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  • Wiley  (34.822)
  • Oxford University Press  (19.048)
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  • 2010-2014  (63.396)
  • 2013  (63.396)
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  • 1
    Publikationsdatum: 2024-03-22
    Beschreibung: The Sr/Ca ratio of coral aragonite is used to reconstruct past sea surface temperature (SST). Twentyone laboratories took part in an interlaboratory study of coral Sr/Ca measurements. Results show interlaboratory bias can be significant, and in the extreme case could result in a range in SST estimates of 7°C. However, most of the data fall within a narrower range and the Porites coral reference material JCp- 1 is now characterized well enough to have a certified Sr/Ca value of 8.838 mmol/mol with an expanded uncertainty of 0.089 mmol/mol following International Association of Geoanalysts (IAG) guidelines. This uncertainty, at the 95% confidence level, equates to 1.5°C for SST estimates using Porites, so is approaching fitness for purpose. The comparable median within laboratory error is 〈0.5°C. This difference in uncertainties illustrates the interlaboratory bias component that should be reduced through the use of reference materials like the JCp-1. There are many potential sources contributing to biases in comparative methods but traces of Sr in Ca standards and uncertainties in reference solution composition can account for half of the combined uncertainty. Consensus values that fulfil the requirements to be certified values were also obtained for Mg/Ca in JCp-1 and for Sr/Ca and Mg/Ca ratios in the JCt-1 giant clam reference material. Reference values with variable fitness for purpose have also been obtained for Li/Ca, B/Ca, Ba/Ca, and U/Ca in both reference materials. In future, studies reporting coral element/Ca data should also report the average value obtained for a reference material such as the JCp-1.
    Materialart: Article , PeerReviewed
    Format: text
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  • 2
    Publikationsdatum: 2024-01-16
    Beschreibung: Earth system climate models generally underestimate dissolved oxygen concentrations in the deep eastern equatorial Pacific. This problem is associated with the "nutrient trapping" problem, described by Najjar et al. [1992], and is, at least partially, caused by a deficient representation of the Equatorial Intermediate Current System (EICS). Here we emulate the unresolved EICS in the UVic earth system climate model by locally increasing the zonal isopycnal diffusivity. An anisotropic diffusivity of ∼50,000 m 2 s-1 yields an improved global representation of temperature, salinity and oxygen. In addition, it (1) resolves most of the local "nutrient trapping" and associated oxygen deficit in the eastern equatorial Pacific and (2) reduces spurious zonal temperature gradients on isopycnals without affecting other physical metrics such as meridional overturning or air-sea heat fluxes. Finally, climate projections of low-oxygenated waters and associated denitrification change sign and apparently become more plausible
    Materialart: Article , PeerReviewed
    Format: text
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  • 3
    Publikationsdatum: 2023-11-29
    Beschreibung: We present data on the co-registered geochemistry (in situ mass spectrometry) and microbiology (pyrosequencing of 16S rRNA genes; V1, V2, V3 regions) in five fluid samples from Irina II in the Logatchev hydrothermal field. Two samples were collected over 24min from the same spot and further three samples were from spatially distinct locations (20cm, 3m and the overlaying plume). Four low-temperature hydrothermal fluids from the Irina II are composed of the same core bacterial community, namely specific Gammaproteobacteria and Epsilonproteobacteria, which, however, differs in the relative abundance. The microbial composition of the fifth sample (plume) is considerably different. Although a significant correlation between sulfide enrichment and proportions of Sulfurovum (Epsilonproteobacteria) was found, no other significant linkages between abiotic factors, i.e. temperature, hydrogen, methane, sulfide and oxygen, and bacterial lineages were evident. Intriguingly, bacterial community compositions of some time series samples from the same spot were significantly more similar to a sample collected 20cm away than to each other. Although this finding is based on three single samples only, it provides first hints that single hydrothermal fluid samples collected on a small spatial scale may also reflect unrecognized temporal variability. However, further studies are required to support this hypothesis.
    Materialart: Article , PeerReviewed
    Format: text
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  • 4
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    AGU (American Geophysical Union) | Wiley
    Publikationsdatum: 2023-01-31
    Beschreibung: We analyze an extensive set of global coupled biogeochemical ocean circulation models. The focus is on the equatorial Pacific. In all simulations, which are consistent with observed standing stocks of relevant biogeochemical species at the surface, we find spuriously enhanced (reduced) macronutrient (oxygen) concentrations in the deep eastern equatorial Pacific. This modeling problem, apparently endemic to global coupled biogeochemical ocean circulation models, was coined “nutrient trapping” by Najjar et al. (1992). In contrast to Aumont et al. (1999), we argue that “nutrient trapping” is still a persistent problem, even in eddy-permitting models and, further, that the scale of the problem retards model projections of nitrogen cycling. In line with previous work, our results indicate that a deficient circulation is at the core of the problem rather than an admittedly poor quantitative understanding of biogeochemical cycles. More specifically, we present indications that “nutrient trapping” in models is a result of a spuriously damped Equatorial Intermediate (zonal) Current System and Equatorial Deep Jets—phenomenon which await a comprehensive understanding and have, to date, not been successfully simulated.
    Materialart: Article , PeerReviewed
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  • 5
    Publikationsdatum: 2023-01-31
    Beschreibung: Lateral diffusivity is computed from a tracer release experiment in the northeastern tropical Atlantic thermocline. The uncertainties of the estimates are inferred from a synthetic particle release using a high-resolution ocean circulation model. The main method employed to compute zonal and meridional components of lateral diffusivity is the growth of the second moment of a cloud of tracer. The application of an areal comparison method for estimating tracer-based diffusivity in the field experiments is also discussed. The best estimate of meridional eddy diffusivity in the Guinea Upwelling region at about 300 m depth is estimated to be inline image m2 s−1. The zonal component of lateral diffusivity is estimated to be inline image m2 s−1, while areal comparison method yields areal equivalent zonal diffusivity component of inline image m2 s−1. In comparison to Ky, Kx is about twice larger, resulting from the tracer patch stretching by zonal jets. Employed conceptual jet model indicates that zonal jet velocities of about inline image m s−1 are required to explain the enhancement of the zonal eddy diffusivity component. Finally, different sampling strategies are tested on synthetic tracer release experiments. They indicate that the best sampling strategy is a sparse regular sampling grid covering most of the tracer patch.
    Materialart: Article , PeerReviewed
    Format: text
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  • 6
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Conservation Physiology 1 (2013): cot006, doi:10.1093/conphys/cot006.
    Beschreibung: Large whales are subjected to a variety of conservation pressures that could be better monitored and managed if physiological information could be gathered readily from free-swimming whales. However, traditional approaches to studying physiology have been impractical for large whales, because there is no routine method for capture of the largest species and there is presently no practical method of obtaining blood samples from free-swimming whales. We review the currently available techniques for gathering physiological information on large whales using a variety of non-lethal and minimally invasive (or non-invasive) sample matrices. We focus on methods that should produce information relevant to conservation physiology, e.g. measures relevant to stress physiology, reproductive status, nutritional status, immune response, health, and disease. The following four types of samples are discussed: faecal samples, respiratory samples (‘blow’), skin/blubber samples, and photographs. Faecal samples have historically been used for diet analysis but increasingly are also used for hormonal analyses, as well as for assessment of exposure to toxins, pollutants, and parasites. Blow samples contain many hormones as well as respiratory microbes, a diverse array of metabolites, and a variety of immune-related substances. Biopsy dart samples are widely used for genetic, contaminant, and fatty-acid analyses and are now being used for endocrine studies along with proteomic and transcriptomic approaches. Photographic analyses have benefited from recently developed quantitative techniques allowing assessment of skin condition, ectoparasite load, and nutritional status, along with wounds and scars from ship strikes and fishing gear entanglement. Field application of these techniques has the potential to improve our understanding of the physiology of large whales greatly, better enabling assessment of the relative impacts of many anthropogenic and ecological pressures.
    Beschreibung: This work was supported by the United States Office of Naval Research (award #N000141110435 to K.E.H., award #N000141110540 to R.M.R., and award #N0001412WX20890 to L.C.Y. and C.E.D.); the United Kingdom Natural Environmental Research Council (supporting A.J.H.); the National Center for Research Resources, a component of the United States National Institutes of Health (NIH; supporting C.E.D.); the NIH Roadmap for Medical Research (UL1 RR024146 supporting C.E.D.); The Hartwell Foundation (supporting C.E.D.) and the 2012 Marine Mammal Breath Workshop, which was funded by the National Oceanic and Atmospheric Administration’s Marine Mammal Health and Stranding Response Program.
    Schlagwort(e): Blow ; Biopsy dart ; Cetacea ; Faecal samples ; Non-invasive ; Visual health assessment
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
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  • 7
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nucleic Acids Research 40 (2012): W82-W87, doi:10.1093/nar/gks418.
    Beschreibung: Amplicon sequencing of the hypervariable regions of the small subunit ribosomal RNA gene is a widely accepted method for identifying the members of complex bacterial communities. Several rRNA gene sequence reference databases can be used to assign taxonomic names to the sequencing reads using BLAST, USEARCH, GAST or the RDP classifier. Next-generation sequencing methods produce ample reads, but they are short, currently ∼100–450 nt (depending on the technology), as compared to the full rRNA gene of ∼1550 nt. It is important, therefore, to select the right rRNA gene region for sequencing. The primers should amplify the species of interest and the hypervariable regions should differentiate their taxonomy. Here, we introduce TaxMan: a web-based tool that trims reference sequences based on user-selected primer pairs and returns an assessment of the primer specificity by taxa. It allows interactive plotting of taxa, both amplified and missed in silico by the primers used. Additionally, using the trimmed sequences improves the speed of sequence matching algorithms. The smaller database greatly improves run times (up to 98%) and memory usage, not only of similarity searching (BLAST), but also of chimera checking (UCHIME) and of clustering the reads (UCLUST). TaxMan is available at http://www.ibi.vu.nl/programs/taxmanwww/.
    Beschreibung: University of Amsterdam under the research priority area ‘Oral Infections and Inflammation’ (to B.W.B.); National Science Foundation [NSF/BDI 0960626 to S.M.H.]; the European Union Seventh Framework Programme (FP7/ 2007-2013) under ANTIRESDEV grant agreement no 241446 (to E.Z.).
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
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  • 8
    Publikationsdatum: 2022-05-25
    Beschreibung: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Briefings in Bioinformatics 15 (2014): 783-787, doi:10.1093/bib/bbt010.
    Beschreibung: The extremely high error rates reported by Keegan et al. in ‘A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE’ (PLoS Comput Biol 2012;8:e1002541) for many next-generation sequencing datasets prompted us to re-examine their results. Our analysis reveals that the presence of conserved artificial sequences, e.g. Illumina adapters, and other naturally occurring sequence motifs accounts for most of the reported errors. We conclude that DRISEE reports inflated levels of sequencing error, particularly for Illumina data. Tools offered for evaluating large datasets need scrupulous review before they are implemented.
    Beschreibung: National Institutes of Health [1UH2DK083993 to M.L.S.]; National Science Foundation [BDI- 096026 to S.M.H.].
    Schlagwort(e): Next-generation sequencing ; Sequencing error ; Adapter ligation ; PCR ; Quality score
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
    Format: application/msword
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  • 9
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    Wiley
    In:  European Climate Vulnerabilities and Adaptation
    Publikationsdatum: 2022-03-21
    Materialart: info:eu-repo/semantics/bookPart
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  • 10
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    Wiley
    In:  European Climate Vulnerabilities and Adaptation
    Publikationsdatum: 2022-03-21
    Materialart: info:eu-repo/semantics/bookPart
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