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  • 1
    Publikationsdatum: 2020-12-14
    Beschreibung: In this study we present an intercomparison of measurements of very low water vapor column content obtained with a Ground-Based Millimeter-wave Spectrometer (GBMS), Vaisala RS92k radiosondes, a Raman Lidar, and an IR Fourier Transform Spectrometer. These sets of measurements were carried out during the primary field campaign of the ECOWAR (Earth COoling by WAter vapor Radiation) project which took place on the Western Italian Alps from 3 to 16 March, 2007.
    Beschreibung: Published
    Beschreibung: 135-138
    Beschreibung: 1.8. Osservazioni di geofisica ambientale
    Beschreibung: N/A or not JCR
    Beschreibung: open
    Schlagwort(e): Precipitable Water Vapor ; ECOWAR ; IR and Millimeter-Wave Spectroscopy ; 01. Atmosphere::01.01. Atmosphere::01.01.01. Composition and Structure ; 01. Atmosphere::01.01. Atmosphere::01.01.02. Climate
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
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  • 2
    Publikationsdatum: 2017-04-04
    Beschreibung: COST (Co-operation in the field of Scientific and Technical Research) is an important instrument supporting co-operation among scientists and researchers across Europe now joining 35 member countries. Scientific projects in the COST framework are called COST Actions and have the objectives embodied in their respective Memorandum of Understanding (MoU). The main objectives of the COST Actions within the European ionospheric and radio propagation community have been: to study the influence of upper atmospheric conditions on terrestrial and Earthspace communications, to develop methods and techniques to improve existing and generate new ionospheric and propagation models over Europe for telecommunication and navigation applications and to transfer the results to the appropriate national and international organizations, institutions and industry dealing with the modern communication systems. This paper summarises in brief the background and historical context of four ionospheric COST Actions and outlines their main objectives and results. In addition, the paper discusses the dissemination of the results and the collaboration among the participating institutions and researchers.
    Beschreibung: DRS Codem Systems Ball Aerospace Corporation University of Massachusetts Lowell
    Beschreibung: Published
    Beschreibung: Lowell, Massachusetts, U.S.A., April 29, 2007
    Beschreibung: 3.9. Fisica della magnetosfera, ionosfera e meteorologia spaziale
    Beschreibung: open
    Schlagwort(e): Physics of the Ionosphere ; 01. Atmosphere::01.02. Ionosphere::01.02.99. General or miscellaneous ; 05. General::05.07. Space and Planetary sciences::05.07.02. Space weather
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: Conference paper
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  • 3
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    American Institute of Physics
    Publikationsdatum: 2020-02-24
    Beschreibung: A high-resolution Fabry–Perot interferometer was inserted in a feedback loop which, by monitoring elements of the fringe pattern, keeps the position of the transmitting window fixed with respect to a given line, taking into account the instability of the radiation source which would produce a wander of the line itself and the noise affecting the tuning of the receiving interferometer. The system, in this preliminary form, is able to lock itself and maintain its position indefinitely for slow and moderately fast varying disturbances.
    Beschreibung: Published
    Beschreibung: 2940-2944
    Beschreibung: 1.7. Osservazioni di alta e media atmosfera
    Beschreibung: JCR Journal
    Beschreibung: reserved
    Schlagwort(e): FABRY-PEROT ; INTERFEROMETER ; SERVOMECHANISMS ; FEEDBACK ; 01. Atmosphere::01.01. Atmosphere::01.01.08. Instruments and techniques
    Repository-Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Materialart: article
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  • 4
    Publikationsdatum: 2022-05-25
    Beschreibung: Author Posting. © National Academy of Sciences, 2006. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 103 (2006): 3675-3680, doi:10.1073/pnas.0600160103.
    Beschreibung: We investigated whether the evolution of electric organs and electric signal diversity in two independently evolved lineages of electric fishes was accompanied by convergent changes on the molecular level. We found that a sodium channel gene (Nav1.4a) that is expressed in muscle in nonelectric fishes has lost its expression in muscle and is expressed instead in the evolutionarily novel electric organ in both lineages of electric fishes. This gene appears to be evolving under positive selection in both lineages, facilitated by its restricted expression in the electric organ. This view is reinforced by the lack of evidence for selection on this gene in one electric species in which expression of this gene is retained in muscle. Amino acid replacements occur convergently in domains that influence channel inactivation, a key trait for shaping electric communication signals. Some amino acid replacements occur at or adjacent to sites at which disease-causing mutations have been mapped in human sodium channel genes, emphasizing that these replacements occur in functionally important domains. Selection appears to have acted on the final step in channel inactivation, but complementarily on the inactivation "ball" in one lineage, and its receptor site in the other lineage. Thus, changes in the expression and sequence of the same gene are associated with the independent evolution of signal complexity.
    Beschreibung: This work was funded by National Institutes of Health Grant R01 NS025513 (to H.H.Z. and Y.L.) and National Science Foundation Integrative Graduate Education and Research Traineeship Program DGE-0114387 (to D.J.Z. and D.M.H.).
    Schlagwort(e): Animal communication ; Electric organ ; Channel inactivation ; Protein evolution ; Positive selection
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
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  • 5
    Publikationsdatum: 2022-05-25
    Beschreibung: Author Posting. © National Academy of Sciences, 2006. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 103 (2006): 6448-6453, doi:10.1073/pnas.0600830103.
    Beschreibung: Submersible exploration of the Samoan hotspot revealed a new, 300-m-tall, volcanic cone, named Nafanua, in the summit crater of Vailulu'u seamount. Nafanua grew from the 1,000-m-deep crater floor in 〈4 years and could reach the sea surface within decades. Vents fill Vailulu'u crater with a thick suspension of particulates and apparently toxic fluids that mix with seawater entering from the crater breaches. Low-temperature vents form Fe oxide chimneys in many locations and up to 1-m-thick layers of hydrothermal Fe floc on Nafanua. High-temperature (81°C) hydrothermal vents in the northern moat (945-m water depth) produce acidic fluids (pH 2.7) with rising droplets of (probably) liquid CO2. The Nafanua summit vent area is inhabited by a thriving population of eels (Dysommina rugosa) that feed on midwater shrimp probably concentrated by anticyclonic currents at the volcano summit and rim. The moat and crater floor around the new volcano are littered with dead metazoans that apparently died from exposure to hydrothermal emissions. Acid-tolerant polychaetes (Polynoidae) live in this environment, apparently feeding on bacteria from decaying fish carcasses. Vailulu'u is an unpredictable and very active underwater volcano presenting a potential long-term volcanic hazard. Although eels thrive in hydrothermal vents at the summit of Nafanua, venting elsewhere in the crater causes mass mortality. Paradoxically, the same anticyclonic currents that deliver food to the eels may also concentrate a wide variety of nektonic animals in a death trap of toxic hydrothermal fluids.
    Beschreibung: This work was supported by the National Oceanic and Atmospheric Administration (NOAA) Oceans Exploration and the Hawaii Undersea Research Laboratory–NOAA Undersea Research Program, the National Science Foundation, the Australian Research Council, and the SERPENT program.
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
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  • 6
    Publikationsdatum: 2022-05-25
    Beschreibung: © 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.
    Beschreibung: 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.
    Beschreibung: 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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  • 7
    Publikationsdatum: 2022-05-25
    Beschreibung: Author Posting. © National Academy of Sciences, 2006. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 103 (2006): 3846-3851, doi:10.1073/pnas.0600035103.
    Beschreibung: Studies of deeply buried, sedimentary microbial communities and associated biogeochemical processes during Ocean Drilling Program Leg 201 showed elevated prokaryotic cell numbers in sediment layers where methane is consumed anaerobically at the expense of sulfate. Here, we show that extractable archaeal rRNA, selecting only for active community members in these ecosystems, is dominated by sequences of uncultivated Archaea affiliated with the Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group, whereas known methanotrophic Archaea are not detectable. Carbon flow reconstructions based on stable isotopic compositions of whole archaeal cells, intact archaeal membrane lipids, and other sedimentary carbon pools indicate that these Archaea assimilate sedimentary organic compounds other than methane even though methanotrophy accounts for a major fraction of carbon cycled in these ecosystems. Oxidation of methane by members of Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group without assimilation of methane–carbon provides a plausible explanation. Maintenance energies of these subsurface communities appear to be orders of magnitude lower than minimum values known from laboratory observations, and ecosystem-level carbon budgets suggest that community turnover times are on the order of 100–2,000 years. Our study provides clues about the metabolic functionality of two cosmopolitan groups of uncultured Archaea.
    Beschreibung: This work was supported by Deutsche Forschungsgemeinschaft (to J.S.L., R.A., M.E., and K.-U.H. at Research Center for Ocean Margins and Grant Hi 616/4 to K.U.-H.); National Aeronautics and Space Administration Astrobiology Institute Grants NNA04CC06A (to J.E.B. and C.H.H. at Pennsylvania State University), NCC 2-1275 (to M.A.L., K.G.L., K.B.S., H.F.F., A.T., and K.-U.H. at the University of Rhode Island), and NCC 2-1054 (to M.L.S. and A.T. at the Marine Biological Laboratory); the G. Unger Vetlesen Foundation; U.S. Department of Energy Grant DE-FG02-93ER20117; and NSF Grant MCB03-48492. J.F.B. was supported by NSF Integrative Graduate Education and Research Traineeship Program Grant DGE-9972759 and a Schlanger fellowship from the Joint Oceanographic Institutions (JOI). M.A.L. was supported in part by postcruise support from JOI.
    Schlagwort(e): Anaerobic methanotrophy ; Deep biosphere ; FISH–secondary ion MS ; Intact polar lipids ; Stable carbon isotopes
    Repository-Name: Woods Hole Open Access Server
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  • 8
    Publikationsdatum: 2022-05-25
    Beschreibung: © 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.
    Beschreibung: 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.
    Beschreibung: 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
    Materialart: Article
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  • 9
    Publikationsdatum: 2022-05-25
    Beschreibung: © 2006 The Authors. 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 Molecular Biology and Evolution 23(2006): 2090-2100, doi:10.1093/molbev/msl080.
    Beschreibung: We have characterized the relationship between accurate phylogenetic reconstruction and sequence similarity, testing whether high levels of sequence similarity can consistently produce accurate evolutionary trees. We generated protein families with known phylogenies using a modified version of the PAML/EVOLVER program that produces insertions and deletions as well as substitutions. Protein families were evolved over a range of 100–400 point accepted mutations; at these distances 63% of the families shared significant sequence similarity. Protein families were evolved using balanced and unbalanced trees, with ancient or recent radiations. In families sharing statistically significant similarity, about 60% of multiple sequence alignments were 95% identical to true alignments. To compare recovered topologies with true topologies, we used a score that reflects the fraction of clades that were correctly clustered. As expected, the accuracy of the phylogenies was greatest in the least divergent families. About 88% of phylogenies clustered over 80% of clades in families that shared significant sequence similarity, using Bayesian, parsimony, distance, and maximum likelihood methods. However, for protein families with short ancient branches (ancient radiation), only 30% of the most divergent (but statistically significant) families produced accurate phylogenies, and only about 70% of the second most highly conserved families, with median expectation values better than 10–60, produced accurate trees. These values represent upper bounds on expected tree accuracy for sequences with a simple divergence history; proteins from 700 Giardia families, with a similar range of sequence similarities but considerably more gaps, produced much less accurate trees. For our simulated insertions and deletions, correct multiple sequence alignments did not perform much better than those produced by T-COFFEE, and including sequences with expressed sequence tag–like sequencing errors did not significantly decrease phylogenetic accuracy. In general, although less-divergent sequence families produce more accurate trees, the likelihood of estimating an accurate tree is most dependent on whether radiation in the family was ancient or recent. Accuracy can be improved by combining genes from the same organism when creating species trees or by selecting protein families with the best bootstrap values in comprehensive studies.
    Beschreibung: This work was supported by National Institutes of Health grant AI1058054 to M. Sogin.
    Schlagwort(e): Simulation ; Phylogenetic analysis ; Accuracy ; Sequence similarity
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
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  • 10
    Publikationsdatum: 2022-05-25
    Beschreibung: Author Posting. © National Academy of Sciences, 2002. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 99 (2002): 14694-14699, doi:10.1073/pnas.232562899.
    Beschreibung: The aryl hydrocarbon receptor (AHR) is a ligand-inducible transcription factor that is best known because it mediates the actions of polycyclic and halogenated aromatic hydrocarbon environmental toxicants such as 3-methylcholanthrene and 2,3,7,8-tetrachlorodibenzo-p-dioxin. We report here the successful identification of an endogenous ligand for this receptor; {approx}20 µg was isolated in pure form from 35 kg of porcine lung. Its structure was deduced as 2-(1'H-indole-3'-carbonyl)-thiazole-4-carboxylic acid methyl ester from extensive physical measurements and quantum mechanical calculations. In a reporter gene assay, this ligand activates the AHR with a potency five times greater than that of {beta}-naphthoflavone, a prototypical synthetic AHR ligand. 2-(1'H-indole-3'-carbonyl)-thiazole-4-carboxylic acid methyl ester competes with 2,3,7,8-[3H]tetrachlorodibenzo-p-dioxin for binding to human, murine, and fish AHRs, thus showing that AHR activation is caused by direct receptor binding, and that recognition of this endogenous ligand is conserved from early vertebrates (fish) to humans.
    Beschreibung: This work was supported by the Wisconsin Alumni Research Foundation, the University of Wisconsin Sea Grant Institute, and the National Institutes of Health.
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  • 11
    Publikationsdatum: 2022-05-25
    Beschreibung: Author Posting. © National Academy of Sciences, 2006. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 103 (2006): 6252-6257, doi:10.1073/pnas.0509950103.
    Beschreibung: 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) and related halogenated aromatic hydrocarbons (HAHs) are highly toxic to most vertebrate animals, but there are dramatic differences in sensitivity among species and strains. Aquatic birds including the common tern (Sterna hirundo) are highly exposed to HAHs in the environment, but are up to 250-fold less sensitive to these compounds than the typical avian model, the domestic chicken (Gallus gallus). The mechanism of HAH toxicity involves altered gene expression subsequent to activation of the aryl hydrocarbon receptor (AHR), a basic helix–loop–helix-PAS transcription factor. AHR polymorphisms underlie mouse strain differences in sensitivity to HAHs and polynuclear aromatic hydrocarbons, but the role of the AHR in species differences in HAH sensitivity is not well understood. Here, we show that although chicken and tern AHRs both exhibit specific binding of [3H]TCDD, the tern AHR has a lower binding affinity and exhibits a reduced ability to support TCDD-dependent transactivation as compared to AHRs from chicken or mouse. We further show through use of chimeric AHR proteins and site-directed mutagenesis that the difference between the chicken and tern AHRs resides in the ligand-binding domain and that two amino acids (Val-325 and Ala-381) are responsible for the reduced activity of the tern AHR. Other avian species with reduced sensitivity to HAHs also possess these residues. These studies provide a molecular understanding of species differences in sensitivity to dioxin-like compounds and suggest an approach to using the AHR as a marker of dioxin susceptibility in wildlife.
    Beschreibung: This research was supported by the National Oceanographic and Atmospheric Administration National Sea Grant College Program, Department of Commerce, under Grants NA46RG0470 and NA16RG2273.
    Schlagwort(e): Basic helix–loop–helix-PAS ; Comparative toxicology ; Mechanisms ; Risk assessment ; Susceptibility
    Repository-Name: Woods Hole Open Access Server
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  • 12
    Publikationsdatum: 2022-05-25
    Beschreibung: © 2007 The Author(s) 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 36 (2008): D607-D611, doi:10.1093/nar/gkm941.
    Beschreibung: The starlet sea anemone, Nematostella vectensis, is a basal metazoan organism that has recently emerged as an important model system in developmental biology and evolutionary genomics. StellaBase, the Nematostella Genomics Database (http://stellabase.org), was developed in 2005 as a resource to support the Nematostella research community. Recently, it has become apparent that Nematostella may be a particularly useful system for studying (i) microevolutionary variation in natural populations, and (ii) the functional evolution of human disease genes. We have developed two new databases that will foster such studies: StellaBase Disease (http://stellabase.org/disease) is a relational database that houses 155 904 invertebrate homologous isoforms of human disease genes from four leading genomic model systems (fly, worm, yeast and Nematostella), including 14 874 predicted genes from the sea anemone itself. StellaBase SNP (http://stellabase.org/SNP) is a relational database that describes the location and underlying type of mutation for 20 063 single nucleotide polymorphisms.
    Beschreibung: This work was supported by NSF grant FP-91656101-0 to J.C.S. and J.R.F. and EPA Grant F5E11155 to A.R.M. and J.R.F. and by a Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution, with funding provided by The Beacon Institute for Rivers and Estuaries, and the J. Seward Johnson Fund to A.M.R.
    Repository-Name: Woods Hole Open Access Server
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  • 13
    Publikationsdatum: 2022-05-25
    Beschreibung: © 2009 The Authors. This article is distributed under the terms of the Creative Commons Attribution Non-Commercial License. The definitive version was published in ICES Journal of Marine Science: Journal du Conseil 67 (2010): 379-394, doi:10.1093/icesjms/fsp242.
    Beschreibung: In principle, measurements of high-frequency acoustic scattering from oceanic microstructure and zooplankton across a broad range of frequencies can reduce the ambiguities typically associated with the interpretation of acoustic scattering at a single frequency or a limited number of discrete narrowband frequencies. With this motivation, a high-frequency broadband scattering system has been developed for investigating zooplankton and microstructure, involving custom modifications of a commercially available system, with almost complete acoustic coverage spanning the frequency range 150–600 kHz. This frequency range spans the Rayleigh-to-geometric scattering transition for some zooplankton, as well as the diffusive roll-off in the spectrum for scattering from turbulent temperature microstructure. The system has been used to measure scattering from zooplankton and microstructure in regions of non-linear internal waves. The broadband capabilities of the system provide a continuous frequency response of the scattering over a wide frequency band, and improved range resolution and signal-to-noise ratios through pulse-compression signal-processing techniques. System specifications and calibration procedures are outlined and the system performance is assessed. The results point to the utility of high-frequency broadband scattering techniques in the detection, classification, and under certain circumstances, quantification of zooplankton and microstructure.
    Beschreibung: The work was supported by the US Office of Naval Research (Grant # N000140210359).
    Schlagwort(e): Broadband acoustic scattering ; Internal waves ; Oceanic microstructure ; Zooplankton
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  • 14
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    Oxford University Press
    Publikationsdatum: 2022-05-25
    Beschreibung: Author Posting. © Society of Systematic Biologists, 2006. This article is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Systematic Biology 55 (2006): 875-885, doi:10.1080/10635150601077683.
    Beschreibung: Penelope-like elements (PLEs) are a relatively little studied class of eukaryotic retroelements, distinguished by the presence of the GIY-YIG endonuclease domain, the ability of some representatives to retain introns, and the similarity of PLE-encoded reverse transcriptases to telomerases. Although these retrotransposons are abundant in many animal genomes, the reverse transcriptase moiety can also be found in several protists, fungi, and plants, indicating its ancient origin. A comprehensive phylogenetic analysis of PLEs was conducted, based on extended sequence alignments and a considerably expanded data set. PLEs exhibit the pattern of evolution similar to that of non-LTR retrotransposons, which form deep-branching clades dating back to the Precambrian era. However, PLEs seem to have experienced a much higher degree of lineage losses than non-LTR retrotransposons. It is suggested that PLEs and non-LTR retrotransposons are included into a larger eTPRT (eukaryotic target-primed) group of retroelements, characterized by 5' truncation, variable target-site duplication, and the potential of the 3' end to participate in formation of non-autonomous derivatives.
    Beschreibung: This work was supported by the U.S. National Science Foundation (MCB 0614142).
    Schlagwort(e): Penelope-like elements ; Retrotransposons ; Reverse transcriptase ; GIY-YIG endonuclease
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  • 15
    Publikationsdatum: 2022-05-25
    Beschreibung: © 2007 The Author(s). 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 Bioinformatics 23 (2007): 1434-1436, doi:10.1093/bioinformatics/btm109.
    Beschreibung: Web content syndication through standard formats such as RSS and ATOM has become an increasingly popular mechanism for publishers, news sources, and blogs to disseminate regularly updated content. These standardized syndication formats deliver content directly to the subscriber, allowing them to locally aggregate content from a variety of sources instead of having to find the information on multiple websites. The uBioRSS application is a "taxonomically intelligent" service customized for the biological sciences. It aggregates syndicated content from academic publishers and science news feeds, then uses a taxonomic name entity recognition algorithm to identify and index taxonomic names within those data streams. The resulting name index is cross-referenced to current global taxonomic datasets to provide context for browsing the publications by taxonomic group. This process, called taxonomic indexing, draws upon services developed specifically for biological sciences, collectively referred to as "taxonomic intelligence." Such value-added enhancements can provide biologists with accelerated and improved access to current biological content.
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  • 16
    Publikationsdatum: 2022-05-26
    Beschreibung: © 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
    Beschreibung: 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.
    Beschreibung: 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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  • 17
    Publikationsdatum: 2022-05-26
    Beschreibung: 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.
    Beschreibung: 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.
    Schlagwort(e): 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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  • 18
    Publikationsdatum: 2022-05-26
    Beschreibung: © 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.
    Beschreibung: 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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  • 19
    Publikationsdatum: 2022-05-26
    Beschreibung: Author Posting. © National Academy of Sciences, 1997. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 94 (1997): 13743-13748.
    Beschreibung: The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor through which halogenated aromatic hydrocarbons such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) cause altered gene expression and toxicity. The AHR belongs to the basic helix-loop-helix/Per-ARNT-Sim (bHLH-PAS) family of transcriptional regulatory proteins, whose members play key roles in development, circadian rhythmicity, and environmental homeostasis; however, the normal cellular function of the AHR is not yet known. As part of a phylogenetic approach to understanding the function and evolutionary origin of the AHR, we sequenced the PAS homology domain of AHRs from several species of early vertebrates and performed phylogenetic analyses of these AHR amino acid sequences in relation to mammalian AHRs and 24 other members of the PAS family. AHR sequences were identified in a teleost (the killifish Fundulus heteroclitus), two elasmobranch species (the skate Raja erinacea and the dogfish Mustelus canis), and a jawless fish (the lamprey Petromyzon marinus). Two putative AHR genes, designated AHR1 and AHR2, were found both in Fundulus and Mustelus. Phylogenetic analyses indicate that the AHR2 genes in these two species are orthologous, suggesting that an AHR gene duplication occurred early in vertebrate evolution and that multiple AHR genes may be present in other vertebrates. Database searches and phylogenetic analyses identified four putative PAS proteins in the nematode Caenorhabditis elegans, including possible AHR and ARNT homologs. Phylogenetic analysis of the PAS gene family reveals distinct clades containing both invertebrate and vertebrate PAS family members; the latter include paralogous sequences that we propose have arisen by gene duplication early in vertebrate evolution. Overall, our analyses indicate that the AHR is a phylogenetically ancient protein present in all living vertebrate groups (with a possible invertebrate homolog), thus providing an evolutionary perspective to the study of dioxin toxicity and AHR function.
    Beschreibung: This work was supported in part by the National Institute of Environmental Health Sciences (Grants R29 ES06272, F32 ES05644, and P42 ES07381), the Donaldson Charitable Trust, and a Christopher Haebler Frantz Fellowship (to M.A.S.).
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  • 20
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    Unbekannt
    American Institute of Physics
    Publikationsdatum: 2022-05-26
    Beschreibung: Author Posting. © American Institute of Physics, 2009. This article is posted here by permission of American Institute of Physics for personal use, not for redistribution. The definitive version was published in Physics Today 62 n.11 (2009): 39-44.
    Beschreibung: Most species of large whales are endangered because for centuries whaling fleets have decimated their populations. In the late 1960s, marine-mammal biologists discovered that fishermen setting nets for tuna in the Pacific Ocean were killing more than 100,000 dolphins a year. The cause of marine-mammal conservation became so popular at the dawn of the environmental movement that one of the first environmental accomplishments of the US Congress was to enact the Marine Mammal Protection Act of 1972, which prohibits the killing or injuring of marine mammals. Today, small remnant populations of whales, such as the North Atlantic right whale, are threatened by entanglement in fishing gear and collisions by ships. Indeed, marine biologists have estimated that hundreds of thousands of marine mammals are killed each year in fishing gear. Inadvertent effects of human activities can pose a serious risk to coastal populations, as evidenced by the recent extinction of the Chinese river dolphin due to fishing, pollution, and overdevelopment of the Yangtze River. A few decades ago, conservation efforts focused on reducing the intentional hunting of marine mammals. Nowadays, when hunts for marine mammals are better controlled, the slow degradation of habitat from a combination of sources may have a bigger impact. For example, biologists have documented cases in which the effects of coastal development—including noise, pollution, and dredging—have caused marine mammals to abandon critical breeding habitat. Noise in particular is at issue in legal actions that have been brought against the US Navy for sonar exercises that may have caused whales to strand and die.
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  • 21
    facet.materialart.
    Unbekannt
    Oxford University Press
    In:  Handbook of Avian Hybrids of the World vol. 76, 1, pp. 59-61
    Publikationsdatum: 2024-01-12
    Schlagwort(e): book review ; geographic distribution ; hybridisation ; birds
    Repository-Name: National Museum of Natural History, Netherlands
    Materialart: info:eu-repo/semantics/review
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  • 22
    facet.materialart.
    Unbekannt
    American Association for the Advancement of Science (AAAS)
    In:  EPIC3Science, American Association for the Advancement of Science (AAAS), 310(5752), pp. 1299-1299, ISSN: 0036-8075
    Publikationsdatum: 2023-06-13
    Beschreibung: 〈jats:p〉Sustained harmonic tremor signals were recorded by the seismographs of the German Neumayer Base seismological network in western Dronning Maud Land, Antarctica. These tremor episodes, lasting up to 16 hours, were recorded up to 820 kilometers from the source. Their spectra show narrow peaks with fundamental frequencies ranging from 0.5 to 6 hertz, more than 30 integer harmonic overtones, and frequency gliding, resembling volcanic tremor. Frequency‐wave number analysis suggested a moving source, which was recognized as iceberg B-09A traveling along the coast of eastern Antarctica. The most probable tremor sources are fluid-flow‐induced vibrations inside the iceberg's tunnel/crevasse systems.〈/jats:p〉
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , isiRev
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  • 23
    Digitale Medien
    Digitale Medien
    Woodbury, NY : American Institute of Physics
    ISSN: 1089-7682
    Quelle: AIP Digital Archive
    Thema: Physik , Elektrotechnik, Elektronik, Nachrichtentechnik
    Notizen: A quarterly journal devoted to increasing the understanding of nonlinear phenomena and describing the manifestations in a manner comprehensible to researchers from a broad spectrum of disciplines
    Materialart: Digitale Medien
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  • 24
    ISSN: 1089-7674
    Quelle: AIP Digital Archive
    Thema: Physik , Elektrotechnik, Elektronik, Nachrichtentechnik
    Notizen: The journal features concise, up-to-date reports on significant new findings in applied physics. Emphasizing rapid dissemination for key data and new physical insights, Physics of Plasmas offers prompt publication of new experimental and theoretical papers bearing on applications of physics phenomena to all branches of science, engineering, and modern technology. The journal emphasizes coverage of significant new topics, such as in recent years, high-Tc superconductors, diamond films, porous silicon, and fullerenes. It prints papers which report results of research in nuclear physics and related fields such as nuclear astrophysics.
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  • 25
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 1059-1066 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: New methods of diffraction stress analysis of polycrystalline materials, consisting of cubic elastically anisotropic crystallites, are proposed and compared with existing methods. Whereas for the existing methods knowledge of the diffraction elastic constants is presupposed, three new methods are presented that require only knowledge of the (macroscopic) mechanical elastic constants. The stress values obtained with these new methods on the basis of the mechanical elastic constants are more reliable than those obtained with the methods on the basis of the diffraction elastic constants. New and existing methods are illustrated by means of measurements of X-ray diffraction from a magnetron-sputtered TiN layer.
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  • 26
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 1102-1112 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Electron crystallography on multilayered three-dimensional microcrystals has been limited in application by the need to define precisely the three-dimensional shape of the diffraction density profiles. A new method is presented here to obtain this profile from experimental spot positions which are shifted in a characteristic way from the expected Bragg positions. While the Bragg positions are defined by the diffraction geometry, the characteristic shift additionally depends on the density profile in Fourier space. In general, these two effects are intermingled. A new correlation approach is presented which uses characteristic shift patterns to separate these effects. This technique also allows the determination of all three crystallographic unit-cell dimensions from a single tilted electron diffraction pattern. It was tested on simulated diffraction patterns and applied to experimental data of frozen hydrated crystals of the protein catalase. Since multilayered catalase crystals with different numbers of crystallographic layers were studied, an inhomogeneous data set had to be evaluated. Processing of such data is now possible using the new correlation approach.
    Materialart: Digitale Medien
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  • 27
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 1136-1142 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Based on the analysis of geometric relations, it is found that the amplitude of the distortion of the full width at half-maximum (FWHM) of a peak after smoothing is the largest among the distortions of the seven parameters of a peak: maximum intensity, FWHM, shape, asymmetry, integral intensity, peak position and integral width. Hence the FWHM distortion is used as a criterion of smoothing. The 1% and 5% error limits of smoothing are calculated. Quadratic and quartic polynomial Savitzky–Golay filters are compared. Aberrations of an X-ray diffraction (XRD) peak caused by using double, matched, 1.5 and 0.7 FWHM filters are described in more detail by means of the analyses of internal and external factors. It is found that the smoothing-induced distortions of an actual XRD peak trend towards those of ideal curves. The distortions are classified according to three types of peak. A possible method to obtain the actual peak parameters, called `system smoothing refinement', is presented.
    Materialart: Digitale Medien
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  • 28
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 1154-1161 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Despite advances in computer technology, computing in macromolecular crystallography keeps pace in its demand for CPU power. Improvements in CPU speed, together with advances in computing methods that depend on it, often translate into the possibility to solve structures that would otherwise require additional experiments. Programs for data reduction, molecular-replacement programs employing multidimensional searches on a grid in real, Patterson or reciprocal space, and phasing and refinement programs, currently have, among others, the highest requirements for CPU power. For these and other programs, speed-up of calculations as a result of parallel execution on multiprocessor computers is possible. This paper outlines the use of the OpenMP programming interface and reports its successful application for parallelization of ESSENS [Kleywegt & Jones (1997). Acta Cryst. D53, 179–185] and SHELXL [Schneider & Sheldrick (1997). Methods Enzymol. 277, 319–343]. Parallel computing, which is possible as a result of the inherent parallelism of crystallographic algorithms, extends the range of problems in macromolecular crystallography that programs can be applied to and can significantly reduce the time required for progressing from a data set to a refined model.
    Materialart: Digitale Medien
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  • 29
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 1189-1189 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Materialart: Digitale Medien
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  • 30
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 1190-1191 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Materialart: Digitale Medien
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  • 31
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 380-386 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Linear and nonlinear optical properties of the four isomorphic orthorhombic (point group mm2) potassium rare earth nitrates K2[RE(NO3)5(H2O)2], with RE = La, Ce, Pr or Nd, have been investigated. Refractive indices in a wavelength range from 0.35 to 2.5 µm and the transmission spectra between 0.25 to 3.0 µm were measured. Using the Maker fringe technique, the d_{ijk}^{\rm\, SHG} coefficients of second-harmonic generation for a fundamental of the Nd–YAP laser (λ = 1079.5 nm) were determined for all four compounds. The d_{ijk}^{\rm\, SHG} coefficients of all four substances are about three times larger than those of KDP, as was first published by Ebbers et al. [IEEE J. Quantum Electron. (1993), 29, 497–507] for K2[La(NO3)5(H2O)2]. These nitrates are promising materials for application to nonlinear optics (e.g. second-harmonic generation of Nd laser radiation). The nonlinear optical properties of these compounds seem to have their origin mainly in the nitrate groups, as indicated by a simple model (summing the molecular hyperpolarizabilities of the NO3 group). Neglecting local field effects, the hyperpolarizability of the NO3 group was calculated as β222 = 2.52 × 10−40 m4 V−1.
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  • 32
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: In the molecular structure of tetraferrocenyl-[3]-cumulene, (Fc)2C=C=C=C(Fc)2, four ferrocene molecules are connected via a linear bridge consisting of four carbon atoms. At room temperature, the crystal structure has space group P21/a (Z = 1) with a = 13.104 (5), b = 6.121 (2), c = 11.194 (4) Å, β = 114.922 (1)° and V = 814.3 (8) Å3. A phase transition during cooling was not observed from room temperature to 75 K. From high-resolution X-ray powder diffraction data, the structure of the room-temperature phase was solved by the method of simulated annealing and refined by the Rietveld method using rigid bodies and restraints. The crystal structure was found to be highly disordered with the molecules occupying two orientations with equal probability and a 50% occupancy of the carbon atoms in the cumulene bridge. The disorder could be modelled by stacking faults in ordered structures. In contrast to other compounds of this class, the ferrocenyl groups are in a syn rather than in an up–down conformation with respect to the cumulene bridge.
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  • 33
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 1212-1216 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: The structure of colloidal particles can be studied with small-angle X-ray and neutron scattering (SAXS and SANS). In the case of randomly oriented systems, the indirect Fourier transformation (IFT) is a well established technique for the calculation of model-free real-space information. Interaction leads to an overlap of inter- and intraparticle scattering effects, preventing most detailed interpretations. The recently developed generalized indirect Fourier transformation (GIFT) technique allows these effects to be separated by assuming various models for the interaction, i.e. the so-called structure factors. The different analytical behaviour of these structure factors from that of the form factors, describing the intraparticle scattering, allows this separation. The mean-deviation surface is defined by the quality of the fit for different parameter sets of the structure factor. Its global minimum represents the solution. The former non-linear least-squares approach has proved to be inefficient and not very reliable. In this paper, the incorporation of the completely different Boltzmann simplex simulated annealing (BSSA) algorithm for finding the global minimum of the hypersurface is presented. This new method increases not only the calculation speed but also the reliability of the evaluation.
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  • 34
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 1241-1245 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: A synchrotron radiation X-ray powder diffractometer for samples of very small amount has been developed to collect high-quality diffraction patterns under extreme conditions, i.e. at low temperature and/or high pressure. A new cylindrical imaging plate (CIP) is used as a detector, in addition to a conventional flat-type imaging plate (FIP). By using the CIP system, the diffraction data in a diffraction angle range −44 ≤ 2θ ≤ 122° are collected with a dynamic range of about 106. The alignment of the diffractometer, measurement and analysis are automatically operated by a workstation. A performance test shows that the CIP system has spatial resolution of about 0.07° with a dynamic range of 106. The diffraction pattern of a standard sample of Si measured by the CIP system has high quality; the refinement of the structure reaches Rw = 3.68% even in the case of a small amount of sample (about 2 µg) and a short exposure time (60 s). Examples of experiments at low temperatures under ambient and high pressures are also presented.
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  • 35
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 1194-1194 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Materialart: Digitale Medien
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  • 36
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 1208-1211 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Accidental overlap constitutes one of the principal limitations for the solution of crystal structures from powder diffraction data, since it reduces the number of available intensities for direct-methods application. In this work, the field of application of the direct-methods sum function is extended to cope with powder patterns with relatively large amounts of accidental overlap. This is achieved by refining not only the phases of the structure factors but also the estimated intensities of the severely overlapped peaks during the structure solution process. This procedure has been specifically devised for inorganic compounds with uncertain cell contents and with probable severe atomic disorder, a situation often found when studying complex minerals with limited crystallinity. It has been successfully applied to the solution of the previously unknown crystal structure of the mineral tinticite. Finally, an estimation of the smallest ratio (number of observations to number of variables) for the procedure to be successful is given.
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  • 37
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 1231-1240 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: A waveguide microdiffraction setup is described for an undulator beamline at the European Synchrotron Radiation Facility. The composite optics consists of a waveguide, which confines the beam vertically, and a horizontally focusing multilayer mirror. A beam size of about 0.1 × 3 µm (vertical × horizontal) at λ = 0.095 nm has been obtained. The sample stage comprises a three-axis gantry with micrometre precision and a three-axis piezo-scanner with about 0.1 µm repeatability. Diffraction experiments are demonstrated for selected inorganic and polymeric samples. Possibilities for scanning diffractometry and small-angle scattering experiments are discussed.
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  • 38
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 1253-1261 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Small-angle neutron scattering (SANS) measurements have been performed on long-flight-path pinhole-collimation SANS instruments using, as a two-dimensional position-sensitive detector, both a neutron imaging plate, incorporating gadolinium, and a two-step transfer method, with dysprosium foil as the image transfer medium. The measurements are compared with corresponding data taken using conventional position-sensitive gas proportional counters on the SANS instruments in order to assess the viability of the imaging techniques. The imaging plates have pixel sizes of about two orders of magnitude smaller than those of the gas proportional counter. The reduced pixel size provides definite advantages over the gas counter in certain specific situations, namely when limited space necessitates a short sample-to-detector distance, when only small samples (comparable in size to the detector pixels) are available, or when used in conjunction with focusing beam optics.
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  • 39
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 1302-1302 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Materialart: Digitale Medien
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  • 40
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 1311-1316 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: The formula of the pseudo-Voigt function expressed by a weighted sum of Gaussian and Lorentzian functions is extended by adding two other types of peak functions in order to improve the accuracy when approximating the Voigt profile. The full width at half-maximum (FWHM) values and mixing parameters of the Gaussian, the Lorentzian and the other two component functions in the extended formula can be approximated by polynomials of a parameter ρ = ΓL/(ΓG + ΓL), where ΓG and ΓL are the FWHM values of the deconvoluted Gaussian and Lorentzian functions, respectively. The maximum deviation of the extended pseudo-Voigt function from the Voigt profile is within 0.12% relative to the peak height when sixth-order polynomial expansions are used. The systematic errors of the integrated intensity ΓG and ΓL, estimated by fitting the extended formula to Voigt profiles, are typically less than 1/10 of the errors arising from the application of the original formula of the pseudo-Voigt approximation proposed by Thompson et al. [J. Appl. Cryst. (1987), 20, 79–83], while the time required for computation of the extended formula is only about 2.5 relative to the computation time required for the original formula.
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  • 41
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 1335-1341 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Nanometre-sized particles are of considerable current interest because of their special size-dependent physical properties. Debye–Scherrer diffraction patterns are often used to characterize samples, as well as to probe the structure of nanoparticles. Unfortunately, the well known `Scherrer formula' is unreliable at estimating particle size, because the assumption of an underlying crystal structure (translational symmetry) is often invalid. A simple approach is presented here which takes the Fourier transform of a Debye–Scherrer diffraction pattern. The method works well on noisy data and when only a narrow range of scattering angles is available.
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  • 42
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 1393-1398 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: It is now possible to build new types of optical elements for neutron beams. These include monochromating crystals with rectangular mosaic profiles, `gradient' monochromating crystals with varying lattice spacing, and collimators with rectangular profiles. Phase-space methods are used to describe the resolution of a combination of two collimators and a monochromating crystal for various combinations of novel beam elements. The description of rectangular-profile elements in this formalism considerably simplifies the normal description of resolution effects and should thus prove useful as a teaching tool.
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  • 43
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 1405-1414 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Expressions for the calculation of multiple-diffraction patterns observed in ω–ψ scans of Bragg reflections are derived within the framework of the kinematical theory, taking into account the divergence and wavelength-spread of the incident beam as well as the mosaicity of the crystal sample. The theoretical results can be applied to X-ray tube radiation as well as synchrotron radiation experiments. A 189.9° experimental Cu Kα \bar2\bar2\bar2 ω–ψ scan of diamond is compared with the corresponding theoretical multiple-diffraction pattern.
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  • 44
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 1447-1447 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Comments are made on a paper by E. Rossmanith [J. Appl. Cryst. (2000), 33, 330–333] concerning the use of asymptotic expressions for the extinction-corrected mean thickness.
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  • 45
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 1450-1450 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Materialart: Digitale Medien
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  • 46
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 20-26 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Contrast is associated with micropipes in X-ray topographs of SiC crystals obtained with prismatic reflections, representing an apparent violation of the g·b = 0 invisibility criterion. This is explained as a population of basal-plane dislocations with Burgers vectors of the set b = {\textstyle{1 \over 3}}〈11{\bar{2}}0〉 that occur in a high density within a few micrometers of the micropipes, below the resolution of X-ray topography. These basal-plane dislocations could be observed under an electron microscope. The presence of the surfaces of the micropipes influences the dislocation images in the topographs taken with prismatic reflections, often resulting in a band of light contrast along the axes of the micropipes.
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  • 47
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 33-41 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: A method is presented for automated best-matching alignment of three-dimensional models represented by ensembles of points. A normalized spatial discrepancy (NSD) is introduced as a proximity measure between three-dimensional objects. Starting from an inertia-axes alignment, the algorithm minimizes the NSD; the final value of the NSD provides a quantitative estimate of similarity between the objects. The method is implemented in a computer program. Simulations have been performed to test its performance on model structures with specified numbers of points ranging from a few to a few thousand. The method can be used for comparative analysis of structural models obtained by different methods, e.g. of high-resolution crystallographic atomic structures and low-resolution models from solution scattering or electron microscopy.
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  • 48
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 1450-1450 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Materialart: Digitale Medien
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  • 49
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 1450-1450 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Materialart: Digitale Medien
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  • 50
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 16-19 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Texture effects caused by preferred orientation can be corrected in Rietveld analysis by an alternative algorithm presented in this contribution. This algorithm is equivalent to models using symmetrized linear combinations of spherical harmonic functions, but it is unique to all Laue classes and to all orders. Positive definiteness of the polar-axis density is achieved by the exponential method. The outlined algorithm was tested during Rietveld refinement of selected polycrystal samples. The algorithm was proven to be numerically robust and satisfactorily described deviations from the ideal intensity ratios of the Bragg reflections caused by the texture of the samples.
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  • 51
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 76-79 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: As the combination of high-intensity synchrotron sources and area detectors allows collection of large data sets in a much shorter time span than previously possible, the use of open helium gas-flow systems is much facilitated. A flow system installed at the SUNY X3 synchrotron beamline at the National Synchrotron Light Source has been used for collection of a number of large data sets at a temperature of ∼16 K. Instability problems encountered when using a helium cryostat for three-dimensional data collection are eliminated. Details of the equipment, its temperature calibration and a typical result are described.
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  • 52
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: The bond energy constant of methionine Sδ—Cε, 170.066 kcal mol−1 Å−2, is given as a default value in X-ray protein structure refinement with X-PLOR [Brünger (1992). X-PLOR Version 3.1. A system for X-ray Crystallography and NMR. New York University Press]. When the atomic parameters of 3564 amino acid residues of bovine heart cytochrome c oxidase were refined at 2.0 Å resolution by using X-PLOR with default restraining parameters, 36 bond lengths deviated by over 0.06 Å from their ideal values. Out of the 36 bonds, 25 were methionine Sδ—Cε bonds. Refinement with an energy parameter of 500.0 kcal mol−1 Å−2 for the methionine Sδ—Cε bond resulted in convergence of the Sδ—Cε bond lengths to within 0.06 Å from their ideal values and reduced the crystallographic R and free-R factors by 0.6 and 0.3%, respectively. Consequently, a strong bond energy constant for Sδ—Cε of 500.0 kcal mol−1 Å−2 is recommended instead of the default value of 170.066 kcal mol−1 Å−2.
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  • 53
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 89-94 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Materialart: Digitale Medien
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  • 54
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 114-118 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: The Rietveld method has proved to be a very effective means to characterize and quantify the crystalline phases and the amorphous phase in glass ceramic materials using X-ray powder diffraction data. The technique was applied to a borosilicate glass of the type used for high-level nuclear-waste containment, in order to measure the proportions of the crystallized phases after heat treatment and, thus, to qualify the thermal stability of the glass. Six crystalline phases were analysed in this way in an almost entirely (〉95 wt%) amorphous material after adding a known proportion of an internal standard (TiO2). The quantitative analyses were corrected to allow for microabsorption effects resulting from grain-size and absorption-contrast effects. In addition to the quantitative data, unit-cell parameters and site-occupancy refinements revealed solid-solution and substitution phenomena in the crystal.
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  • 55
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 478-482 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: NiO-based xerogels were prepared by sol-gel processing starting from the NiCl2-BuOH-H2O system. Structural features associated to the porosity of xerogels were studied by small-angle X-ray scattering. Xerogels heat-treated at low temperatures (423 and 573 K) are composed of hydrated NiCl2 small crystals and exhibit an essentially single mode nanoporous structure with an average pore radius of ∼75 Å. Xerogels heat-treated at 973 and 1173 K are composed of aggregates of NiO crystals which only contain intergrain mesopores with radii exceeding 200 Å. A mixture of phases is observed in xerogels heat-treated at 773 K. Xerogels with a water concentration of 2 mol/(mol NiCl2) exhibit a narrow nanopore size distribution. Water concentrations higher or lower than 2 mol promote the formation of nanoporous structures with wider size distributions.
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  • 56
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 483-487 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: The sintering behaviour of two new types of coated ceramics, made from alumina grains coated with a zirconia shell and from zirconia grains coated with an alumina shell, was analyzed with small angle neutron scattering (SANS). Measurements were performed both for the plain samples, and with contrast variation using D2 O as immersion liquid. The size distribution and the volume fraction of grains and pores were determined from the corrected scattering curves using a direct model fitting, applying two different approaches, a sphere model and a combined sphere/spherical shell model. Results are discussed in context with the macroscopic density of the samples. The sintering behaviour of the two ceramics types was found to be very different.
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  • 57
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 488-491 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: In-situ small-angle neutron scattering was performed on polycrystals and single crystals of Ni-10 to 12 at.% Ti at temperatures between 900 and 1240 K. A plateau in the integrated intensity as a function of aging time for polycrystalline Ni-11.3 at.% Ti at 900 K indicates the presence of a precursor state γ'' preceding the formation of the metastable γ' state, with a Ti concentration of 16.5(1.0) at.% in the particles. In the scattering patterns of a Ni-12.0 at.% Ti single crystal aged at 1200 and 1240 K, strong scattering intensities along 〈100〉 related to the coherent γ''/γ' states, and sharp streaks along 〈111〉 related to plates of the stable η phase appear successively. At 1240 K, the presence of the L12-related intensities along 〈100〉 is unexpected, as this temperature lies above the metastable miscibility gap suggested in the literature.
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  • 58
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 492-495 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: The glass with composition 13Na2O-11CaO-76SiO2 (mol%) undergoes subliquidus phase separation via a binodal mechanism. At temperatures below the binodal temperature, Tb = 978 K, the glass separates into two amorphous phases, silica-enriched droplets and a silica-poor matrix. Small-angle X-ray scattering was used to study the formation of the droplet phase at 923 K as well as the process of reversion where the precipitates dissolve after an increase in temperature. After a heat treatment of 48 h at 923 K the system is in the stage of coarsening. However, the equilibrium volume fraction of the droplet phase, we = 0.073, has not yet precipitated. The reversion of the droplets was studied at T = 983 K and T = 963 K. For T 〉 Tb, the precipitates dissolve completely by an interdiffusion process resulting in a decrease of the silica concentration of the droplets, while the phase boundary is preserved over long times. For T 〈 Tb, the reversion process shows two distinct stages. In the first stage, the silica concentration inside the droplets decreases and all precipitates shrink until the concentration in the matrix reaches its new equilibrium value. Afterwards, the largest droplets grow again by slow coarsening.
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  • 59
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 496-499 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Zirconia precursor gels, prepared in the zirconium n-propoxide, n-propanol, acetylacetone and water system, are studied by small angle X-ray scattering (SAXS). The SAXS intensity pattern exhibits a pronounced maximum for a scattering vector q different from zero. The intensity maximum of the finite q-vector peak increases during gelation while its position qm moves towards smaller and smaller q—vectors. The SAXS intensity distribution is well accounted for by recent direct numerical calculations of diffusion-limited cluster aggregation (DLCA). The structural aspects of cluster growth can be described by scaling assumptions. The position qm of the intensity maximum and the structure function S(q/qm,t) are shown to scale according to S(q/qm,t) = qm(t)−d F(q/qm) where F(q/qm) is a time-independent scaling function. This scaling requires d=Df, the fractal dimension of the clusters, instead of d=3 for spinodal decomposition. The gel structure is made up of connected fractal clusters, around 50 nm in size, with an apparent fractal dimension of 1.7, resulting from the aggregation of very small primary particles about 2.5 nm in diameter.
    Materialart: Digitale Medien
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  • 60
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 500-503 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Small-angle neutron scattering experiments were performed on the bulk amorphous alloy Zr41.2Ti13.8Cu12.5Ni10Be22.5 (Vit1®, subscripts indicate at.%) and on other alloys, where the (Zr,Ti) and (Cu,Be) contents were varied by following the line in composition space connecting Vit1 and Zr46.8Ti8.2Cu7.5Ni10Be27.5 (Vit4®). The small-angle neutron scattering data of the samples, annealed at temperatures between 603 K and 663 K, show interference peaks, giving evidence for spatially correlated arrangements of inhomogeneities. The Q values of the interference peaks, Qmax, decrease with increasing annealing temperature Ta and, at a given annealing temperature, with composition following the connecting line from Vit1 to Vit4. Down to the glass transition temperature Tg, the data follow a relation 1/L2 ∝ (Ts − Ta) as predicted by the linearized Cahn theory, with L = 2π/Qmax the characteristic wavelength of the decomposition and Ts the apparent spinodal temperature. Below Tg, a different behavior is observed, which may be either due to a change in atomic diffusion or due to an insufficient relaxation of the samples.
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  • 61
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 504-506 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Results obtained using the Brunauer-Emmett-Teller method, small-angle x-ray scattering and wide angle x-ray diffraction in the study of porous silicon are compared. The BET method seems to fail when the porosity of samples is smaller than 50%, giving unrealistically large values for the specific surface area, but giving results similar to SAXS when the porosity is larger than 50%. In the comparison of the WAXD and SAXS data quite large differences between the average particle size and chord length were observed in low-porosity samples. The possible origin of the differences is discussed.
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  • 62
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 507-510 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: MgAl2O4 nanoparticles have been prepared using a microemulsion synthesis technique (ME) and a chemical vapour deposition (CVD) approach. In the wet-chemical route, the chain length of the surfactant molecules used to stabilise the microemulsion as well as the annealing conditions (temperature and time) after preparation were varied. For CVD samples, the influence of the target temperature and the consecutive annealing temperature were investigated. A pinhole small-angle X-ray scattering camera was employed to determine the size and size distribution of primary particles as well as agglomerates. ME material is primarily obtained in the form of amorphous non-agglomerated particles; CVD raw material is crystalline and agglomerated. Upon annealing, agglomerates of ME material form and then grow faster than the primary particles do; in CVD material the agglomerates do not grow. Agglomeration is suppressed if the CVD process is carried out at elevated target temperature.
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  • 63
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 511-514 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Molecular structure of pathologically changed biological tissue differs greatly from the normal one. It gives the opportunity to diagnose different diseases by using methods of structural tissue analysis. The present paper is based on Ultra-Low Angle X-ray (ULAX) coherent scattering data from 1000 paired samples of mammary gland tissue dissected during the surgical treatment from 500 patients with different types of breast tumours (malignant or benign) and tumour-like formations (fibrocystic change). The medical data (histological and histostereometrical analysis) and the digital scattering information have been compared by regression analysis to produce the scattering pattern recognition code that demonstrates the high sensitivity of the ULAX method.
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  • 64
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Three different small-angle neutron scattering facilities, the "YUMO" camera at JINR (Dubna, Russia), the V4 camera at HMI (Berlin, Germany) and D11 camera at ILL (Grenoble, France), were used in the investigation of 30S ribosomal subunit from Thermus thermophilus. Parallel X-ray measurements on X33 camera at DESY (Hamburg, Germany) were used to control the identity of deuterated particles. The neutron and x-ray contrast variation data were interpreted by direct method using spherical harmonics. Structural models of the 30S ribosomal subunit from Thermus thermophilus and its RNA -rich core with the resolution 3.5 nm were constructed. A comparison between the 30S Thermus thermophilus and 30S E.coli models shows that primary difference between them consists in the special distributions of the protein component whereas the special distributions of the RNA component coincide well in both models.
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  • 65
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 524-525 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Materialart: Digitale Medien
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  • 66
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 519-523 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: X-ray crystallography is the single most powerful method for the determination of accurate and precise macromolecular structures. The study of macromolecular motions, however, is, despite some successes with time-resolved crystallography not within the realms of the method. Further, the study of large macromolecular complexes sometimes poses tremendous problems of various kinds for x-ray crystallography and many laboratories approach large structures by solving individual domains. We herein present two examples employing small-angle x-ray and/or neutron scattering (SAXS, SANS) to study (i) conformational changes, and (ii) protein-lipid complexes complementing information from x-ray crystallography. The structural changes of creatine kinase upon substrate binding were investigated as an example of conformational changes not comprehensible from crystallography in the absence of crystal structures of the substrate-ligated enzyme. We also present studies of apolipoprotein E, reconstituted with lipid, in which a combined approach using SAXS/SANS, x-ray crystallography and other techniques yields a model of the complex not accessible by either of the methods alone.
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  • 67
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 526-529 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: We have measured the static form factor of superhelical DNA by SANS in dilute aqueous solution as a function of salt concentration. Theoretical static form factors were calculated by Monte Carlo simulations. Simulated and measured form factors are in very good agreement and can be interpreted in terms of the superhelix diameter, which decreases from (16.0±0.9) nm at 10 mM to (9.0±0.7) nm at 100 mM Na+ concentration. This result contradicts a lateral collapse of the DNA superhelix in physiological salt concentrations as recently found by cryo-electron microscopy.
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  • 68
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 530-534 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: A method for ab initio low-resolution shape and internal structure retrieval from contrast variation solution scattering data is described. The method uses a multiphase model of a particle build from densely packed dummy atoms and employs simulated annealing to find a compact interconnected configuration of phases that fits the available experimental data. In the particular case of a single phase particle (shape determination) the method is compared to another ab initio method using low resolution envelope functions. Examples of the shape determination of several proteins from experimental X-ray scattering data are presented.
    Materialart: Digitale Medien
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  • 69
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 540-543 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: We have investigated the scattering properties of mixtures of aggregated-whey-protein colloid (AWC) particles and an exocellular polysaccharide (EPS) from a lactic acid bacterium. Exceeding a certain concentration leads to a phase separation, which can be explained by an effective depletion attraction between the AWCs due to non-adsorbing EPS. The measured scattering intensity of a AWC/EPS mixture shows that the structure factor of the AWC particles increases at low wave vectors with increasing EPS concentration. The measurements can be described qualitatively in terms of the structure factor, calculated using integral theory including an expression for the depletion interaction potential.
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  • 70
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 480-483 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Planarity and similarity restraints are described using a unified framework for the computation layout. In both cases, the gradient and Hessian of the restraint residual with respect to atomic coordinates are derived. All computed quantities (residual, gradient, Hessian, normal and distance to the plane for planarity restraints, rotation and translation in the case of similarity) can be obtained directly, without iterative procedure.
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  • 71
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 613-624 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: A Monte Carlo code for the simulation of neutron strain scanning experiments on a reactor-based two-axis diffractometer is described. In order to validate this code, several experiments have been performed. A comparison is made between experimental and simulated results for instrumental resolution, primary beam divergence and wavelength distribution in the incident neutron beam. Finally, the application of the simulation results to the analysis of a real neutron strain scanning experiment is outlined.
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  • 72
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 608-612 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: The possibility of finding, for a given X-ray wavelength, the conditions for obtaining multiple coplanar reflections in a single block of crystal is investigated. It is found that by introducing a small relative tilt between two parts of the crystal, the conditions for a high-resolution X-ray monochromator for conventional and synchrotron X-ray sources can be obtained. The design of a new high-resolution monochromator–collimator based on a single crystal, which takes advantage of the existence for almost any wavelength of n and m planes in the single crystal that lie near the Bragg condition, is presented. A weak link between the two reflecting surfaces is used to align the crystal planes and to obtain efficient reflections in the dispersive configuration. DuMond diagrams are used to evaluate the total diffracted intensity and the resolution of such a monochromator. The experimental results obtained from prototypes made of single crystals of silicon and germanium are in good agreement with theoretical predictions. This new type of monochromator offers the advantages of a compact design and simple alignment.
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  • 73
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 646-653 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: The use of bent asymmetric Laue crystals to focus synchrotron X-rays sagittally from 15 to 50 keV is described. A four-bar bender, bending a rectangular planar crystal, produced the necessary sagittal and meridional bending for this unique application. Adjustments of the tilt angle and height of the bent crystal resulted in first- and second-order corrections, respectively, to the dependence of the angle of diffraction on the horizontal position on the crystal. After these corrections, the remaining variation of the diffraction angle was of the order of 10 µrad. The theoretical sagittal focal length was verified. A prototype of a double-crystal sagittally focusing monochromator was constructed and tested, using two identical Laue crystals. A horizontal divergence of 3 mrad was focused to a horizontal dimension of about 0.4 mm. The X-ray flux density at the focus was a few hundred times larger than that of unfocused X-rays.
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  • 74
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 663-665 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: In past years, both experimental and analytical approaches have been developed for eliminating preferred orientation effects on powder X-ray diffraction patterns. The state of the art does not allow one to face the problem without difficult sample treatments, mechanical randomization, pole-figure study or pattern fitting based on the Rietveld approach. These methods are time consuming or need the knowledge of all the structural parameters, and, moreover, must be managed by specialized operators. Besides, none of the above techniques can be applied to powder samples of drugs loaded into polymeric carriers, the diffraction patterns of which present a structured amorphous halo from which the crystalline drug peaks rise up. In this paper, it is shown that micro X-ray diffraction on capillary powder samples, combined with a two-dimensional detector, is a promising solution to preferred orientation problems, since it provides easy and rapid preparation of randomly oriented powder samples, fast measurements (acquisition times of a few minutes) and correct powder diffraction patterns.
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  • 75
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 691-698 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: A modified least-squares analysis is presented that allows reliable structural parameters to be extracted from a powder diffraction pattern even in the presence of a substantial unmodelled impurity contribution. The algorithm is developed within the context of Bayesian probability theory. Experimental points that fall above those calculated, and are thus more probably from impurity peaks, are systematically down-weighted. This approach is illustrated with a two-phase example.
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  • 76
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 681-690 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: A new method for analysing X-ray peak broadening caused by compositional fluctuation is proposed. The method is applicable to epitaxial layers with diamond or zinc-blende structure on (001) substrates. In the new method, a rescaling procedure with a difference variable ΔA is applied to measured X-ray profiles and the dependence of the profiles on various reflection indices hkl is analysed. The theoretical formula reveals that X-ray peak profiles become independent of hkl after the rescaling. A new criterion is proposed; an experimental examination based on the criterion makes it possible simply to judge whether or not X-ray peak broadening is caused by compositional fluctuation. The method is verified experimentally and demonstrated by applying it to an InGaAs multilayer sample having artificial compositional fluctuation.
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  • 77
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 577-581 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: In this study small angle neutron scattering was used to characterize the formation of micelles in aqueous solutions of the detergents DMG and SPC as a function of detergent concentration and ionic strength of the solvent. The effects on the micelle structure of the additives glycerol and PEG, alone as well as in combination typical for membrane protein crystallization, were also explored. This study suggests that the micelles are rod-like in form at the concentrations studied. The size of the micelles was observed to increase with increasing ionic strength but decrease with the addition of glycerol or PEG.
    Materialart: Digitale Medien
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  • 78
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 569-573 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: We applied small-angle neutron scattering (SANS) contrast variation to samples where a microphase separation occurred. The samples contain multilamellar vesicles in equilibrium with excess "solvent" that produce a very common powder pattern in SANS: a Debye-Sherrer ring produced by the regular bilayer packing superposed to a sharply decaying Porod behaviour. These two features of the SANS pattern have distinct contrast match points (CMP). We exploit here the small angle signal to determine the partition of sugars between two coexisting microphases. The net result is an exclusion of small sugar molecules from the liquid crystalline domains of the sample. We discuss this exclusion in relation with the observed maximum swelling, headgroup hydration and bilayer softening induced by the presence of the sugar molecules.
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  • 79
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 582-586 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: We have developed a cell allowing in situ measurement of the osmotic pressure of solutions under Ultra Small-Angle X-ray Scattering (USAXS) examination. The coupled set-up made of a Bonse/Hart camera and a deionisation close circuit allows the combined determination of the structure factor and the equation of state of colloidal suspensions. A precise control of ions concentration inside the reservoir allows to vary the ionic strength of the suspensions from the very pure case of colloidal crystals to sols with tunable screening of electrostatic repulsive interactions. We describe in detail the experimental set-ups and the data treatment methodology that we have been developing in the last years to allow detailed measurements of interactions and correlations between spherical particles. A review of our recent results obtained on the model system of negatively charged parabromostyrene latex particles forming solutions, crystals and microcrystals, is given as an illustration.
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  • 80
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 574-576 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: We discuss the analysis of the volume transition in thermosensitive colloidal core-shell particles by synchrotron small-angle X-ray scattering. The latex-particles are dispersed in water and consist of a solid poly(styrene) core (diameter: 107 nm) and a shell of a thermosensitive crosslinked polymer chains. The thermosensitive shell is built up from poly(N-isopropylacrylamide) chains (PNIPA) crosslinked by N,N'-methylenbisacrylamide (BIS). The scattering intensities measured as function of temperature may be decomposed into a part deriving from the overall structure and a part originating from the fluctuations within the network. The analysis of the overall structure leads to the volume fraction of the swollen network at different temperatures. The intensity caused by the fluctuations of the network becomes the leading contribution at high scattering angles. It may be described by a Lorentzian below and above the volume transition. The analysis demonstrates that critical fluctuations of the network around the transition temperature are fully suppressed. This finding is explained by the strong steric constraint of the network by its confinement within a shell of colloidal dimensions: i) The swelling and shrinking can only take place along the radial direction, and ii) the chains are bound to the solid surface of the cores which remains constant during the transition.
    Materialart: Digitale Medien
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  • 81
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 34 (2001), S. 737-743 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Much of crystallography is concerned with the accurate location of the centre of diffraction peak profiles. Simple analytical expressions are derived for estimating the precision of diffraction peak location that can be achieved for Gaussian diffraction peaks with a flat background, in terms of the standard deviation, integrated intensity and peak height (H) to background (B) ratio. Two formulations are derived using standard methods: one for the case of very low background, the other for significant backgrounds. It is found that in cases of significant background, peak position is less well determined by a factor of [1+2(21/2)B/H]1/2 compared with the case of no background. The applicability of the expression has been demonstrated by Monte Carlo simulation of Gaussian profiles and by the analysis of real data collected at a large number of neutron and synchrotron sources, largely as part of the VAMAS TWA20 project. While the solution is presented for Gaussian peak shapes, it is believed to be approximately correct for a wide range of other common diffraction peak shapes (Lorentzian, Voigtian etc.). The method is applied to the assessment of the variation in optimal measuring time as a function of the depth of the gauge volume for residual strain scanning measurements.
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  • 82
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 659-663 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Small angle X-ray fibre diffraction on aligned elongated macromolecules has been a routine tool for the structure of materials that either can not be crystallized or in cases in which one wants to study the structure of the molecule as close as possible to those occurring in solution. One of the problems with this approach is that quite often it is not possible to obtain completely aligned samples but only samples in which there is an angular distribution around the main orientation axis. This has as a consequence that atlarger scattering angles the contributions from different layer lines start to overlap. A possible method to overcome this problem can be found in combining results from small angle solution scattering with small angle fibre diffraction from molecules aligned with their long axis parallel with respect to the X-ray beam. In the latter case one only observes the projection of the molecule on the basal plane. We show how this method can be applied to hydrated microtubules.
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  • 83
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 695-699 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Simultaneous small-angle scattering and wide-angle diffraction using a synchrotron radiation microbeam was applied for the first time to investigate single carbon fibers in a position-resolved way. Taking into account the exact X-ray beam profile and examining the fibers in two scattering geometries allowed a discrimination between different models for the internal arrangement of carbon layers and pores. For a fiber based on polyacrylnitrile the carbon layers were randomly oriented within the fiber cross section, whereas in a mesophase-pitch based fiber the layers were arranged in a radial structure.
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  • 84
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 704-708 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Two examples are presented that illustrate the capabilities of DND-CAT instrumentation for the study of the effects of processing on polymers. Firstly, a thermoplastic elastomer, Hytrel®, was stretched while 2-D data were collected simultaneously. The Hytrel® data show that the yield point of the stress-strain curve is associated with the sudden appearance of a four-point pattern. At higher deformations, strain-induced crystallization and the destruction of the hard segment domains lead to a substantial decrease of the contrast as monitored by the SAXS invariant. Prior to breakage, the extent and intensity of an equatorial streak develops as the material fibrillates. Secondly, SAXS and WAXS data were collected from quenched and annealed Poly(ethylene terephthalate) (PET) samples mounted on a DSC cell, to characterize the pre-melting shoulder in this material. Results show that substantial melting and re-crystallization occurs within the range of this shoulder in the quenched sample.
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  • 85
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 714-717 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: We report a study of metallocene isotactic poly(propylene) (m-iPP) which crystallizes into α and γ crystal modifications. Simultaneous in-situ small- and wide-angle X-ray scattering (SAXS and WAXS) were used to study kinetics during crystallization. Both techniques provide information about time development of crystallinity, while WAXS gives also kinetics of formation of α and γ crystals. During the earliest stages of crystal formation, the SAXS Bragg peak occurs simultaneously, or slightly lags, the appearance of crystalline WAXS reflections. We conclude crystallization occurs by a nucleation and growth process in this m-iPP.
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  • 86
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 749-752 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Details of structure and composition at interfaces may be obtained by Small Angle Neutron Scattering (SANS) contrast variation. At the curved oil/surfactant/water interfaces of microemulsion droplets useful results may be obtained by simultaneous fits of core-shell models to SANS data measured at different scattering contrasts. Results for small ethyl octanoate/dimethyldodecylamineoxide/water droplets, where the oil core penetrates the surfactant layer, will illustrate this method. For block-copolymer micelles with deuterated poly(lactic acid) core, the composition profiles of thicker poly(ethylene glycol) shells were obtained using a model with a vertical step and two diffuse shells. One of the three water contrasts used was close to the "mean contrast" match point for the whole micelle, as opposed to "shell" contrast, providing a peak in the form factor very sensitive to the model used.
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  • 87
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 804-806 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: With the start-up of the neutron spallation source SINQ at PSI an instrument for small angle neutron scattering became operational and is open for the user community. The instrument is equipped with state-of-the-art components and compares well with the world's largest and most powerful facilities of this kind. Great emphasis was put on providing a flexible, universal multi-user facility which guaranties a comfortable and reliable operation. In the present paper, the layout of the instrument is presented, the main components are described, and the performance is illustrated by selected examples
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  • 88
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 812-816 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Data acquisition packages developed at different small angle scattering facilities use different formats both for raw and processed data storage. To facilitate the data exchange between laboratories, a consensus in the small angle scattering community has been reached on an ASCII format for one-dimensional data which includes a self-describing header containing relevant information about the sample and instrumental conditions followed by raw or reduced data in a tabular form. This format called sasCIF was implemented as an extension of core CIF (Crystallographic Information File) dictionary.
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  • 89
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 824-828 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Evaluation of small-angle neutron scattering (SANS) data is often complicated by multiple scattering effects if large particles of relatively high volume fraction have to be studied and dilution or contrast reduction is impossible. The use of pin-hole SANS instruments is often limited due to the contradictory requirements of high resolution and short wavelength needed to keep scattering contrast as low as possible. Double crystal (DC) SANS diffractometers of Bonse-Hart and bent-crystal type are useful alternatives in such cases, as they permit reaching very high resolution with thermal neutrons. A method for SANS data evaluation suited to DC instruments is presented. It includes the common scheme of the indirect Fourier transformation method, but takes multiple scattering into account. The scattering medium is described by the frequency function g(x) defined as the cosine Fourier transform of slit-smeared data. Although a simplistic model of polydisperse spheres is used to represent g(x), resulting g(x) function and some integral parameters are independent of this model. Tests on simulated data show, that the method reproduce well true values of microstructural parameters, though systematic errors are observed in the cases when the unscattered part of incident beam completely disappears. If the scattering power 〈N〉 is known and kept fixed during fitting, then other parameters are reproduced well also in the regime of strong multiple scattering. The evaluation procedure permits simultaneously fitting to several sets of data measured for different Q-regions, resolutions and sample thicknesses. It has proved to provide reliable results for particle sizes ranging from about 100 Å to several microns and 〈N〉 〈 10.
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  • 90
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 839-842 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: The scattering intensity equals the Fourier-transform of the distance distribution function p(t) = t2Δ\tilde{\rho}2(t) of the sample, where Δ\tilde{\rho}2(t) is the autocorrelation function of the scattering contrast Δρ(r). Δ\tilde{\rho}2(t) carries information both on the structure of the elementary scatterers and on their spatial distribution. In the present paper a method is described how to separate the two types of information in a system of interacting hard spheres.
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  • 91
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 876-881 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: The anomalous signals from scatterers such as sulfur (S) and arsenic (As) were compared in diffraction data sets collected from an X-ray source with three different targets, Au, Cu and Cr, on a multi-target rotating anode. HIV-1 integrase crystals served as the test case for this study. The crystalline specimen of HIV-1 integrase contains in each protein molecule two As atoms, each covalently bound to a cysteine S atom, and two additional S atoms derived from methionine. It was found that the Cr Kα radiation gave the clearest peaks in anomalous difference Fourier maps, although the signal-to-noise ratios of the anomalous signal for the Cu Kα and Cr Kα data were similar but better than that for Au Lα. This result was in spite of the fourfold higher flux from the Cu anode versus the Cr anode. For all three X-ray wavelengths, anomalous difference Fourier maps calculated with bias-removed phases derived from the known atomic model revealed clear peaks at the two As sites. However, only in the map calculated using the Cr Kα data were both peaks of the expected ellipsoidal shape, enveloping the As atom and the adjacent S atom. None of the S sites was apparent in difference maps calculated using the Au Lα data. The ability to enhance the S-derived anomalous signal using Cr Kα radiation has particularly useful applications in the structure determination of proteins, for example in resolving ambiguities in the chain tracing of a protein with numerous disulfide bonds and in assigning amino acid identities. Additionally, anomalous difference Patterson maps calculated from the Cr Kα data were sufficiently clear to identify the As-related peaks. These results form the groundwork for in-house phase determination with the multi-wavelength anomalous diffraction method.
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  • 92
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 899-908 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Techniques and methods to facilitate the solution of structures by simulated annealing have been developed from the starting point of a space group and lattice parameters. The simulated-annealing control parameters have been systematically investigated and optimum values characterized and determined. Most significant is the inclusion of electrostatic-potential penalty functions in a non-linear least-squares Rietveld refinement procedure. The long-range electrostatic potentials are calculated using a general real-space summation which can be used for all space groups. In addition, a general weighting scheme for penalty functions negates the need to determine weighting schemes experimentally. Also investigated and improved is the non-linear least-squares minimization procedure used in the refinement of structural parameters. The behaviour and success of the techniques have been tested on X-ray diffraction powder data against the known structures of AlVO4 in P1 with 18 atoms in the asymmetric unit, K2HCr2AsO10 in P31 with 15 atoms in the asymmetric unit excluding hydrogen, and [Co(NH3)5CO3]NO3.H2O in P121 with 15 atoms in the asymmetric unit excluding hydrogen.
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  • 93
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 928-937 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Single crystals of Cu–2.5 at.% Ti have been studied by small-angle and large-angle X-ray scattering to determine the displacements induced by the formation and the coarsening of ordered Cu4Ti precipitates. The variation of the atomic scattering factor of Cu near its absorption edge was used to confirm the nature of the precipitates and to show that the scattering appearing near Bragg peaks was due to the displacements of the atoms from their ideal positions, induced by the formation of the precipitates, and not to the segregation of the Ti atoms. The displacement field was found to be dependent on the precipitate mean size, with a single component aligned along a soft 〈100〉 direction: it is composed of a region of dilatation, where the Cu-atom positions follow the increase of the atomic distance induced by the Cu4Ti precipitate formation, followed by a region of contraction. This effect is responsible for the pile-up of the precipitates along the soft directions: the interaction between precipitates is repulsive at long distances and attractive at shorter distances.
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  • 94
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 964-974 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: A distribution of crystallite size reduces the width of a powder diffraction line profile, relative to that for a single crystallite, and lengthens its tails. It is shown that estimates of size from the integral breadth or Fourier methods differ from the arithmetic mean of the distribution by an amount which depends on its dispersion. It is also shown that the form of `size' line profiles for a unimodal distribution is generally not Lorentzian. A powder pattern can be simulated for a given distribution of sizes, if it is assumed that on average the crystallites have a regular shape, and this can then be compared with experimental data to give refined parameters defining the distribution. Unlike `traditional' methods of line-profile analysis, this entirely physical approach can be applied to powder patterns with severe overlap of reflections, as is demonstrated by using data for nanocrystalline ceria. The procedure is compared with alternative powder-pattern fitting methods, by using pseudo-Voigt and Pearson VII functions to model individual line profiles, and with transmission electron microscopy (TEM) data.
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
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  • 95
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 980-981 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: The phase problem is reduced to a sign problem once the anomalous-scatterer or the replacing-heavy-atom sites are located. OASIS adopts the CCP4 format [Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760–763]. It applies a direct-method procedure to break the phase ambiguity intrinsic to one-wavelength anomalous scattering (OAS) or single isomorphous replacement (SIR) data.
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 96
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 986-987 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: An air-filled ionization chamber with a three-way split anode can be used to measure the tilt and the translation of a collimated X-ray beam with respect to the chamber axis.
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
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  • 97
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 982-985 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: A maximum-entropy formalism aimed at the production of a `maximally noncommittal' map is a standard method in fields of science like radioastronomy, but a rare exception in both X-ray crystallography and electron microscopy (or crystallography). This is rather unfortunate, given the wealth of information that a maximum-entropy map can reveal, especially when the map itself is the end product (for example, low-resolution electron or potential density maps, Patterson functions, deformation maps). The program GraphEnt attempts to automate the procedure of calculating maximum-entropy maps, with emphasis on the calculation of difference Patterson functions for macromolecular crystallographic problems, while providing a useful graphical output of the current stage of the calculation.
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
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  • 98
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 988-989 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Notizen: Excessive nucleation often leads to a large number of small macromolecular crystals that are not useful for X-ray diffraction analysis. Crystals with dimensions suitable for data collection can be reproducibly obtained by releasing, for a discrete amount of time, the vapour pressure in both hanging- and sitting-drop experiments, set up at lower precipitant concentrations than those required for crystallization.
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
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  • 99
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 992-992 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
  • 100
    Digitale Medien
    Digitale Medien
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 33 (2000), S. 994-994 
    ISSN: 1600-5767
    Quelle: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Thema: Geologie und Paläontologie , Physik
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
    BibTip Andere fanden auch interessant ...
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