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  • 2005-2009  (154,310)
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  • 1
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    Oxford University Press
    In:  Handbook of Avian Hybrids of the World vol. 76, 1, pp. 59-61
    Publication Date: 2024-01-12
    Keywords: book review ; geographic distribution ; hybridisation ; birds
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/review
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  • 2
    Publication Date: 2024-01-07
    Description: Drift is a prominent parameter characterizing the Arctic sea ice cover that has a deep impact on the climate system. Hence it is a key issue to both the remote sensing as well as the modeling community, to provide reliable sea ice drift fields. This study focuses on the comparison of sea ice drift results from different sea ice‐ocean coupled models and the validation with observational data in the period 1979–2001. The models all take part in the Arctic Ocean Model Intercomparison Project (AOMIP) and the observations are mainly based on satellite imagery. According to speed distributions, one class of models has a mode at drift speeds around 3 cm s −1 and a short tail toward higher speeds. Another class shows a more even frequency distribution with large probability of drift speeds of 10 to 20 cm s −1 . Observations clearly agree better with the first class of model results. Reasons for these differences are manifold and lie in discrepancies of wind stress forcing as well as sea ice model characteristics and sea ice‐ocean coupling. Moreover, we investigated the drift patterns of anticyclonic and cyclonic wind‐driven regimes. The models are capable of producing realistic drift pattern variability. The winter of 1994/1995 stands out because of its maximum in Fram Strait ice export. Although export estimates of some models agree with observations, the corresponding inner Arctic drift pattern is not reproduced. The reason for this is found in the wind‐forcing as well as in differences in ocean velocities.
    Type: Article , PeerReviewed
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  • 3
    Publication Date: 2023-11-17
    Description: Structure and growth of the Izu‐Bonin‐Mariana arc crust: 1. Seismic constraint on crust and mantle structure of the Mariana arc–back‐arc system Narumi Takahashi Institute for Research on Earth Evolution Japan Agency for Marine‐Earth Science and Technology Kanagawa Japan Shuichi Kodaira Institute for Research on Earth Evolution Japan Agency for Marine‐Earth Science and Technology Kanagawa Japan Yoshiyuki Tatsumi Institute for Research on Earth Evolution Japan Agency for Marine‐Earth Science and Technology Kanagawa Japan Yoshiyuki Kaneda Institute for Research on Earth Evolution Japan Agency for Marine‐Earth Science and Technology Kanagawa Japan Kiyoshi Suyehiro Institute for Research on Earth Evolution Japan Agency for Marine‐Earth Science and Technology Kanagawa Japan A high‐resolution seismic velocity model is presented for the crust and upper mantle of the Mariana arc–back‐arc system (MABS) based on active source seismic profiling. The major characteristics are (1) slow mantle velocity of 〈8 km s −1 in the uppermost mantle, especially, and deep reflectors under the Mariana arc (MA) and the West Mariana Ridge (WMR), (2) a deep reflector in the upper mantle beneath the relative thick crust of the Mariana Trough (MT) axis, (3) distribution of lower‐velocity lower crusts (6.7–6.9 km s −1 ) beneath the volcanic front and adjacent to the MT, and (4) high‐velocity lower crust (7.2–7.4 km s −1 ) beneath the boundary regions between the MA and MT, and between the WMR and the Parece Vela Basin (PVB), adding to structural characteristics of crust and upper mantle beneath the MABS. Of the characteristics described above, characteristic 1 suggests that the origins of the slow mantle velocity and the deep reflectors be explained by transfer of the lower crustal residues to the upper mantle across the Moho, considering that the WMR is extinct arc currently. On the other hand, characteristic 2 suggests that the origin of deep reflectors beneath the MT axis might be lower velocity materials due to the diffractive signals with strong amplitudes, characteristic 3 suggests that the lower‐velocity lower crust advanced crustal growth and characteristic 4 suggests that the high‐velocity lower crust beneath arc–back‐arc transition zone is composed of mafic/ultramafic materials created by extensive partial melting of mantle peridotites or last stage of the arc magmatism rather than serpentinized peridotite.
    Type: Article , PeerReviewed
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  • 4
    Publication Date: 2023-11-08
    Description: On the Pacific margin off central Costa Rica, an anomalous lens-shaped zone is located between the overriding plate and the subducting oceanic lithosphere approximately 25 km landward of the deformation front. This feature was previously recognized in reflection seismic data when it was termed 'megalens'. Its origin and seismic velocity structure, however, could not unambiguously be derived from earlier studies. Therefore during RV SONNE cruise SO163, seismic wide-angle data were acquired in 2002 using closely spaced ocean bottom hydrophones and seismometers along two parallel strike and two parallel dip lines above the 'megalens', intersecting on the middle slope. The P-wave velocities and structure of the subducting oceanic Cocos Plate and overriding Caribbean Plate were determined by modelling the wide-angle seismic data in combination with the analysis of coincident reflection seismic data and the use of synthetic seismograms. The margin wedge is defined by high seismic velocities (4.3-6.1 km s(-1)) identified within a wedge-shaped body covered by a slope sediment drape. It is divided into two layers with different velocity gradients. The lower margin wedge is clearly constrained by decreasing velocities trenchward and terminates beneath the middle slope at the location of the 'megalens'. Seismic velocities of the 'megalens' are lower (3.8-4.3 km s(-1)) relative to the margin wedge. We propose that the 'megalens' represents hybrid material composed of subducted sediment and eroded fragments from the base of the upper plate. Upward-migrating overpressured fluids weaken the base of the margin wedge through hydrofracturing, thus causing material transfer from the upper plate to the lower plate. Results from amplitude modelling support that the 'megalens' observed off central Costa Rica is bound by a low-velocity zone documenting fluid drainage from the plate boundary to the upper plate.
    Type: Article , PeerReviewed
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  • 5
    Publication Date: 2023-03-22
    Description: Lilliput was discovered in 2005 as the southernmost known hydrothermal field along the Mid-Atlantic Ridge. It is exceptional in that it lacks high-temperature venting probably because of a thickened crust. The absence of thermophilic and hyperthermophilic prokaryotes in emissions supports the argument against the presence of a hot subsurface at Lilliput, as is typically suggested for diffuse emissions from areas of high-temperature venting. The high phylogenetic diversity and novelty of bacteria observed could be because of the low-temperature influence, the distinct location of the hydrothermal field or the Bathymodiolus assemblages covering the sites of discharge. The low-temperature fluids at the Lilliput are characterized by lowered pH and slightly elevated hydrogen (16 nM) and methane (∼2.6 μM) contents compared with ambient seawater. No typical hydrogen and methane oxidizing prokaryotes were detected. The higher diversity of reverse tricarboxylic acid genes and the form II RubisCO genes of the Calvin Benson-Bassham (CBB) cycle compared with the form I RubisCO genes of the CBB cycle suggests that the chemoautotrophic community is better adapted to low oxygen concentrations. Thiomicrospira spp. and Epsilonproteobacteria dominated the autotrophic community. Sulfide is the most abundant inorganic energy source (0.5 mM). Diverse bacteria were associated with sulfur cycling, including Gamma-, Delta- and Epsilonproteobacteria, with the latter being the most abundant bacteria according to fluorescence in situ hybridization. With members of various Candidate Divisions constituting for 25% of clone library sequences we suggest that their role in vent ecosystems might be more important than previously assumed and propose potential mechanisms they might be involved in at the Lilliput hydrothermal field.
    Type: Article , PeerReviewed
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  • 6
    Publication Date: 2022-05-26
    Description: © 2008 The Authors. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in Nucleic Acids Research 36 (2008): 2522-2529, doi:10.1093/nar/gkm1166
    Description: Penelope-like elements (PLEs) represent a new class of retroelements identified in more than 80 species belonging to at least 10 animal phyla. Penelope isolated from Drosophila virilis is the only known transpositionally active representative of this class. Although the size and structure of the Penelope major transcript has been previously described in both D. virilis and D. melanogaster transgenic strains, the architecture of the Penelope regulatory region remains unknown. In order to determine the localization of presumptive Penelope promoter and enhancer-like elements, segments of the putative Penelope regulatory region were linked to a CAT reporter gene and introduced into D. melanogaster by P-element-mediated transformation. The results obtained using ELISA to measure CAT expression levels and RNA studies, including RT–PCR, suggest that the active Penelope transposon contains an internal promoter similar to the TATA-less promoters of LINEs. The results also suggest that some of the Penelope regulatory sequences control the preferential expression in the ovaries of the adult flies by enhancing expression in the ovary and reducing expression in the carcass. The possible significance of the intron within Penelope for the function and evolution of PLEs, and the effect of Penelope insertions on adjacent genes, are discussed.
    Description: This work was supported by grants from Russian Academy of Sciences (Cell and Molecular Biology to M.E.), and Welcome Trust Grant (075698) to M.E and D.J.F.
    Repository Name: Woods Hole Open Access Server
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  • 7
    Publication Date: 2022-05-26
    Description: This paper is not subject to U.S. copyright. The definitive version was published in ICES Journal of Marine Science: Journal du Conseil 67 (2010): 1-9, doi:10.1093/icesjms/fsp221.
    Description: Effective marine ecosystem-based management (EBM) requires understanding the key processes and relationships controlling the aspects of biodiversity, productivity, and resilience to perturbations. Unfortunately, the scales, complexity, and non-linear dynamics that characterize marine ecosystems often confound managing for these properties. Nevertheless, scientifically derived decision-support tools (DSTs) are needed to account for impacts resulting from a variety of simultaneous human activities. Three possible methodologies for revealing mechanisms necessary to develop DSTs for EBM are: (i) controlled experimentation, (ii) iterative programmes of observation and modelling ("learning by doing"), and (iii) comparative ecosystem analysis. We have seen that controlled experiments are limited in capturing the complexity necessary to develop models of marine ecosystem dynamics with sufficient realism at appropriate scales. Iterative programmes of observation, model building, and assessment are useful for specific ecosystem issues but rarely lead to generally transferable products. Comparative ecosystem analyses may be the most effective, building on the first two by inferring ecosystem processes based on comparisons and contrasts of ecosystem response to human-induced factors. We propose a hierarchical system of ecosystem comparisons to include within-ecosystem comparisons (utilizing temporal and spatial changes in relation to human activities), within-ecosystem-type comparisons (e.g. coral reefs, temperate continental shelves, upwelling areas), and cross-ecosystem-type comparisons (e.g. coral reefs vs. boreal, terrestrial vs. marine ecosystems). Such a hierarchical comparative approach should lead to better understanding of the processes controlling biodiversity, productivity, and the resilience of marine ecosystems. In turn, better understanding of these processes will lead to the development of increasingly general laws, hypotheses, functional forms, governing equations, and broad interpretations of ecosystem responses to human activities, ultimately improving DSTs in support of EBM.
    Keywords: Comparative marine ecosystem analysis ; Decision-support tools ; EAM ; EBM ; Ecological modelling ; Ecosystem approaches to management ; Ecosystem-based management
    Repository Name: Woods Hole Open Access Server
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  • 8
    Publication Date: 2022-05-26
    Description: © The Author 2006. This article is posted here by permission of Oxford University Press. The definitive version was published in Nucleic Acids Research 34 (2006): 1-9, doi:10.1093/nar/gkj405.
    Description: The goal of this group project has been to coordinate and bring up-to-date information on all genes of Escherichia coli K-12. Annotation of the genome of an organism entails identification of genes, the boundaries of genes in terms of precise start and end sites, and description of the gene products. Known and predicted functions were assigned to each gene product on the basis of experimental evidence or sequence analysis. Since both kinds of evidence are constantly expanding, no annotation is complete at any moment in time. This is a snapshot analysis based on the most recent genome sequences of two E.coli K-12 bacteria. An accurate and up-to-date description of E.coli K-12 genes is of particular importance to the scientific community because experimentally determined properties of its gene products provide fundamental information for annotation of innumerable genes of other organisms. Availability of the complete genome sequence of two K-12 strains allows comparison of their genotypes and mutant status of alleles.
    Repository Name: Woods Hole Open Access Server
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  • 9
    Publication Date: 2022-05-25
    Description: © 2008 The Authors. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License. The definitive version was published in Nucleic Acids Research 37 (2009): D526-D530, doi:10.1093/nar/gkn631.
    Description: GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia and Trichomonas vaginalis, respectively, and represent the latest additions to the EuPathDB (http://EuPathDB.org) family of functional genomic databases. GiardiaDB and TrichDB employ the same framework as other EuPathDB sites (CryptoDB, PlasmoDB and ToxoDB), supporting fully integrated and searchable databases. Genomic-scale data available via these resources may be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs and other protein characteristics. Functional queries may also be formulated, based on transcript and protein expression data from a variety of platforms. Phylogenetic relationships may also be interrogated. The ability to combine the results from independent queries, and to store queries and query results for future use facilitates complex, genome-wide mining of functional genomic data.
    Description: Federal funds from the National Institute of Allergy and Infectious Diseases; Department of Health and Human Services, National Institutes of Health (HHSN266200400037C). Funding for open access charge: National Institutes of Health (HHSN266200400037C).
    Repository Name: Woods Hole Open Access Server
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  • 10
    Publication Date: 2022-05-25
    Description: © 2007 The Author et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in Nucleic Acids Research 35 (2007): 2107-2115, doi:10.1093/nar/gkm049.
    Description: Trypanosomatids contain an unusual DNA base J (ß-D-glucosylhydroxymethyluracil), which replaces a fraction of thymine in telomeric and other DNA repeats. To determine the function of base J, we have searched for enzymes that catalyze J biosynthesis. We present evidence that a protein that binds to J in DNA, the J-binding protein 1 (JBP1), may also catalyze the first step in J biosynthesis, the conversion of thymine in DNA into hydroxymethyluracil. We show that JBP1 belongs to the family of Fe2+ and 2-oxoglutarate-dependent dioxygenases and that replacement of conserved residues putatively involved in Fe2+ and 2-oxoglutarate-binding inactivates the ability of JBP1 to contribute to J synthesis without affecting its ability to bind to J-DNA. We propose that JBP1 is a thymidine hydroxylase responsible for the local amplification of J inserted by JBP2, another putative thymidine hydroxylase.
    Description: This work was funded by a grant from the Netherlands Organization for Scientific Research and Chemical Sciences (NWO-CW) to P.B., NIH grant A1063523 to R.S. and NIH grant GM063584 to R.P.H.
    Repository Name: Woods Hole Open Access Server
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