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  • Springer  (80,797)
  • American Chemical Society  (55,090)
  • Krefeld : Geologischer Dienst Nordhein-Westfalen
  • National Academy of Sciences
  • 2015-2019  (143,600)
  • 2005-2009
  • 1985-1989
  • 2018  (143,600)
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  • 2015-2019  (143,600)
  • 2005-2009
  • 1985-1989
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  • 1
    Publication Date: 2020-10-13
    Description: Mount Etna is the highest relief in Sicily and represents a unique environment because of its long established and almost continuous eruptive activity, that has moulded its landforms and which has produced distinctive landscapes. Over the past 60 ka both destructive and constructive geological processes have produced the principal morphological features of the volcano such as the wide Valle del Bove depression, monogenic scoria cones and extensive lava flow fields. Relationships between Etna, its environment and human activity began in the Neolithic Period within the mountain foot region and have developed over millennia. Even though there has been a rapid rate of resurfacing by lava during historic times, the impact on human activity has been short-lived, recovery has been rapid and society has adjusted to the ever present hazard in distinctive ways.
    Description: Published
    Description: 467-478
    Description: 1V. Storia eruttiva
    Description: N/A or not JCR
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book chapter
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  • 2
    Publication Date: 2020-10-13
    Description: Volcanoes hold a fascination for human beings and, before they were recorded by literate observers, eruptions were portrayed in art, were recalled in legend and became incorporated into religious practices: being viewed as agents of punishment, bounty or intimidation depending upon their state of activity and the culture involved. In the Middle East the earliest record dates from the third millennium BCE and knowledge of volcanoes increased progressively over time. In the first century CE written records noted nine volcanoes in the Mediterranean region plus Mount Cameroon in West Africa, yet by 1380 AD the record only totalled 48, with volcanoes in Japan, Indonesia and Iceland being added. After this the list of continued to increase, but important regions such as New Zealand and Hawaii were only added during the last 200 years. Only from 1900 did the rate of growth decline significantly, but it is sobering to recall that in the twentieth century major eruptions have occurred from volcanoes that were considered inactive or extinct, examples including: Mount Lamington—Papua New Guinea, 1951; Mount Arenal—Costa Rica, 1968 and Nyos—Cameroon, 1986. Although there were instances where the human impact of historical eruptions were studied in detail, with examples including the 1883 eruption of Krakatau and 1943–1952 eruption of Parícutin, these were exceptions and before 1980 there was a significant knowledge gap about both the short and long-term effects of major eruptions on societies. Following a global review, this chapter provides a discussion of the ways in which information has been collected, compiled and disseminated from the earliest times until the 1980s in two case study areas: the Azores Islands (Portugal) and southern Italy. In Italy information on eruptions stretches back to prehistoric times and has become progressively better known over more than 2,000 years, yet even here there remain significant gaps in the record even for events that took place between 1900 and 1990. In contrast, located in the middle of the Atlantic, the Azores have been isolated for much of their history and illustrate the difficulties involved in using indigenous sources to compile, not only assessments of impact, but also at a more basic level a complete list of historical events with accurate dates.
    Description: Published
    Description: 1-25
    Description: 1V. Storia eruttiva
    Description: N/A or not JCR
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book chapter
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  • 3
    Publication Date: 2019-02-14
    Description: Mineral ballasting enhances carbon export from the surface to the deep ocean; however, little is known about the role of this process in the ice-covered Arctic Ocean. Here, we propose gypsum ballasting as a new mechanism that likely facilitated enhanced vertical carbon export from an under-ice phytoplankton bloom dominated by the haptophyte Phaeocystis. In the spring 2015 abundant gypsum crystals embedded in Phaeocystis aggregates were collected throughout the water column and on the sea floor at a depth below 2 km. Model predictions supported by isotopic signatures indicate that 2.7 g m−2 gypsum crystals were formed in sea ice at temperatures below −6.5°C and released into the water column during sea ice melting. Our finding indicates that sea ice derived (cryogenic) gypsum is stable enough to survive export to the deep ocean and serves as an effective ballast mineral. Our findings also suggest a potentially important and previously unknown role of Phaeocystis in deep carbon export due to cryogenic gypsum ballasting. The rapidly changing Arctic sea ice regime might favour this gypsum gravity chute with potential consequences for carbon export and food partitioning between pelagic and benthic ecosystems.
    Repository Name: EPIC Alfred Wegener Institut
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  • 4
    Publication Date: 2018-06-14
    Description: Sea-ice ecosystems are among the most extensive of Earth’s habitats; yet its autotrophic and heterotrophic activities remain poorly constrained. We employed the in situ aquatic eddy-covariance (AEC) O2 flux method and laboratory incubation techniques (H14CO3−, [3H] thymidine and [3H] leucine) to assess productivity in Arctic sea-ice using different methods, in conditions ranging from land-fast ice during winter, to pack ice within the central Arctic Ocean during summer. Laboratory tracer measurements resolved rates of bacterial C demand of 0.003–0.166 mmol C m−2 day−1 and primary productivity rates of 0.008–0.125 mmol C m−2 day−1 for the different ice floes. Pack ice in the central Arctic Ocean was overall net autotrophic (0.002–0.063 mmol C m−2 day−1), whereas winter land-fast ice was net heterotrophic (− 0.155 mmol C m−2 day−1). AEC measurements resolved an uptake of O2 by the bottom-ice environment, from ~ − 2 mmol O2 m−2 day−1 under winter land-fast ice to~ − 6 mmol O2 m−2 day−1 under summer pack ice. Flux of O2-deplete meltwater and changes in water flow velocity masked potential biological-mediated activity. AEC estimates of primary productivity were only possible at one study location. Here, productivity rates of 1.3 ± 0.9 mmol O2 m−2 day−1, much larger than concurrent laboratory tracer estimates (0.03 mmol C m−2 day−1), indicate that ice algal production and its importance within the marine Arctic could be underestimated using traditional approaches. Given careful flux interpretation and with further development, the AEC technique represents a promising new tool for assessing oxygen dynamics and sea-ice productivity in ice-covered regions.
    Repository Name: EPIC Alfred Wegener Institut
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  • 5
    Publication Date: 2018-11-12
    Description: The study investigates the in-situ strength of sediments across a plate boundary décollement using drilling parameters recorded when a 1180-m-deep borehole was established during International Ocean Discovery Program (IODP)Expedition 370, Temperature-Limit of the Deep Biosphere off Muroto (T-Limit). Information of the in-situ strength of the shallow portion in/around a plate boundary fault zone is critical for understanding the development of accretionary prisms and of the décollement itself. Studies using seismic reflection surveys and scientific ocean drillings have recently revealed the existence of high pore pressure zones around frontal accretionary prisms, which may reduce the effective strength of the sediments. A direct measurement of in-situ strength by experiments, however, has not been executed due to the difficulty in estimating in-situ stress conditions. In this study, we derived a depth profile for the in-situ strength of a frontal accretionary prism across a décollement from drilling parameters using the recently established equivalent strength (EST) method. At site C0023, the toe of the accretionary prism area off Cape Muroto, Japan, the EST gradually increases with depth but undergoes a sudden change at ~ 800 mbsf, corresponding to the top of the subducting sediment. At this depth, directly below the décollement zone, the EST decreases from ~ 10 to 2 MPa, with a change in the baseline. This mechanically weak zone in the subducting sediments extends over 250 m (~ 800–1050 mbsf), corresponding to the zone where the fluid influx was discovered, and high-fluid pressure was suggested by previous seismic imaging observations. Although the origin of the fluids or absolute values of the strength remain unclear, our investigations support previous studies suggesting that elevated pore pressure beneath the décollement weakens the subducting sediments.
    Repository Name: EPIC Alfred Wegener Institut
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  • 6
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    American Chemical Society
    In:  EPIC3Environmental Science & Technology, American Chemical Society, 52(22), pp. 13279-13288
    Publication Date: 2019-03-13
    Repository Name: EPIC Alfred Wegener Institut
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  • 7
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    Springer
    In:  EPIC3Cham, Springer, 259 p., ISBN: 978-3-319-93284-2
    Publication Date: 2020-06-12
    Description: This open access book presents the proceedings volume of the YOUMARES 8 conference, which took place in Kiel, Germany, in September 2017, supported by the German Association for Marine Sciences (DGM). The YOUMARES conference series is entirely bottom-up organized by and for YOUng MARine RESearchers. Qualified early career scientists moderated the scientific sessions during the conference and provided literature reviews on aspects of their research field. These reviews and the presenters’ conference abstracts are compiled here. Thus, this book discusses highly topical fields of marine research and aims to act as a source of knowledge and inspiration for further reading and research.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Book , peerRev
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  • 8
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    Springer
    In:  EPIC3Handbook on Marine Environment Protection, Handbook on Marine Environment Protection, Berlin, Springer, 1024 p., pp. 463-485, ISBN: 978-3-319-60154-0
    Publication Date: 2018-07-23
    Description: Underwater sound is ubiquitous throughout the world’s oceans. Evaluating its impact and relevance for the marine fauna is highly complex and hampered by a paucity of data, lack of understanding and ambiguity of terms. When comparing sound (an energetic pollutant) with substantial pollutants (chemical, biological or marine litter) two notable differences emerge: Firstly, while sound propagates instantaneously away from the source, it also ceases immediately within minutes of shutting off the source. Anthropogenic noise is hence per-se ephemeral, lending itself to a set of in-situ mitigation strategies unsuitable for mitigation of persistent pollutants. Secondly, while pollution with hazardous substances can readily be described quantitatively with few parameters (environmental concentration as the most important one), the description of sound and its impact on aquatic life is of much higher complexity, as to be evidenced by the issues multifaceted description following hereinafter.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Inbook , peerRev
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  • 9
    Publication Date: 2019-04-11
    Description: This study forms part II of two papers describing ECHAM6-FESOM, a newly established global climate model with a unique multi-resolution sea ice-ocean component. While part I deals with the model description and the mean climate state, here we examine the internal climate variability of the model under constant present-day (1990) conditions. We (1) assess the internal variations in the model in terms of objective variability performance indices, (2) analyze variations in global mean surface temperature and put them in context to variations in the observed record, with particular emphasis on the recent warming slowdown, (3) analyze and validate the most common atmospheric and oceanic variability patterns, (4) diagnose the potential predictability of various climate indices, and (5) put the multi-resolution approach to the test by comparing two setups that differ only in oceanic resolution in the equatorial belt, where one ocean mesh keeps the coarse ~1° resolution applied in the adjacent open-ocean regions and the other mesh is gradually refined to ~0.25°. Objective variability performance indices show that, in the considered setups, ECHAM6-FESOM performs overall favourably compared to five well-established climate models. Internal variations of the global mean surface temperature in the model are consistent with observed fluctuations and suggest that the recent warming slowdown can be explained as a once-in-one-hundred-years event caused by internal climate variability; periods of strong cooling in the model (‘hiatus’ analogs) are mainly associated with ENSO-related variability and to a lesser degree also to PDO shifts, with the AMO playing a minor role. Common atmospheric and oceanic variability patterns are simulated largely consistent with their real counterparts. Typical deficits also found in other models at similar resolutions remain, in particular too weak non-seasonal variability of SSTs over large parts of the ocean and episodic periods of almost absent deep-water formation in the Labrador Sea, resulting in overestimated North Atlantic SST variability. Concerning the influence of locally (isotropically) increased resolution, the ENSO pattern and index statistics improve significantly with higher resolution around the equator, illustrating the potential of the novel unstructured-mesh method for global climate modeling.
    Repository Name: EPIC Alfred Wegener Institut
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  • 10
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    Springer
    In:  EPIC3Boundary Layer Meteorol., Springer, 166, pp. 301-325
    Publication Date: 2019-02-15
    Description: In climate and weather prediction models the near-surface turbulent fluxes of heat and momentum and related transfer coefficients are usually parametrized on the basis of Monin–Obukhov similarity theory (MOST). To avoid iteration, required for the numerical solution of the MOST equations, many models apply parametrizations of the transfer coefficients based on an approach relating these coefficients to the bulk Richardson number Rib.However, the parametrizations that are presently used in most climate models are valid only for weaker stability and larger surface roughnesses than those documented during the Surface Heat Budget of the Arctic Ocean campaign (SHEBA). The latter delivered a well-accepted set of turbulence data in the stable surface layer over polar sea-ice. Using stability functions based on the SHEBA data, we solve the MOST equations applying a new semi-analytic approach that results in transfer coefficients as a function of Rib and roughness lengths for momentum and heat. It is shown that the new coefficients reproduce the coefficients obtained by the numerical iterative method with a good accuracy in the most relevant range of stability and roughness lengths. For small Rib , the new bulk transfer coefficients are similar to the traditional coefficients, but for large Ri b they are much smaller than currently used coefficients. Finally, a possible adjustment of the latter and the implementation of the new proposed parametrizations in models are discussed.
    Repository Name: EPIC Alfred Wegener Institut
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  • 11
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    Springer
    In:  EPIC3Global Ecology and Oceanography of Harmful Algal Blooms, Global Ecology and Oceanography of Harmful Algal Blooms, Springer, 16 p., pp. 187-203, ISBN: 978-3-319-7006
    Publication Date: 2018-06-23
    Description: Coastal systems partially surrounded by land such as coastal embayments, estuaries and fjords have characteristics that affect the development of harmful algal blooms. Among these, shallow water depths and geophysical constraints from surrounding land masses favour stronger links between the water column and bottom sediments. Typical circulation patterns (e.g., in estuaries) can limit the exchange with offshore waters and favour cell retention. Sub-mesoscale and high-frequency processes are particularly important physical factors that influence pattern and persistence of HABs in coastal systems. Coupling with benthic nutrient fluxes or seed banks from the bottom is enhanced as the degree of physical robustness of coastal systems decreases. The links between bottom cyst distribution patterns and intensity or extension of HABs are still not fully understood. The importance of intra-specific diversity has been highlighted for many HAB species but tools are needed to assist in situ identification of these various life cycle stages. Alternative metabolic strategies, such as mixotrophy or reliance on organic nutrients and allelochemically mediated species interactions, can play a critical role in the development of HA blooms particularly in semi-confined coastal environments. Future work should address the influence of climate change and of coastal aquaculture on blooms of these harmful species in coastal environments.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Inbook , peerRev
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  • 12
    Publication Date: 2019-10-04
    Description: An integrative inventory of the amphipod scavenging fauna (Lysianassoidea), combining morphological identifications with DNA barcoding, is provided here for the Filchner area situated in the south-eastern Weddell Sea. Over 4400 lysianassoids were investigated for species richness and relative abundances, covering 20 different stations and using different sampling devices, including the southernmost baited traps deployed so far (76°S). High species richness was observed: 29 morphospecies of which 5 were new to science. Molecular species delimitation methods were carried out with 109 cytochrome c oxidase I gene (COI) sequences obtained during this study as well as sequences from specimens sampled in other Antarctic regions. These distance-based analyses (trees and the Automatic Barcode Gap Discovery method) indicated the presence of 42 lineages; for 4 species, several (cryptic) lineages were found. More than 96% of the lysianassoids collected with baited traps belonged to the species Orchomenella pinguides s. l. The diversity of the amphipod scavenger guild in this ice-bound ecosystem of the Weddell Sea is discussed in the light of bottom–up selective forces. In this southernmost part of the Weddell Sea, harbouring spawning and nursery grounds for silverfish and icefishes, abundant fish and mammalian food falls are likely to represent the major food for scavengers. Finally, the importance of biodiversity surveys in the context of the establishment of a marine protected area in this region (Weddell Sea MPA) is highlighted and how future studies can contribute to a better understanding the ecological role of scavengers in this system is discussed.
    Repository Name: EPIC Alfred Wegener Institut
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  • 13
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    Springer
    In:  EPIC3Handbook on Marine Environment Protection, Cham, Switzerland, Springer, 21 p., pp. 353-373, ISBN: 978-3-319-60156-4
    Publication Date: 2018-02-09
    Description: In this chapter, the effects of temperature change—as a main aspect of climate change—on marine biodiversity are assessed. Starting from a general discussion of species responses to temperature, the chapter presents how species respond to warming. These responses comprise adaptation and phenotypic plasticity as well as range shifts. The observed range shifts show more rapid shifts at the poleward range edge than at the equator-near edge, which probably reflects more rapid immigration than extinction in a warming world. A third avenue of changing biodiversity is change in species interactions, which can be altered by temporal and spatial shifts in interacting species. We then compare the potential changes in biodiversity to actual trends recently addressed in empirical synthesis work on local marine biodiversity, which lead to conceptual issues in quantifying the degree of biodiversity change. Finally we assess how climate change impacts the protection of marine environments.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Inbook , peerRev
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  • 14
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    American Chemical Society
    In:  EPIC3Crystal Growth & Design, American Chemical Society, 18, pp. 2563-2571
    Publication Date: 2018-04-23
    Description: The morphology and growth kinetics of ice single crystals in aqueous solutions of type III antifreeze protein (AFP-III) have been studied in detail over a range of AFP-III concentrations and supercoolings. In pure water, the shape of ice crystals changes from the circular disklike to planar dendritic with increasing supercooling. In AFP-III solutions, ice crystals in the form of faceted plates, irregular dendrites with polygonized tips, and needles appear with increasing supercooling and AFP-III concentration. The growth rate of ice crystals in the crystallographic a direction is 2 orders of magnitude higher than that in the c direction. AFP-III molecules cause the stoppage of the growth of the prismatic and basal faces at low supercoolings. When supercooling exceeds the critical value, AFP-III favors the acceleration of the growth in both a and c directions. The observed behavior of AFP-III is explained in terms of the Cabrera-Vermilyea pinning model and the specificity of the dissipation of latent heat from the growing crystals with different shapes.
    Repository Name: EPIC Alfred Wegener Institut
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  • 15
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    Springer
    In:  EPIC3Building Bridges at the Science-Stakeholder Interface, Building Bridges at the Science-Stakeholder Interface, Springer, 133 p., pp. 73-78, ISBN: 978-3-319-75919-7
    Publication Date: 2019-08-15
    Repository Name: EPIC Alfred Wegener Institut
    Type: Inbook , peerRev , info:eu-repo/semantics/other
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  • 16
    Publication Date: 2019-04-17
    Description: In fall 1995, during a survey in Abrolhos coral reef system (southwestern Atlantic, Brazil), significant densities (143–6174 cells L-1) of small thecate dinoflagellates were detected. Analysis of this material in scanning and transmission electron microscopy confirmed the presence of four taxa assigned to the potentially toxic genus Azadinium: A. dexteroporum Percopo et Zingone, A. luciferelloides Tillmann et Akselman, A. cf. polongum Tillmann and Azadinium sp. The latter taxon showed external morphological features quite distinct from any Azadinium taxon yet described, but its formal description as a new species depends on more detailed analysis. Species of Azadinium have never been confirmed in Brazilian waters until now, although the toxins produced by these dinoflagellates, the azaspiracids, have been detected in Brazilian southern coast without recognition of their producing organisms. The highest densities of Azadinium spp. occurred at stations south of and over the Abrolhos Bank, which receive higher nutrient concentrations due to upwelling of deep and nutrient-rich water masses.
    Repository Name: EPIC Alfred Wegener Institut
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  • 17
    Publication Date: 2018-06-27
    Description: This study focusses on the last glacial–deglacial–Holocene spatial and temporal variability in sea-ice cover based on organic geochemical analyses of marine sediment cores from the subarctic Pacific and the Bering Sea. By means of the sea-ice proxy “IP25” and phytoplankton-derived biomarkers (specific sterols and alkenones), we reconstruct the spring sea-ice conditions, (summer) sea-surface temperature (SST) and primary productivity, respectively. The large variability of sea ice was explained by a combination of local and global factors, such as solar insolation, global climate anomalies and sea-level changes controlling the oceanographic circulation and water mass exchange between the subarctic Pacific and the Bering Sea. During the Last Glacial Maximum, extensive sea-ice cover prevailed over large part of the subarctic Pacific and the Bering Sea. The following deglaciation is characterized by a rapid sea-ice advance and retreat. During cold periods (Heinrich Stadial 1 and Younger Dryas) seasonal sea-ice cover generally coincided with low alkenone SSTs and low primary productivity. Conversely, during warmer intervals (Bølling/Allerød, Early Holocene) reduced sea-ice or ice-free conditions prevailed in the study area. At the northern Bering Sea continental shelf a late-Early/Mid Holocene shift to marginal sea-ice conditions is in line with the simultaneous wide-spread sea-ice recovery observed in the other Arctic marginal seas and is likely initiated by the lower Northern Hemisphere insolation and surface-water cooling.
    Repository Name: EPIC Alfred Wegener Institut
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  • 18
    Publication Date: 2018-09-28
    Repository Name: EPIC Alfred Wegener Institut
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  • 19
    Publication Date: 2021-04-25
    Keywords: 551 ; VKB 350 ; 38.20
    Language: English
    Type: anthologyArticle , publishedVersion
    Format: 186-209
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  • 20
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    Springer | Berlin [u.a.]
    Publication Date: 2021-04-25
    Description: Colonial non-zooxanthellate corals from deep-water coral reefs, Lophelia pertusa and Madrepora oculata, produce large amounts of extracellular mucus (EMS). This mucus has various functions, e.g., an antifouling capability protecting the coral skeleton from attacks of endolithic and boring organisms. Both corals show thick epithecal and exothecal skeletal parts with a clear lamellar growth pattern. The formation of the epitheca is unclear. It is supposed that the EMS play a central role during the calcification process of the epithecal skeletal parts. Staining with the fluorochrome tetracycline has shown an enrichment of Ca2+ ions in the mucus. In order to investigate this hypothesis, the protein content of the mucus and the intracrystalline organic matter from newly formed epithecal aragonite of Madrepora oculata was determined via sodium dodecyl sulfate (SDS) gel electrophoresis. Identical band patterns within both substances could be detected, one around 45 kDa molecular weight and a cluster around 30-35 kDa molecular weight. The occurrence of identical protein patterns within the mucus and in the newly formed aragonite confirms the idea that the mucus plays an important role during the organomineralization of the coral epitheca.
    Keywords: 551 ; VU 000 ; 38.20
    Language: English
    Type: anthologyArticle , publishedVersion
    Format: 731-744
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  • 21
    Publication Date: 2021-03-29
    Description: The incorporation of hydrogen in enstatite in a hydrous system containing various amounts of NaCl was investigated at 25 kbar. The hydrogen content in enstatite shows a clear negative correlation to the NaCl-concentration in the system. The most favourable explanation is the reduction of water fugacity due to dilution. Other reasons for the limited hydrogen incorporation at high NaCl levels, such as a significant influence of Na+ on the defect chemistry or an exchange between OH- and Cl-in enstatite, appear much less important. A partition coefficient D Na En/Fluid = 0.0013 could be determined, demonstrating that Na is less incompatible in enstatite than H. The new results support the idea that dissolved components have to be considered when the total hydrogen storage capacity in nominally anhydrous minerals is estimated, especially in geological settings with high levels of halogens, such as subduction zones.
    Keywords: KEnstatite; Hydrogen incorporation;Water activity; Sodium; Chlorine ; 551
    Language: English
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  • 22
    Publication Date: 2021-03-29
    Description: The coprecipitation of U (VI) with iron corrosion products from aqueous solutions by zero valent iron was investigated. The evidence of coprecipitation was demonstrated by conducting experiments with well characterized scrap iron,pyrite and a mixture of both materials with experimental durations of up to four months. Results indicate that under anoxic conditions only less than one tenth of the immobilized U(VI) was associated with the surface of scrap iron, whereas theremaining amount is entrapped in aging corrosion products.
    Keywords: 551
    Language: English
    Type: anthologyArticle , acceptedVersion
    Format: 577-586
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  • 23
    Publication Date: 2018-03-08
    Description: This contribution proposes a cautious way of constructing the susceptibility classes obtained from favourability modeling of landslide occurrences. It is based on the ranks of the numerical values obtained by the modelling. Such ranks can be displayed in the form of histograms, cumulative curves, and prediction patterns resembling maps. A number of models have been proposed and in this contribution the following will be compared in terms of their respective rankings for equal area classes: fuzzy set function, empirical likelihood ratio, linear and logistic regression, and Bayesian prediction function. The analyses performed and contrasted exemplify a generalized methodology for comparing predictions that should allow evaluating prediction patterns from any model. Unfortunately, many applications in the scientific literature use methods of characterizing prediction quality that make comparison hard or impossible. A database from a study area in the Mountain Community of Tirano in Valtellina, Lombardy Region, northern Italy, is used to illustrate how the results of the different models and strategies of analysis show the relevance of the properties of the database over those of the models.
    Description: Published
    Description: 1135-1144
    Description: 2TR. Ricostruzione e modellazione della struttura crostale
    Keywords: Landslide susceptibility, spatial support, spatial relationships, prediction models, prediction patterns, target pattern, ranked classes, cross-validation, database signature ; 04.04. Geology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book chapter
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  • 24
    Publication Date: 2018-04-06
    Description: The EOS-1 Terra ASTER (Advanced Spaceborne Thermal Emission and Reflection Radiometer) has acquired about 200 images (100 of them sufficiently cloud-free to be used) over Mt. Etna since 1999. This chapter shows the results from the analysis of 10 years Mt Etna activity using thermal infrared (TIR) high spatial resolution data by a semi-automatic procedure that extracts radiance values of the summit area with the goal of detecting variation related to eruptive events. Night time data showed a good correlation with the main eruptive events that occurred both in the summit and in the flank areas. A comparison of the variance of maximum ASTER TIR radiance with variance of the maximum AVHRR TIR radiance (Advanced Very High Resolution Radiometer) for the same area confirms good correlation in terms of trend and values between the two data sets. Finally this study emphasizes the importance of high spatial resolution TIR data during background monitoring to detect changes in the thermal emission that may be related to an impending eruption and the need to further improve the spatial resolution in the TIR channels to better separate the thermal active areas in volcanic systems.
    Description: Published
    Description: 409-428
    Description: 5V. Dinamica dei processi eruttivi e post-eruttivi
    Description: 2SR. VULCANI - Servizi e ricerca per la Società
    Description: 5IT. Osservatori
    Keywords: Remote sensing observation, volcano monitoring ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 25
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    Springer
    Publication Date: 2018-02-16
    Description: No abstract
    Description: Published
    Description: 6A. Geochimica per l'ambiente
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 26
    Publication Date: 2018-02-19
    Description: No abstract
    Description: Published
    Description: 6A. Geochimica per l'ambiente
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book
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  • 27
    Publication Date: 2018-03-16
    Description: In this paper, we analyze the tropospheric delay observed on some ground-based CGPS stations in a dense small regional network and its time evolution during extreme weather conditions. In particular, we studied two severe weather events occurring in the Campanian Region (Italy) on October 12, 2012 and December 2, 2014, reaching 42 and 28 mm rainfall during about 1 h at Naples (MAFE) and Gragnano (GRAG) stations respectively. The main concern of this study is the retrieval of the precipitable water (PW) from co-located GPS and meteorological stations. We investigate the correlation between PW and rain amount at ground level. We analyse phase residuals for each visible GPS satellite using sky plots of the phase residuals along the GPS satellites tracks, showing that the two phenomena are shown in the phase residual plots. Moreover, we compare PWdata retrieved from observed meteorological data and from models (GPT2 and ECMWF), evidencing that there is a need for co-located CGPS and weather stations to improve the assessment of water content in the troposphere.
    Description: Published
    Description: 293-302
    Description: 4A. Oceanografia e clima
    Description: 7A. Geofisica per il monitoraggio ambientale e geologia medica
    Keywords: Precipitable water ; Tropospheric delay ; GPT2 ; ECMWF ; GPS ; 01.01. Atmosphere
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book chapter
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  • 28
    Publication Date: 2018-03-19
    Description: The importance of historical earthquake data is largely recognized by both seismologists and engineers, who use such data in a wide range of applications. At the European-Mediterranean scale, several databases dealing with historical earthquake data – mostly intensity data points – exist and are constantly maintained and updated, as well as national earthquake catalogues. In addition, a number of studies on historical earthquakes are published every year. Most of these activities are being performed at a national scale, depending on each country’s needs, and according to diverse methodologies. As a result, the earthquake history of Europe is today fragmented in a puzzle of different, only partially overlapping sets of data, which, at the continent scale, are not homogeneously collected and interpreted. This situation is particularly evident in the frontier areas, where historical earthquakes are often interpreted in a conflicting and/or partial way by the catalogues of the bordering countries. In addition, the background information upon which several historical catalogues are built is not published or not easily accessible. In recent years, a major effort was made to bridge over these gaps, by establishing cooperation among existing national databases, and creating new ones according to common standards. Particular attention was devoted to retrieve the earthquake background information, that is, the results of historical earthquake investigation in terms of a paper, a report, a book chapter, a map, etc. As most of the information on an historical earthquake can be summarized in a set of Macroseismic Data Points (MDPs) – i.e. a list of localities (name and coordinates) with a macroseismic intensity assessment and the related macroseismic scale – a dedicated effort was addressed to make such data publicly available. The described activities resulted in the European Archive of Historical Earthquake Data (AHEAD). The Archive is conceived as a pan-European common and open platform supporting the research activities in the field of historical seismology by (i) tracing back, preserving and granting access to the sources of data on the earthquake history of Europe (papers, reports, MDPs, and catalogues), and (ii) establishing relations among these data. AHEAD inventories multiple sets of information concerning each European earthquake in the time-window 1000–1899. The AHEAD web portal (http://www.emidius.eu/AHEAD/) gives access, as of today, to 4,722 earthquakes and the related background information as provided by 338 data sources. All these data can be queried by earthquake and by study, through a user-friendly web-interface. The distinguishing feature of AHEAD is to grant access not only to one study, but to all the available (published) data sources dealing with each individual earthquake, allowing researchers to take into account the different point of views and interpretations.
    Description: Published
    Description: 359-369
    Description: 3T. Storia Sismica
    Description: 4T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: 4IT. Banche dati
    Keywords: historical seismology ; seismicity ; historical earthquakes ; 04.06. Seismology ; 05.02. Data dissemination
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: book chapter
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  • 29
    Publication Date: 2019-03-26
    Description: The shallow vertical temperature profile has been measured in the proximity of an eruptive fissure far about 4 km north-northeast from Mt. Etna central craters. The monitoring site was a steam-heated soil lying between a group of flank fractures on the upper northeast flank of Mt. Etna (Italy), i.e., on the northeast rift. We chose this area because it was close to an eruptive fissure, that opened in 2002 and extended from about 2500 to about 1500 m a.s.l., with our aim being to determine a connection between this fracture system and the ongoing volcanic activity. Heat flux anomalies from the ground from September 2009 to September 2012 were evaluated. Changes in the hydrothermal release—which can be related to variations in volcanic activity—are discussed and compared to the published geophysical data. The heat flux ranges varied during the pre-eruptive (from about 7 to 38 W×m−2), syn-eruptive (from about 3 to 49W×m−2), and post-eruptive phases, with the heat released being lowest at the latter phase (from about 1 to 20 W×m−2). Moreover, the heat flux time variation was strongly correlated with the eruption rate from the new southeast crater between January 2011 and April 2012. The migration of magma through active conduits acts as a changing heating source for steam-heated soils located above the active fractures. Our findings suggest that tracking the heat flux above active fractures constitutes a useful investigation field for low-cost thermal monitoring of volcanic activity. Time variations in their emissions could highlight the relationship between a hydrothermal circuit and the local network of fractures, possibly indicating variation in the structural weakness of a volcanic edifice. Continuous monitoring of heat flux, combined with a realistic model, would contribute to multidisciplinary investigations aimed at evaluating changes in volcano dynamics.
    Description: National Department of Civil Protection
    Description: Published
    Description: 31
    Description: 5V. Processi eruttivi e post-eruttivi
    Description: JCR Journal
    Keywords: Volcanic activity ; Ground temperature ; Heat flux ; Continuous monitoring ; 04.08. Volcanology ; 05.04. Instrumentation and techniques of general interest
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 30
    Publication Date: 2021-03-29
    Description: Five volcanic tuffs ranging from dacitic tuffs of Hungary to rhyolite, phonolite and basaltic tuffs of Germany were consolidated under laboratory conditions. Prior to consolidation an anti-hygro, a hydrous consolidant, which reduces the swelling ability of clay minerals, was applied. The three consolidants, a silicic acid ester (SAE), an elastic silicic acid ester (eSAE) and an acrylate resin (PMMA) were applied on test specimens under vacuum. Petrographic characterisation (polarizing microscopy, XRD, SEM) provided data for fabric analyses and the mineral composition of the tuffs. Changes in fabric, effective porosity, density, tensile strength, ultrasonic wave velocity were evaluated after the treatment. Weathering simulation tests such as hygric dilatation and thermal dilatation aimed to prove the effectiveness of consolidation and the durability of consolidated tuff samples. More than 500 samples were analysed. The tests showed that SAE caused the highest increase in indirect tensile strength. The water absorption and the pore size distribution of the tuffs were modified by consolidation. The PMMA reduced the water absorption the most, whereas SAE modified it the least. All the tested consolidants increased the thermal dilatation of the tuffs. The changes in hygric dilatation were not uniform: for most tuffs SAE increased and PMMA decreased the hygric dilatation, although the clay-rich Habichtswald tuff showed the opposite trend. The changes in hygric and thermal behaviour of consolidated tuff require special care when specific consolidants are chosen. These products modify the physical properties of consolidated tuffs and change the behaviour of weathering.
    Keywords: Strengthening agents; Tuff; Silicic acid ester; PMMA; Durability ; 551
    Language: English
    Type: article , publishedVersion
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  • 31
    Publication Date: 2021-03-29
    Keywords: Albrecht-von-Haller-Institut für Pflanzenwissenschaften / Abteilung für Palynologie und Klimadynamik ; Palaeolimnology; Holocene climate; Diatoms; Green algae; Pollen; Karst ; 551
    Language: English
    Type: article , publishedVersion
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  • 32
    Publication Date: 2021-03-29
    Description: A 782 d solubilization study using not shaken batch experiments and involving one uranium-bearing rock and three natural carbonate minerals was conducted to characterize uranium (U) leaching under oxic conditions. Results showed that aqueous U concentration increased continuously with a solubilization rate of 0.16 mgm-2h-1 for the first 564 d (1.5 y). After 1.5 y, U concentration reached a maximum value (saturation) and decreased afterwards. The saturation concentration of 54 mgL-1 (mean value) was influenced to various extent by the presence of carbonate minerals. Dissolution/precipitation, adsorption or ion exchange processes appear to control U solubilization.
    Keywords: 551
    Language: English
    Type: anthologyArticle , acceptedVersion
    Format: 425-435
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  • 33
    Publication Date: 2021-04-25
    Keywords: 551 ; VU 000 ; 38.20
    Language: English
    Type: anthologyArticle , publishedVersion
    Format: 179-211
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  • 34
    Publication Date: 2021-04-25
    Keywords: 551 ; VU 000 ; 38.20
    Language: English
    Type: anthologyArticle , publishedVersion
    Format: 102-120
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  • 35
    Publication Date: 2021-04-25
    Keywords: 551 ; VU 000 ; 38.20
    Language: English
    Type: anthologyArticle , publishedVersion
    Format: 121-133
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  • 36
    Publication Date: 2021-03-29
    Description: The veneer cladding of the Oeconomicum (OEC, Göttingen), the State Theatre of Darmstadt (STD, Darmstadt) and of the State and University Library (SUB, Göttingen) is characterised by pronounced bowing after a short time of exposure. Direct comparison of bowing data related to measurements from 2000 to 2003 at the SUB clearly show that the amplitude in bowing had significantly increased. The bowing is different in intensity and orientation (concave, convex). The cladding material (Peccia marble, Rosa Estremoz marble and Carrara marble) are different in lattice preferred orientation, grain size distribution and grain interlocking. Depending on the bowing, panels may show cracks mostly initiated at the dowels. The percentage of visible cracks and breakouts increases with the amplitude of bowing except for the STD. Repetitive heatingcooling under dry conditions leads to considerable inelastic residual strain only after the first or second thermal cycle. The residual strain continuously increases again if water is present, whereby the moisture content after a thermal cycle has a certain impact on the decay rate. The water-enhanced thermal dilatation strongly correlates with the deterioration rate obtained from the laboratory bow test. Detailed petrophysical investigations provide evidence that with increasing bowing a decrease of mechanical properties (flexural strength or breaking load at dowel hole) occur. Marble degradation is also connected with the increase in porosity and a general shift of the maximum pore radii to larger pore sizes...
    Keywords: Bowing; Marble; Building mapping;Residual strain;Thermal expansion; Bowing potential ; 551
    Language: English
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  • 37
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    In:  EPIC3Ocean Dynamics, Springer, pp. 1-17
    Publication Date: 2019-01-23
    Description: Mesoscale eddies in the open ocean are mostly formed by baroclinic instability, in which the available potential energy from the large-scale slope of the isopycnals is converted into the kinetic energy of the flow around the eddy. As a permissible form of motion within a rapidly rotating and stratified fluid eddies driven by baroclinic instability are important for the poleward and vertical transport, not only of physical properties, but also biogeochemical ones. In this paper, we present observations from four cyclonic eddies in the Antarctic Circumpolar Current. We have sorted them by apparent age, based on altimeter data and consideration of the degree of homogenisation of the potential temperature-salinity(θS) relationship, and then looked at the spatial distribution of measures of fine-scale variability in the upper thermocline. The youngest eddy shows isopycnals which are domed upwards and it contains a variety of waters with differing temperature-salinity characteristics. The fine-scale variability is higher in the core of the eddy. The older eddies show a core which is more homogeneous in potential temperature and salinity. The isopycnals are flatter in the centre of the eddy, and in cross-section, they can be M-shaped, so that the steepest gradients are concentrated around the edge. The fine-scale variability is more concentrated around the edges where the density gradients are stronger. We hypothesise that lateral stirring and mixing processes within the eddy homogenise the water so that the temperature-salinity relationship becomes tighter. When the eddy eventually collapses, this modified water can be released back into the flow. Thus, we see how the interplay of mesoscale and small-scale processes are modifying water mass properties and, potentially, regulate biogeochemical processes.
    Repository Name: EPIC Alfred Wegener Institut
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  • 38
    facet.materialart.
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    Springer
    In:  EPIC3YOUMARES 8 - Ocean across boundaries: Learning from each other, Kiel, Germany, 2017-09-13-2017-09-15Cham, Springer
    Publication Date: 2019-09-13
    Repository Name: EPIC Alfred Wegener Institut
    Type: Conference , notRev
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  • 39
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Proceedings of the National Academy of Sciences.of the United States of America 115 (2018): 3398-3403, doi:10.1073/pnas.1715382115.
    Description: Plant nitrogen (N) use is a key component of the N cycle in terrestrial ecosystems. The supply of N to plants affects community species composition and ecosystem processes such as photosynthesis and carbon (C) accumulation. However, the availabilities and relative importance of different N forms to plants are not well understood. While nitrate (NO3−) is a major N form used by plants worldwide, it is discounted as a N source for Arctic tundra plants because of extremely low NO3− concentrations in Arctic tundra soils, undetectable soil nitrification, and plant-tissue NO3− that is typically below detection limits. Here we reexamine NO3− use by tundra plants using a sensitive denitrifier method to analyze plant-tissue NO3−. Soil-derived NO3− was detected in tundra plant tissues, and tundra plants took up soil NO3− at comparable rates to plants from relatively NO3−-rich ecosystems in other biomes. Nitrate assimilation determined by 15N enrichments of leaf NO3− relative to soil NO3− accounted for 4 to 52% (as estimated by a Bayesian isotope-mixing model) of species-specific total leaf N of Alaskan tundra plants. Our finding that in situ soil NO3− availability for tundra plants is high has important implications for Arctic ecosystems, not only in determining species compositions, but also in determining the loss of N from soils via leaching and denitrification. Plant N uptake and soil N losses can strongly influence C uptake and accumulation in tundra soils. Accordingly, this evidence of NO3− availability in tundra soils is crucial for predicting C storage in tundra.
    Description: his study was supported by the Kyoto University Foundation, the Sumitomo Foundation, Program for Next Generation World-Leading Researcher (Grant GS008) and Grant-in-Aid for Scientific Research (KAKENHI Grants 26252020, 26550004, 17H06297, and P09316) from the Japan Society for Promotion of Science, the National Natural Science Foundation of China (Grants 41730855, 41522301, and 41473081), the National Key Research and Development Program of China (Grants 2016YFA0600802 and 2017YFC0210101), and the 11th Recruitment Program of Global Experts (the Thousand Talents Plan) for Young Professionals granted by the central budget of China.
    Keywords: Arctic tundra plants ; Nitrogen dynamics ; Plant nitrate ; Soil nitrate ; Stable isotopes
    Repository Name: Woods Hole Open Access Server
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  • 40
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Proceedings of the National Academy of Sciences.of the United States of America 115 (2018): 6756–6761, doi:10.1073/pnas.1804351115.
    Description: The existence of a chemosynthetic subseafloor biosphere was immediately recognized when deep-sea hot springs were discovered in 1977. However, quantifying how much new carbon is fixed in this environment has remained elusive. In this study, we incubated natural subseafloor communities under in situ pressure/temperature and measured their chemosynthetic growth efficiency and metabolic rates. Combining these data with fluid flux and in situ chemical measurements, we derived empirical constraints on chemosynthetic activity in the natural environment. Our study shows subseafloor microorganisms are highly productive (up to 1.4 Tg C produced yearly), fast-growing (turning over every 17–41 hours), and physiologically diverse. These estimates place deep-sea hot springs in a quantitative framework and allow us to assess their importance for global biogeochemical cycles.
    Description: This research was funded by a grant of the Dimensions of Biodiversity program of the US National Science Foundation (NSF-OCE-1136727 to S.M.S. and J.S.S.). Funding for J.M. was further provided by doctoral fellowships from the Natural Sciences and Engineering Research Council of Canada (PGSD3-430487-2013, PGSM-405117-2011) and the National Aeronautics and Space Administration Earth Systems Science Fellowship (PLANET14F-0075), an award from the Canadian Meteorological and Oceanographic Society, and the WHOI Academic Programs Office.
    Repository Name: Woods Hole Open Access Server
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  • 41
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Population Ecology 60 (2018): 21-36, doi:10.1007/s10144-018-0615-8.
    Description: Models of sexually-reproducing populations that consider only a single sex cannot capture the effects of sex-specific demographic differences and mate availability. We present a new framework for two-sex demographic models that implements and extends the birth-matrix mating-rule approach of Pollak. The model is a continuous-time matrix model that explicitly includes the processes of mating (which is nonlinear but homogeneous), offspring production, and demographic transitions and survival. The resulting nonlinear model converges to exponential growth with an equilibrium population composition. The model can incorporate age- or stage-structured life histories and flexible mating functions. As an example, we apply the model to analyze the effects of mating strategies (polygamy or monogamy, and mated unions composed of males and females, of variable duration) on the response to sex-biased harvesting. The combination of demographic complexity with the interaction of the sexes can have major population dynamic effects and can change the outcome of evolution on sex-related characters.
    Description: This work was supported by a National Science Foundation Graduate Research Fellowship to ES, under Grant 1122374. HC acknowledges support from NSF Grants DEB1145017 and DEB1257545 and support from the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013), ERC Advanced Grant 322989. ES acknowledges support from the Academic Programs office of the Woods Hole Oceanographic Institution.
    Keywords: Birth matrix-mating rule ; BMMR ; Demography ; Matrix population models ; Sex-biased harvest ; Two-sex models
    Repository Name: Woods Hole Open Access Server
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  • 42
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Progress in Earth and Planetary Science 5 (2018): 19, doi:10.1186/s40645-018-0167-8.
    Description: The Quaternary hemipelagic sediments of the Japan Sea are characterized by centimeter- to decimeter-scale alternation of dark and light clay to silty clay, which are bio-siliceous and/or bio-calcareous to a various degree. Each of the dark and light layers are considered as deposited synchronously throughout the deeper (〉 500 m) part of the sea. However, attempts for correlation and age estimation of individual layers are limited to the upper few tens of meters. In addition, the exact timing of the depositional onset of these dark and light layers and its synchronicity throughout the deeper part of the sea have not been explored previously, although the onset timing was roughly estimated as ~ 1.5 Ma based on the result of Ocean Drilling Program legs 127/128. Consequently, it is not certain exactly when their deposition started, whether deposition of dark and light layers was synchronous and whether they are correlatable also in the earlier part of their depositional history. The Quaternary hemipelagic sediments of the Japan Sea were drilled at seven sites during Integrated Ocean Drilling Program Expedition 346 in 2013. Alternation of dark and light layers was recovered at six sites whose water depths are 〉 ~ 900 m, and continuous composite columns were constructed at each site. Here, we report our effort to correlate individual dark layers and estimate their ages based on a newly constructed age model at Site U1424 using the best available paleomagnetic datum and marker tephras. The age model is further tuned to LR04 δ18O curve using gamma ray attenuation density (GRA) since it reflects diatom contents that are higher during interglacial high-stands. The constructed age model for Site U1424 is projected to other sites using correlation of dark layers to form a high-resolution and high-precision paleo-observatory network that allows to reconstruct changes in material fluxes with high spatio-temporal resolutions.
    Description: This work was supported by a grant from IODP Exp. 346 After Cruise Research Program, JAMSTEC, awarded to TR, IK, Irino T, Itaki T, ST, KY, SS, and KA and from JSPS KAKENHI grant number 16H01765 awarded to TR.
    Keywords: Quaternary sediments ; Japan Sea ; Inter-site correlation ; High-resolution age model ; IODP ; Expedition 346 ; U1424 ; U1425 ; U1426 ; U1430
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  • 43
    Publication Date: 2022-05-25
    Description: Author Posting. © American Chemical Society, 2018. This is an open access article published under an ACS AuthorChoice License. The definitive version was published in Environmental Science and Technology Letters 5 (2018): 226–231, doi:10.1021/acs.estlett.8b00084.
    Description: Chemical dispersants are one of many tools used to mitigate the overall environmental impact of oil spills. In principle, dispersants break up floating oil into small droplets that disperse into the water column where they are subject to multiple fate and transport processes. The effectiveness of dispersants typically decreases as oil weathers in the environment. This decrease in effectiveness is often attributed to evaporation and emulsification, with the contribution of photochemical weathering assumed to be negligible. Here, we aim to test this assumption using Macondo well oil released during the Deepwater Horizon spill as a case study. Our results indicate that the effects of photochemical weathering on Deepwater Horizon oil properties and dispersant effectiveness can greatly outweigh the effects of evaporative weathering. The decrease in dispersant effectiveness after light exposure was principally driven by the decreased solubility of photo-oxidized crude oil residues in the solvent system that comprises COREXIT EC9500A. Kinetic modeling combined with geospatial analysis demonstrated that a considerable fraction of aerial applications targeting Deepwater Horizon surface oil had low dispersant effectiveness. Collectively, the results of this study challenge the paradigm that photochemical weathering has a negligible impact on the effectiveness of oil spill response and provide critical insights into the “window of opportunity” to apply chemical dispersants in response to oil spills in sunlit waters.
    Description: This work was supported, in part, by National Science Foundation Grant OCE-1333148, Gulf of Mexico Research Initiative Grants 015, SA 16-30, the DEEP-C consortium, and the Clark Family Foundation, Inc. EPA funding was provided to R.N.C. from the Oil Spill Liability Trust Fund.
    Repository Name: Woods Hole Open Access Server
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  • 44
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Proceedings of the National Academy of Sciences.of the United States of America 115 (2018): 7729-7734, doi:10.1073/pnas.1805428115.
    Description: Identifying physical processes responsible for historical coastal sea-level changes is important for anticipating future impacts. Recent studies sought to understand the drivers of interannual to multidecadal sea-level changes on the United States Atlantic and Gulf coasts. Ocean dynamics, terrestrial water storage, vertical land motion, and melting of land ice were highlighted as important mechanisms of sea-level change along this densely populated coast on these time scales. While known to exert an important control on coastal ocean circulation, variable river discharge has been absent from recent discussions of drivers of sea-level change. We update calculations from the 1970s, comparing annual river-discharge and coastal sea-level data along the Gulf of Maine, Mid-Atlantic Bight, South Atlantic Bight, and Gulf of Mexico during 1910–2017. We show that river-discharge and sea-level changes are significantly correlated (p〈0.01), such that sea level rises between 0.01 and 0.08 cm for a 1 km3 annual river-discharge increase, depending on region. We formulate a theory that describes the relation between river-discharge and halosteric sea-level changes (i.e., changes in sea level related to salinity) as a function of river discharge, Earth’s rotation, and density stratification. This theory correctly predicts the order of observed increment sea-level change per unit river-discharge anomaly, suggesting a causal relation. Our results have implications for remote sensing, climate modeling, interpreting Common Era proxy sea-level reconstructions, and projecting coastal flood risk.
    Description: C.G.P. and R.M.P. acknowledge support from NASA Contract NNH16CT01C (which also supported C.M.L.), NASA Jet Propulsion Laboratory Subcontract 1569246, and National Science Foundation Award 1558966. C.G.P. also acknowledges support from The Investment in Science Fund at Woods Hole Oceanographic Institution. A.C.K. and S.E.E. acknowledge NSF Awards OCE-1458921 and OCE-1458903, respectively.
    Keywords: Coastal sea level ; Coastal river plumes ; Coastal flood risk ; Climate modeling ; Physical oceanography
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  • 45
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Progress in Earth and Planetary Science 5 (2018): 74, doi:10.1186/s40645-018-0232-3.
    Description: South Chamorro Seamount (SCS) is a blueschist-bearing serpentinite mud volcano in the Mariana forearc. Previous scientific drilling conducted at SCS revealed highly alkaline, sulfate-rich formation fluids resulting from slab-derived fluid upwelling combined with serpentinization both beneath and within the seamount. In the present study, a time-series of ROV dives spanning 1000 days was conducted to collect discharging alkaline fluids from the cased Ocean Drilling Program (ODP) Hole 1200C (hereafter the CORK fluid). The CORK fluids were analyzed for chemical compositions (including dissolved gas) and microbial community composition/function. Compared to the ODP porewater, the CORK fluids were generally identical in concentration of major ions, with the exception of significant sulfate depletion and enrichment in sulfide, alkalinity, and methane. Microbiological analyses of the CORK fluids revealed little biomass and functional activity, despite habitable temperature conditions. The post-drilling sulfate depletion is likely attributable to sulfate reduction coupled with oxidation of methane (and hydrogen), probably triggered by the drilling and casing operations. Multiple lines of evidence suggest that abiotic organic synthesis associated with serpentinization is the most plausible source of the abundant methane in the CORK fluid. The SCS formation fluid regime presented here may represent the first example on Earth where abiotic syntheses are conspicuous with little biotic processes, despite a condition with sufficient bioavailable energy potentials and temperatures within the habitable range.
    Description: This work was partly supported by JSPS KAKENHI Grant Number 25701004 (SK).
    Keywords: Forearc serpentinite mud volcano ; South Chamorro Seamount ; Limit of biosphere ; Present-days’ chemical evolution ; Radio-isotope-tracer carbon assimilation estimation
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  • 46
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 115 (2018): 8161-8166, doi:10.1073/pnas.1806296115.
    Description: Copper is an essential cofactor of cytochrome c oxidase (CcO), the terminal enzyme of the mitochondrial respiratory chain. Inherited loss-of-function mutations in several genes encoding proteins required for copper delivery to CcO result in diminished CcO activity and severe pathologic conditions in affected infants. Copper supplementation restores CcO function in patient cells with mutations in two of these genes, COA6 and SCO2, suggesting a potential therapeutic approach. However, direct copper supplementation has not been therapeutically effective in human patients, underscoring the need to identify highly efficient copper transporting pharmacological agents. By using a candidate-based approach, we identified an investigational anticancer drug, elesclomol (ES), that rescues respiratory defects of COA6-deficient yeast cells by increasing mitochondrial copper content and restoring CcO activity. ES also rescues respiratory defects in other yeast mutants of copper metabolism, suggesting a broader applicability. Low nanomolar concentrations of ES reinstate copper-containing subunits of CcO in a zebrafish model of copper deficiency and in a series of copper-deficient mammalian cells, including those derived from a patient with SCO2 mutations. These findings reveal that ES can restore intracellular copper homeostasis by mimicking the function of missing transporters and chaperones of copper, and may have potential in treating human disorders of copper metabolism.
    Description: This work was supported by National Institutes of Health Awards R01GM111672 (to V.M.G.), R01 DK110195 (to B.-E.K.), and DK 44464 (to J.D.G.); Welch Foundation Grant A-1810 (to V.M.G.); and Canadian Institutes of Health Research Operating Grant MOP 133562 (to S.C.L.).
    Keywords: Copper ; Mitochondria ; Elesclomol ; Cytochrome c oxidase
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  • 47
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of the History of Biology 51 (2018): 693–805, doi:10.1007/s10739-018-9538-7.
    Description: The Bermuda Principles for DNA sequence data sharing are an enduring legacy of the Human Genome Project (HGP). They were adopted by the HGP at a strategy meeting in Bermuda in February of 1996 and implemented in formal policies by early 1998, mandating daily release of HGP-funded DNA sequences into the public domain. The idea of daily sharing, we argue, emanated directly from strategies for large, goal-directed molecular biology projects first tested within the “community” of C. elegans researchers, and were introduced and defended for the HGP by the nematode biologists John Sulston and Robert Waterston. In the C. elegans community, and subsequently in the HGP, daily sharing served the pragmatic goals of quality control and project coordination. Yet in the HGP human genome, we also argue, the Bermuda Principles addressed concerns about gene patents impeding scientific advancement, and were aspirational and flexible in implementation and justification. They endured as an archetype for how rapid data sharing could be realized and rationalized, and permitted adaptation to the needs of various scientific communities. Yet in addition to the support of Sulston and Waterston, their adoption also depended on the clout of administrators at the US National Institutes of Health (NIH) and the UK nonprofit charity the Wellcome Trust, which together funded 90% of the HGP human sequencing effort. The other nations wishing to remain in the HGP consortium had to accommodate to the Bermuda Principles, requiring exceptions from incompatible existing or pending data access policies for publicly funded research in Germany, Japan, and France. We begin this story in 1963, with the biologist Sydney Brenner’s proposal for a nematode research program at the Laboratory of Molecular Biology (LMB) at the University of Cambridge. We continue through 2003, with the completion of the HGP human reference genome, and conclude with observations about policy and the historiography of molecular biology.
    Repository Name: Woods Hole Open Access Server
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  • 48
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Climate Dynamics 51 (2018): 3275–3289, doi:10.1007/s00382-018-4078-6.
    Description: The atmospheric jet and blocking distributions, especially in the North Atlantic sector, have been challenging features for a climate model to realistically reproduce. This study examines climatological distributions of winter (December–February) daily jet latitude and blocking in the North Atlantic from the 40-member Community Earth System Model version 1 Large Ensemble (CESM1LE) simulations. This analysis aims at examining whether a broad range of internal climate variability encompassed by a large ensemble of simulations results in an improved representation of the jet latitude distributions and blocking days in CESM1LE. In the historical runs (1951–2005), the daily zonal wind at 850 hPa exhibits three distinct preferred latitudes for the eddy-driven jet position as seen in the reanalysis datasets, which represents a significant improvement from the previous version of the same model. However, the meridional separations between the three jet latitudes are much smaller than those in the reanalyses. In particular, the jet rarely migrates to the observed southernmost position around 37°N. This leads to the bias in blocking frequency that is too low over Greenland and too high over the Azores. These features are shown to be remarkably stable across the 40 ensemble members with negligible member-to-member spread. This result implies the range of internal variability of winter jet latitude and blocking frequency within the 55-year segment from each ensemble member is comparable to that represented by the full large ensemble. Comparison with 2046–2100 from the RCP8.5 future projection runs suggests that the daily jet position is projected to maintain the same three preferred latitudes, with a slightly higher frequency of occurrence over the central latitude around 50°N, instead of shifting poleward in the future as documented in some previous studies. In addition, the daily jet speed is projected not to change significantly between 1951–2005 and 2046–2100. On the other hand, the climatological mean jet is projected to become slightly more elongated and stronger on its southern flank, and the blocking frequency over the Azores is projected to decrease.
    Description: Authors gratefully acknowledge support from the UCAR Significant Opportunities in Atmospheric Research and Science (SOARS) and WHOI Summer Student Fellowship programs. AC and CM were supported in part by the SOARS program, NSF Grant AGS- 1120459. In addition, the supports by the NSF AGS Climate and Largescale Dynamics program and OCE Physical Oceanography program (AGS-1355339) to Y-OK and HS, the DOE BER Regional and Global Climate Modeling program (DE-SC0014433) to Y-OK, and the NSF EaSM3 Sustainability Research Networks program (OCE-1419235) to HS are acknowledged.
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  • 49
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    In:  EPIC3YOUMARES 8 – Oceans Across Boundaries: Learning from each other, YOUMARES 8 – Oceans Across Boundaries: Learning from each other, Cham, Springer, 6 p., pp. 1-6, ISBN: 978-3-319-93284-2
    Publication Date: 2020-06-12
    Description: YOUMARES is an annual early-career scientist conference series. It is an initiative of the German Society for Marine Research (DGM) and takes place in changing cities of northern Germany. The conference series is organized in a bottom-up structure: from and for YOUng MARine RESearchers. In this chapter, we describe the concept of YOUMARES together with its historical development from a single-person initiative to a conference venue of about 200 participants. Furthermore, the three authors added some personals experiences and insights, what YOUMARES means to them.
    Repository Name: EPIC Alfred Wegener Institut
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  • 50
    Publication Date: 2022-05-24
    Description: Is Europe-wide operational earthquake forecasting (OEF) possible? We discuss the myriad problems that prevent it today, many of which relate to heterogeneities in earthquake recording, processing, and reporting. We contemplate the difficulty of building models that cross political boundaries, and we consider the prospect of European OEF in light of recent efforts to harmonize long-term seismic hazard assessment among several nations. Emphasizing the Strategies and Tools for Real-time Earthquake Risk Reduction (REAKT) project, we report achievements related to short-term seismicity forecasting in Iceland and Italy that could apply elsewhere in Europe. In Iceland, collaboration fostered by REAKT resulted in a revised earthquake catalog and a prototype OEF system. We report results from an experiment conducted with this prototype; these results suggest ensemble models provide an information gain, updating models more frequently improves their forecast skill, and that OEF is computationally feasible. In Italy, REAKT supported the creation of an ensemble model that now issues weekly hazard forecasts. We present examples of these forecasts, highlighting the problem that OEF often yields low probabilities, which are difficult to interpret and convert into actionable decisions. Motivated by such low hazard probabilities, we highlight Europe’s pioneering efforts in operational earthquake loss forecasting and mention solutions to problems that currently prevent OEF at the European scale.
    Description: Published
    Description: 2459-2469
    Description: 5T. Modelli di pericolosità sismica e da maremoto
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 51
    Publication Date: 2022-05-24
    Description: Investigating relationships between macroseismic intensity and strong-motion data requires the existence of these two records for the same seismic event and site. In Italy, this comparison is feasible through the cross-matching of the Italian Macroseismic Database (DBMI) and the Italian Strong-Motion Database (ITACA) which are the most comprehensive sources of both data. However, the two databases lack a direct link which would allow performing joint analysis of macroseismic data points and strong-motion recordings, making the comparison a time consuming job for the researcher. This paper demonstrates the usefulness of cross-database identifiers, and presents their use in a webtool called Rosetta, an initial proof-of-concept that helped testing linking procedures among DBMI and ITACA, and user friendly visual solutions. The development allowed the working group to exchange expertise on their respective database structures and workflows, laying the groundwork for a consistent, low-maintenance, and durable solution that will be easily updatable each time a new version of DBMI or ITACA will be released.
    Description: Italian Department of Civil Protection to the project INGV-DPC S2-2014 “Constraining Observations into Seismic Hazard”
    Description: Published
    Description: 2429–2443
    Description: 3T. Storia Sismica
    Description: 4T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: 4IT. Banche dati
    Description: JCR Journal
    Keywords: seismology ; macroseismic intensity ; strong-motion ; stations ; historical earthquakes ; database ; identifiers ; 04.06. Seismology ; 05.02. Data dissemination
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 52
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    In:  EPIC3YOUMARES 8--Oceans Across Boundaries: Learning from each other, Springer, ISBN: 978-3-319-93284-2
    Publication Date: 2022-07-18
    Description: The Earth’s climate is changing and the poles are particularly sensitive to the global warming, with most evident implications over the Arctic. While summer sea ice reduced significantly compared to the previous decades, and the atmospheric warming is amplified over the Arctic, changes in the ocean are less obvious due to its higher inertia. Still, impacts of the changing climate on high-latitude and polar oceans are already observable and expected to further increase. The northern seas are essential regions for the maintenance of the Atlantic Meridional Overturning Circulation, which in turn is a key aspect of the maritime climate. Alterations in heat and freshwater/salinity content in the Arctic Ocean and adjacent seas impact and are closely linked to buoyancy flux distributions, which control the vertical and horizontal motion of water masses, thus impacting the climate system on a longer time scale. In this context, we set our focus on the Arctic Ocean and Atlantic subarctic seas, review some of the contemporary knowledge and speculations on the complex coupling between atmosphere, sea ice, and ocean, and describe the important elements of its physical oceanography. This assessment is an attempt to raise awareness that investigating the pathways and timescales of oceanic responses and contributions is fundamental to better understand the current climate change.
    Repository Name: EPIC Alfred Wegener Institut
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  • 53
    Publication Date: 2022-05-26
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Aquatic Sciences 80 (2018): 44, doi:10.1007/s00027-018-0594-z.
    Description: Complex natural systems are affected by multiple anthropogenic stressors, and therefore indirect effects within food webs are increasingly investigated. In this context, dead organic matter (OM) or detritus provides a food source sustaining detrital food webs that recycle the retained energy through microbial decomposition and invertebrate consumption. In aquatic environments, poorly water-soluble contaminants, including nanoparticles (NPs), quickly adsorb onto OM potentially modifying OM-associated microbial communities. Since invertebrates often depend on microbial conditioning to enhance OM quality, adverse effects on OM-associated microbial communities could potentially affect invertebrate performances. Therefore, this study assessed the effect of environmentally relevant concentrations of the model emerging contaminant, silver nanoparticles (AgNPs), on OM-associated microorganisms and subsequent indirect effects on growth of the invertebrate Asellus aquaticus. At low concentrations (0.8 ug/L), AgNPs inhibited activity and altered metabolic diversity of the OM-associated microbial community. This was observed to coincide with a negative effect on the growth of A. aquaticus due to antimicrobial properties, as a decreased growth was observed when offered AgNP-contaminated OM. When A. aquaticus were offered sterile OM in the absence of AgNPs, invertebrate growth was observed to be strongly retarded, illustrating the importance of microorganisms in the diet of this aquatic invertebrate. This outcome thus hints that environmentally relevant concentrations of AgNPs can indirectly affect the growth of aquatic invertebrates by affecting OM-associated microbial communities, and hence that microorganisms are an essential link in understanding bottom-up directed effects of chemical stressors in food webs.
    Description: The Chinese Scholarship Council (CSC) is gratefully acknowledged for its financial support to Yujia Zhai [201506510003]. Martina G. Vijver is funded by NWO-VIDI [project number 864.13.010].
    Keywords: Asellus aquaticus ; Food web ; Freshwater biofilms ; Decomposition and consumption ; Silver nanoparticles ; Ecosystem functioning
    Repository Name: Woods Hole Open Access Server
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  • 54
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Climate Dynamics 50 (2018): 1291–1305, doi:10.1007/s00382-017-3685-y.
    Description: The role of the oceanic water cycle in the record-breaking 2015 warm-season precipitation in the US is analyzed. The extreme precipitation started in the Southern US in the spring and propagated northward to the Midwest and the Great Lakes in the summer of 2015. This seasonal evolution of precipitation anomalies represents a typical mode of variability of US warm-season precipitation. Analysis of the atmospheric moisture flux suggests that such a rainfall mode is associated with moisture export from the subtropical North Atlantic. In the spring, excessive precipitation in the Southern US is attributable to increased moisture flux from the northwestern portion of the subtropical North Atlantic. The North Atlantic moisture flux interacts with local soil moisture which enables the US Midwest to draw more moisture from the Gulf of Mexico in the summer. Further analysis shows that the relationship between the rainfall mode and the North Atlantic water cycle has become more significant in recent decades, indicating an increased likelihood of extremes like the 2015 case. Indeed, two record-high warm-season precipitation events, the 1993 and 2008 cases, both occurred in the more recent decades of the 66 year analysis period. The export of water from the North Atlantic leaves a marked surface salinity signature. The salinity signature appeared in the spring preceding all three extreme precipitation events analyzed in this study, i.e. a saltier-than-normal subtropical North Atlantic in spring followed by extreme Midwest precipitation in summer. Compared to the various sea surface temperature anomaly patterns among the 1993, 2008, and 2015 cases, the spatial distribution of salinity anomalies was much more consistent during these extreme flood years. Thus, our study suggests that preseason salinity patterns can be used for improved seasonal prediction of extreme precipitation in the Midwest.
    Description: LL is supported by the Postdoctoral Scholar Program at WHOI, with funding provided by the Oceans and Climate Change Institute. RWS is supported by NASA Grants NNX12AF59G and NNX14AH38G, and NSF Grant OCE-1129646. CCU is supported by NSF Grant AGS-1355339.
    Keywords: US extreme precipitation ; Oceanic water cycle ; Ocean-to-land moisture transport ; Sea surface salinity
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  • 55
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Progress in Earth and Planetary Science 4 (2017): 41, doi:10.1186/s40645-017-0154-5.
    Description: During the past several decades, the Earth system has changed significantly, especially across Northern Eurasia. Changes in the socio-economic conditions of the larger countries in the region have also resulted in a variety of regional environmental changes that can have global consequences. The Northern Eurasia Future Initiative (NEFI) has been designed as an essential continuation of the Northern Eurasia Earth Science Partnership Initiative (NEESPI), which was launched in 2004. NEESPI sought to elucidate all aspects of ongoing environmental change, to inform societies and, thus, to better prepare societies for future developments. A key principle of NEFI is that these developments must now be secured through science-based strategies co-designed with regional decision-makers to lead their societies to prosperity in the face of environmental and institutional challenges. NEESPI scientific research, data, and models have created a solid knowledge base to support the NEFI program. This paper presents the NEFI research vision consensus based on that knowledge. It provides the reader with samples of recent accomplishments in regional studies and formulates new NEFI science questions. To address these questions, nine research foci are identified and their selections are briefly justified. These foci include warming of the Arctic; changing frequency, pattern, and intensity of extreme and inclement environmental conditions; retreat of the cryosphere; changes in terrestrial water cycles; changes in the biosphere; pressures on land use; changes in infrastructure; societal actions in response to environmental change; and quantification of Northern Eurasia’s role in the global Earth system. Powerful feedbacks between the Earth and human systems in Northern Eurasia (e.g., mega-fires, droughts, depletion of the cryosphere essential for water supply, retreat of sea ice) result from past and current human activities (e.g., large-scale water withdrawals, land use, and governance change) and potentially restrict or provide new opportunities for future human activities. Therefore, we propose that integrated assessment models are needed as the final stage of global change assessment. The overarching goal of this NEFI modeling effort will enable evaluation of economic decisions in response to changing environmental conditions and justification of mitigation and adaptation efforts.
    Description: Support for most of the US authors and contributors of this paper as well as the multiannual support for the office of the NEESPI Project Scientist was provided by the NASA Land Cover and Land Use Change (LCLUC) Program, in particular, by grants NNX13AC66G, NNX11AB77G, NNX13AN58G, NNX15AD10G, NAG5–11084, 08–LCLUC08–2–0003, NNX14AD88G, NNX08AW51G, NNX12AD34G, NNX14AD91G, and NNX15AP81G. The research carried out at the Jet Propulsion Laboratory, California Institute of Technology, was also supported by the NASA LCLUC Program. Support of NASA grants 08–TE08–029 and NNH09ZDA001N–IDS for AS and NT are acknowledged. Research of MS is supported by Newton-al-Farabi Fund (grant 172722855). Grant 14.B25.31.0026 of the Ministry of Education and Science of the Russian Federation provided support to PG, SG, NT, AS, OB, BP, and IP for their work conducted at the P.P. Shirshov Institute of Oceanology. The Project “ARCTIC-ERA: ARCTIC climate change and its impact on Environment, infrastructures, and Resource Availability” sponsored by: ANR (France), RFBR (Russia), and the US NSF (grants 1717770 and 1558389) in response to Belmont Forum Collaborative Research Action on Arctic Observing and Research for Sustainability provided support for OZ, SG, BP, PG, and NS. A part of the paper is based on the research carried out with the financial support of the Russian Foundation for Basic Research (Project No. 15–06–08163 “Assessment and forecast of the socioeconomic and environmental implications of the climate change in the Arctic region”). Support for AP is provided by the Russian Government Program of Competitive Growth of Kazan Federal University (OpenLab Initiative). Support for JA is provided by grant NPUILO1417 of the Ministry of Education, Youth and Sports of Czechia.
    Keywords: Environmental changes ; Northern Eurasia ; Ecosystems dynamics ; Terrestrial water cycle ; Cryosphere retreat ; Extreme and inclement environmental conditions ; Sustainable development ; Land cover and land use change ; Integrated assessment models for decision-makers
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  • 56
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    In:  EPIC3Building bridges at the science-stakeholder interface - Towards knowledge exchange in Earth System Science, SpringerBriefs in Earth System Sciences, Cham, Switzerland, Springer, pp. 69-72, ISBN: 978-3-319-75918-0
    Publication Date: 2023-06-21
    Description: The new knowledge and data portal ‘meereisportal.de’ is a contribution to the cross-linking of scientifically qualified information on climate change. It focuses deliberately on the theme ‘sea ice in both Polar Regions’. With the establishment of ‘meereisportal.de’, science adapts to changing societal demands and embarks on new ways of communication between science and society.
    Repository Name: EPIC Alfred Wegener Institut
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  • 57
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    In:  EPIC3YOUMARES 8 – Oceans Across Boundaries: Learning from each other, Cham, Springer, pp. 109-124, ISBN: 978-3-319-93283-5
    Publication Date: 2023-06-21
    Description: From the depths of the oceans to the shallow estuaries and wetlands of our coasts, organisms of the marine environment are teeming with unique adaptations to cope with a multitude of varying environmental conditions. With millions of years and a vast volume of water to call their home, they have become quite adept at developing specialized and unique techniques for survival and – given increasing human mediated transport – biological invasions. A growing world human population and a global economy drives the transportation of goods across the oceans and with them invasive species via ballast water and attached to ship hulls. In any given 24-hour period, there are about 10,000 species being transported across different biogeographic regions. If any of them manage to take hold and establish a range in an exotic habitat, the implications for local ecosystems can be costly. This review on marine invasions highlights trends among successful non-indigenous species (NIS), from vectors of transport to ecological and physiological plasticity. Apart from summarizing patterns of successful invasions, it discusses the implications of how successfully established NIS impact the local environment, economy and human health. Finally, it looks to the future and discusses what questions need to be addressed and what models can tell us about what the outlook on future marine invasions is.
    Repository Name: EPIC Alfred Wegener Institut
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  • 58
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    In:  EPIC3Building bridges at the science-stakeholder interface - Towards knowledge exchange in earth system science, SpringerBriefs in Earth System Sciences, Cham, Switzerland, Springer, 132 p., pp. 19-29, ISBN: 987-3-319-75918-0
    Publication Date: 2023-06-21
    Repository Name: EPIC Alfred Wegener Institut
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  • 59
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    In:  EPIC3YOUMARES 8 – Oceans Across Boundaries: Learning from each other, YOUMARES 8 – Oceans Across Boundaries: Learning from each other, Phytoplankton Responses to Marine Climate Change – An Introduction, Springer, pp. 55-71, ISBN: 978-3-319-93284-2
    Publication Date: 2023-06-21
    Description: Phytoplankton are one of the key players in the ocean and contribute approximately 50% to global primary production. They serve as the basis for marine food webs, drive chemical composition of the global atmosphere and thereby climate. Seasonal environmental changes and nutrient availability naturally influence phytoplankton species composition. Since the industrial era, anthropogenic climatic influences have increased noticeably – also within the ocean. Our changing climate, however, affects the composition of phytoplankton species composition on a long-term basis and requires the organisms to adapt to this changing environment, influencing micronutrient bioavailability and other biogeochemical parameters. At the same time, phytoplankton themselves can influence the climate with their responses to environmental changes. Due to its key role, phytoplankton has been of interest in marine sciences for quite some time and there are several methodical approaches implemented in oceanographic sciences. There are ongoing attempts to improve predictions and to close gaps in the understanding of this sensitive ecological system and its responses.
    Repository Name: EPIC Alfred Wegener Institut
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  • 60
    Publication Date: 2018-12-21
    Description: Growth rate is one of the most important and most complex phenotypic characteristics of unicellular microorganisms, which determines the genetic mutations that dominate at the population level, and ultimately whether the population will survive. Translating changes at the genetic level to their growth-rate consequences remains a subject of intense interest, since such a mapping could rationally direct experiments to optimize antibiotic efficacy or bioreactor productivity. In this work, we directly map transcriptional profiles to growth rates by gathering published gene-expression data from Escherichia coli and Saccharomyces cerevisiae with corresponding growth-rate measurements. Using a machine-learning technique called k-nearest-neighbors regression, we build a model which predicts growth rate from gene expression. By exploiting the correlated nature of gene expression and sparsifying the model, we capture 81% of the variance in growth rate of the E. coli dataset, while reducing the number of features from 〉4,000 to 9. In S. cerevisiae, we account for 89% of the variance in growth rate, while reducing from 〉5,500 dimensions to 18. Such a model provides a basis for selecting successful strategies from among the combinatorial number of experimental possibilities when attempting to optimize complex phenotypic traits like growth rate.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 61
    Publication Date: 2018-01-08
    Description: Increasing evidence suggests that early neurodevelopmental defects in Huntington’s disease (HD) patients could contribute to the later adult neurodegenerative phenotype. Here, by using HD-derived induced pluripotent stem cell lines, we report that early telencephalic induction and late neural identity are affected in cortical and striatal populations. We show that a large CAG expansion causes complete failure of the neuro-ectodermal acquisition, while cells carrying shorter CAGs repeats show gross abnormalities in neural rosette formation as well as disrupted cytoarchitecture in cortical organoids. Gene-expression analysis showed that control organoid overlapped with mature human fetal cortical areas, while HD organoids correlated with the immature ventricular zone/subventricular zone. We also report that defects in neuroectoderm and rosette formation could be rescued by molecular and pharmacological approaches leading to a recovery of striatal identity. These results show that mutant huntingtin precludes normal neuronal fate acquisition and highlights a possible connection between mutant huntingtin and abnormal neural development in HD.
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  • 62
    Publication Date: 2018-06-18
    Description: Phenotypic novelties are an important but poorly understood category of morphological diversity. They can provide insights into the origins of phenotypic variation, but we know relatively little about their genetic origins. Cichlid fishes display remarkable diversity in craniofacial anatomy, including several novelties. One aspect of this variation is a conspicuous, exaggerated snout that has evolved in a single Malawi cichlid lineage and is associated with foraging specialization and increased ecological success. We examined the developmental and genetic origins for this phenotype and found that the snout is composed of two hypertrophied tissues: the intermaxillary ligament (IML), which connects the right and left sides of the upper jaw, and the overlying loose connective tissue. The IML is present in all cichlids, but in its exaggerated form it interdigitates with the more superficial connective tissue and anchors to the epithelium, forming a unique ligament–epithelial complex. We examined the Transforming growth factor β (Tgfβ) → Scleraxis (Scx) candidate pathway and confirmed a role for these factors in snout development. We demonstrate further that experimental up-regulation of Tgfβ is sufficient to produce an expansion of scx expression and concomitant changes in snout morphology. Genetic and genomic mapping show that core members of canonical Tgfβ signaling segregate with quantitative trait loci (QTL) for snout variation. These data also implicate a candidate for ligament development, adam12, which we confirm using the zebrafish model. Collectively, these data provide insights into ligament morphogenesis, as well as how an ecologically relevant novelty can arise at the molecular level.
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  • 63
    Publication Date: 2018-07-02
    Description: Throughout three domains of life, alanyl-tRNA synthetases (AlaRSs) recognize a G3:U70 base pair in the acceptor stem of tRNAAla as the major identity determinant of tRNAAla. The crystal structure of the archaeon Archaeoglobus fulgidus AlaRS in complex with tRNAAla provided the basis for G3:U70 recognition with residues (Asp and Asn) that are conserved in the three domains [Naganuma M, et al. (2014) Nature 510:507–511]. The recognition mode is unprecedented, with specific accommodation of the dyad asymmetry of the G:U wobble pair and exclusion of the dyad symmetry of a Watson–Crick pair. With this conserved mode, specificity is based more on “fit” than on direct recognition of specific atomic groups. Here, we show that, in contrast to the archaeal complex, the Escherichia coli enzyme uses direct positive (energetically favorable) minor groove recognition of the unpaired 2-amino of G3 by Asp and repulsion of a competing base pair by Asn. Strikingly, mutations that disrupted positive recognition by the E. coli enzyme had little or no effect on G:U recognition by the human enzyme. Alternatively, Homo sapiens AlaRS selects G:U without positive recognition and uses Asp instead to repel a competitor. Thus, the widely conserved Asp-plus-Asn architecture of AlaRSs can select G:U in a straightforward (bacteria) or two different unconventional (eukarya/archaea) ways. The adoption of different modes for recognition of a widely conserved G:U pair in alanine tRNAs suggests an early and insistent role for G:U in the development of the genetic code.
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  • 64
    Publication Date: 2018-06-05
    Description: In the field of X-ray microcomputed tomography (μCT) there is a growing need to reduce acquisition times at high spatial resolution (approximate micrometers) to facilitate in vivo and high-throughput operations. The state of the art represented by synchrotron light sources is not practical for certain applications, and therefore the development of high-brightness laboratory-scale sources is crucial. We present here imaging of a fixed embryonic mouse sample using a compact laser–plasma-based X-ray light source and compare the results to images obtained using a commercial X-ray μCT scanner. The radiation is generated by the betatron motion of electrons inside a dilute and transient plasma, which circumvents the flux limitations imposed by the solid or liquid anodes used in conventional electron-impact X-ray tubes. This X-ray source is pulsed (duration 1010 photons per pulse), small (diameter 15 keV. Stable X-ray performance enabled tomographic imaging of equivalent quality to that of the μCT scanner, an important confirmation of the suitability of the laser-driven source for applications. The X-ray flux achievable with this approach scales with the laser repetition rate without compromising the source size, which will allow the recording of high-resolution μCT scans in minutes.
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  • 65
    Publication Date: 2018-08-01
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  • 66
    Publication Date: 2018-09-18
    Description: Materials and structures that enable long-term, intimate coupling of flexible electronic devices to biological systems are critically important to the development of advanced biomedical implants for biological research and for clinical medicine. By comparison with simple interfaces based on arrays of passive electrodes, the active electronics in such systems provide powerful and sometimes essential levels of functionality; they also demand long-lived, perfect biofluid barriers to prevent corrosive degradation of the active materials and electrical damage to the adjacent tissues. Recent reports describe strategies that enable relevant capabilities in flexible electronic systems, but only for capacitively coupled interfaces. Here, we introduce schemes that exploit patterns of highly doped silicon nanomembranes chemically bonded to thin, thermally grown layers of SiO2 as leakage-free, chronically stable, conductively coupled interfaces. The results can naturally support high-performance, flexible silicon electronic systems capable of amplified sensing and active matrix multiplexing in biopotential recording and in stimulation via Faradaic charge injection. Systematic in vitro studies highlight key considerations in the materials science and the electrical designs for high-fidelity, chronic operation. The results provide a versatile route to biointegrated forms of flexible electronics that can incorporate the most advanced silicon device technologies with broad applications in electrical interfaces to the brain and to other organ systems.
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  • 67
    Publication Date: 2018-06-25
    Description: Protein homeostasis is critically important for cell viability. Key to this process is the refolding of misfolded or aggregated proteins by molecular chaperones or, alternatively, their degradation by proteases. In most prokaryotes and in chloroplasts and mitochondria, protein degradation is performed by the caseinolytic protease ClpP, a tetradecamer barrel-like proteolytic complex. Dysregulating ClpP function has shown promise in fighting antibiotic resistance and as a potential therapy for acute myeloid leukemia. Here we use methyl–transverse relaxation-optimized spectroscopy (TROSY)–based NMR, cryo-EM, biochemical assays, and molecular dynamics simulations to characterize the structural dynamics of ClpP from Staphylococcus aureus (SaClpP) in wild-type and mutant forms in an effort to discover conformational hotspots that regulate its function. Wild-type SaClpP was found exclusively in the active extended form, with the N-terminal domains of its component protomers in predominantly β-hairpin conformations that are less well-defined than other regions of the protein. A hydrophobic site was identified that, upon mutation, leads to unfolding of the N-terminal domains, loss of SaClpP activity, and formation of a previously unobserved split-ring conformation with a pair of 20-Å-wide pores in the side of the complex. The extended form of the structure and partial activity can be restored via binding of ADEP small-molecule activators. The observed structural plasticity of the N-terminal gates is shown to be a conserved feature through studies of Escherichia coli and Neisseria meningitidis ClpP, suggesting a potential avenue for the development of molecules to allosterically modulate the function of ClpP.
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  • 68
    Publication Date: 2018-07-30
    Description: Humans can integrate social contextual information into decision-making processes to adjust their responses toward inequity. This context dependency emerges when individuals receive more (i.e., advantageous inequity) or less (i.e., disadvantageous inequity) than others. However, it is not clear whether context-dependent processing of advantageous and disadvantageous inequity involves differential neurocognitive mechanisms. Here, we used fMRI to address this question by combining an interactive game that modulates social contexts (e.g., interpersonal guilt) with computational models that enable us to characterize individual weights on inequity aversion. In each round, the participant played a dot estimation task with an anonymous coplayer. The coplayer would receive pain stimulation with 50% probability when either of them responded incorrectly. At the end of each round, the participant completed a variant of dictator game, which determined payoffs for him/herself and the coplayer. Computational modeling demonstrated the context dependency of inequity aversion: when causing pain to the coplayer (i.e., guilt context), participants cared more about the advantageous inequity and became more tolerant of the disadvantageous inequity, compared with other conditions. Consistently, neuroimaging results suggested the two types of inequity were associated with differential neurocognitive substrates. While the context-dependent processing of advantageous inequity was associated with social- and mentalizing-related processes, involving left anterior insula, right dorsolateral prefrontal cortex, and dorsomedial prefrontal cortex, the context-dependent processing of disadvantageous inequity was primarily associated with emotion- and conflict-related processes, involving left posterior insula, right amygdala, and dorsal anterior cingulate cortex. These results extend our understanding of decision-making processes related to inequity aversion.
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  • 69
    Publication Date: 2018-11-05
    Description: Electrochemistry is an old but still flourishing field of research due to the importance of the efficiency and kinetics of electrochemical reactions in industrial processes and (bio-)electrochemical devices. The heterogeneous electron transfer from an electrode to a reactant in the solution has been well studied for metal, semiconductor, metal oxide, and carbon electrodes. For those electrode materials, there is little correlation between the electronic transport within the electrode material and the electron transfer occurring at the interface between the electrode and the solution. Here, we investigate the heterogeneous electron transfer between a conducting polymer electrode and a redox couple in an electrolyte. As a benchmark system, we use poly(3,4-ethylenedioxythiophene) (PEDOT) and the Ferro/ferricyanide redox couple in an aqueous electrolyte. We discovered a strong correlation between the electronic transport within the PEDOT electrode and the rate of electron transfer to the organometallic molecules in solution. We attribute this to a percolation-based charge transport within the polymer electrode directly involved in the electron transfer. We show the impact of this finding by optimizing an electrochemical thermogalvanic cell that transforms a heat flux into electrical power. The power generated by the cell increased by four orders of magnitude on changing the morphology and conductivity of the polymer electrode. As all conducting polymers are recognized to have percolation transport, we believe that this is a general phenomenon for this family of conductors.
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  • 70
    Publication Date: 2018-07-18
    Description: We derive a principled information-theoretic account of cross-language semantic variation. Specifically, we argue that languages efficiently compress ideas into words by optimizing the information bottleneck (IB) trade-off between the complexity and accuracy of the lexicon. We test this proposal in the domain of color naming and show that (i) color-naming systems across languages achieve near-optimal compression; (ii) small changes in a single trade-off parameter account to a large extent for observed cross-language variation; (iii) efficient IB color-naming systems exhibit soft rather than hard category boundaries and often leave large regions of color space inconsistently named, both of which phenomena are found empirically; and (iv) these IB systems evolve through a sequence of structural phase transitions, in a single process that captures key ideas associated with different accounts of color category evolution. These results suggest that a drive for information-theoretic efficiency may shape color-naming systems across languages. This principle is not specific to color, and so it may also apply to cross-language variation in other semantic domains.
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  • 71
    Publication Date: 2018-11-12
    Description: The nuclear receptor peroxisome proliferator-activated receptor γ (PPARγ) is a master regulator of adipocyte differentiation and is the target for the insulin-sensitizing thiazolidinedione (TZD) drugs used to treat type 2 diabetes. In cell-based in vitro studies, the transcriptional activity of PPARγ is inhibited by covalent attachment of small ubiquitin-related modifier (SUMOylation) at K107 in its N terminus. However, whether this posttranslational modification is relevant in vivo remains unclear. Here, using mice homozygous for a mutation (K107R) that prevents SUMOylation at this position, we demonstrate that PPARγ is SUMOylated at K107 in white adipose tissue. We further show that in the context of diet-induced obesity PPARγ-K107R–mutant mice have enhanced insulin sensitivity without the corresponding increase in adiposity that typically accompanies PPARγ activation by TZDs. Accordingly, the PPARγ-K107R mutation was weaker than TZD treatment in stimulating adipocyte differentiation in vitro. Moreover, we found that both the basal and TZD-dependent transcriptomes of inguinal and epididymal white adipose tissue depots were markedly altered in the K107R-mutant mice. We conclude that PPARγ SUMOylation at K107 is physiologically relevant and may serve as a pharmacologic target for uncoupling PPARγ’s beneficial insulin-sensitizing effect from its adverse effect of weight gain.
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  • 72
    Publication Date: 2018-01-18
    Description: To compensate for sensory processing delays, the visual system must make predictions to ensure timely and appropriate behaviors. Recent work has found predictive information about the stimulus in neural populations early in vision processing, starting in the retina. However, to utilize this information, cells downstream must be able to read out the predictive information from the spiking activity of retinal ganglion cells. Here we investigate whether a downstream cell could learn efficient encoding of predictive information in its inputs from the correlations in the inputs themselves, in the absence of other instructive signals. We simulate learning driven by spiking activity recorded in salamander retina. We model a downstream cell as a binary neuron receiving a small group of weighted inputs and quantify the predictive information between activity in the binary neuron and future input. Input weights change according to spike timing–dependent learning rules during a training period. We characterize the readouts learned under spike timing–dependent synaptic update rules, finding that although the fixed points of learning dynamics are not associated with absolute optimal readouts they convey nearly all of the information conveyed by the optimal readout. Moreover, we find that learned perceptrons transmit position and velocity information of a moving-bar stimulus nearly as efficiently as optimal perceptrons. We conclude that predictive information is, in principle, readable from the perspective of downstream neurons in the absence of other inputs. This suggests an important role for feedforward prediction in sensory encoding.
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  • 73
    Publication Date: 2018-05-29
    Description: One-quarter of the 28 types of natural collagen exist as heterotrimers. The oligomerization state of collagen affects the structure and mechanics of the extracellular matrix, providing essential cues to modulate biological and pathological processes. A lack of high-resolution structural information limits our mechanistic understanding of collagen heterospecific self-assembly. Here, the 1.77-Å resolution structure of a synthetic heterotrimer demonstrates the balance of intermolecular electrostatics and hydrogen bonding that affects collagen stability and heterospecificity of assembly. Atomistic simulations and mutagenesis based on the solved structure are used to explore the contributions of specific interactions to energetics. A predictive model of collagen stability and specificity is developed for engineering novel collagen structures.
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  • 74
    Publication Date: 2018-10-17
    Description: Global climate models robustly predict that global mean precipitation should increase at roughly 2–3%K−1, but the origin of these values is not well understood. Here we develop a simple theory to help explain these values. This theory combines the well-known radiative constraint on precipitation, which says that condensation heating from precipitation is balanced by the net radiative cooling of the free troposphere, with an invariance of radiative cooling profiles when expressed in temperature coordinates. These two constraints yield a picture in which mean precipitation is controlled primarily by the depth of the troposphere, when measured in temperature coordinates. We develop this theory in idealized simulations of radiative–convective equilibrium and also demonstrate its applicability to global climate models.
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  • 75
    Publication Date: 2018-12-24
    Description: Food security relies on the resilience of staple food crops to climatic variability and extremes, but the climate resilience of European wheat is unknown. A diversity of responses to disturbance is considered a key determinant of resilience. The capacity of a sole crop genotype to perform well under climatic variability is limited; therefore, a set of cultivars with diverse responses to weather conditions critical to crop yield is required. Here, we show a decline in the response diversity of wheat in farmers’ fields in most European countries after 2002–2009 based on 101,000 cultivar yield observations. Similar responses to weather were identified in cultivar trials among central European countries and southern European countries. A response diversity hotspot appeared in the trials in Slovakia, while response diversity “deserts” were identified in Czechia and Germany and for durum wheat in southern Europe. Positive responses to abundant precipitation were lacking. This assessment suggests that current breeding programs and cultivar selection practices do not sufficiently prepare for climatic uncertainty and variability. Consequently, the demand for climate resilience of staple food crops such as wheat must be better articulated. Assessments and communication of response diversity enable collective learning across supply chains. Increased awareness could foster governance of resilience through research and breeding programs, incentives, and regulation.
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  • 76
    Publication Date: 2018-11-20
    Description: T cell receptor (TCR) repertoire data contain information about infections that could be used in disease diagnostics and vaccine development, but extracting that information remains a major challenge. Here we developed a statistical framework to detect TCR clone proliferation and contraction from longitudinal repertoire data. We applied this framework to data from three pairs of identical twins immunized with the yellow fever vaccine. We identified 600 to 1,700 responding TCRs in each donor and validated them using three independent assays. While the responding TCRs were mostly private, albeit with higher overlap between twins, they could be well-predicted using a classifier based on sequence similarity. Our method can also be applied to samples obtained postinfection, making it suitable for systematic discovery of new infection-specific TCRs in the clinic.
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  • 77
    Publication Date: 2018-02-05
    Description: The diamond anvil cell (DAC) is considered one of the dominant devices to generate ultrahigh static pressure. The development of the DAC technique has enabled researchers to explore rich high-pressure science in the multimegabar pressure range. Here, we investigated the behavior of the DAC up to 400 GPa, which is the accepted pressure limit of a conventional DAC. By using a submicrometer synchrotron X-ray beam, double cuppings of the beveled diamond anvils were observed experimentally. Details of pressure loading, distribution, gasket-thickness variation, and diamond anvil deformation were studied to understand the generation of ultrahigh pressures, which may improve the conventional DAC techniques.
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  • 78
    Publication Date: 2018-11-13
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  • 79
    Publication Date: 2018-06-04
    Description: The resurrection of ancestral enzymes of now-extinct organisms (paleogenetics) is a developing field that allows the study of evolutionary hypotheses otherwise impossible to be tested. In the present study, we target fungal peroxidases that play a key role in lignin degradation, an essential process in the carbon cycle and often a limiting step in biobased industries. Ligninolytic peroxidases are secreted by wood-rotting fungi, the origin of which was recently established in the Carboniferous period associated with the appearance of these enzymes. These first peroxidases were not able to degrade lignin directly and used diffusible metal cations to attack its phenolic moiety. The phylogenetic analysis of the peroxidases of Polyporales, the order in which most extant wood-rotting fungi are included, suggests that later in evolution these enzymes would have acquired the ability to degrade nonphenolic lignin using a tryptophanyl radical interacting with the bulky polymer at the surface of the enzyme. Here, we track this powerful strategy for lignin degradation as a phenotypic trait in fungi and show that it is not an isolated event in the evolution of Polyporales. Using ancestral enzyme resurrection, we study the molecular changes that led to the appearance of the same surface oxidation site in two distant peroxidase lineages. By characterization of the resurrected enzymes, we demonstrate convergent evolution at the amino acid level during the evolution of these fungi and track the different changes leading to phylogenetically distant ligninolytic peroxidases from ancestors lacking the ability to degrade nonphenolic lignin.
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  • 80
    Publication Date: 2018-08-20
    Description: The hydroxyl radical (OH) is the primary oxidant in the troposphere, and the impact of its fluctuations on the methane budget has been disputed in recent years, however measurements of OH are insufficient to characterize global interannual fluctuations relevant for methane. Here, we use a 6,000-y control simulation of preindustrial conditions with a chemistry-climate model to quantify the natural variability in OH and internal feedbacks governing that variability. We find that, even in the absence of external forcing, maximum OH changes are 3.8 ± 0.8% over a decade, which is large in the context of the recent methane growth from 2007–2017. We show that the OH variability is not a white-noise process. A wavelet analysis indicates that OH variability exhibits significant feedbacks with the same periodicity as the El Niño–Southern Oscillation (ENSO). We find intrinsically generated modulation of the OH variability, suggesting that OH may show periods of rapid or no change in future decades that are solely due to the internal climate dynamics (as opposed to external forcings). An empirical orthogonal function analysis further indicates that ENSO is the dominant mode of OH variability, with the modulation of OH occurring primarily through lightning NOx. La Niña is associated with an increase in convection in the Tropical Pacific, which increases the simulated occurrence of lightning and allows for more OH production. Understanding this link between OH and ENSO may improve the predictability of the oxidative capacity of the troposphere and assist in elucidating the causes of current and historical trends in methane.
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  • 81
    Publication Date: 2018-03-05
    Description: Induced B7-H1 expression in the tumor microenvironment initiates adaptive resistance, which impairs immune functions and leads to tumor escape from immune destruction. Antibody blockade of the B7-H1/PD-1 interaction overcomes adaptive resistance, leading to regression of advanced human cancers and survival benefits in a significant fraction of patients. In addition to cancer cells, B7-H1 is expressed on dendritic cells (DCs), but its role in DC functions is less understood. DCs can present multiple antigens (Ags) to stimulate dominant or subdominant T cell responses. Here, we show that immunization with multiple tumor Ag-loaded DCs, in the absence of B7-H1, vastly enhances cytotoxic T lymphocyte (CTL) responses to dominant Ag. In sharp contrast, CTL responses to subdominant Ag were paradoxically suppressed, facilitating outgrowth of tumor variants carrying only subdominant Ag. Suppressed CTL responses to subdominant Ag are largely due to the loss of B7-H1–mediated protection of DCs from the lysis of CTL against dominant Ag. Therefore, B7-H1 expression on DCs may help maintain the diversity of CTL responses to multiple tumor Ags. Interestingly, a split immunization approach, which presents dominant and subdominant Ags with different DCs, promoted CTL responses to all Ags and prevented tumor escape in murine tumor models. These findings have implications for the design of future combination cancer immunotherapies.
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  • 82
    Publication Date: 2018-01-08
    Description: Lung adenocarcinoma (ADC) and squamous cell carcinoma (SCC) are two distinct and predominant types of human lung cancer. IκB kinase α (IKKα) has been shown to suppress lung SCC development, but its role in ADC is unknown. We found inactivating mutations and homologous or hemizygous deletions in the CHUK locus, which encodes IKKα, in human lung ADCs. The CHUK deletions significantly reduced the survival time of patients with lung ADCs harboring KRAS mutations. In mice, lung-specific Ikkα ablation (IkkαΔLu) induces spontaneous ADCs and promotes KrasG12D-initiated ADC development, accompanied by increased cell proliferation, decreased cell senescence, and reactive oxygen species (ROS) accumulation. IKKα deletion up-regulates NOX2 and down-regulates NRF2, leading to ROS accumulation and blockade of cell senescence induction, which together accelerate ADC development. Pharmacologic inhibition of NADPH oxidase or ROS impairs KrasG12D-mediated ADC development in IkkαΔLu mice. Therefore, IKKα modulates lung ADC development by controlling redox regulatory pathways. This study demonstrates that IKKα functions as a suppressor of lung ADC in human and mice through a unique mechanism that regulates tumor cell-associated ROS metabolism.
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  • 83
    Publication Date: 2018-11-27
    Description: Hepatocellular carcinoma (HCC) is one of the most frequent forms of liver cancer, and effective treatment methods are limited due to tumor heterogeneity. There is a great need for comprehensive approaches to stratify HCC patients, gain biological insights into subtypes, and ultimately identify effective therapeutic targets. We stratified HCC patients and characterized each subtype using transcriptomics data, genome-scale metabolic networks and network topology/controllability analysis. This comprehensive systems-level analysis identified three distinct subtypes with substantial differences in metabolic and signaling pathways reflecting at genomic, transcriptomic, and proteomic levels. These subtypes showed large differences in clinical survival associated with altered kynurenine metabolism, WNT/β-catenin–associated lipid metabolism, and PI3K/AKT/mTOR signaling. Integrative analyses indicated that the three subtypes rely on alternative enzymes (e.g., ACSS1/ACSS2/ACSS3, PKM/PKLR, ALDOB/ALDOA, MTHFD1L/MTHFD2/MTHFD1) to catalyze the same reactions. Based on systems-level analysis, we identified 8 to 28 subtype-specific genes with pivotal roles in controlling the metabolic network and predicted that these genes may be targeted for development of treatment strategies for HCC subtypes by performing in silico analysis. To validate our predictions, we performed experiments using HepG2 cells under normoxic and hypoxic conditions and observed opposite expression patterns between genes expressed in high/moderate/low-survival tumor groups in response to hypoxia, reflecting activated hypoxic behavior in patients with poor survival. In conclusion, our analyses showed that the heterogeneous HCC tumors can be stratified using a metabolic network-driven approach, which may also be applied to other cancer types, and this stratification may have clinical implications to drive the development of precision medicine.
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  • 84
    Publication Date: 2018-04-23
    Description: Hepatocellular carcinoma (HCC) is a highly lethal cancer that has a high rate of recurrence, in part because of cancer stem cell (CSC)-dependent field cancerization. Acyclic retinoid (ACR) is a synthetic vitamin A-like compound capable of preventing the recurrence of HCC. Here, we performed a genome-wide transcriptome screen and showed that ACR selectively suppressed the expression of MYCN, a member of the MYC family of basic helix–loop–helix–zipper transcription factors, in HCC cell cultures, animal models, and liver biopsies obtained from HCC patients. MYCN expression in human HCC was correlated positively with both CSC and Wnt/β-catenin signaling markers but negatively with mature hepatocyte markers. Functional analysis showed repressed cell-cycle progression, proliferation, and colony formation, activated caspase-8, and induced cell death in HCC cells following silencing of MYCN expression. High-content single-cell imaging analysis and flow cytometric analysis identified a MYCN+ CSC subpopulation in the heterogeneous HCC cell cultures and showed that these cells were selectively killed by ACR. Particularly, EpCAM+ cells isolated using a cell-sorting system showed increased MYCN expression and sensitivity to ACR compared with EpCAM− cells. In a long-term (〉10 y) follow-up study of 102 patients with HCC, MYCN was expressed at higher levels in the HCC tumor region than in nontumor regions, and there was a positive correlation between MYCN expression and recurrence of de novo HCC but not metastatic HCC after curative treatment. In summary, these results suggest that MYCN serves as a prognostic biomarker and therapeutic target of ACR for liver CSCs in de novo HCC.
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  • 85
    Publication Date: 2018-07-11
    Description: What forces direct brain organization and its plasticity? When brain regions are deprived of their input, which regions reorganize based on compensation for the disability and experience, and which regions show topographically constrained plasticity? People born without hands activate their primary sensorimotor hand region while moving body parts used to compensate for this disability (e.g., their feet). This was taken to suggest a neural organization based on functions, such as performing manual-like dexterous actions, rather than on body parts, in primary sensorimotor cortex. We tested the selectivity for the compensatory body parts in the primary and association sensorimotor cortex of people born without hands (dysplasic individuals). Despite clear compensatory foot use, the primary sensorimotor hand area in the dysplasic subjects showed preference for adjacent body parts that are not compensatorily used as effectors. This suggests that function-based organization, proposed for congenital blindness and deafness, does not apply to the primary sensorimotor cortex deprivation in dysplasia. These findings stress the roles of neuroanatomical constraints like topographical proximity and connectivity in determining the functional development of primary cortex even in extreme, congenital deprivation. In contrast, increased and selective foot movement preference was found in dysplasics’ association cortex in the inferior parietal lobule. This suggests that the typical motor selectivity of this region for manual actions may correspond to high-level action representations that are effector-invariant. These findings reveal limitations to compensatory plasticity and experience in modifying brain organization of early topographical cortex compared with association cortices driven by function-based organization.
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  • 86
    Publication Date: 2018-07-05
    Description: Sal-like 4 (SALL4) is a nuclear factor central to the maintenance of stem cell pluripotency and is a key component in hepatocellular carcinoma, a malignancy with no effective treatment. In cancer cells, SALL4 associates with nucleosome remodeling deacetylase (NuRD) to silence tumor-suppressor genes, such as PTEN. Here, we determined the crystal structure of an amino-terminal peptide of SALL4(1–12) complexed to RBBp4, the chaperone subunit of NuRD, at 2.7 Å, and subsequent design of a potent therapeutic SALL4 peptide (FFW) capable of antagonizing the SALL4–NURD interaction using systematic truncation and amino acid substitution studies. FFW peptide disruption of the SALL4–NuRD complex resulted in unidirectional up-regulation of transcripts, turning SALL4 from a dual transcription repressor-activator mode to singular transcription activator mode. We demonstrate that FFW has a target affinity of 23 nM, and displays significant antitumor effects, inhibiting tumor growth by 85% in xenograft mouse models. Using transcriptome and survival analysis, we discovered that the peptide inhibits the transcription-repressor function of SALL4 and causes massive up-regulation of transcripts that are beneficial to patient survival. This study supports the SALL4–NuRD complex as a drug target and FFW as a viable drug candidate, showcasing an effective strategy to accurately target oncogenes previously considered undruggable.
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  • 87
    Publication Date: 2018-03-19
    Description: Facial expressions of emotion in humans are believed to be produced by contracting one’s facial muscles, generally called action units. However, the surface of the face is also innervated with a large network of blood vessels. Blood flow variations in these vessels yield visible color changes on the face. Here, we study the hypothesis that these visible facial colors allow observers to successfully transmit and visually interpret emotion even in the absence of facial muscle activation. To study this hypothesis, we address the following two questions. Are observable facial colors consistent within and differential between emotion categories and positive vs. negative valence? And does the human visual system use these facial colors to decode emotion from faces? These questions suggest the existence of an important, unexplored mechanism of the production of facial expressions of emotion by a sender and their visual interpretation by an observer. The results of our studies provide evidence in favor of our hypothesis. We show that people successfully decode emotion using these color features, even in the absence of any facial muscle activation. We also demonstrate that this color signal is independent from that provided by facial muscle movements. These results support a revised model of the production and perception of facial expressions of emotion where facial color is an effective mechanism to visually transmit and decode emotion.
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  • 88
    Publication Date: 2018-11-05
    Description: Prostate cancer is a leading cause of cancer death in men over 50 years of age, and there is a characteristic marked decrease in Zn content in the malignant prostate cells. The cause and consequences of this loss have thus far been unknown. We found that in middle-aged rats a Zn-deficient diet reduces prostatic Zn levels (P = 0.025), increases cellular proliferation, and induces an inflammatory phenotype with COX-2 overexpression. This hyperplastic/inflammatory prostate has a human prostate cancer-like microRNA profile, with up-regulation of the Zn-homeostasis–regulating miR-183-96-182 cluster (fold change = 1.41–2.38; P = 0.029–0.0003) and down-regulation of the Zn importer ZIP1 (target of miR-182), leading to a reduction of prostatic Zn. This inverse relationship between miR-182 and ZIP1 also occurs in human prostate cancer tissue, which is known for Zn loss. The discovery that the Zn-depleted middle-aged rat prostate has a metabolic phenotype resembling that of human prostate cancer, with a 10-fold down-regulation of citric acid (P = 0.0003), links citrate reduction directly to prostatic Zn loss, providing the underlying mechanism linking dietary Zn deficiency with miR-183-96-182 overexpression, ZIP1 down-regulation, prostatic Zn loss, and the resultant citrate down-regulation, changes mimicking features of human prostate cancer. Thus, dietary Zn deficiency during rat middle age produces changes that mimic those of human prostate carcinoma and may increase the risk for prostate cancer, supporting the need for assessment of Zn supplementation in its prevention.
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  • 89
    Publication Date: 2018-07-02
    Description: Brain “inflammaging,” a low-grade and chronic inflammation, is a major hallmark for aging-related neurodegenerative diseases. Here, by profiling H3K27ac and gene expression patterns in human and mouse brains, we found that age-related up-regulated (Age-Up) and down-regulated (Age-Down) genes have distinct H3K27ac patterns. Although both groups show promoter H3K27ac, the Age-Up genes, enriched for inflammation-related functions, are additionally marked by broad H3K27ac distribution over their gene bodies, which is progressively reduced during aging. Age-related gene expression changes can be predicted by gene-body H3K27ac level. Contrary to the presumed transcription activation function of promoter H3K27ac, we found that broad gene-body hyper H3K27ac suppresses overexpression of inflammaging genes. Altogether, our findings revealed opposite regulations by H3K27ac of Age-Up and Age-Down genes and a mode of broad gene-body H3K27ac in repressing transcription.
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  • 90
    Publication Date: 2018-02-06
    Description: Although the motility of the flagellated bacteria,Escherichia coli, has been widely studied, the effect of viscosity on swimming speed remains controversial. The swimming mode of wild-typeE. coliis often idealized as a run-and-tumble sequence in which periods of swimming at a constant speed are randomly interrupted by a sudden change of direction at a very low speed. Using a tracking microscope, we follow cells for extended periods of time in Newtonian liquids of varying viscosity and find that the swimming behavior of a single cell can exhibit a variety of behaviors, including run and tumble and “slow random walk” in which the cells move at a relatively low speed. Although the characteristic swimming speed varies between individuals and in different polymer solutions, we find that the skewness of the speed distribution is solely a function of viscosity and can be used, in concert with the measured average swimming speed, to determine the effective running speed of each cell. We hypothesize that differences in the swimming behavior observed in solutions of different viscosity are due to changes in the flagellar bundling time, which increases as the viscosity rises, due to the lower rotation rate of the flagellar motor. A numerical simulation and the use of resistive force theory provide support for this hypothesis.
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  • 91
    Publication Date: 2018-03-05
    Description: Eukaryotic gene regulation is a complex process, often coordinated by the action of tens to hundreds of proteins. Although previous biochemical studies have identified many components of the basal machinery and various ancillary factors involved in gene regulation, numerous gene-specific regulators remain undiscovered. To comprehensively survey the proteome directing gene expression at a specific genomic locus of interest, we developed an in vitro nuclease-deficient Cas9 (dCas9)-targeted chromatin-based purification strategy, called “CLASP” (Cas9 locus-associated proteome), to identify and functionally test associated gene-regulatory factors. Our CLASP method, coupled to mass spectrometry and functional screens, can be efficiently adapted for isolating associated regulatory factors in an unbiased manner targeting multiple genomic loci across different cell types. Here, we applied our method to isolate the Drosophila melanogaster histone cluster in S2 cells to identify several factors including Vig and Vig2, two proteins that bind and regulate core histone H2A and H3 mRNA via interaction with their 3′ UTRs.
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  • 92
    Publication Date: 2018-07-02
    Description: The ability to control the activity of CRISPR-dCas9 with precise spatiotemporal resolution will enable tight genome regulation of user-defined endogenous genes for studying the dynamics of transcriptional regulation. Optogenetic devices with minimal phototoxicity and the capacity for deep tissue penetration are extremely useful for precise spatiotemporal control of cellular behavior and for future clinic translational research. Therefore, capitalizing on synthetic biology and optogenetic design principles, we engineered a far-red light (FRL)-activated CRISPR-dCas9 effector (FACE) device that induces transcription of exogenous or endogenous genes in the presence of FRL stimulation. This versatile system provides a robust and convenient method for precise spatiotemporal control of endogenous gene expression and also has been demonstrated to mediate targeted epigenetic modulation, which can be utilized to efficiently promote differentiation of induced pluripotent stem cells into functional neurons by up-regulating a single neural transcription factor, NEUROG2. This FACE system might facilitate genetic/epigenetic reprogramming in basic biological research and regenerative medicine for future biomedical applications.
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  • 93
    Publication Date: 2018-11-14
    Description: That fire facilitated the late Miocene C4 grassland expansion is widely suspected but poorly documented. Fire potentially tied global climate to this profound biosphere transition by serving as a regional-to-local driver of vegetation change. In modern environments, seasonal extremes in moisture amplify the occurrence of fire, disturbing forest ecosystems to create niche space for flammable grasses, which in turn provide fuel for frequent fires. On the Indian subcontinent, C4 expansion was accompanied by increased seasonal extremes in rainfall (evidenced by δ18Ocarbonate), which set the stage for fuel accumulation and fire-linked clearance during wet-to-dry seasonal transitions. Here, we test the role of fire directly by examining the abundance and distribution patterns of fire-derived polycyclic aromatic hydrocarbons (PAHs) and terrestrial vegetation signatures in n-alkane carbon isotopes from paleosol samples of the Siwalik Group (Pakistan). Two million years before the C4 grassland transition, fire-derived PAH concentrations increased as conifer vegetation declined, as indicated by a decrease in retene. This early increase in molecular fire signatures suggests a transition to more fire-prone vegetation such as a C3 grassland and/or dry deciduous woodland. Between 8.0 and 6.0 million years ago, fire, precipitation seasonality, and C4-grass dominance increased simultaneously (within resolution) as marked by sharp increases in fire-derived PAHs, δ18Ocarbonate, and 13C enrichment in n-alkanes diagnostic of C4 grasses. The strong association of evidence for fire occurrence, vegetation change, and landscape opening indicates that a dynamic fire–grassland feedback system was both a necessary precondition and a driver for grassland ecology during the first emergence of C4 grasslands.
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  • 94
    Publication Date: 2018-06-18
    Description: To quantitatively evaluate brain tissue and its corresponding function, knowledge of the 3D cellular distribution is essential. The gold standard to obtain this information is histology, a destructive and labor-intensive technique where the specimen is sliced and examined under a light microscope, providing 3D information at nonisotropic resolution. To overcome the limitations of conventional histology, we use phase-contrast X-ray tomography with optimized optics, reconstruction, and image analysis, both at a dedicated synchrotron radiation endstation, which we have equipped with X-ray waveguide optics for coherence and wavefront filtering, and at a compact laboratory source. As a proof-of-concept demonstration we probe the 3D cytoarchitecture in millimeter-sized punches of unstained human cerebellum embedded in paraffin and show that isotropic subcellular resolution can be reached at both setups throughout the specimen. To enable a quantitative analysis of the reconstructed data, we demonstrate automatic cell segmentation and localization of over 1 million neurons within the cerebellar cortex. This allows for the analysis of the spatial organization and correlation of cells in all dimensions by borrowing concepts from condensed-matter physics, indicating a strong short-range order and local clustering of the cells in the granular layer. By quantification of 3D neuronal “packing,” we can hence shed light on how the human cerebellum accommodates 80% of the total neurons in the brain in only 10% of its volume. In addition, we show that the distribution of neighboring neurons in the granular layer is anisotropic with respect to the Purkinje cell dendrites.
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  • 95
    Publication Date: 2018-09-04
    Description: The animal kingdom exhibits a great diversity of organismal form (i.e., disparity). Whether the extremes of disparity were achieved early in animal evolutionary history or clades continually explore the limits of possible morphospace is subject to continuing debate. Here we show, through analysis of the disparity of the animal kingdom, that, even though many clades exhibit maximal initial disparity, arthropods, chordates, annelids, echinoderms, and mollusks have continued to explore and expand the limits of morphospace throughout the Phanerozoic, expanding dramatically the envelope of disparity occupied in the Cambrian. The “clumpiness” of morphospace occupation by living clades is a consequence of the extinction of phylogenetic intermediates, indicating that the original distribution of morphologies was more homogeneous. The morphological distances between phyla mirror differences in complexity, body size, and species-level diversity across the animal kingdom. Causal hypotheses of morphologic expansion include time since origination, increases in genome size, protein repertoire, gene family expansion, and gene regulation. We find a strong correlation between increasing morphological disparity, genome size, and microRNA repertoire, but no correlation to protein domain diversity. Our results are compatible with the view that the evolution of gene regulation has been influential in shaping metazoan disparity whereas the invasion of terrestrial ecospace appears to represent an additional gestalt, underpinning the post-Cambrian expansion of metazoan disparity.
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  • 96
    Publication Date: 2018-06-05
    Description: In plants, plasma membrane-embedded CELLULOSE SYNTHASE (CESA) enzyme complexes deposit cellulose polymers into the developing cell wall. Cellulose synthesis requires two different sets of CESA complexes that are active during cell expansion and secondary cell wall thickening, respectively. Hence, developing xylem cells, which first undergo cell expansion and subsequently deposit thick secondary walls, need to completely reorganize their CESA complexes from primary wall- to secondary wall-specific CESAs. Using live-cell imaging, we analyzed the principles underlying this remodeling. At the onset of secondary wall synthesis, the primary wall CESAs ceased to be delivered to the plasma membrane and were gradually removed from both the plasma membrane and the Golgi. For a brief transition period, both primary wall- and secondary wall-specific CESAs coexisted in banded domains of the plasma membrane where secondary wall synthesis is concentrated. During this transition, primary and secondary wall CESAs displayed discrete dynamic behaviors and sensitivities to the inhibitor isoxaben. As secondary wall-specific CESAs were delivered and inserted into the plasma membrane, the primary wall CESAs became concentrated in prevacuolar compartments and lytic vacuoles. This adjustment in localization between the two CESAs was accompanied by concurrent decreased primary wall CESA and increased secondary wall CESA protein abundance. Our data reveal distinct and dynamic subcellular trafficking patterns that underpin the remodeling of the cellulose biosynthetic machinery, resulting in the removal and degradation of the primary wall CESA complex with concurrent production and recycling of the secondary wall CESAs.
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  • 97
    Publication Date: 2018-04-13
    Description: The discovery that endoplasmic reticulum (ER) luminal chaperones such as GRP78/BiP can escape to the cell surface upon ER stress where they regulate cell signaling, proliferation, apoptosis, and immunity represents a paradigm shift. Toward deciphering the mechanisms, we report here that, upon ER stress, IRE1α binds to and triggers tyrosine kinase SRC activation, leading to ASAP1 phosphorylation and Golgi accumulation of ASAP1 and Arf1-GTP, resulting in KDEL receptor dispersion from the Golgi and suppression of retrograde transport. At the cell surface, GRP78 binds to and acts in concert with a glycosylphosphatidylinositol-anchored protein, CD109, in blocking TGF-β signaling by promoting the routing of the TGF-β receptor to the caveolae, thereby disrupting its binding to and activation of Smad2. Collectively, we uncover a SRC-mediated signaling cascade that leads to the relocalization of ER chaperones to the cell surface and a mechanism whereby GRP78 counteracts the tumor-suppressor effect of TGF-β.
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  • 98
    Publication Date: 2018-03-05
    Description: Treatment of bacterial infections is becoming a serious clinical challenge due to the global dissemination of multidrug antibiotic resistance, necessitating the search for alternative treatments to disarm the virulence mechanisms underlying these infections. Uropathogenic Escherichia coli (UPEC) employs multiple chaperone–usher pathway pili tipped with adhesins with diverse receptor specificities to colonize various host tissues and habitats. For example, UPEC F9 pili specifically bind galactose or N-acetylgalactosamine epitopes on the kidney and inflamed bladder. Using X-ray structure-guided methods, virtual screening, and multiplex ELISA arrays, we rationally designed aryl galactosides and N-acetylgalactosaminosides that inhibit the F9 pilus adhesin FmlH. The lead compound, 29β-NAc, is a biphenyl N-acetyl-β-galactosaminoside with a Ki of ∼90 nM, representing a major advancement in potency relative to the characteristically weak nature of most carbohydrate–lectin interactions. 29β-NAc binds tightly to FmlH by engaging the residues Y46 through edge-to-face π-stacking with its A-phenyl ring, R142 in a salt-bridge interaction with its carboxylate group, and K132 through water-mediated hydrogen bonding with its N-acetyl group. Administration of 29β-NAc in a mouse urinary tract infection (UTI) model significantly reduced bladder and kidney bacterial burdens, and coadministration of 29β-NAc and mannoside 4Z269, which targets the type 1 pilus adhesin FimH, resulted in greater elimination of bacteria from the urinary tract than either compound alone. Moreover, FmlH specifically binds healthy human kidney tissue in a 29β-NAc–inhibitable manner, suggesting a key role for F9 pili in human kidney colonization. Thus, these glycoside antagonists of FmlH represent a rational antivirulence strategy for UPEC-mediated UTI treatment.
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  • 99
    Publication Date: 2018-05-14
    Description: The bright ultrafast pulses of X-ray Free-Electron Lasers allow investigation into the structure of matter under extreme conditions. We have used single pulses to ionize and probe water as it undergoes a phase transition from liquid to plasma. We report changes in the structure of liquid water on a femtosecond time scale when irradiated by single 6.86 keV X-ray pulses of more than 106 J/cm2. These observations are supported by simulations based on molecular dynamics and plasma dynamics of a water system that is rapidly ionized and driven out of equilibrium. This exotic ionic and disordered state with the density of a liquid is suggested to be structurally different from a neutral thermally disordered state.
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  • 100
    Publication Date: 2018-12-17
    Description: The E3 ubiquitin ligase X-linked inhibitor of apoptosis (XIAP) acts as a molecular rheostat for the immune deficiency (IMD) pathway of the tick Ixodes scapularis. How XIAP activates the IMD pathway in response to microbial infection remains ill defined. Here, we identified the XIAP enzymatic substrate p47 as a positive regulator of the I. scapularis IMD network. XIAP polyubiquitylates p47 in a lysine 63-dependent manner and interacts with the p47 ubiquitin-like (UBX) module. p47 also binds to Kenny (IKKγ/NEMO), the regulatory subunit of the inhibitor of nuclear factor (NF)- κB kinase complex. Replacement of the amino acid lysine to arginine within the p47 linker region completely abrogated molecular interactions with Kenny. Furthermore, mitigation of p47 transcription levels through RNA interference in I. scapularis limited Kenny accumulation, reduced phosphorylation of IKKβ (IRD5), and impaired cleavage of the NF-κB molecule Relish. Accordingly, disruption of p47 expression increased microbial colonization by the Lyme disease spirochete Borrelia burgdorferi and the rickettsial agent Anaplasma phagocytophilum. Collectively, we highlight the importance of ticks for the elucidation of paradigms in arthropod immunology. Manipulating immune signaling cascades within I. scapularis may lead to innovative approaches to reducing the burden of tick-borne diseases.
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