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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Merga, Lemessa; Redondo-Hasselerharm, P.E.; van den Brink, P.J.; Koelmans, A.A.;

    Abstract Pollution with microplastics has become an environmental concern worldwide. Yet, little information is available on the distribution of microplastics in lakes. Lake Ziway is one of the largest lakes in Ethiopia and is known for its fishing and drinking water supply. This study aims to examine the distribution of plastic particles, of all sizes (micro- and small macro-plastics) in four of the major fish species of the lake and in its shoreline sediment. The gastrointestinal tracts analysis showed that 35% of the sampled fishes ingested plastic particles. The median number of particles per fish was 4 (range 1–26). Benthic (Clarias gariepinus) and benthopelagic (Cyprinus carpio and Carassius carassius) fish species were found to contain a significantly higher number of plastic particles in comparison to the planktivorous fish species (Oreochromis niloticus). More fishes ingested plastic particles in the wet compared to the dry season. The maximum plastic size (40 mm fibre) was found in C. carpio. Estimated median mass of plastic particles in fish was 0.07 (0.0002–385.2) mg/kg_ww. Fish and sediment samples close to known potential sources of plastic particles had a higher plastic ingestion frequency (52% of the fish) and higher plastic concentration compared to the other parts of the lake. The median count and mass of plastic particles measured in sediment of the lake were 30,000 (400–124,000) particles/m3 and 764 (0.05–36,233) mg/kg_dw, respectively, the upper limits of which exceed known effect thresholds. Attenuated total reflection (ATR) - Fourier-transform infrared (FTIR) spectroscopy showed that polypropylene, polyethylene and alkyd-varnish were the dominant polymers in fishes and in sediment. The plastic particles size distributions were Log-linear and were identical for plastic particles found in fish and in sediment, suggesting strong benthic-pelagic coupling of plastic particles transfer.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ NARCIS; Research@WURarrow_drop_down
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    NARCIS; Research@WUR
    Article . 2020
    License: CC BY
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    The Science of The Total Environment
    Article . 2020 . Peer-reviewed
    License: CC BY
    Data sources: Crossref; NARCIS
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ NARCIS; Research@WURarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      NARCIS; Research@WUR
      Article . 2020
      License: CC BY
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      The Science of The Total Environment
      Article . 2020 . Peer-reviewed
      License: CC BY
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    Authors: Kleyheeg, Erik; van Leeuwen, C.H.A.; Nolet, B.A.; Soons, Merel; +2 Authors

    Plant populations in fragmented ecosystems rely largely on internal dispersal by animals. To unravel the mechanisms underlying this mode of dispersal, an increasing number of experimental feeding studies is carried out. However, while physical activity is known to affect vertebrate digestive processes, almost all current knowledge on mechanisms of internal seed dispersal has been obtained from experiments with resting animals. We investigated how physical activity of the mallard Anas platyrhynchos, probably the quantitatively most important biotic dispersal agent in aquatic habitats in the entire Northern Hemisphere, affects gut passage survival and retention time of ingested plant seeds. We fed seeds of nine common wetland plants to mallards trained to subsequently swim for six hours in a flume tank at different swimming speeds (activity levels). We compared gut passage survival and retention times of seeds against a control treatment with mallards resting in a conventional dry cage. Intact gut passage of seeds increased significantly with mallard activity (up to 80% in the fastest swimming treatment compared to the control), identifying reduced digestive efficiency due to increased metabolic rates as a mechanism enhancing the dispersal potential of ingested seeds. Gut passage speed was modestly accelerated (13% on average) by increased mallard activity, an effect partly obscured by the interaction between seed retention time and probability of digestion. Gut passage acceleration will be more pronounced in digestion‐resilient seed species, thereby modulating their dispersal distances. Our findings imply that seed dispersal potential by mallards calculated from previous experiments with resting birds is highly underestimated, while dispersal distances may be overestimated for some plant species. Similar effects of physical activity on digestive efficiency of mammals suggests that endozoochorous dispersal of plant seeds by vertebrates is more effective and plays a quantitatively more important ecological role in both terrestrial and aquatic ecosystems than previously thought.

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    Oikos
    Article . 2015
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    Oikos
    Article . 2014
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    Oikos
    Article . 2014 . Peer-reviewed
    License: CC BY NC ND
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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    NARCIS
    Article . 2014
    Data sources: NARCIS
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      Oikos
      Article . 2015
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Oikos
      Article . 2014
      Data sources: NARCIS
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Oikos
      Article . 2014 . Peer-reviewed
      License: CC BY NC ND
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
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      Article . 2014
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Hoitink, A.J.F.; Peters, H.C.; Schroevers, M.;

    Abstract Acoustic Doppler current profilers (ADCPs) can measure orbital velocities induced by surface gravity waves, yet the ADCP estimates of these velocities are subject to a relatively high noise level. The present paper introduces a linear filtration technique to significantly reduce the influence of noise and turbulence from energy spectra of combined orbital velocity measurements. Data were collected in 13-m-deep water with a 1.2-MHz ADCP sampling in mode 12, where a collocated wave buoy was used for verification. The surface elevation spectra derived from the filtrated and nonfiltrated measurements were compared with corresponding wave buoy spectra. In the frequency range between 0.12 and 0.5 Hz, ADCP- and wave-buoy-derived spectral estimates matched very well, even without applying the filtration technique. At frequencies below 0.12 Hz, the ADCP-derived surface elevation spectra are biased, caused by a depth-varying excess of spectral energy density in the measured orbital velocities, peaking at middepth. Internal waves may provide an explanation for the energy excess, as the experiment was conducted in the region of influence of the Rhine freshwater plume. Alternatively, infragravity waves may be the cause of the depth variation of low-frequency spectral energy density.

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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ NARCIS; Research@WURarrow_drop_down
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    Authors: M. Lizotte; B. Juhls; B. Juhls; B. Juhls; +52 Authors

    Climate warming and related drivers of soil thermal change in the Arctic are expected to modify the distribution and dynamics of carbon contained in perennially frozen grounds. Thawing of permafrost in the Mackenzie Delta region of northwestern Canada, coupled with increases in river discharge and coastal erosion, trigger the release of terrestrial organic matter (OMt) from the largest Arctic drainage basin in North America into the Arctic Ocean. While this process is ongoing, well-established, and its rate is accelerating, the fate of the newly-mobilized organic matter, as it transits from the watershed through the delta and into the marine system, remains poorly understood. In the framework of the European Horizon 2020 Nunataryuk programme, and as part of the Work Package 4 (WP4) Coastal Waters theme, four field expeditions were conducted in the Mackenzie Delta region and southern Beaufort Sea from April to September 2019. The temporal sampling design allowed the survey of ambient conditions in the coastal waters under full ice cover prior to the spring freshet, during ice break-up in summer, as well as anterior to the freeze-up period in fall. To capture the fluvial-marine transition zone, and with distinct challenges related to shallow waters and changing seasonal and meteorological conditions, the field sampling was conducted in close partnership with members of the communities of Aklavik, Inuvik and Tuktoyaktuk, using several platforms: helicopters, snowmobiles and small boats. Water column profiles of physical and optical variables were measured in situ, while surface water, groundwater and sediment samples were collected and preserved for the determination of the composition and sources of OMt, including particulate and dissolved organic carbon (POC, DOC), and chromophoric dissolved organic matter (CDOM), as well as a suite of physical, chemical and biological variables. Here we present an overview of the standardized datasets, including hydrographic profiles, remote sensing reflectance, temperature and salinity, particle absorption, nutrients, dissolved organic carbon, particulate organic carbon, particulate organic nitrogen, colored dissolved organic matter absorption, fluorescent dissolved organic matter intensity, suspended particulate matter, total particulate carbon, total particulate nitrogen, stable water isotopes, radon in water, bacterial abundance, and a string of phytoplankton pigments including total chlorophyll. Datasets and related metadata can be found in Juhls et al. 2021. https://doi.pangaea.de/10.1594/PANGAEA.937587.

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    https://doi.org/10.5194/essd-2...
    Preprint . 2022 . Peer-reviewed
    License: CC BY
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    Earth System Science Data
    Article . 2023
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    ZENODO; Earth System Science Data (ESSD)
    Article . 2023 . Peer-reviewed
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      https://doi.org/10.5194/essd-2...
      Preprint . 2022 . Peer-reviewed
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      Article . 2023
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      ZENODO; Earth System Science Data (ESSD)
      Article . 2023 . Peer-reviewed
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      Earth System Science Data
      Article . 2023
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    Authors: X. Wen; X. Wen; V. Unger; G. Jurasinski; +15 Authors

    The rewetting of drained peatlands alters peat geochemistry and often leads to sustained elevated methane emission. Although this methane is produced entirely by microbial activity, the distribution and abundance of methane-cycling microbes in rewetted peatlands, especially in fens, is rarely described. In this study, we compare the community composition and abundance of methane-cycling microbes in relation to peat porewater geochemistry in two rewetted fens in northeastern Germany, a coastal brackish fen and a freshwater riparian fen, with known high methane fluxes. We utilized 16S rRNA high-throughput sequencing and quantitative polymerase chain reaction (qPCR) on 16S rRNA, mcrA, and pmoA genes to determine microbial community composition and the abundance of total bacteria, methanogens, and methanotrophs. Electrical conductivity (EC) was more than 3 times higher in the coastal fen than in the riparian fen, averaging 5.3 and 1.5 mS cm−1, respectively. Porewater concentrations of terminal electron acceptors (TEAs) varied within and among the fens. This was also reflected in similarly high intra- and inter-site variations of microbial community composition. Despite these differences in environmental conditions and electron acceptor availability, we found a low abundance of methanotrophs and a high abundance of methanogens, represented in particular by Methanosaetaceae, in both fens. This suggests that rapid (re)establishment of methanogens and slow (re)establishment of methanotrophs contributes to prolonged increased methane emissions following rewetting.

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    DOAJ
    Article . 2018
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    Biogeosciences
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    Biogeosciences
    Article . 2018 . Peer-reviewed
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    Article . 2018
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    Copernicus Publications
    Other literature type . 2019
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      Biogeosciences
      Article . 2018 . Peer-reviewed
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      Other literature type . 2019
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      Article . 2018
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    Authors: Cózar, Andrés; Martí, Elisa; Duarte, Carlos M; García-de-Lomas, Juan; +10 Authors

    Tara Oceans particularly acknowledges the commitment of the following sponsors: the CNRS (in particular Groupement de Recherche GDR3280), the European Molecular Biology Laboratory, Genoscope/CEA, French Government “Investissements d’Avenir” programs OCEANOMICS (ANR-11-BTBR-0008) and FRANCE GENOMIQUE (ANR-10-INBS-09-08), Agence Nationale de la Recherche, and European Union FP7 (Micro B3 no. 287589). We appreciate the support and commitment of agnès b. and E. Bourgois, Veolia Environment Foundation, Region Bretagne, Lorient Agglomeration, World Courier, Illumina, Eléctricité de France Foundation, Fondation pour la recherche sur la biodiversité, Prince Albert II de Monaco Foundation, Tara Foundation, its schooner, and its teams. We are also grateful to the French Ministry of Foreign Affairs for supporting the expedition and to the countries that granted sampling permissions. Tara Oceans would not exist without continuous support from 23 institutes (http://oceans.taraexpeditions.org/en/m/science/les-labos-impliques/). This article is contribution number 52 of Tara Oceans. This study is funded by Tara Oceans and the Malaspina 2010 Expedition project (Spanish Ministry of Economy and Competitiveness, CSD2008-00077) and has received additional support from the King Abdullah University of Science and Technology through baseline funding to X.I. and C.M.D., Campus de Excelencia Internacional del Mar (CEIMAR), and PLASTREND (BBVA Foundation) and MIDaS (CTM2016-77106-R, AEI/FEDER/UE) projects. The subtropical ocean gyres are recognized as great marine accummulation zones of floating plastic debris; however, the possibility of plastic accumulation at polar latitudes has been overlooked because of the lack of nearby pollution sources. In the present study, the Arctic Ocean was extensively sampled for floating plastic debris from the Tara Oceans circumpolar expedition. Although plastic debris was scarce or absent in most of the Arctic waters, it reached high concentrations (hundreds of thousands of pieces per square kilometer) in the northernmost and easternmost areas of the Greenland and Barents seas. The fragmentation and typology of the plastic suggested an abundant presence of aged debris that originated from distant sources. This hypothesis was corroborated by the relatively high ratios of marine surface plastic to local pollution sources. Surface circulation models and field data showed that the poleward branch of the Thermohaline Circulation transfers floating debris from the North Atlantic to the Greenland and Barents seas, which would be a dead end for this plastic conveyor belt. Given the limited surface transport of the plastic that accumulated here and the mechanisms acting for the downward transport, the seafloor beneath this Arctic sector is hypothesized as an important sink of plastic debris. Peer reviewed

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    Science Advances
    Article . 2017
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    Authors: Darawalee Wangsa; Rüdiger Braun; Madison Schiefer; Edward Michael Gertz; +15 Authors

    Intratumor heterogeneity is a major challenge in cancer treatment. To decipher patterns of chromosomal heterogeneity, we analyzed six colorectal cancer cell lines by multiplex interphase FISH (miFISH). The mismatch-repair-deficient cell lines DLD-1 and HCT116 had the most stable copy numbers, whereas aneuploid cell lines (HT-29, SW480, SW620 and H508) displayed a higher degree of instability. We subsequently assessed the clonal evolution of single cells in two colorectal carcinoma cell lines, SW480 and HT-29, which both have aneuploid karyotypes but different degrees of chromosomal instability. The clonal compositions of the single cell-derived daughter lines, as assessed by miFISH, differed for HT-29 and SW480. Daughters of HT-29 were stable, clonal, with little heterogeneity. Daughters of SW480 were more heterogeneous, with the single cell-derived daughter lines separating into two distinct populations with different ploidy (hyper-diploid and near-triploid), morphology, gene expression and tumorigenicity. To better understand the evolutionary trajectory for the two SW480 populations, we constructed phylogenetic trees which showed ongoing instability in the daughter lines. When analyzing the evolutionary development over time, most single cell-derived daughter lines maintained their major clonal pattern, with the exception of one daughter line that showed a switch involving a loss of APC. Our meticulous analysis of the clonal evolution and composition of these colorectal cancer models shows that all chromosomes are subject to segregation errors, however, specific net genomic imbalances are maintained. Karyotype evolution is driven by the necessity to arrive at and maintain a specific plateau of chromosomal copy numbers as the drivers of carcinogenesis.

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    Europe PubMed Central
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    Carcinogenesis
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    Carcinogenesis
    Article . 2018 . Peer-reviewed
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      Carcinogenesis
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  • image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Authors: Luke F. Gockowski; Neil D. Dolinski; Roberto Chavez; Noy Cohen; +5 Authors

    Multimaterial additive manufacturing is an enabling tool for exploring difficult to access structure-property relationships. In this work, a recently developed multimaterial printing approach, solution mask liquid lithography, is used to produce porous polymer-polymer composites inspired by tough, hierarchical structures found in nature. The results demonstrate that varying the size and packing of pores in the core structure leads to significant enhancement in crack deflection. Finite element analysis reveals that this enhancement is linked to geometry-dependent stress distribution. 

    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Materials Horizonsarrow_drop_down
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Materials Horizons
    Article . 2020
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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
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    Article . 2020
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Materials Horizonsarrow_drop_down
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      Materials Horizons
      Article . 2020
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
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    Authors: Versteegh, Emma A. A.; Van Dover, Cindy; Van Audenhaege, Loïc; Coleman, Max; +2 Authors

    Alvinocaridid shrimp occurring in dense assemblages close to vigorously venting orifices are characteristic of many vent fields on the Mid-Atlantic Ridge, Central Indian Ridge, and Mid-Cayman Rise. Episymbiotic bacteria of these shrimp are exposed to vent fluids enriched in inorganic nutrients (carbon dioxide, sulfide) that, together with dissolved oxygen in the surrounding seawater, sustain autotrophic growth and supply nourishment to the shrimp. Enigmatically, conspecific shrimp may also be found sparsely distributed in the periphery of a vent field, where there is little visual evidence of vent fluid flux. We tested the null hypothesis that nourishment sources were identical for the central (dense) and peripheral shrimp assemblages, using gut content and stable isotope analyses. Rimicaris hybisae were sampled from central and peripheral assemblages at the Von Damm Vent Field (Mid-Cayman Rise). Guts of centrally aggregated shrimp contained a white material inferred to be bacteria, while peripheral individuals contained this white material and/or pieces of crustacean exoskeletons. C, N, and S isotopic compositions of shrimp muscle tissues were significantly different between central and peripheral shrimp assemblages, and little overlap in isotopic space was found. A comparison of δ13C and δ34S values of gut contents and abdominal tissues revealed that abdominal tissue composition reflects the shrimp's source of nourishment. Slight but significantly elevated δ15N values in peripheral shrimp, together with crustacean exoskeleton fragments in the gut, suggest facultative carnivory in peripherally aggregated shrimp. The lower δ13C and δ34S values in individuals from the peripheral assemblages are also consistent with a mixotrophic diet. We conclude that central and peripheral assemblages of R. hybisae have different nourishment sources, with central assemblages relying on episymbionts, while peripheral assemblages have diverse nourishment sources comprising bacteria and Crustacea.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ NARCIS; Utrecht Univ...arrow_drop_down
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    Deep Sea Research Part I Oceanographic Research Papers; ZENODO
    Other literature type . Article . 2022 . 2023 . Peer-reviewed
    License: Elsevier TDM
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      Deep Sea Research Part I Oceanographic Research Papers; ZENODO
      Other literature type . Article . 2022 . 2023 . Peer-reviewed
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    Authors: Jaime Pitarch; Marco Bellacicco; Emanuele Organelli; Gianluca Volpe; +3 Authors

    Particulate optical backscattering (bbp) is a crucial parameter for the study of ocean biology and oceanic carbon estimations. In this work, bbp retrieval, by the quasi-analytical algorithm (QAA), is assessed using a large in situ database of matched bbp and remote-sensing reflectance (Rrs). The QAA is also applied to satellite Rrs (ESA OC-CCI project) as well, after their validation against in situ Rrs. Additionally, the effect of Raman Scattering on QAA retrievals is studied. Results show negligible biases above random noise when QAA-derived bbp is compared to in situ bbp. In addition, Rrs from the CCI archive shows good agreement with in situ data. The QAA’s functional form of spectral backscattering slope, as derived from in situ radiometry, is validated. Finally, we show the importance of correcting for Raman Scattering over clear waters prior to semi-analytical retrieval. Overall, this work demonstrates the high efficiency of QAA in the bbp detection in case of both in situ and ocean color data, but it also highlights the necessity to increase the number of observations that are severely under-sampled in respect to others environmental parameters.

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    Remote Sensing; NARCIS
    Other literature type . Article . 2020 . 2019 . Peer-reviewed
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    NIOZ Repository
    Article . 2020
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    DOAJ
    Article . 2019
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    CNR ExploRA
    Article . 2020
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    ENEA Open Archive
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    Article . 2020
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    Authors: Merga, Lemessa; Redondo-Hasselerharm, P.E.; van den Brink, P.J.; Koelmans, A.A.;

    Abstract Pollution with microplastics has become an environmental concern worldwide. Yet, little information is available on the distribution of microplastics in lakes. Lake Ziway is one of the largest lakes in Ethiopia and is known for its fishing and drinking water supply. This study aims to examine the distribution of plastic particles, of all sizes (micro- and small macro-plastics) in four of the major fish species of the lake and in its shoreline sediment. The gastrointestinal tracts analysis showed that 35% of the sampled fishes ingested plastic particles. The median number of particles per fish was 4 (range 1–26). Benthic (Clarias gariepinus) and benthopelagic (Cyprinus carpio and Carassius carassius) fish species were found to contain a significantly higher number of plastic particles in comparison to the planktivorous fish species (Oreochromis niloticus). More fishes ingested plastic particles in the wet compared to the dry season. The maximum plastic size (40 mm fibre) was found in C. carpio. Estimated median mass of plastic particles in fish was 0.07 (0.0002–385.2) mg/kg_ww. Fish and sediment samples close to known potential sources of plastic particles had a higher plastic ingestion frequency (52% of the fish) and higher plastic concentration compared to the other parts of the lake. The median count and mass of plastic particles measured in sediment of the lake were 30,000 (400–124,000) particles/m3 and 764 (0.05–36,233) mg/kg_dw, respectively, the upper limits of which exceed known effect thresholds. Attenuated total reflection (ATR) - Fourier-transform infrared (FTIR) spectroscopy showed that polypropylene, polyethylene and alkyd-varnish were the dominant polymers in fishes and in sediment. The plastic particles size distributions were Log-linear and were identical for plastic particles found in fish and in sediment, suggesting strong benthic-pelagic coupling of plastic particles transfer.

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    NARCIS; Research@WUR
    Article . 2020
    License: CC BY
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    The Science of The Total Environment
    Article . 2020 . Peer-reviewed
    License: CC BY
    Data sources: Crossref; NARCIS
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      Article . 2020
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      The Science of The Total Environment
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    Authors: Kleyheeg, Erik; van Leeuwen, C.H.A.; Nolet, B.A.; Soons, Merel; +2 Authors

    Plant populations in fragmented ecosystems rely largely on internal dispersal by animals. To unravel the mechanisms underlying this mode of dispersal, an increasing number of experimental feeding studies is carried out. However, while physical activity is known to affect vertebrate digestive processes, almost all current knowledge on mechanisms of internal seed dispersal has been obtained from experiments with resting animals. We investigated how physical activity of the mallard Anas platyrhynchos, probably the quantitatively most important biotic dispersal agent in aquatic habitats in the entire Northern Hemisphere, affects gut passage survival and retention time of ingested plant seeds. We fed seeds of nine common wetland plants to mallards trained to subsequently swim for six hours in a flume tank at different swimming speeds (activity levels). We compared gut passage survival and retention times of seeds against a control treatment with mallards resting in a conventional dry cage. Intact gut passage of seeds increased significantly with mallard activity (up to 80% in the fastest swimming treatment compared to the control), identifying reduced digestive efficiency due to increased metabolic rates as a mechanism enhancing the dispersal potential of ingested seeds. Gut passage speed was modestly accelerated (13% on average) by increased mallard activity, an effect partly obscured by the interaction between seed retention time and probability of digestion. Gut passage acceleration will be more pronounced in digestion‐resilient seed species, thereby modulating their dispersal distances. Our findings imply that seed dispersal potential by mallards calculated from previous experiments with resting birds is highly underestimated, while dispersal distances may be overestimated for some plant species. Similar effects of physical activity on digestive efficiency of mammals suggests that endozoochorous dispersal of plant seeds by vertebrates is more effective and plays a quantitatively more important ecological role in both terrestrial and aquatic ecosystems than previously thought.

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    Oikos
    Article . 2015
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    Oikos
    Article . 2014
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    Oikos
    Article . 2014 . Peer-reviewed
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    Article . 2014
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      Article . 2015
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      Oikos
      Article . 2014
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      Article . 2014 . Peer-reviewed
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      Article . 2014
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    Authors: Hoitink, A.J.F.; Peters, H.C.; Schroevers, M.;

    Abstract Acoustic Doppler current profilers (ADCPs) can measure orbital velocities induced by surface gravity waves, yet the ADCP estimates of these velocities are subject to a relatively high noise level. The present paper introduces a linear filtration technique to significantly reduce the influence of noise and turbulence from energy spectra of combined orbital velocity measurements. Data were collected in 13-m-deep water with a 1.2-MHz ADCP sampling in mode 12, where a collocated wave buoy was used for verification. The surface elevation spectra derived from the filtrated and nonfiltrated measurements were compared with corresponding wave buoy spectra. In the frequency range between 0.12 and 0.5 Hz, ADCP- and wave-buoy-derived spectral estimates matched very well, even without applying the filtration technique. At frequencies below 0.12 Hz, the ADCP-derived surface elevation spectra are biased, caused by a depth-varying excess of spectral energy density in the measured orbital velocities, peaking at middepth. Internal waves may provide an explanation for the energy excess, as the experiment was conducted in the region of influence of the Rhine freshwater plume. Alternatively, infragravity waves may be the cause of the depth variation of low-frequency spectral energy density.

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    Authors: M. Lizotte; B. Juhls; B. Juhls; B. Juhls; +52 Authors

    Climate warming and related drivers of soil thermal change in the Arctic are expected to modify the distribution and dynamics of carbon contained in perennially frozen grounds. Thawing of permafrost in the Mackenzie Delta region of northwestern Canada, coupled with increases in river discharge and coastal erosion, trigger the release of terrestrial organic matter (OMt) from the largest Arctic drainage basin in North America into the Arctic Ocean. While this process is ongoing, well-established, and its rate is accelerating, the fate of the newly-mobilized organic matter, as it transits from the watershed through the delta and into the marine system, remains poorly understood. In the framework of the European Horizon 2020 Nunataryuk programme, and as part of the Work Package 4 (WP4) Coastal Waters theme, four field expeditions were conducted in the Mackenzie Delta region and southern Beaufort Sea from April to September 2019. The temporal sampling design allowed the survey of ambient conditions in the coastal waters under full ice cover prior to the spring freshet, during ice break-up in summer, as well as anterior to the freeze-up period in fall. To capture the fluvial-marine transition zone, and with distinct challenges related to shallow waters and changing seasonal and meteorological conditions, the field sampling was conducted in close partnership with members of the communities of Aklavik, Inuvik and Tuktoyaktuk, using several platforms: helicopters, snowmobiles and small boats. Water column profiles of physical and optical variables were measured in situ, while surface water, groundwater and sediment samples were collected and preserved for the determination of the composition and sources of OMt, including particulate and dissolved organic carbon (POC, DOC), and chromophoric dissolved organic matter (CDOM), as well as a suite of physical, chemical and biological variables. Here we present an overview of the standardized datasets, including hydrographic profiles, remote sensing reflectance, temperature and salinity, particle absorption, nutrients, dissolved organic carbon, particulate organic carbon, particulate organic nitrogen, colored dissolved organic matter absorption, fluorescent dissolved organic matter intensity, suspended particulate matter, total particulate carbon, total particulate nitrogen, stable water isotopes, radon in water, bacterial abundance, and a string of phytoplankton pigments including total chlorophyll. Datasets and related metadata can be found in Juhls et al. 2021. https://doi.pangaea.de/10.1594/PANGAEA.937587.

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    https://doi.org/10.5194/essd-2...
    Preprint . 2022 . Peer-reviewed
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    Earth System Science Data
    Article . 2023
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    Earth System Science Data (ESSD)
    Other literature type . 2022
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    ZENODO; Earth System Science Data (ESSD)
    Article . 2023 . Peer-reviewed
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    Article . 2023
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      https://doi.org/10.5194/essd-2...
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      Article . 2023
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      ZENODO; Earth System Science Data (ESSD)
      Article . 2023 . Peer-reviewed
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      Article . 2023
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    Authors: X. Wen; X. Wen; V. Unger; G. Jurasinski; +15 Authors

    The rewetting of drained peatlands alters peat geochemistry and often leads to sustained elevated methane emission. Although this methane is produced entirely by microbial activity, the distribution and abundance of methane-cycling microbes in rewetted peatlands, especially in fens, is rarely described. In this study, we compare the community composition and abundance of methane-cycling microbes in relation to peat porewater geochemistry in two rewetted fens in northeastern Germany, a coastal brackish fen and a freshwater riparian fen, with known high methane fluxes. We utilized 16S rRNA high-throughput sequencing and quantitative polymerase chain reaction (qPCR) on 16S rRNA, mcrA, and pmoA genes to determine microbial community composition and the abundance of total bacteria, methanogens, and methanotrophs. Electrical conductivity (EC) was more than 3 times higher in the coastal fen than in the riparian fen, averaging 5.3 and 1.5 mS cm−1, respectively. Porewater concentrations of terminal electron acceptors (TEAs) varied within and among the fens. This was also reflected in similarly high intra- and inter-site variations of microbial community composition. Despite these differences in environmental conditions and electron acceptor availability, we found a low abundance of methanotrophs and a high abundance of methanogens, represented in particular by Methanosaetaceae, in both fens. This suggests that rapid (re)establishment of methanogens and slow (re)establishment of methanotrophs contributes to prolonged increased methane emissions following rewetting.

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    DOAJ
    Article . 2018
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    Biogeosciences
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    Biogeosciences
    Article . 2018 . Peer-reviewed
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      Biogeosciences
      Article . 2018 . Peer-reviewed
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      Copernicus Publications
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    Authors: Cózar, Andrés; Martí, Elisa; Duarte, Carlos M; García-de-Lomas, Juan; +10 Authors

    Tara Oceans particularly acknowledges the commitment of the following sponsors: the CNRS (in particular Groupement de Recherche GDR3280), the European Molecular Biology Laboratory, Genoscope/CEA, French Government “Investissements d’Avenir” programs OCEANOMICS (ANR-11-BTBR-0008) and FRANCE GENOMIQUE (ANR-10-INBS-09-08), Agence Nationale de la Recherche, and European Union FP7 (Micro B3 no. 287589). We appreciate the support and commitment of agnès b. and E. Bourgois, Veolia Environment Foundation, Region Bretagne, Lorient Agglomeration, World Courier, Illumina, Eléctricité de France Foundation, Fondation pour la recherche sur la biodiversité, Prince Albert II de Monaco Foundation, Tara Foundation, its schooner, and its teams. We are also grateful to the French Ministry of Foreign Affairs for supporting the expedition and to the countries that granted sampling permissions. Tara Oceans would not exist without continuous support from 23 institutes (http://oceans.taraexpeditions.org/en/m/science/les-labos-impliques/). This article is contribution number 52 of Tara Oceans. This study is funded by Tara Oceans and the Malaspina 2010 Expedition project (Spanish Ministry of Economy and Competitiveness, CSD2008-00077) and has received additional support from the King Abdullah University of Science and Technology through baseline funding to X.I. and C.M.D., Campus de Excelencia Internacional del Mar (CEIMAR), and PLASTREND (BBVA Foundation) and MIDaS (CTM2016-77106-R, AEI/FEDER/UE) projects. The subtropical ocean gyres are recognized as great marine accummulation zones of floating plastic debris; however, the possibility of plastic accumulation at polar latitudes has been overlooked because of the lack of nearby pollution sources. In the present study, the Arctic Ocean was extensively sampled for floating plastic debris from the Tara Oceans circumpolar expedition. Although plastic debris was scarce or absent in most of the Arctic waters, it reached high concentrations (hundreds of thousands of pieces per square kilometer) in the northernmost and easternmost areas of the Greenland and Barents seas. The fragmentation and typology of the plastic suggested an abundant presence of aged debris that originated from distant sources. This hypothesis was corroborated by the relatively high ratios of marine surface plastic to local pollution sources. Surface circulation models and field data showed that the poleward branch of the Thermohaline Circulation transfers floating debris from the North Atlantic to the Greenland and Barents seas, which would be a dead end for this plastic conveyor belt. Given the limited surface transport of the plastic that accumulated here and the mechanisms acting for the downward transport, the seafloor beneath this Arctic sector is hypothesized as an important sink of plastic debris. Peer reviewed

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    Science Advances
    Article . 2017
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    Authors: Darawalee Wangsa; Rüdiger Braun; Madison Schiefer; Edward Michael Gertz; +15 Authors

    Intratumor heterogeneity is a major challenge in cancer treatment. To decipher patterns of chromosomal heterogeneity, we analyzed six colorectal cancer cell lines by multiplex interphase FISH (miFISH). The mismatch-repair-deficient cell lines DLD-1 and HCT116 had the most stable copy numbers, whereas aneuploid cell lines (HT-29, SW480, SW620 and H508) displayed a higher degree of instability. We subsequently assessed the clonal evolution of single cells in two colorectal carcinoma cell lines, SW480 and HT-29, which both have aneuploid karyotypes but different degrees of chromosomal instability. The clonal compositions of the single cell-derived daughter lines, as assessed by miFISH, differed for HT-29 and SW480. Daughters of HT-29 were stable, clonal, with little heterogeneity. Daughters of SW480 were more heterogeneous, with the single cell-derived daughter lines separating into two distinct populations with different ploidy (hyper-diploid and near-triploid), morphology, gene expression and tumorigenicity. To better understand the evolutionary trajectory for the two SW480 populations, we constructed phylogenetic trees which showed ongoing instability in the daughter lines. When analyzing the evolutionary development over time, most single cell-derived daughter lines maintained their major clonal pattern, with the exception of one daughter line that showed a switch involving a loss of APC. Our meticulous analysis of the clonal evolution and composition of these colorectal cancer models shows that all chromosomes are subject to segregation errors, however, specific net genomic imbalances are maintained. Karyotype evolution is driven by the necessity to arrive at and maintain a specific plateau of chromosomal copy numbers as the drivers of carcinogenesis.

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    Europe PubMed Central
    Other literature type . 2018
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    Carcinogenesis
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    Carcinogenesis
    Article . 2018 . Peer-reviewed
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      Europe PubMed Central
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    Authors: Luke F. Gockowski; Neil D. Dolinski; Roberto Chavez; Noy Cohen; +5 Authors

    Multimaterial additive manufacturing is an enabling tool for exploring difficult to access structure-property relationships. In this work, a recently developed multimaterial printing approach, solution mask liquid lithography, is used to produce porous polymer-polymer composites inspired by tough, hierarchical structures found in nature. The results demonstrate that varying the size and packing of pores in the core structure leads to significant enhancement in crack deflection. Finite element analysis reveals that this enhancement is linked to geometry-dependent stress distribution. 

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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
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    Authors: Versteegh, Emma A. A.; Van Dover, Cindy; Van Audenhaege, Loïc; Coleman, Max; +2 Authors

    Alvinocaridid shrimp occurring in dense assemblages close to vigorously venting orifices are characteristic of many vent fields on the Mid-Atlantic Ridge, Central Indian Ridge, and Mid-Cayman Rise. Episymbiotic bacteria of these shrimp are exposed to vent fluids enriched in inorganic nutrients (carbon dioxide, sulfide) that, together with dissolved oxygen in the surrounding seawater, sustain autotrophic growth and supply nourishment to the shrimp. Enigmatically, conspecific shrimp may also be found sparsely distributed in the periphery of a vent field, where there is little visual evidence of vent fluid flux. We tested the null hypothesis that nourishment sources were identical for the central (dense) and peripheral shrimp assemblages, using gut content and stable isotope analyses. Rimicaris hybisae were sampled from central and peripheral assemblages at the Von Damm Vent Field (Mid-Cayman Rise). Guts of centrally aggregated shrimp contained a white material inferred to be bacteria, while peripheral individuals contained this white material and/or pieces of crustacean exoskeletons. C, N, and S isotopic compositions of shrimp muscle tissues were significantly different between central and peripheral shrimp assemblages, and little overlap in isotopic space was found. A comparison of δ13C and δ34S values of gut contents and abdominal tissues revealed that abdominal tissue composition reflects the shrimp's source of nourishment. Slight but significantly elevated δ15N values in peripheral shrimp, together with crustacean exoskeleton fragments in the gut, suggest facultative carnivory in peripherally aggregated shrimp. The lower δ13C and δ34S values in individuals from the peripheral assemblages are also consistent with a mixotrophic diet. We conclude that central and peripheral assemblages of R. hybisae have different nourishment sources, with central assemblages relying on episymbionts, while peripheral assemblages have diverse nourishment sources comprising bacteria and Crustacea.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ NARCIS; Utrecht Univ...arrow_drop_down
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    Deep Sea Research Part I Oceanographic Research Papers; ZENODO
    Other literature type . Article . 2022 . 2023 . Peer-reviewed
    License: Elsevier TDM
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      Deep Sea Research Part I Oceanographic Research Papers; ZENODO
      Other literature type . Article . 2022 . 2023 . Peer-reviewed
      License: Elsevier TDM
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    Authors: Jaime Pitarch; Marco Bellacicco; Emanuele Organelli; Gianluca Volpe; +3 Authors

    Particulate optical backscattering (bbp) is a crucial parameter for the study of ocean biology and oceanic carbon estimations. In this work, bbp retrieval, by the quasi-analytical algorithm (QAA), is assessed using a large in situ database of matched bbp and remote-sensing reflectance (Rrs). The QAA is also applied to satellite Rrs (ESA OC-CCI project) as well, after their validation against in situ Rrs. Additionally, the effect of Raman Scattering on QAA retrievals is studied. Results show negligible biases above random noise when QAA-derived bbp is compared to in situ bbp. In addition, Rrs from the CCI archive shows good agreement with in situ data. The QAA’s functional form of spectral backscattering slope, as derived from in situ radiometry, is validated. Finally, we show the importance of correcting for Raman Scattering over clear waters prior to semi-analytical retrieval. Overall, this work demonstrates the high efficiency of QAA in the bbp detection in case of both in situ and ocean color data, but it also highlights the necessity to increase the number of observations that are severely under-sampled in respect to others environmental parameters.

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    Remote Sensing; NARCIS
    Other literature type . Article . 2020 . 2019 . Peer-reviewed
    License: CC BY
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    NIOZ Repository
    Article . 2020
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    DOAJ
    Article . 2019
    Data sources: DOAJ
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    CNR ExploRA
    Article . 2020
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    Article . 2020
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    Article . 2020
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