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  • Articles  (513,563)
  • American Institute of Physics  (205,510)
  • Oxford University Press  (147,717)
  • Cell Press  (85,946)
  • International Union of Crystallography  (67,904)
  • International Union of Crystallography (IUCr)
  • 2010-2014  (237,918)
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  • 1
    Publication Date: 2020-11-20
    Description: Siwi caldera, in the Vanuatu arc (Tanna island), is a rare volcanic complex where both persistent eruptive activity (Yasur volcano)and rapid block resurgence (Yenkahe horst) can be investigated simultaneously during a post-caldera stage. Here we provide new constraints on the feeding system of this volcanic complex, based on a detailed study of the petrology, geochemistry and volatile content of Yasur^Siwi bulk-rocks and melt inclusions, combined with measurements of the chemical composition and mass fluxes of Yasur volcanic gases. Major and trace element analyses of Yasur^ Siwi volcanic rocks, together with literature data for other volcanic centers, point to a single magmatic series and possibly long-lived feeding of Tanna volcanism by a homogeneous arc basalt. Olivine-hosted melt inclusions show that the parental basaltic magma, which produces basaltic-trachyandesites to trachyandesites by 50^70% crystal fractionation, is moderately enriched in volatiles ( 1wt % H2O, 0·1wt % S and 0·055 wt % Cl). The basaltic-trachyandesite magma, emplaced at between 4^5 km depth and the surface, preserves a high temperature (1107 158C) and constant H2O content ( 1wt %) until very shallow depths, where it degasses extensively and crystallizes. These conditions, maintained over the past 1400 years of Yasur activity, require early water loss during basalt differentiation, prevalent open-system degassing, and a relatively high heat flow ( 109W). Yasur volcano releases on average 13·4 103 tons d 1 of H2O and 680 tons d 1 of SO2, but moderate amounts of CO2 (840 tons d 1), HCl (165 tons d 1), and HF (23 tons d 1). Combined with melt inclusion data, these gas outputs constrain a bulk magma degassing rate of 5 107 m3 a 1, about a half of which is due to degassing of the basaltic-trachyandesite. We compute that 25 km3 of this magma have degassed without erupting and have accumulated beneath Siwi caldera over the past 1000 years, which is one order of magnitude larger than the accumulated volume uplift of the Yenkahe resurgent block. Hence, basalt supply and gradual storage of unerupted degassed basaltictrachyandesite could easily account for (or contribute to) the Yenkahe block resurgence.
    Description: Published
    Description: 1077-1105
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: 2.4. TTC - Laboratori di geochimica dei fluidi
    Description: JCR Journal
    Description: restricted
    Keywords: Vanuatu arc ; Yasur ; gas fluxes ; volatiles ; melt inclusions ; resurgent block ; volcano thermal budget ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 2
    Publication Date: 2020-12-14
    Description: 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.
    Description: Published
    Description: 135-138
    Description: 1.8. Osservazioni di geofisica ambientale
    Description: N/A or not JCR
    Description: open
    Keywords: 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)
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  • 3
    Publication Date: 2020-11-26
    Description: So far, the role of appendicularians in the biogeochemical cycling of organic matter has been largely overlooked. Appendicularians represent only a fraction of total mesozooplankton biomass, however these ubiquitous zooplankters have very high filtration and growth rates compared to copepods, and produce numerous fecal pellets and filtering houses contributing to export production by aggregating small marine particles. To study their quantitative impact on biogeochemical flux, we have included this group in the biogeochemical flux model, using a recently developed ecophysiological model. One-dimensional annual simulations of the pelagic ecosystem including appendicularians were conducted with realistic surface forcing for the year 2000, using data from the DyFAMed open ocean station. The appendicularian grazing impact was generally low, but appendicularians increased detritus production by 8% and export production by 55% compared to a simulation without appendicularians. Therefore, current biogeochemical models lacking appendicularians probably under, or misestimate the detritus and export production by omitting the pathway from small-sized plankton to fast sinking detritus. Detritus production and export rates are 60% lower than the estimates from mesotrophic sites, showing that appendicularians’ role is lower but still significant in oligotrophic environments. The simulated annual export at 200 m exceeds sediment trap values by 44%, suggesting an intense degradation during the sinking of appendicularian detritus, supported by observations made at other sites. Thus, degradation and grazing of appendicularian detritus need better quantification if we are to accurately assess the role of appendicularia in export flux.
    Description: EU-FP6 project SESAME GOCE-036949
    Description: Published
    Description: 855-872
    Description: 3.7. Dinamica del clima e dell'oceano
    Description: JCR Journal
    Description: reserved
    Keywords: BFM ; zooplankton ; 03. Hydrosphere::03.01. General::03.01.01. Analytical and numerical modeling ; 03. Hydrosphere::03.01. General::03.01.07. Physical and biogeochemical interactions ; 03. Hydrosphere::03.04. Chemical and biological::03.04.01. Biogeochemical cycles ; 03. Hydrosphere::03.04. Chemical and biological::03.04.04. Ecosystems
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
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    Oxford University Press
    In:  EPIC3Journal of Experimental Botany, Oxford University Press, ISSN: 0022-0957
    Publication Date: 2019-07-17
    Repository Name: EPIC Alfred Wegener Institut
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  • 5
    Publication Date: 2017-04-04
    Description: 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.
    Description: DRS Codem Systems Ball Aerospace Corporation University of Massachusetts Lowell
    Description: Published
    Description: Lowell, Massachusetts, U.S.A., April 29, 2007
    Description: 3.9. Fisica della magnetosfera, ionosfera e meteorologia spaziale
    Description: open
    Keywords: 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)
    Type: Conference paper
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  • 6
    Publication Date: 2017-04-04
    Description: Crystal-rich lithic clasts occurring in volcanic deposits are key tools to understand processes of storage, cooling, and fractionation of magmas in pre-eruptive volcanic systems. These clasts, indeed, represent snapshots of the magma-chamber/host-rock interface before eruptions and provide information on crystallization, differentiation, and degrees of interaction between magma and wall-rocks. In this study, with the aim to shed light on magma-carbonate interaction and CO2 emission in volcanic areas, we focused on the petrology of cumulate and skarn rocks by using as case study a suite of mafic and calcite-bearing lithic clasts from the Colli Albani Volcanic District. By means of phase relations, bulk rock chemistry, phase compositions, and stable isotope data we have recognized different types of cumulates and skarns. Cumulates containing either clinopyroxene±olivine associated with Cr-bearing spinel or glass+phlogopite have been divided in primitive and differentiated, respectively. Primitive cumulates originate at the interface between a relatively primitive magma and carbonate-bearing rocks and show evidences of olivine instability (i.e. heteradcumulate texture) due to carbonate assimilation. Differentiated cumulates, characterized by Ca-rich olivines, phlogopite, and glass containing calcite, form from a differentiated magma in a system open to CaO-contamination. Skarns has been divided in exoskarns, characterized by xenomorphic texture and abundant calcite, and endoskarns, characterized by hypidiomorphic texture, Ca-Tschermak-rich mineral phases, and interstitial glass. Exoskarns formed by means of solid state reactions in a dolostone protolith whereas endoskarns crystallized at subliquidus temperature from a silicate melt that experienced exoskarns assimilation. Our study evidences that magma-carbonate interaction can not be considered a one step process exhausting just after the formation of skarn shells. Magma and carbonate rocks, when in contact, continuously interact leading to the formation of exoskarns, endoskarns, cumulates (primitive and differentiated ones), and differentiated melts. Finally, by means of oxygen and carbon isotope compositions of calcite in equilibrium with skarns, we demonstrate that carbonate assimilation represents a source of massive CO2 degassing mechanism due to the consumption of calcite and removing of CO2 during the decarbonation process.
    Description: Sapienza Universita' di Roma INGV-DPC [Project V 3.1, Colli Albani].
    Description: Published
    Description: 2307-2332
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: JCR Journal
    Description: reserved
    Keywords: magma/carbonate interaction ; CO2 degassing ; c umulate and skarn ; Colli Albani ; 04. Solid Earth::04.04. Geology::04.04.05. Mineralogy and petrology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 7
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    American Institute of Physics
    Publication Date: 2020-02-24
    Description: 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.
    Description: Published
    Description: 2940-2944
    Description: 1.7. Osservazioni di alta e media atmosfera
    Description: JCR Journal
    Description: reserved
    Keywords: 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)
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  • 8
    Publication Date: 2017-04-04
    Description: Stromboli is known for its persistent degassing and rhythmic strombolian activity occasionally punctuated by paroxysmal eruptions. The basaltic pumice and scoria emitted during paroxysms and strombolian activity, respectively, differ in their textures, crystal contents and glass matrix compositions, which testify to distinct conditions of crystallization, degassing and magma ascent. We present here an extensive dataset on major elements and volatiles (CO2, H2O, S and Cl) in olivine-hosted melt inclusions and embayments from pyroclasts emplaced during explosive eruptions of variable magnitude. Magma saturation pressures were assessed from the dissolved amounts of H2O and CO2 taking into account the melt composition evolution. Both pressures and melt inclusion compositions indicate that (1) Ca-basaltic melts entrapped in high-Mg olivines (Fo89–90) generate Stromboli basalts through crystal fractionation, and (2) the Stromboli plumbing system can be imaged as a succession of magma ponding zones connected by dikes. The 7–10 km interval, where magmas are stored and differentiate, is periodically recharged by new magma batches, possibly ranging from Ca-basalts to basalts, with a CO2-rich gas phase. These deep recharges promote the formation of bubbly basalt blobs, which are able to intrude the shallow plumbing system (2–4 km), where CO2 gas fluxing enhances H2O loss, crystallization and generation of crystal-rich, dense, degassed magma. Chlorine partitioning into the H2O–CO2-bearing gas phase accounts for its efficient degassing (≥69%) under the open-system conditions of strombolian activity. Paroxysms, however, are generated through predominantly closed-system ascent of basaltic magma batches from the deep storage zone. In this situation crystallization is negligible and sulfur exsolution starts at ≤170 MPa. Chlorine remains dissolved in the melt until lower pressures, only 16% being lost upon eruption. Finally, we propose a continuum in explosive eruption energy, from strombolian activity to large paroxysmal events, ultimately controlled by variable pressurization of the deep feeding system associated with magma and gas recharges.
    Description: Published
    Description: 603-626
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: 3.5. Geologia e storia dei vulcani ed evoluzione dei magmi
    Description: JCR Journal
    Description: reserved
    Keywords: Stromboli ; melt inclusions ; magmatic volatiles ; CO2 fluxing ; magma degassing ; 04. Solid Earth::04.04. Geology::04.04.05. Mineralogy and petrology ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 9
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    Oxford University Press
    In:  EPIC3Ocean Acidification, Oxford, Oxford University Press, pp. 291-311, ISBN: 978-0-19-959109-1
    Publication Date: 2014-04-15
    Repository Name: EPIC Alfred Wegener Institut
    Type: Inbook , peerRev
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  • 10
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    Cell Press
    In:  EPIC3Current Biology, Cell Press, 23(14), pp. 1330-1334, ISSN: 09609822
    Publication Date: 2019-07-17
    Repository Name: EPIC Alfred Wegener Institut
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  • 11
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    Oxford University Press
    In:  EPIC3Journal of Plankton Research, Oxford University Press, 34(5), pp. 399-415, ISSN: 0142-7873
    Publication Date: 2019-07-17
    Description: This study investigates the relationships between the spring phytoplankton community and environmental factors in the Brazil-Malvinas confluence region. Phytoplankton community composition was determined by the high performance liquid chromatography/CHEMTAX approach, complemented with microscopic examination. Abiotic factors included temperature, salinity, dissolved inorganic macronutrients (ammonium, nitrite, nitrate, phosphate and silicate), water column stability and upper mixed layer depth (UMLD). These environmental variables were reasonably informative to explain the variability of the phytoplankton communities (44% of variation explained). Cluster and canonical correspondence analyses allowed discrimination of four zones (coastal, Sub-Antarctic, tropical and intermediate zones), also identifiable in the T–S diagrams and in the nutrient spatial distribution patterns. The presence of nutrient-rich Sub-Antarctic waters was a major oceanographic feature, associated with diatoms and dinoflagellates. However, in the Sub-Antarctic zone, biomass was particularly low, probably as a result of grazing pressure, as suggested by chemical and biological indicators. In contrast, in oligotrophic tropical waters, phytoplankton was mainly composed by small nanoflagellates and cyanobacteria. A large intermediate zone was also dominated by nanoflagellates, mainly Phaeocystis antarctica, probably favored by strong water column stability. The coastal zone exhibited fairly similar conditions to those in the intermediate zone, but with deeper UMLD, a favorable condition for diatom growth. These results emphasize the importance of the properties of water masses and also biological processes such as grazing in structuring phytoplankton communities in the region.
    Repository Name: EPIC Alfred Wegener Institut
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  • 12
    Publication Date: 2022-05-25
    Description: © 2008 The Authors. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License. The definitive version was published in Nucleic Acids Research 37 (2009): D526-D530, doi:10.1093/nar/gkn631.
    Description: GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia and Trichomonas vaginalis, respectively, and represent the latest additions to the EuPathDB (http://EuPathDB.org) family of functional genomic databases. GiardiaDB and TrichDB employ the same framework as other EuPathDB sites (CryptoDB, PlasmoDB and ToxoDB), supporting fully integrated and searchable databases. Genomic-scale data available via these resources may be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs and other protein characteristics. Functional queries may also be formulated, based on transcript and protein expression data from a variety of platforms. Phylogenetic relationships may also be interrogated. The ability to combine the results from independent queries, and to store queries and query results for future use facilitates complex, genome-wide mining of functional genomic data.
    Description: Federal funds from the National Institute of Allergy and Infectious Diseases; Department of Health and Human Services, National Institutes of Health (HHSN266200400037C). Funding for open access charge: National Institutes of Health (HHSN266200400037C).
    Repository Name: Woods Hole Open Access Server
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  • 13
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Conservation Physiology 1 (2013): cot006, doi:10.1093/conphys/cot006.
    Description: Large whales are subjected to a variety of conservation pressures that could be better monitored and managed if physiological information could be gathered readily from free-swimming whales. However, traditional approaches to studying physiology have been impractical for large whales, because there is no routine method for capture of the largest species and there is presently no practical method of obtaining blood samples from free-swimming whales. We review the currently available techniques for gathering physiological information on large whales using a variety of non-lethal and minimally invasive (or non-invasive) sample matrices. We focus on methods that should produce information relevant to conservation physiology, e.g. measures relevant to stress physiology, reproductive status, nutritional status, immune response, health, and disease. The following four types of samples are discussed: faecal samples, respiratory samples (‘blow’), skin/blubber samples, and photographs. Faecal samples have historically been used for diet analysis but increasingly are also used for hormonal analyses, as well as for assessment of exposure to toxins, pollutants, and parasites. Blow samples contain many hormones as well as respiratory microbes, a diverse array of metabolites, and a variety of immune-related substances. Biopsy dart samples are widely used for genetic, contaminant, and fatty-acid analyses and are now being used for endocrine studies along with proteomic and transcriptomic approaches. Photographic analyses have benefited from recently developed quantitative techniques allowing assessment of skin condition, ectoparasite load, and nutritional status, along with wounds and scars from ship strikes and fishing gear entanglement. Field application of these techniques has the potential to improve our understanding of the physiology of large whales greatly, better enabling assessment of the relative impacts of many anthropogenic and ecological pressures.
    Description: This work was supported by the United States Office of Naval Research (award #N000141110435 to K.E.H., award #N000141110540 to R.M.R., and award #N0001412WX20890 to L.C.Y. and C.E.D.); the United Kingdom Natural Environmental Research Council (supporting A.J.H.); the National Center for Research Resources, a component of the United States National Institutes of Health (NIH; supporting C.E.D.); the NIH Roadmap for Medical Research (UL1 RR024146 supporting C.E.D.); The Hartwell Foundation (supporting C.E.D.) and the 2012 Marine Mammal Breath Workshop, which was funded by the National Oceanic and Atmospheric Administration’s Marine Mammal Health and Stranding Response Program.
    Keywords: Blow ; Biopsy dart ; Cetacea ; Faecal samples ; Non-invasive ; Visual health assessment
    Repository Name: Woods Hole Open Access Server
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  • 14
    Publication Date: 2022-05-25
    Description: © 2007 The Author et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in Nucleic Acids Research 35 (2007): 2107-2115, doi:10.1093/nar/gkm049.
    Description: Trypanosomatids contain an unusual DNA base J (ß-D-glucosylhydroxymethyluracil), which replaces a fraction of thymine in telomeric and other DNA repeats. To determine the function of base J, we have searched for enzymes that catalyze J biosynthesis. We present evidence that a protein that binds to J in DNA, the J-binding protein 1 (JBP1), may also catalyze the first step in J biosynthesis, the conversion of thymine in DNA into hydroxymethyluracil. We show that JBP1 belongs to the family of Fe2+ and 2-oxoglutarate-dependent dioxygenases and that replacement of conserved residues putatively involved in Fe2+ and 2-oxoglutarate-binding inactivates the ability of JBP1 to contribute to J synthesis without affecting its ability to bind to J-DNA. We propose that JBP1 is a thymidine hydroxylase responsible for the local amplification of J inserted by JBP2, another putative thymidine hydroxylase.
    Description: This work was funded by a grant from the Netherlands Organization for Scientific Research and Chemical Sciences (NWO-CW) to P.B., NIH grant A1063523 to R.S. and NIH grant GM063584 to R.P.H.
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  • 15
    Publication Date: 2022-05-25
    Description: © 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.
    Description: 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.
    Description: This work was supported by National Institutes of Health grant AI1058054 to M. Sogin.
    Keywords: Simulation ; Phylogenetic analysis ; Accuracy ; Sequence similarity
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  • 16
    Publication Date: 2022-05-25
    Description: © 2010 The Authors. This article is distributed under the terms of the Creative Commons Attribution-Noncommercial License. The definitive version was published in ICES Journal of Marine Science: Journal du Conseil 67 (2010): 365-378, doi:10.1093/icesjms/fsp262.
    Description: A commercial acoustic system, originally designed for seafloor applications, has been adapted for studying fish with swimbladders. The towed system contains broadband acoustic channels collectively spanning the frequency range 1.7–100 kHz, with some gaps. Using a pulse-compression technique, the range resolution of the echoes is ~20 and 3 cm in the lower and upper ranges of the frequencies, respectively, allowing high-resolution imaging of patches and resolving fish near the seafloor. Measuring the swimbladder resonance at the lower frequencies eliminates major ambiguities normally associated with the interpretation of fish echo data: (i) the resonance frequency can be used to estimate the volume of the swimbladder (inferring the size of fish), and (ii) signals at the lower frequencies do not depend strongly on the orientation of the fish. At-sea studies of Atlantic herring demonstrate the potential for routine measurements of fish size and density, with significant improvements in accuracy over traditional high-frequency narrowband echosounders. The system also detected patches of scatterers, presumably zooplankton, at the higher frequencies. New techniques for quantitative use of broadband systems are presented, including broadband calibration and relating target strength and volume-scattering strength to quantities associated with broadband signal processing.
    Description: The research was supported by the US Office of Naval Research, grants number N00014-04-1-0440 and N00014-04-1-0475, NOAA/CICOR cooperative agreement NA17RJ1223, NOAA/ National Marine Fisheries Service, and the J. Seward Johnson Chair of the WHOI Academic Programs Office.
    Keywords: Acoustic scattering ; Broadband ; Echosounder ; Fish ; Resonance
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  • 17
    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nucleic Acids Research 40 (2012): W82-W87, doi:10.1093/nar/gks418.
    Description: Amplicon sequencing of the hypervariable regions of the small subunit ribosomal RNA gene is a widely accepted method for identifying the members of complex bacterial communities. Several rRNA gene sequence reference databases can be used to assign taxonomic names to the sequencing reads using BLAST, USEARCH, GAST or the RDP classifier. Next-generation sequencing methods produce ample reads, but they are short, currently ∼100–450 nt (depending on the technology), as compared to the full rRNA gene of ∼1550 nt. It is important, therefore, to select the right rRNA gene region for sequencing. The primers should amplify the species of interest and the hypervariable regions should differentiate their taxonomy. Here, we introduce TaxMan: a web-based tool that trims reference sequences based on user-selected primer pairs and returns an assessment of the primer specificity by taxa. It allows interactive plotting of taxa, both amplified and missed in silico by the primers used. Additionally, using the trimmed sequences improves the speed of sequence matching algorithms. The smaller database greatly improves run times (up to 98%) and memory usage, not only of similarity searching (BLAST), but also of chimera checking (UCHIME) and of clustering the reads (UCLUST). TaxMan is available at http://www.ibi.vu.nl/programs/taxmanwww/.
    Description: University of Amsterdam under the research priority area ‘Oral Infections and Inflammation’ (to B.W.B.); National Science Foundation [NSF/BDI 0960626 to S.M.H.]; the European Union Seventh Framework Programme (FP7/ 2007-2013) under ANTIRESDEV grant agreement no 241446 (to E.Z.).
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  • 18
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Briefings in Bioinformatics 15 (2014): 783-787, doi:10.1093/bib/bbt010.
    Description: The extremely high error rates reported by Keegan et al. in ‘A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE’ (PLoS Comput Biol 2012;8:e1002541) for many next-generation sequencing datasets prompted us to re-examine their results. Our analysis reveals that the presence of conserved artificial sequences, e.g. Illumina adapters, and other naturally occurring sequence motifs accounts for most of the reported errors. We conclude that DRISEE reports inflated levels of sequencing error, particularly for Illumina data. Tools offered for evaluating large datasets need scrupulous review before they are implemented.
    Description: National Institutes of Health [1UH2DK083993 to M.L.S.]; National Science Foundation [BDI- 096026 to S.M.H.].
    Keywords: Next-generation sequencing ; Sequencing error ; Adapter ligation ; PCR ; Quality score
    Repository Name: Woods Hole Open Access Server
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  • 19
    Publication Date: 2022-05-25
    Description: © 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.
    Description: 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.
    Description: 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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  • 20
    Publication Date: 2022-05-25
    Description: © 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.
    Description: 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.
    Description: The work was supported by the US Office of Naval Research (Grant # N000140210359).
    Keywords: Broadband acoustic scattering ; Internal waves ; Oceanic microstructure ; Zooplankton
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  • 21
    Publication Date: 2022-05-25
    Description: 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.
    Description: 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.
    Description: This work was supported by the U.S. National Science Foundation (MCB 0614142).
    Keywords: Penelope-like elements ; Retrotransposons ; Reverse transcriptase ; GIY-YIG endonuclease
    Repository Name: Woods Hole Open Access Server
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  • 22
    Publication Date: 2022-05-25
    Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution-Noncommercial License. The definitive version was published in Journal of Plankton Research 32 (2010): 1355-1368, doi:10.1093/plankt/fbq062.
    Description: Increasing availability and extent of biological ocean time series (from both in situ and satellite data) have helped reveal significant phenological variability of marine plankton. The extent to which the range of this variability is modified as a result of climate change is of obvious importance. Here we summarize recent research results on phenology of both phytoplankton and zooplankton. We suggest directions to better quantify and monitor future plankton phenology shifts, including (i) examining the main mode of expected future changes (ecological shifts in timing and spatial distribution to accommodate fixed environmental niches vs. evolutionary adaptation of timing controls to maintain fixed biogeography and seasonality), (ii) broader understanding of phenology at the species and community level (e.g. for zooplankton beyond Calanus and for phytoplankton beyond chlorophyll), (iii) improving and diversifying statistical metrics for indexing timing and trophic synchrony and (iv) improved consideration of spatio-temporal scales and the Lagrangian nature of plankton assemblages to separate time from space changes.
    Description: This study was supported by NSF grants to R.J.: OCE-0727033, 0815838 and 0732152. NSF grants to A.C.T.: OCE-0535386, 0815051 and 0814413. NSF grant to J.A.R.: OCE 0815336.
    Keywords: Plankton ; Phenology ; Life history ; Climate change
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  • 23
    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cell Reports 2 (2012): 242–248, doi:10.1016/j.celrep.2012.06.016.
    Description: Ion selectivity of metazoan voltage-gated Na+ channels is critical for neuronal signaling and has long been attributed to a ring of four conserved amino acids that constitute the ion selectivity filter (SF) at the channel pore. Yet, in addition to channels with a preference for Ca2+ ions, the expression and characterization of Na+ channel homologs from the sea anemone Nematostella vectensis, a member of the early-branching metazoan phylum Cnidaria, revealed a sodium-selective channel bearing a noncanonical SF. Mutagenesis and physiological assays suggest that pore elements additional to the SF determine the preference for Na+ in this channel. Phylogenetic analysis assigns the Nematostella Na+-selective channel to a channel group unique to Cnidaria, which diverged 〉540 million years ago from Ca2+-conducting Na+ channel homologs. The identification of Cnidarian Na+-selective ion channels distinct from the channels of bilaterian animals indicates that selectivity for Na+ in neuronal signaling emerged independently in these two animal lineages.
    Description: This study was supported by a research grant from the Austrian National Science Foundation (FWF P 21108-B17) to U.T., and by a United States-Israel Binational Agricultural Research and Development Grant (IS-4313-10) and an Israeli Science Foundation grant (107/08) to M.G.
    Repository Name: Woods Hole Open Access Server
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  • 24
    Publication Date: 2022-05-25
    Description: © 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.
    Description: 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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  • 25
    Publication Date: 2022-05-25
    Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution-Noncommercial 2.5 License. The definitive version was published in Genome Biology and Evolution 2 (2010): 304, doi:10.1093/gbe/evq022.
    Description: Reduction of various biological processes is a hallmark of the parasitic lifestyle. Generally, the more intimate the association between parasites and hosts the stronger the parasite relies on its host's physiology for survival and reproduction. However, some systems have been held to be indispensable, for example, the core pathways of carbon metabolism that produce energy from sugars. Even the most hardened anaerobes that lack oxidative phosphorylation and the tricarboxylic acid cycle have retained glycolysis and some downstream means to generate ATP. Here we describe the deep-coverage genome resequencing of the pathogenic microsporidiian, Enterocytozoon bieneusi, which shows that this parasite has crossed this line and abandoned complete pathways for the most basic carbon metabolism. Comparing two genome sequence surveys of E. bieneusi to genomic data from four other microsporidia reveals a normal complement of 353 genes representing 30 functional pathways in E. bieneusi, except that only 2 out of 21 genes collectively involved in glycolysis, pentose phosphate, and trehalose metabolism are present. Similarly, no genes encoding proteins involved in the processing of spliceosomal introns were found. Altogether, E. bieneusi appears to have no fully functional pathway to generate ATP from glucose. Therefore, this intracellular parasite relies on transporters to import ATP from its host.
    Description: This work was supported by grants from the Canadian Institutes for Health Research (MOP-84265), the National Institutes of Health (NIH AI31788, R21 AI52792, and R21 AI064118), and the National Science Foundation (MCB- 0135272). N.C. is a Scholar of the Canadian Institute for Advanced Research and is supported by a fellowship from the Swiss National Science Foundation (NSF) (PA00P3- 124166). D.E. is supported by the Swiss NSF. P.J.K. is a Fellow of the Canadian Institute for Advanced Research and a Senior Scholar of the Michael Smith Foundation for Health Research.
    Keywords: Microsporidia ; Parasite ; Glycolysis ; Carbon metabolism ; Reduction ; Evolution
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    Publication Date: 2022-05-25
    Description: Author Posting. © The Authors, 2014. This article is posted here by permission of The Royal Astronomical Society for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 197 (2014): 697-704, doi:10.1093/gji/ggu048.
    Description: After the 1960 M9.5 Valdivia, Chile earthquake, three types of geodetic observations were made during four time periods at nearby locations. These post-seismic observations were previously explained by post-seismic afterslip on the downdip extension of the 1960 rupture plane. In this study, we demonstrate that the post-seismic observations can be explained alternatively by volumetric viscoelastic relaxation of the asthenosphere mantle. In searching for the best-fitting viscosity model, we invert for two variables, the thickness of the elastic lithosphere, He, and the effective Maxwell decay time of the asthenosphere mantle, TM, assuming a 100-km-thick asthenosphere mantle. The best solutions to fit the observations in four sequential time periods, 1960–1964, 1960–1968, 1965–1973 and 1980–2010, each yield a similar He value of about 65 km but significantly increasing TM values of 0.7, 6, 10 and 80 yr, respectively. We calculate the corresponding viscoelastic Coulomb stress increase since 1960 on the future rupture plane of the 2010 M8.8 Maule, Chile earthquake. The calculated viscoelastic stress increase on the 2010 rupture plane varies gradually from 13.1 bars at the southern end to 0.1 bars at the northern end. In contrast, the stress increase caused by an afterslip model has a similar spatial distribution but slightly smaller values of 0.1–3.2 bars on the 2010 rupture plane.
    Description: This work was supported by a MIT/WHOI Joint Program Student Fellowship and a Graduate Student Fellowship from the WHOI Deep Ocean Exploration Institute (MD), as well as NSF Grant OCE-1141785 and a Deerbrook Foundation Award (JL).
    Keywords: Seismic cycle ; Transient deformation ; Seismicity and tectonics ; Subduction zone processes ; Dynamics: seismotectonics ; South America
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  • 27
    Publication Date: 2017-04-04
    Description: The effect of pressure on melt viscosity was investigated for five compositions along the join An(CaAl2Si2O8)–Di(CaMgSi2O6) and four alkali silicates containing lithium, sodium, and potassium in constant ratio of ∼ 1:1:1, but alkali-silica ratios are varying. The experiments were performed in an internally heated gas pressure vessel at pressures from 50 to 400 MPa in the viscosity range from 108 to 1011.5 Pa⋅s using parallel plate viscometry. The polymerized An composition shows a negative pressure dependence of viscosity while the other, more depolymerized compositions of the join An–Di have neutral to positive pressure coefficients. The alkali silicates display neutral to slightly positive pressure coefficients for melt viscosity. These findings in the high viscosity range of 108–1011 Pa⋅s, where pressure appears to be more efficient than in low viscous melts at high temperature, are consistent with previous results on the viscosity of polymerized to depolymerized melts in the system NaAlSi3O8–CaMgSi2O6 by Behrens and Schulze [ H. Behrens and F. Schulze, Am. Mineral. 88, 1351 (2003) ]. Thus we confirm that the sign of the pressure coefficient for viscosity is mainly related to the degree of melt polymerization in silicate and aluminosilicate melts.
    Description: DFG Grant n.°BE1720/9
    Description: Published
    Description: 044504-14
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: JCR Journal
    Description: open
    Keywords: viscosity ; polymerisation ; anorthite ; diopside ; 04. Solid Earth::04.08. Volcanology::04.08.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 28
    Publication Date: 2017-04-04
    Description: A series of computed microtomography experiments are reported which were performed by using a third-generation synchrotron radiation source on volcanic rocks from various active hazardous volcanoes in Italy and other volcanic areas in the world. The applied technique allowed the internal structure of the investigated material to be accurately imaged at the micrometre scale and three-dimensional views of the investigated samples to be produced as well as three-dimensional quantitative measurements of textural features. The geometry of the vesicle (gas-filled void) network in volcanic products of both basaltic and trachytic compositions were particularly focused on, as vesicle textures are directly linked to the dynamics of volcano degassing. This investigation provided novel insights into modes of gas exsolution, transport and loss in magmas that were not recognized in previous studies using solely conventional two-dimensional imaging techniques. The results of this study are important to understanding the behaviour of volcanoes and can be combined with other geosciences disciplines to forecast their future activity.
    Description: Published
    Description: 215-221
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: JCR Journal
    Description: reserved
    Keywords: high-resolution three-dimensional imaging ; X-ray computed microtomography ; volcanic eruptions ; volcanic rock textures ; 04. Solid Earth::04.08. Volcanology::04.08.05. Volcanic rocks ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 29
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    Oxford University Press
    In:  EPIC3Geophysical Journal International, Oxford University Press, 193(3), pp. 1399-1414, ISSN: 0956-540X
    Publication Date: 2019-07-16
    Description: The Boreas Basin is located in the Norwegian-Greenland Sea between Northeast Greenland and Svalbard. Towards the east, it is bounded by the ultraslow mid-ocean Knipovich Ridge. Here, we present a 340-km-long seismic refraction line acquired during the expedition ARK-XXIV/3 of research vessel Polarstern in 2009, using 18 ocean bottom seismometers. It crosses the central Boreas Basin from the Knipovich Ridge to the Northeast Greenland margin. Thus, the line provides the first reliable crustal structure information of this basin. In addition, the gravity data acquired parallel to the seismic refraction line are used to calculate a 2.5-D gravity model. The P-wave velocity model shows an unusual ∼3-km-thin oceanic crust with seismic velocities less than 6.3 km s−1, indicating the absence of a significant oceanic layer 3. Mantle velocities vary between 7.5 kms−1 in the uppermost mantle and 8.0 km s−1 at approximately 15 km depth. The low velocities within the upper mantle may be explained by 13 per cent serpentinisation, which is negligible at about 15 km depth. Furthermore, the S-wave velocity model shows low Vp/Vs ratios in the mantle, indicating a highly serpentinised mantle at shallow depths. The gravity model has crustal densities between 2.3 and 2.9 g cm−3, which also point towards the absence of a significant thick oceanic layer 3. The results of our seismic refraction line and other geophysical data indicate that the entire Boreas Basin opened at ultraslow spreading rates since at least ∼28 Ma. No evidence for an extinct spreading ridge in the centre of the Boreas Basin was found.
    Repository Name: EPIC Alfred Wegener Institut
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  • 30
    Publication Date: 2022-05-26
    Description: © 2008 The Authors. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in Nucleic Acids Research 36 (2008): 2522-2529, doi:10.1093/nar/gkm1166
    Description: Penelope-like elements (PLEs) represent a new class of retroelements identified in more than 80 species belonging to at least 10 animal phyla. Penelope isolated from Drosophila virilis is the only known transpositionally active representative of this class. Although the size and structure of the Penelope major transcript has been previously described in both D. virilis and D. melanogaster transgenic strains, the architecture of the Penelope regulatory region remains unknown. In order to determine the localization of presumptive Penelope promoter and enhancer-like elements, segments of the putative Penelope regulatory region were linked to a CAT reporter gene and introduced into D. melanogaster by P-element-mediated transformation. The results obtained using ELISA to measure CAT expression levels and RNA studies, including RT–PCR, suggest that the active Penelope transposon contains an internal promoter similar to the TATA-less promoters of LINEs. The results also suggest that some of the Penelope regulatory sequences control the preferential expression in the ovaries of the adult flies by enhancing expression in the ovary and reducing expression in the carcass. The possible significance of the intron within Penelope for the function and evolution of PLEs, and the effect of Penelope insertions on adjacent genes, are discussed.
    Description: This work was supported by grants from Russian Academy of Sciences (Cell and Molecular Biology to M.E.), and Welcome Trust Grant (075698) to M.E and D.J.F.
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  • 31
    Publication Date: 2022-05-26
    Description: This paper is not subject to U.S. copyright. The definitive version was published in ICES Journal of Marine Science: Journal du Conseil 67 (2010): 1-9, doi:10.1093/icesjms/fsp221.
    Description: Effective marine ecosystem-based management (EBM) requires understanding the key processes and relationships controlling the aspects of biodiversity, productivity, and resilience to perturbations. Unfortunately, the scales, complexity, and non-linear dynamics that characterize marine ecosystems often confound managing for these properties. Nevertheless, scientifically derived decision-support tools (DSTs) are needed to account for impacts resulting from a variety of simultaneous human activities. Three possible methodologies for revealing mechanisms necessary to develop DSTs for EBM are: (i) controlled experimentation, (ii) iterative programmes of observation and modelling ("learning by doing"), and (iii) comparative ecosystem analysis. We have seen that controlled experiments are limited in capturing the complexity necessary to develop models of marine ecosystem dynamics with sufficient realism at appropriate scales. Iterative programmes of observation, model building, and assessment are useful for specific ecosystem issues but rarely lead to generally transferable products. Comparative ecosystem analyses may be the most effective, building on the first two by inferring ecosystem processes based on comparisons and contrasts of ecosystem response to human-induced factors. We propose a hierarchical system of ecosystem comparisons to include within-ecosystem comparisons (utilizing temporal and spatial changes in relation to human activities), within-ecosystem-type comparisons (e.g. coral reefs, temperate continental shelves, upwelling areas), and cross-ecosystem-type comparisons (e.g. coral reefs vs. boreal, terrestrial vs. marine ecosystems). Such a hierarchical comparative approach should lead to better understanding of the processes controlling biodiversity, productivity, and the resilience of marine ecosystems. In turn, better understanding of these processes will lead to the development of increasingly general laws, hypotheses, functional forms, governing equations, and broad interpretations of ecosystem responses to human activities, ultimately improving DSTs in support of EBM.
    Keywords: Comparative marine ecosystem analysis ; Decision-support tools ; EAM ; EBM ; Ecological modelling ; Ecosystem approaches to management ; Ecosystem-based management
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  • 32
    Publication Date: 2022-05-26
    Description: © The Author 2006. This article is posted here by permission of Oxford University Press. The definitive version was published in Nucleic Acids Research 34 (2006): 1-9, doi:10.1093/nar/gkj405.
    Description: The goal of this group project has been to coordinate and bring up-to-date information on all genes of Escherichia coli K-12. Annotation of the genome of an organism entails identification of genes, the boundaries of genes in terms of precise start and end sites, and description of the gene products. Known and predicted functions were assigned to each gene product on the basis of experimental evidence or sequence analysis. Since both kinds of evidence are constantly expanding, no annotation is complete at any moment in time. This is a snapshot analysis based on the most recent genome sequences of two E.coli K-12 bacteria. An accurate and up-to-date description of E.coli K-12 genes is of particular importance to the scientific community because experimentally determined properties of its gene products provide fundamental information for annotation of innumerable genes of other organisms. Availability of the complete genome sequence of two K-12 strains allows comparison of their genotypes and mutant status of alleles.
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  • 33
    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 5 (2013): 2368-2381, doi:10.1093/gbe/evt179.
    Description: The dinoflagellates are an evolutionarily and ecologically important group of microbial eukaryotes. Previous work suggests that horizontal gene transfer (HGT) is an important source of gene innovation in these organisms. However, dinoflagellate genomes are notoriously large and complex, making genomic investigation of this phenomenon impractical with currently available sequencing technology. Fortunately, de novo transcriptome sequencing and assembly provides an alternative approach for investigating HGT. We sequenced the transcriptome of the dinoflagellate Alexandrium tamarense Group IV to investigate how HGT has contributed to gene innovation in this group. Our comprehensive A. tamarense Group IV gene set was compared with those of 16 other eukaryotic genomes. Ancestral gene content reconstruction of ortholog groups shows that A. tamarense Group IV has the largest number of gene families gained (314–1,563 depending on inference method) relative to all other organisms in the analysis (0–782). Phylogenomic analysis indicates that genes horizontally acquired from bacteria are a significant proportion of this gene influx, as are genes transferred from other eukaryotes either through HGT or endosymbiosis. The dinoflagellates also display curious cases of gene loss associated with mitochondrial metabolism including the entire Complex I of oxidative phosphorylation. Some of these missing genes have been functionally replaced by bacterial and eukaryotic xenologs. The transcriptome of A. tamarense Group IV lends strong support to a growing body of evidence that dinoflagellate genomes are extraordinarily impacted by HGT.
    Description: J.H.W. was supported by the NSF IGERT Program in Comparative Genomics at the University of Arizona (grant number DGE-0654435). This work was supported by grants from the National Science Foundation (grant numbers OCE-0723498, EF-0732440) and funding provided by the BIO5 Institute at the University of Arizona to J.D.H.
    Keywords: Gene innovation ; Alexandrium tamarense Group IV ; Phylogenetic profile ; Phylogenomics ; De novo transcriptome assembly ; Mitochondrial metabolism
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  • 34
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cell 7 (2014): 1601–1613, doi:10.1016/j.celrep.2014.04.047.
    Description: We used high-speed optogenetic mapping technology to examine the spatial organization of local inhibitory circuits formed by cerebellar interneurons. Transgenic mice expressing channelrhodopsin-2 exclusively in molecular layer interneurons allowed us to focally photostimulate these neurons, while measuring resulting responses in postsynaptic Purkinje cells. This approach revealed that interneurons converge upon Purkinje cells over a broad area and that at least seven interneurons form functional synapses with a single Purkinje cell. The number of converging interneurons was reduced by treatment with gap junction blockers, revealing that electrical synapses between interneurons contribute substantially to the spatial convergence. Remarkably, gap junction blockers affected convergence in sagittal slices, but not in coronal slices, indicating a sagittal bias in electrical coupling between interneurons. We conclude that electrical synapse networks spatially coordinate interneurons in the cerebellum and may also serve this function in other brain regions.
    Description: This work was supported by a CRP grant from the National Research Foundation of Singapore and by the World Class Institute (WCI) Program of the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology of Korea (NRF grant number WCI 2009-003).
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  • 35
    Publication Date: 2022-05-26
    Description: Author Posting. © Author, 2014. This article is posted here by permission of The Royal Astronomical Society for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 198 (2014): 622-636, doi: 10.1093/gji/ggu121.
    Description: The robust statistical model of a Gaussian core contaminated by outlying data that underlies robust estimation of the magnetotelluric (MT) response function has been re-examined. The residuals from robust estimators are systematically long tailed compared to a distribution based on the Gaussian, and hence are inconsistent with the robust model. Instead, MT data are pervasively described by the alpha stable distribution family whose variance and sometimes mean are undefined. A maximum likelihood estimator (MLE) that exploits the stable nature of MT data is formulated, and its two-stage implementation in which stable parameters are first fit to the data and then the MT responses are solved for is described. The MLE is shown to be inherently robust, but differs from the conventional robust estimator because it is based on a model derived from the data, while robust estimators are ad hoc, being based on the robust model that is inconsistent with actual data. Propriety versus impropriety of the complex MT response was investigated, and a likelihood ratio test for propriety and its null distribution was established. The Cramér-Rao lower bounds for the covariance matrix of proper and improper MT responses were specified. The MLE was applied to exemplar long period and broad-band data sets from South Africa. Both are shown to be significantly stably distributed using the Kolmogorov–Smirnov goodness of fit and Ansari-Bradley non-parametric dispersion tests. Impropriety of the MT responses at both sites is pervasive, hence the improper Cramér-Rao bound was used to estimate the MLE covariance. The MLE is shown to be nearly unbiased and well described by a Gaussian distribution based on bootstrap simulation. The MLE was compared to a conventional robust estimator, establishing that the standard errors of the former are systematically smaller than for the latter and that the standardized differences between them exhibit excursions that are both too frequent and too large to be described by a Gaussian model. This is ascribed to pervasive bias of the robust estimator that is to some degree obscured by their systematically large confidence bounds. Finally, a series of topics for further investigation is proposed.
    Description: This work was supported by NSF grant EAR0809074.
    Keywords: Time series analysis ; Numerical approximations and analysis ; Fractals and multifractals ; Probability distributions ; Magnetotellurics
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  • 36
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Plankton Research 36 (2014): 943-955, doi:10.1093/plankt/fbu029.
    Description: The mechanisms by which phytoplankton cope with stressors in the marine environment are neither fully characterized nor understood. As viruses are the most abundant entities in the global ocean and represent a strong top-down regulator of phytoplankton abundance and diversity, we sought to characterize the cellular response of two marine haptophytes to virus infection in order to gain more knowledge about the nature and diversity of microalgal responses to this chronic biotic stressor. We infected laboratory cultures of the haptophytes Haptolina ericina and Phaeocystis pouchetii with CeV-01B or PpV-01B dsDNA viruses, respectively, and assessed the extent to which host cellular responses resemble programmed cell death (PCD) through the activation of diagnostic molecular and biochemical markers. Pronounced DNA fragmentation and activation of cysteine aspartate-specific proteases (caspases) were only detected in virus-infected cultures of these phytoplankton. Inhibition of host caspase activity by addition of the pan-caspase inhibitor z-VAD-fmk did not impair virus production in either host–virus system, differentiating it from the Emiliania huxleyi-Coccolithovirus model of haptophyte–virus interactions. Nonetheless, our findings point to a general conservation of PCD-like activation during virus infection in ecologically diverse haptophytes, with the subtle heterogeneity of cell death biochemical responses possibly exerting differential regulation on phytoplankton abundance and diversity.
    Description: Funding to J.L.R, R.-A.S. and A.L. was provided by the Norwegian Research Council for the “VIPMAP” (nr. 186142) and “HAPTODIV” (nr. 190307) projects, and by the European Research Council Advanced Grant ERC-AG-LS8 “Microbial Network Organisation” (MINOS, project number 250254). J.L.R. received a FRIBIO overseas research fellowship from the Norwegian Research Council. K.D.B. and B.V.M. were supported by funding from the United States National Science Foundation (OCE-1061883).
    Keywords: Caspase ; DNA fragmentation ; IETD ; Phycodnaviridae ; z-VAD-fmk ; Haptophyte
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  • 37
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 6 (2014): 2210-2217, doi:10.1093/gbe/evu177.
    Description: The alpha subunits of voltage-gated calcium channels (Cavs) are large transmembrane proteins responsible for crucial physiological processes in excitable cells. They are assisted by three auxiliary subunits that can modulate their electrical behavior. Little is known about the evolution and roles of the various subunits of Cavs in nonbilaterian animals and in nonanimal lineages. For this reason, we mapped the phyletic distribution of the four channel subunits and reconstructed their phylogeny. Although alpha subunits have deep evolutionary roots as ancient as the split between plants and opistokonths, beta subunits appeared in the last common ancestor of animals and their close-relatives choanoflagellates, gamma subunits are a bilaterian novelty and alpha2/delta subunits appeared in the lineage of Placozoa, Cnidaria, and Bilateria. We note that gene losses were extremely common in the evolution of Cavs, with noticeable losses in multiple clades of subfamilies and also of whole Cav families. As in vertebrates, but not protostomes, Cav channel genes duplicated in Cnidaria. We characterized by in situ hybridization the tissue distribution of alpha subunits in the sea anemone Nematostella vectensis, a nonbilaterian animal possessing all three Cav subfamilies common to Bilateria. We find that some of the alpha subunit subtypes exhibit distinct spatiotemporal expression patterns. Further, all six sea anemone alpha subunit subtypes are conserved in stony corals, which separated from anemones 500 MA. This unexpected conservation together with the expression patterns strongly supports the notion that these subtypes carry unique functional roles.
    Keywords: Voltage-gated calcium channel ; Ion channel ; Cnidaria ; Nematostella vectensis ; Evolution of nervous system
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  • 38
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    American Institute of Physics
    Publication Date: 2022-05-26
    Description: 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.
    Description: 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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  • 39
    Publication Date: 2022-05-26
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nucleic Acids Research 40 (2012): 7132-7149, doi:10.1093/nar/gks467.
    Description: The capacity of microorganisms to respond to variable external conditions requires a coordination of environment-sensing mechanisms and decision-making regulatory circuits. Here, we seek to understand the interplay between these two processes by combining high-throughput measurement of time-dependent mRNA profiles with a novel computational approach that searches for key genetic triggers of transcriptional changes. Our approach helped us understand the regulatory strategies of a respiratorily versatile bacterium with promising bioenergy and bioremediation applications, Shewanella oneidensis, in minimal and rich media. By comparing expression profiles across these two conditions, we unveiled components of the transcriptional program that depend mainly on the growth phase. Conversely, by integrating our time-dependent data with a previously available large compendium of static perturbation responses, we identified transcriptional changes that cannot be explained solely by internal network dynamics, but are rather triggered by specific genes acting as key mediators of an environment-dependent response. These transcriptional triggers include known and novel regulators that respond to carbon, nitrogen and oxygen limitation. Our analysis suggests a sequence of physiological responses, including a coupling between nitrogen depletion and glycogen storage, partially recapitulated through dynamic flux balance analysis, and experimentally confirmed by metabolite measurements. Our approach is broadly applicable to other systems.
    Description: Office of Science (BER), U.S. Department of Energy [DE-FG02-07ER64388 to D.S. and DE-FG02- 08ER64511 to M.H.S.]; National Aeronautics and Space Administration, NASA Astrobiology Institute [NNA08CN84A to D.S.].
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  • 40
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    Oxford University Press
    In:  Handbook of Avian Hybrids of the World vol. 76, 1, pp. 59-61
    Publication Date: 2024-01-12
    Keywords: book review ; geographic distribution ; hybridisation ; birds
    Repository Name: National Museum of Natural History, Netherlands
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  • 41
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 18 (1985), S. 53-54 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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    Applied crystallography online 18 (1985), S. 54-54 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 18 (1985), S. 54-54 
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    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 18 (1985), S. 55-60 
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    Topics: Geosciences , Physics
    Notes: The requirements imposed on the magnitude of the noise in a scattering curve in order to minimize the corresponding error in the structure functions are estimated for a given value of the time T in which the scattering curve is recorded. Typical small-angle X-ray scattering (SAXS) curves have been used to check how these conditions are fulfilled when different counting modes are applied for the measurement. It is shown that fixed-time counting is the most practical technique and produces error bands in the structure functions with magnitudes close to the smallest values attainable in SAXS investigations.
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    Applied crystallography online 18 (1985), S. 61-64 
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    Notes: Following the procedure suggested by May, Ibel & Haas [J. Appl. Cryst. (1982), 15, 15–19] for the correlation of transmission data with the level of neutrons scattered incoherently into the full solid angle 4π measurements have been made of the transmission and incoherent scattering intensities of aqueous buffers of different H2O/D2O ratios at temperatures between 280 and 343 K. That it is possible to extend the proposed calibration procedure to absorbing-ions-containing buffers is also shown.
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    Applied crystallography online 18 (1985), S. 65-70 
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    Topics: Geosciences , Physics
    Notes: Small-angle neutron scattering experiments have been performed with aqueous dispersions of binary lipid mixtures. One component was protonated, the other was partly deuterated. By varying the mole fraction of the deuterated species the mean scattering-length density of the lipid lamellas and hence the contrast between liposomes and the solvent was changed. It is shown that this inverse contrast variation has the advantage of (i) a simpler data analysis, (ii) an increased resolution of homogeneous and heterogenous lipid distributions and (iii) a considerably increased sensitivity for the evaluation of phase diagrams in segregated lipid mixtures. Phase boundaries can now be determined to an accuracy of better than 1 mol%.
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  • 47
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    Applied crystallography online 18 (1985), S. 71-74 
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    Notes: A very simple method is described to align accurately any full four-circle diffractometer with respect to the incident beam. This method relies on anomalous transmission measurements. It has been found that the centroids of the Ge 220 anomalous transmission intensity distributions measured at the four main positions of the χ circle, that is 0, 90, 180, and 270°, not only provide an accurate determination of the reference angles for ω and φ, but also provide an accurate method to align the χ circle with respect to the direction of the incident beam. This procedure promises to be even more helpful for diffractometers installed at synchrotron radiation laboratories than for in-house installations.
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  • 48
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    Applied crystallography online 18 (1985), S. 75-79 
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    Notes: A computer program to calculate the contributions of crystal, capillary and a simple model of mother liquor to the overall absorption of X-rays has been written. It is based on the Gaussian quadrature method of integration; the crystal is described by the polyhedral faces bounding it, the capillary by its diameter, thickness and orientation with respect to the diffractometer axes and the mother liquor by the crystal faces that trap it between crystal and inner capillary wall. The program is written in Fortran for a VAX 11/780 computer and incorporates tables of mass absorption coefficients for silver, molybdenum and copper radiations for easy calculation of linear absorption coefficients.
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    Applied crystallography online 18 (1985), S. 80-84 
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    Notes: A method is described for semiquantitative X-ray diffraction phase analysis, which involves the addition to the investigated multicomponent system of known large (about 80–95%) amounts of a crystalline substance originally not contained in the system. This results in a decrease of the diffraction line intensities of the components to be measured to small but detectable values. The weight fraction of a component is related to the added fraction of the doping substance and to the fraction of that component remaining in the doped sample. The method is very simple and yields the weight fractions of the major components in the system with a typical error of a few percent. The weight fractions of the minor components cannot be determined with fair accuracy in this way. The method is appropriate in cases where only a small amount of the investigated system is available. Optimum conditions to attain maximum accuracy of the method are discussed.
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    Applied crystallography online 18 (1985), S. 85-92 
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    Notes: The use of a varying-step algorithm now allows the simulation of traverse topographs and of section topographs taking into account the real width of the incident beam. However, computation time remains a critical factor in practical use. With an array processor it is possible to decrease the computation time significantly. It is shown that pictures of good quality may be obtained in a reasonable time using local facilities. The influence of various parameters on the accuracy of the simulations is discussed. It is demonstrated that local machines can be more useful, in crystallography, than giant computers often difficult to reach through the network of communications.
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    Applied crystallography online 18 (1985), S. 106-109 
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    Notes: A simple method for in situ alignment of samples in a double-crystal X-ray topography system is described. This method permits a specific crystallographic axis to be made coincident with the sample rotation axis used to set the Bragg angle. Surface reflections from approximately orthogonal crystallographic planes are required and tables of such planes suitable for alignment of cubic crystals are given. This procedure allows rapid setup for the other accessible surface reflection or transmission topographs.
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  • 52
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    Applied crystallography online 18 (1985), S. 114-119 
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    Topics: Geosciences , Physics
    Notes: This article presents mathematical methods for calculating the shoulder limit and detection limit for two merging Pearson VII functions. Results are given for the particular case of the modified Lorentzian (n = 2). The modified Marquardt algorithm of the data reduction program used by the authors is briefly discussed. Synthetic diffraction patterns are used to determine a practical detection limit for this program that compares favourably with the theoretical detection limit.
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  • 53
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    Applied crystallography online 18 (1985), S. 110-113 
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    Notes: With a highly convergent electron beam entering a small crystal area, the Bragg condition may be fulfilled simultaneously for many diffraction orders along a reciprocal-lattice direction, and reflections with (sin θ)/λ 〉 2 Å−1 are accessible. Considerations based on the dynamical theory of electron diffraction suggest that for Bragg reflections with (sin θ)/λ 〉 1 Å−1, 100 keV electrons can be treated quasi-kinematically when the crystal thickness is less than 1000 Å, and this is supported by experiments. This simple approach has been used to determine the D-induced static displacement modulation δ of V along the a axis (monoclinic indexing) in the β phase of V2D. From visual inspection of the Bragg intensities for large diffraction orders, up to (sin θ)/λ = 2.35 Å−1, it is concluded that δ = 0.070 (5) Å.
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    Applied crystallography online 18 (1985), S. 120-122 
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    Notes: It is shown that an X-ray interferometer consisting of two crystals cut from different pieces of silicon material can be successfully operated. The dependence of the visibility of the interference pattern on different thicknesses of beam splitter and analyzer is investigated.
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    Applied crystallography online 18 (1985), S. 93-105 
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    Notes: A systematic study of the variations of the contrast of a dislocation in silicon on section topographs with the depth of the line was performed both experimentally and with computer simulations. Mo Kα1 radiation and 33{\bar 3} and {\bar 3}{\bar 3}3 symmetric reflections were used. The crystal thickness was 440 μm so that the value of μt was 0.64. The influence of the orientation of the dislocation was studied for values of the angle between the line and its Burgers vector ranging between 60 and 90° in the glide plane. It was observed that when the dislocation lies close to the entrance surface, whatever its orientation, its image is centred around the trace of the plane of incidence passing through the intersection of the dislocation with the direct beam while when the dislocation lies close to the exit surface its image is centred around the projection of the dislocation on the section pattern. The variation of the orientation of the image for intermediate depths of the dislocation is interpreted by means of the geometrical construction of the dynamical image. The values of the orientation of the image calculated according to this simple model are in good agreement with those measured on both experimental and simulated topographs. The same geometrical model enables the difference in the relative positions of the direct and dynamic images of stereo pairs to be explained. A new feature was observed in the simulated images and several of the experimental ones, namely a concentration of intensity along the projection of the dislocation in the reflected direction. Slit width was taken into account in the simulations for a better fit with experimental topographs but not polarization, which was taken to be normal to the plane of incidence. Because of the small value of the crystal thickness and of μt, the variation of the contrast with the Burgers vector is very small, making its determination very difficult.
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    Applied crystallography online 18 (1985), S. 130-130 
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    Applied crystallography online 18 (1985), S. 122-125 
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    Topics: Geosciences , Physics
    Notes: The Rayleigh scattering of Mössbauer radiation has recently been applied to the study of disordered macromolecular systems. A general program has been developed for the analysis of the scattering intensities obtained with this technique. The methodology, which follows the line of the X-ray analysis of disordered systems, has been improved and it can provide information on the static and dynamic structures from the Fourier transform of the total and elastic scattering intensities. A flow-chart of the whole program with its main features and the organization of input-output are also described.
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    Applied crystallography online 18 (1985), S. 126-130 
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    Topics: Geosciences , Physics
    Notes: A computer program for simulating convergent-beam electron diffraction patterns from single crystals and bicrystals is described. The program is based on the dynamical theory of electron diffraction, and the intensity of a convergent-beam disc is constructed from the individual intensities of a number of plane waves incident on the specimen. For the bicrystal case, this program allows the influence of parameters such as the location of the boundary plane and a rigid translation at the boundary to be investigated. These effects are discussed for a horizontal (111) twin boundary in silicon.
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    Applied crystallography online 18 (1985), S. 131-134 
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    Notes: A simple analytic method to correct the experimentally observed spin-flip and non-spin-flip scattering cross sections in neutron polarization analysis experiments for the effects of multiple scattering is presented. From known parameters of the constituent elements of a specimen and from the measured experimental cross sections the single scattering cross sections can readily be determined. This is particularly useful in situations where the scattering is isotropic or exhibits only slight angular dependence.
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    Applied crystallography online 18 (1985), S. 135-140 
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    Notes: Reflecting properties of a double-crystal (DC) monochromator consisting of two elastically bent perfect silicon crystals in the parallel non-dispersive (1, −1) setting were experimentally treated. Using an unconventional fully asymmetric geometry, the effective mosaicity may be significantly enhanced up to the value of about 10−2 rad. Test experiments were performed on the 111 and 400 reflections for wavelengths of 0.2 nm and 0.157 nm, respectively. The experimental results obtained are found to be in good agreement with the theoretical predictions published in a previous paper [Mikula, Kulda, Vrána & Chalupa (1984). J. Appl. Cryst. 17, 189–195].
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    Applied crystallography online 18 (1985), S. 141-144 
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    Notes: Crystallographic properties of depleted uranium alloys (0.75 wt% Ti) with two different heat treatments were studied by neutron powder diffraction methods. The crystal structures are essentially the same as that of pure α-uranium metal, but with somewhat different unit-cell dimensions. The super-saturated Ti impurity in the quenched sample is primarily substitutional. Diffraction lines of the quenched uranium alloy showed a clear strain broadening. The r.m.s. strain obtained from the broadening was 0.0019.
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    Applied crystallography online 18 (1985), S. 145-149 
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    Notes: A new technique is described for performing high-pressure single-crystal neutron diffraction [up to 20 kbar (2 GPa) at room temperature], using a BeCu pressure cell, an area detector and the Los Alamos National Laboratory pulsed neutron source. Success of this method depends on the increase in information available with a multi-wavelength pulse neutron source, a novel orientation of a cylindrically symmetric pressure cell with its axis coincident with the neutron beam and a specific crystal orientation within the pressure cell. Bragg scattering from the pressure cell is avoided and background for a given 2θ is constant. For a crystal of orthorhombic or higher symmetry oriented with the incident beam passing midway between the major lattice vectors, it will be possible to refine a complete three-dimensional structure with data collected from only one pressure loading. Preliminary investigations of Tl3PSe4 lattice parameters (space group Pcmn) at 15(1)kbar yielded linear compressibilities (× 1000 in kbar−1) of Ka = 1.05(8), Kb = 1.50(10), Kc = 1.20(8). The anisotropic compressibility is explained by examination of the ambient-pressure room-temperature structure.
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    Applied crystallography online 18 (1985), S. 150-155 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: An X-ray powder diffractometric procedure has been developed to determine the lattice parameters of long-chain hydrocarbons and mixtures thereof. Useful information was limited to low diffraction angles owing to the large size of the unit cell. Intensities were measured in the reflection mode for thick samples with low absorption. Centroids of the diffraction profiles were corrected for axial beam divergence, sample flatness, displacement and transparency and goniometer scale zero position. An internal Si standard was mixed with the sample to determine the displacement of the sample surface from the goniometer axis. The values of a, b and c for the orthorhombic structures n-tricosane (n-C23H48) are 4.965(3), 7.462(4) and 62.12(2) Å and for n-pentacosane (n-C25H52) are 4.964(3), 7.450(4) and 67.21(2) Å. The values agree well with earlier single-crystal studies except for c for which a larger value is reported in the earlier work, probably due to sample impurity.
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  • 64
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    Applied crystallography online 18 (1985), S. 156-158 
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    Notes: Crystal lattice parameters of mixtures of the normal alkanes n-C23H48 and n-C25H52 have been determined by X-ray powder diffractometry. The c-axis length increases nearly monotonically with increasing C25H52 content, a and b are larger for the mixtures than for the pure substances with maximum values at 15% n-C25H52. The small but significant increases in a of 0.6% and b of 0.9% have not been previously reported.
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  • 65
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    Applied crystallography online 18 (1985), S. 159-164 
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    Topics: Geosciences , Physics
    Notes: An interactive program for comparison of experimental with theoretical martensitic transformation data and for orientation determination from Laue and zero-layer reciprocal-lattice photographs is described. The program can generate orthographic, gnomonic, Laue and zero-layer reciprocal-lattice projections of lattice vectors, circles and latitude-longitude nets. A utility for habit-plane calculation from surface trace data and its diagrammatical representation is provided. Drawings before and after transformation can be superimposed. Output from program MRTNST [Ledbetter & Wayman (1971). Mater. Sci. Eng. 7, 151–157] (altered to handle triclinic lattices) can be read directly by COATI, which also facilitates the graphical method of martensitic calculations. A lucid command language allows easy manipulation of previously complex procedures.
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  • 66
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    Applied crystallography online 18 (1985), S. 165-169 
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    Topics: Geosciences , Physics
    Notes: A rigid-body refinement method and program for crystallography of macromolecules is described. Orientational and translational parameters are refined by fitting the molecular Fourier transforms to the observed structure-factor amplitudes. The range of convergence of the method has been tested on four examples with known crystal structure: PTI, chymotrypsinogen and two forms of α1 anti-trypsin. It was successfully applied in the structure solution of two unknown crystal structures: a third form of α1 anti-trypsin and C-phycocyanin.
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  • 67
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    Applied crystallography online 18 (1985), S. 170-172 
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    Notes: A chemical reaction, the hydration of CaSO4.½D2O, was followed in real time in an on-line neutron diffraction experiment at different temperatures. The results of the reactions are presented as diagrams showing the evolution of the intensities of CaSO4.2D2O in real time. The hydration passes through the formation of a gel interphase. The dehydration of CaSO4.2D2O was followed in the same way at temperatures up to 420 K.
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  • 68
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    Applied crystallography online 18 (1985), S. 173-180 
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    Topics: Geosciences , Physics
    Notes: Analyses of high-resolution neutron powder diffraction data, using both the Pearson VII and pseudo-Voigt peak shape functions, have revealed a range of peak shapes from essentially Gaussian to Lorentzian and beyond. Moreover, the refinements show that the Lorentzian character of the peaks in each pattern increases with increasing diffraction angle. Both kinds of shape change are associated with varying relative contributions to the peak profiles of the instrumental resolution, isotropic crystallite strain and crystallite size effects. Rietveld analysis of powder data with the standard Gaussian form when the peaks have significant Lorentzian character has little effect on atomic positional parameters, but it leads to an overestimation of the thermal vibration coefficients and higher least-squares residuals.
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  • 69
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    Applied crystallography online 18 (1985), S. 181-183 
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    Notes: The anomalous scattering factors of zinc and silver in samples of Al-rich Al–Zn–Ag have been measured near their K-absorption edges. EXAFS spectra obtained from the Stanford Synchrotron Radiation Laboratory were converted to the imaginary part of the atomic scattering factor f′′ using the optical theorem. With a knowledge of f′′(E), f′, the real part of the atomic scattering factor, was determined from the Kramers–Kronig dispersion relation.
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    Applied crystallography online 18 (1985), S. 183-184 
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    Notes: From a given initial unit cell the program generates new lattices that are distributed among crystal systems by a purely metrical criterion and sorted according to an empirical figure of merit. For each solution the output contains the new cell parameters along with the corresponding transformation matrix to be applied to the initial unit cell.
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    Applied crystallography online 18 (1985), S. 188-189 
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    Applied crystallography online 18 (1985), S. 190-190 
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    Applied crystallography online 18 (1985), S. 185-188 
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    Notes: The restrained reciprocal-space least-squares refinement program of Hendrickson & Konnert [Computing in Crystallography, edited by R. Diamond, S. Ramaseshan & K. Venkatesan, pp. 13.01–13.25. (1980). Bangalore: Indian Academy of Sciences] has been modified to include non-bonded and/or hydrogen-bonded contacts between molecules related by symmetry operations and/or unit-cell translations. The modified program has been tested on an inhibited form of aspartate aminotransferase, which is an α2 dimeric enzyme with a crystallographic twofold axis relating the subunits. A number of heretofore unseen close contacts between atoms of separate subunits were located and correctly dealt with by the modified program.
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    Applied crystallography online 18 (1985), S. 189-190 
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    Applied crystallography online 18 (1985), S. 190-190 
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    Applied crystallography online 18 (1985), S. 191-196 
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    Notes: A new method is described to determine accurately the intensities of reflexions in the case of oblique texture electron diffraction. The method is based on a comparison between experimental values of intensities and those calculated with a formalism that takes into account the orientation function of the particles. It allows the problems that arise from frequent overlapping of reflexions to be surmounted. A concrete example of the application of this method is given the structure refinement of a mica with muscovite–phengite composition.
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    Applied crystallography online 18 (1985), S. 197-204 
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    Notes: Convergent-beam electron diffraction has been used to confirm the accepted space group of rutile (TiO2) and to study in detail the dependence of the intensity of the space-group-forbidden reflections on crystal thickness and orientation. The observations are shown to be in detailed agreement with computer-simulated patterns calculated using the standard structural parameters. The diffraction results provide a basis for understanding the high-resolution electron-microscope images of rutile crystals oriented close to the [001] zone in which the effects of the space-group-forbidden reflections are important. It is concluded that satisfactory agreement exists between experimental and calculated images provided that allowance is made for uncertainty in the orientation of the crystal.
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    Applied crystallography online 18 (1985), S. 214-218 
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    Notes: A new integrated device for the structural study of liquid or amorphous compounds is described. The X-ray scattering pattern produced by the sample is quickly recorded by a micro-computer-controlled goniometer with position-sensitive detection. Interactive software allows both experimental data processing and simulation from structural models.
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  • 79
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    Applied crystallography online 18 (1985), S. 205-213 
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    Notes: An improved transform technique has been developed [Gerber (1983). Thesis, Wilhelm-Pieck-University Rostock, German Democratic Republic] for calculating the particle size distribution N(R) for spherical particles with radii R from small-angle X-ray scattering data. This method permits N(R) to be calculated from analytical expressions that were derived for point collimation and for infinitely long slit collimation. A special procedure has been introduced in order to reduce termination errors. The technique described and those developed by Schmidt [Brill, Weil & Schmidt (1968). J. Colloid Interface Sci. 27, 479–492], Vonk [J. Appl. Cryst. (1976), 9, 433–440] and Glatter [J. Appl. Cryst. (1980), 13, 7–11] were used for calculating particle size distributions from theoretical scattering curves and from an experimental scattering curve of suspended SiO2 particles (Ludox). The results obtained by the different techniques were compared, and reasonable results are given by all methods employed. The accuracy of the size distributions calculated by the improved method is somewhat higher than that obtained by Schmidt's transform technique. With Glatter's procedure, the deviations from the exact distributions are comparable to those from this improved transform technique, but the use of Glatter's program requires a large computer, whereas the new method has the advantage of being suitable for a small computer. Vonk's program also requires a large computer, and the deviations obtained are larger than those produced by other methods. The experimental scattering curve of the Ludox sample was also evaluated by assuming a log-normal distribution for the particles. The parameters μ and σ of this function were determined from a set of small-angle X-ray scattering structural parameters. The resulting log-normal distribution is significantly different from the size distribution calculated by our method.
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    Applied crystallography online 18 (1985), S. 237-240 
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    Notes: It is shown by anomalous X-ray scattering that the absolute configuration of LiIO3, originally determined by Li Yin-yuan, Fan Hai-fu & Chia Shou-chuan [Sci. Sin. (1973), 16, 130–135], is incorrect, in accordance with the prediction of Glazer & Stadnicka [(1985). Submitted to J. Appl. Cryst.]. Measurements of the optical rotatory dispersion are also reported.
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  • 81
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    Applied crystallography online 18 (1985), S. 219-229 
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    Notes: Different functional parameterizations of the radiation intensity scattered by an N-component amorphous sample are considered. Each parameterization is such that (i) it depends only on the areas and on the angularities of the samples' interphase surfaces, (ii) it fulfils all the known physical constraints and (iii) it yields a rather simple algebraic expression both for the correlation function and for the scattered intensity. The parameterizations have been used for analysing the scattering data relevant to some three-component catalysts. Provided the volume fraction of the metal is not very small, the best fit yields satisfactory results only for some of the considered parameterizations. In this way, the determination of both the areas and the angularities of catalysts appears possible.
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    Applied crystallography online 18 (1985), S. 230-236 
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    Notes: Solute partitioning during decomposition of a ternary alloy may be evaluated through the inversion of a system of linear equations, obtained by performing at least three independent small-angle scattering experiments. The merits of neutron scattering (with isotopic contrast) and of anomalous X-ray scattering (near the absorption edges) are compared. It appears that neutron scattering, although having good contrast, is not suited to these studies since slight structural differences between the three samples may lead to erroneous results. On the other hand, the use of the same sample in anomalous scattering avoids this problem, but with the drawback of a more ill-conditioned system. Nevertheless, the possibility of performing more than three anomalous experiments may improve the results and a new analysis of data is proposed.
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    Applied crystallography online 18 (1985), S. 253-257 
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    Notes: An algorithm for a safe generation of the table of expected reflections in the Arndt–Wonnacott rotation camera is given. It relies upon classic quadratic matrix algebra. Some mathematical theorems are recalled. This algorithm is part of a series of programs developed at Orsay for the treatment of rotation-camera photographs.
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  • 84
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    Applied crystallography online 18 (1985), S. 248-252 
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    Notes: The fast Fourier transform algorithm commonly used for line profile analysis requires a list of values of the diffracted intensity with constant sinθ step; raw data are usually obtained at constant 2θ step; to interpolate between the measured values an analytic expression of the profile function is very useful. Statistical estimation is used to fit an analytic function to data; the only assumption made is the continuity of this function and no critical initialization is needed. Three different expressions are used: a Fourier sum for the peak and two polynomials of a suitable variable for the tails; the algorithm provides continuity for the function and its first derivative. Simulated examples using a Lorentzian and a Gaussian function are given and several criteria of goodness of fit are examined. The program runs on a PDP 11/03 Digital computer with only 45 kbytes available memory.
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    Applied crystallography online 18 (1985), S. 241-247 
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    Notes: Although the quality of a structure model obtained from small-angle X-ray or neutron scattering curves for polymers can be determined qualitatively by comparing the isotropic scattering curve calculated for the model with the experimental scattering data for a solution of polymer molecules, other methods are needed for a more precise evaluation. A model resolution function has been defined to permit quantitative comparisons. With this function, the quality of the approximation can be assessed, and the structure resolution can be determined. An overinterpretation of scattering curves by use of complex but uniform-density models can thus be avoided. Furthermore, the value of the Porod volume calculated from the scattering data has been found to depend strongly on the interval in which the scattering data are recorded or selected for evaluation. The calculations with the atomic model curves showed that it is impossible to compute physically meaningful values of the hydration of the molecules from the Porod volume and the dry volume by use of extrapolated scattering curves with an insufficient resolution. The theory of the model resolution function and the interpretation of the Porod volume have been verified and tested with experimental scattering curves from solutions of RNA molecules.
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    Applied crystallography online 18 (1985), S. 263-263 
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    Applied crystallography online 18 (1985), S. 258-262 
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    Notes: STRUPL084 is a Fortran plot program for drawing crystal structures in polyhedral or skeletal representation. All data are read in free format by standard Fortran routines. Atomic positions are also accepted in formats compatible with the input for the programs SHELX and ORFLS. The structure can be rotated by three rotation angles applied to the orthogonal axes. Instead of giving the rotation angles a view direction can be specified. The output includes a list of direct and orthogonal coordinates and tables with interatomic distances and angles. Atoms that were found to form coordination polyhedra are listed separately. The program is `user friendly' inasmuch as an acceptable plot can be achieved with minimum input by making use of the default options. Atoms not belonging to any polyhedra can be drawn as circles with specified radii.
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    Applied crystallography online 18 (1985), S. 264-264 
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    Applied crystallography online 18 (1985), S. 263-264 
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    Applied crystallography online 18 (1985), S. 264-265 
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    Applied crystallography online 18 (1985), S. 265-265 
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    Applied crystallography online 18 (1985), S. 265-266 
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    Applied crystallography online 18 (1985), S. 267-271 
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    Notes: The diffraction pattern of cathodically charged austenite consists of broad diffraction bands, often composed of more than one maximum and located close to the position of the regular diffraction peak of the f.c.c. austenitic lattice. The source of these bands was attributed to a nonuniform spatial distribution of hydrogen within the thin surface layer of the material. Calculated diffraction profiles are in good qualitative agreement with the observed profiles. Measurements of the shift of the centroid of the diffraction band were used to estimate the effective diffusion coefficient of hydrogen in austenite.
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    Applied crystallography online 18 (1985), S. 272-274 
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    Notes: Reflection from a perfect crystal is used to produce a parallel beam of Kα1 radiation. The losses due to large distances, which are needed for elimination of the Kα2 component, are compensated by a totally reflecting guide tube. The measured flux of Kα1 from a Cu-target X-ray tube at 40 kV and 40 mA was 5 × 105 counts s−1 on an area of 0.5 mm2, when an Si(220) monochromator and a glass guide tube were used. It is estimated that 1 × 107 counts s−1 are available with a Ge(111) monochromator and a gold-plated guide tube. The angular resolution is about 0.1 mrad.
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    Applied crystallography online 18 (1985), S. 275-278 
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    Notes: Growth defects were studied by X-ray topography in a succession of plates cut parallel to the basal planes of two quartz crystals from an Italian druse (Rocca dei Cristalli, Val Malenco, Italy). Growth bands, dislocations and precipitates are the dominant defects. Defect configurations, Burgers vectors and orientations of line defects were found to be similar in both crystals. Distinctive growth marks characterize the growth history of the druse: in particular, characterization was made of unreported dislocations with 〈a〉 Burgers vectors, whose line orientations deviate from the basal plane by an angle of about 10°. These dislocations, referred to here as pseudo-basal dislocations (p.b.d.), were found to be perpendicular to the x {51{\bar 6}1} faces.
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    Notes: The film absorption factors for CEA Reflex 25 X-ray film have been estimated by three different methods as a function of wavelength in the range 0.3 ≤ λ ≤ 2 Å. This wavelength range encompasses many absorption edges of interest in X-ray crystallography to optimize anomalous dispersion, those wavelengths used to reduce protein crystal absorption (λ ≤ 1 Å), and the spectral range utilized for protein crystal Laue diffraction at synchrotron radiation sources. The value of the film factor at a given λ is important to many protein structural projects.
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    Applied crystallography online 18 (1985), S. 279-295 
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    Notes: Diffraction intensity pole figures are often used for the determination of orientation distribution function (o.d.f.) expansion coefficients. The intensity can be seen as a convolution of the o.d.f. times unity with respect to one rotation angle (about the direction of measurement). The `normal' polycrystalline diffraction experiment only yields the even-order o.d.f. coefficients. The experiment itself imposes a centre of inversion even upon non-centrosymmetric crystals. Crystals may exhibit a centre of inversion themselves. The hkl and {\bar h}{\bar k}{\bar l}contributions to the intensity are indistinguishable then owing to the centre of inversion. As a consequence, the odd-order coefficients cannot be determined. The mean value of a general physical property determined by means of diffraction can be taken as a convolution of the o.d.f. times the single-crystal value of the physical property with respect to the rotation angle mentioned before. The dependency of the physical property on the rotation angle leads to more information being extracted from the o.d.f. in the property's mean-value pole figure. Then, all o.d.f. coefficients may be present in the mean value, i.e. the measurement. Consequently, diffraction-line-shift strain pole figures exhibit even- and odd-order o.d.f. coefficients, present or induced centres of inversion notwithstanding. If the dependency of the single-crystal strain on the rotation angle is known no model of elastic polycrystal coupling is needed. However, this does not occur in practice. The present state of the art does not allow the Kröner model to be used for textured materials. In this paper the Reuss model is used. If the (applied) macrostresses are known, the o.d.f. coefficients can be obtained from the formulae presented.
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    Applied crystallography online 18 (1985), S. 301-307 
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    Notes: A method allowing the calculation of the diffraction line profiles of a powder, whose crystallites are convex polyhedrons, is described. The decomposition of the crystallite volume into elementary prisms distinguishes three cases. The analytical expression of the results allows their derivation in the case of a linear size distribution. With instrumental broadening causes taken into account, an application of this method is given in restoring the whole X-ray diffraction pattern of samples of finely divided powders of boehmite, AlOOH.
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  • 99
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 18 (1985), S. 308-315 
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: An error analysis is performed for a slit-length-smeared SAXS curve of polystyrene in benzene. The desmearing and further calculations are done by indirect Fourier transformation. Four different functions are considered. The results are compared and the different error propagation properties of the chosen functions are discussed.
    Type of Medium: Electronic Resource
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  • 100
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 18 (1985), S. 316-319 
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: To improve the growing of single crystals for structural analysis, especially those of low-melting-point materials, a new technique and the appropriate apparatus have been developed. The heat radiation of a halogen lamp of adjustable intensity is focused by a parabolic mirror on the sample capillary, which is mounted on a diffractometer and cooled by a gas stream at a controlled temperature. The focus can be moved along the length of the capillary in any direction, for horizontal or vertical miniature zone melting or Bridgman techniques. The heat source and the movable mirror are controlled by a microprocessor, which allows systematic and software-supported search and reproduction of suitable experimental growing conditions.
    Type of Medium: Electronic Resource
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