemble at the mineral interface remains elusive. Organic matter is thought to layer sequentially onto the mineral surface, forming molecular architecture stratified by bond strength and compound polarity. However, prominent complexation models lack experimental backing, despite the role of such architecture in fractionated, compound-dependent persistence of organic matter and modulating future perturbations in mineral stabilization capacity. Here, we use kinetic assays and ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry under high temporal frequency to directly detect the molecular partitioning of organic matter onto an iron oxyhydroxide during adsorption. We observed three sequential intervals of discrete molecular composition throughout the adsorption reaction, ...
TL;DR: This article decompose scale-specific changes in richness into proximate components attributed to: 1) the species abundance distribution, 2) density of individuals, and 3) the spatial arrangement of individuals.
Abstract: 1. Little consensus has emerged regarding how proximate and ultimate drivers such as abundance, productivity, disturbance, and temperature may affect species richness and other aspects of biodiversity. Part of the confusion is that most studies examine species richness at a single spatial scale and ignore how the underlying components of species richness can vary with spatial scale.
2. We provide an approach for the measurement of biodiversity (MoB) that decomposes scale-specific changes in richness into proximate components attributed to: 1) the species abundance distribution, 2) density of individuals, and 3) the spatial arrangement of individuals. We decompose species richness using a nested comparison of individual- and plot-based species rarefaction and accumulation curves.
3. Each curve provides some unique scale-specific information on the underlying components of species richness. We tested the validity of our method on simulated data, and we demonstrate it on empirical data on plant species richness in invaded and uninvaded woodlands. We integrated these methods into a new R package (mobr).
4. The metrics that mobr provides will allow ecologists to move beyond comparisons of species richness at a single spatial scale towards a more mechanistic understanding of the drivers of community organization that incorporates information on the scale dependence of the proximate components of species richness.
TL;DR: A PAMP-independent mechanism of immune stimulation is identified and candidalysin and EGFR signalling components are highlighted as potential targets for prophylactic and therapeutic intervention of mucosal candidiasis.
Abstract: Candida albicans is a fungal pathobiont, able to cause epithelial cell damage and immune activation. These functions have been attributed to its secreted toxin, candidalysin, though the molecular mechanisms are poorly understood. Here, we identify epidermal growth factor receptor (EGFR) as a critical component of candidalysin-triggered immune responses. We find that both C. albicans and candidalysin activate human epithelial EGFR receptors and candidalysin-deficient fungal mutants poorly induce EGFR phosphorylation during murine oropharyngeal candidiasis. Furthermore, inhibition of EGFR impairs candidalysin-triggered MAPK signalling and release of neutrophil activating chemokines in vitro, and diminishes neutrophil recruitment, causing significant mortality in an EGFR-inhibited zebrafish swimbladder model of infection. Investigation into the mechanism of EGFR activation revealed the requirement of matrix metalloproteinases (MMPs), EGFR ligands and calcium. We thus identify a PAMP-independent mechanism of immune stimulation and highlight candidalysin and EGFR signalling components as potential targets for prophylactic and therapeutic intervention of mucosal candidiasis. Candida albicans is an opportunistic fungus primarily affecting immunocompromised patients. Here, the authors identify a novel mechanism of host immune stimulation and highlight candidalysin and EGFR signalling components as potential targets for prophylactic and therapeutic intervention of mucosal candidiasis.
University of Nottingham1, York St John University2, University of Amsterdam3, VU University Amsterdam4, University of Oulu5, British Geological Survey6, The Nature Conservancy7, Northern Arizona University8, University of Minho9, Instituto Geológico y Minero de España10, Michigan State University11, University of St Andrews12, Queen Mary University of London13, Commonwealth Scientific and Industrial Research Organisation14, University of Maine15, University of Washington16, University of Plymouth17, Bryn Mawr College18, NASA Headquarters19
TL;DR: Consideration of geodiversity is an important part of developing nature-based solutions to global environmental challenges and demands for natural resources, particularly in relation to human well-being and ecosystem functioning.
Abstract: Rapid environmental change is driving the need for complex and comprehensive scientific information that supports policies aimed at managing natural resources through international treaties, platforms, and networks. One successful approach for delivering such information has been the development of essential variables for climate (1), oceans (2), biodiversity (3), and sustainable development goals (4) (ECVs, EOVs, EBVs, and ESDGVs, respectively). These efforts have improved consensus on terminology and identified essential sets of measurements for characterizing and monitoring changes on our planet. In doing so, they have advanced science and informed policy. As an important but largely unanticipated consequence, conceptualizing these variables has also given rise to discussions regarding data discovery, data access, and governance of research infrastructures. Such discussions are vital to ensure effective storage, distribution, and use of data among management agencies, researchers, and policymakers (5, 6).
Mining is one example of the human impact on geodiversity. Active mines cause a decrease in local biodiversity, but in some cases they can provide an important habitat for specialized and rare species after the mine has been abandoned. Image credit: Shutterstock/1968.
Although the current essential variables frameworks account for the biosphere, atmosphere, and some aspects of the hydrosphere (1⇓⇓–4), they largely overlook geodiversity—the variety of abiotic features and processes of the land surface and subsurface (7). Analogous to biodiversity, geodiversity is important for the maintenance of ecosystem functioning and services (8), and areas high in geodiversity have been shown to support high biodiversity (9). Thus, consideration of geodiversity is an important part of developing nature-based solutions to global environmental challenges and demands for natural resources, particularly in relation to human well-being and ecosystem functioning.
And yet, despite many facets of sustainable development being underpinned by access to geological assets, key elements of geodiversity are yet to …
[↵][1]1To whom correspondence may be addressed. Email: Franziska.Schrodt1{at}nottingham.ac.uk.
[1]: #xref-corresp-1-1
TL;DR: Recovery of stratigraphically discontinuous ice more than two million years old from the Allan Hills Blue Ice Area, East Antarctica confirms that the amplitudes of glacial–interglacial variations in atmospheric greenhouse gases and Antarctic climate were reduced in the 40k world, and that the transition from the 40K to the 100k world was accompanied by a decline in minimum carbon dioxide concentrations during glacial maxima.
Abstract: Over the past eight hundred thousand years, glacial-interglacial cycles oscillated with a period of one hundred thousand years ('100k world'1). Ice core and ocean sediment data have shown that atmospheric carbon dioxide, Antarctic temperature, deep ocean temperature, and global ice volume correlated strongly with each other in the 100k world2-6. Between about 2.8 and 1.2 million years ago, glacial cycles were smaller in magnitude and shorter in duration ('40k world'7). Proxy data from deep-sea sediments suggest that the variability of atmospheric carbon dioxide in the 40k world was also lower than in the 100k world8-10, but we do not have direct observations of atmospheric greenhouse gases from this period. Here we report the recovery of stratigraphically discontinuous ice more than two million years old from the Allan Hills Blue Ice Area, East Antarctica. Concentrations of carbon dioxide and methane in ice core samples older than two million years have been altered by respiration, but some younger samples are pristine. The recovered ice cores extend direct observations of atmospheric carbon dioxide, methane, and Antarctic temperature (based on the deuterium/hydrogen isotope ratio δDice, a proxy for regional temperature) into the 40k world. All climate properties before eight hundred thousand years ago fall within the envelope of observations from continuous deep Antarctic ice cores that characterize the 100k world. However, the lowest measured carbon dioxide and methane concentrations and Antarctic temperature in the 40k world are well above glacial values from the past eight hundred thousand years. Our results confirm that the amplitudes of glacial-interglacial variations in atmospheric greenhouse gases and Antarctic climate were reduced in the 40k world, and that the transition from the 40k to the 100k world was accompanied by a decline in minimum carbon dioxide concentrations during glacial maxima.
TL;DR: Novel hybrid panel composites based on wood, fungal mycelium, and cellulose nanofibrils (CNF) resulted in enhanced physical and mechanical properties compared to the ones made by physically mixing wood, mycelia, and CNF.
Abstract: Novel hybrid panel composites based on wood, fungal mycelium, and cellulose nanofibrils (CNF) were developed and investigated in the present study. In one set of experiments, mycelium was grown on softwood particles to produce mycelium-modified wood which was then hybridized with various levels of CNF as binder. The other set of experiments were conducted on unmodified wood particles mixed with CNF and pure mycelium tissue. It was found that the composites made of mycelium-modified wood and CNF resulted in enhanced physical and mechanical properties compared to the ones made by physically mixing wood, mycelium, and CNF. Scanning electron microscopy (SEM) images showed that mycelium modification covered wood particles with a network of fungal hyphae whereas CNF formed a uniform mycelial film over wood particles. Mycelium modification had a significant effect on reducing water absorption and thickness swelling of the hybrid composites and CNF increased the modulus of rupture and modulus of elasticity, optimally at 2.5% addition. We also present results and analysis pertaining to the development of unique lightweight composite systems with physical and mechanical properties optimized at 5% CNF addition with potential to be used in packaging and furniture applications.
TL;DR: If synergy in toxicological response is a function of simultaneous occurrence of multiple distinct modes of action, then a high frequency of potential synergies was found in pollen and wax-comb samples, which would indicate differences in pesticide exposure risk to honey bees among colonies in the same apiary and by year and location.
Abstract: Pollinators, including honey bees, are responsible for the successful reproduction of more than 87% of flowering plant species: they are thus vital to ecosystem health and agricultural services world-wide. To investigate honey bee exposure to pesticides, 168 pollen samples and 142 wax comb samples were collected from colonies within six stationary apiaries in six U.S. states. These samples were analyzed for evidence of pesticides. Samples were taken bi-weekly when each colony was active. Each apiary included thirty colonies, of which five randomly chosen colonies in each apiary were sampled for pollen. The pollen samples were separately pooled by apiary. There were a total of 714 detections in the collected pollen and 1008 detections in collected wax. A total of 91 different compounds were detected: of these, 79 different pesticides and metabolites were observed in the pollen and 56 were observed in the wax. In all years, insecticides were detected more frequently than were fungicides or herbicides: one third of the detected pesticides were found only in pollen. The mean (standard deviation (SD)) number of detections per pooled pollen sample varied by location from 1.1 (1.1) to 8.7 (2.1). Ten different modes of action were found across all four years and nine additional modes of action occurred in only one year. If synergy in toxicological response is a function of simultaneous occurrence of multiple distinct modes of action, then a high frequency of potential synergies was found in pollen and wax-comb samples. Because only pooled pollen samples were obtained from each apiary, and these from only five colonies per apiary per year, more data are needed to adequately evaluate the differences in pesticide exposure risk to honey bees among colonies in the same apiary and by year and location.
TL;DR: In this article, the authors exploit the sensitivity of organic matter preservation in marine sediments to bottom water oxygen concentration to constrain the level of dissolved oxygen in the deep central equatorial Pacific Ocean during the last glacial period (18,000-28,000 years BP).
Abstract: Enhanced ocean carbon storage during the Pleistocene ice ages lowered atmospheric CO2 concentrations by 80 to 100 ppm relative to interglacial levels. Leading hypotheses to explain this phenomenon invoke a greater efficiency of the ocean's biological pump, in which case carbon storage in the deep sea would have been accompanied by a corresponding reduction in dissolved oxygen. We exploit the sensitivity of organic matter preservation in marine sediments to bottom water oxygen concentration to constrain the level of dissolved oxygen in the deep central equatorial Pacific Ocean during the last glacial period (18,000–28,000 years BP) to have been within the range of 20–50 μmol/kg, much less than the modern value of ~168 μmol/kg. We further demonstrate that reduced oxygen levels characterized the water column below a depth of ~1,000 m. Converting the ice age oxygen level to an equivalent concentration of respiratory CO2, and extrapolating globally, we estimate that deep‐sea CO2 storage during the last ice age exceeded modern values by as much as 850 Pg C, sufficient to balance the loss of carbon from the atmosphere (~200 Pg C) and from the terrestrial biosphere (~300–600 Pg C). In addition, recognizing the enhanced preservation of organic matter in ice age sediments of the deep Pacific Ocean helps reconcile previously unexplained inconsistencies among different geochemical and micropaleontological proxy records used to assess past changes in biological productivity of the ocean.
TL;DR: This work proposes defining macroecology as “the study at the aggregate level of aggregate ecological entities made up of large numbers of particles for the purposes of pursuing generality” and proposes that returning to a focus on studying assemblages of a large number of particles is a helpful view.
Abstract: Macroecology is a growing and important subdiscipline of ecology, but it is becoming increasingly diffuse, without an organizing principle that is widely agreed upon. I highlight two main current views of macroecology: as the study of large‐scale systems and as the study of emergent systems. I trace the history of both these views through the writings of the founders of macroecology. I also highlight the transmutation principle that identifies serious limitations to the study of large‐scale systems with reductionist approaches. And I suggest that much of the underlying goal of macroecology is the pursuit of general principles and the escape from contingency. I highlight that there are many intertwined aspects of macroecology, with a number of resulting implications. I propose that returning to a focus on studying assemblages of a large number of particles is a helpful view. I propose defining macroecology as “the study at the aggregate level of aggregate ecological entities made up of large numbers of particles for the purposes of pursuing generality”.
Leibniz Institute for Baltic Sea Research1, Monterey Bay Aquarium Research Institute2, University of Washington3, Cooperative Research Centre4, Indian National Centre for Ocean Information Services5, University of Maine6, Plymouth Marine Laboratory7, Commonwealth Scientific and Industrial Research Organisation8
TL;DR: The Biogeochemical-Argo program (BGCArgo) as mentioned in this paper is a new profiling-float-based, ocean wide, and distributed ocean monitoring program which is tightly linked to, and has benefited significantly from, the Argo program.
Abstract: The Biogeochemical-Argo program (BGC-Argo) is a new profiling-float-based, ocean wide, and distributed ocean monitoring program which is tightly linked to, and has benefited significantly from, the Argo program. The community has recommended for BGC-Argo the addition of six measurements in addition to pressure, temperature and salinity measured by Argo, to include oxygen, pH, nitrate, downwelling light, chlorophyll fluorescence and the optical backscattering coefficient. The purpose of this addition is to enable the monitoring of ocean biogeochemistry and health, and in particular, monitor major processes such as ocean deoxygenation, acidification and warming and their effect on phytoplankton, the main source of energy of marine ecosystems. Here we describe the salient issues associated with the operation of the BGC-Argo network, with information useful for those interested in deploying and using the data it produces. These include, float testing, deployment and increasingly, recovery. Aspect of data management, processing and quality control are covered as well as specific issues associated with each of the six BGC-Argo sensors. In particular, it is recommended that water samples be collected during float deployment to be used for validation of sensor output.
TL;DR: A mouse model of low-grade candidemia characterized by highly localized cerebritis, accumulation of amyloid precursor protein and beta peptides, and mild memory impairment that resolves with fungal clearance is presented.
Abstract: Bloodborne infections with Candida albicans are an increasingly recognized complication of modern medicine. Here, we present a mouse model of low-grade candidemia to determine the effect of disseminated infection on cerebral function and relevant immune determinants. We show that intravenous injection of 25,000 C. albicans cells causes a highly localized cerebritis marked by the accumulation of activated microglial and astroglial cells around yeast aggregates, forming fungal-induced glial granulomas. Amyloid precursor protein accumulates within the periphery of these granulomas, while cleaved amyloid beta (Aβ) peptides accumulate around the yeast cells. CNS-localized C. albicans further activate the transcription factor NF-κB and induce production of interleukin-1β (IL-1β), IL-6, and tumor necrosis factor (TNF), and Aβ peptides enhance both phagocytic and antifungal activity from BV-2 cells. Mice infected with C. albicans display mild memory impairment that resolves with fungal clearance. Our results warrant additional studies to understand the effect of chronic cerebritis on cognitive and immune function. The potential links between infections and neurodegenerative disorders are unclear. Here, Wu et al. present a mouse model of low-grade candidemia characterized by highly localized cerebritis, accumulation of amyloid precursor protein and beta peptides, and mild memory impairment that resolves with fungal clearance.
TL;DR: Observations from a satellite-mounted light-detection-and-ranging (lidar) instrument are used to describe global distributions of an optical signal from DVM animals that arrive in the surface ocean at night, revealing that these animals generally constitute a greater fraction of total plankton abundance in the clear subtropical gyres.
Abstract: Every night across the world’s oceans, numerous marine animals arrive at the surface of the ocean to feed on plankton after an upward migration of hundreds of metres. Just before sunrise, this migration is reversed and the animals return to their daytime residence in the dark mesopelagic zone (at a depth of 200–1,000 m). This daily excursion, referred to as diel vertical migration (DVM), is thought of primarily as an adaptation to avoid visual predators in the sunlit surface layer1,2 and was first recorded using ship-net hauls nearly 200 years ago3. Nowadays, DVMs are routinely recorded by ship-mounted acoustic systems (for example, acoustic Doppler current profilers). These data show that night-time arrival and departure times are highly conserved across ocean regions4 and that daytime descent depths increase with water clarity4,5, indicating that animals have faster swimming speeds in clearer waters4. However, after decades of acoustic measurements, vast ocean areas remain unsampled and places for which data are available typically provide information for only a few months, resulting in an incomplete understanding of DVMs. Addressing this issue is important, because DVMs have a crucial role in global ocean biogeochemistry. Night-time feeding at the surface and daytime metabolism of this food at depth provide an efficient pathway for carbon and nutrient export6–8. Here we use observations from a satellite-mounted light-detection-and-ranging (lidar) instrument to describe global distributions of an optical signal from DVM animals that arrive in the surface ocean at night. Our findings reveal that these animals generally constitute a greater fraction of total plankton abundance in the clear subtropical gyres, consistent with the idea that the avoidance of visual predators is an important life strategy in these regions. Total DVM biomass, on the other hand, is higher in more productive regions in which the availability of food is increased. Furthermore, the 10-year satellite record reveals significant temporal trends in DVM biomass and correlated variations in DVM biomass and surface productivity. These results provide a detailed view of DVM activities globally and a path for refining the quantification of their biogeochemical importance. Satellite-derived analysis of daily vertical migrations of ocean animals shows that the relative abundance and total biomass of these animals differ between different regions globally, depending on the availability of food and necessity to avoid predators.