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  • Oxford University Press  (97,647)
  • American Association of Petroleum Geologists (AAPG)
  • International Union of Crystallography (IUCr)
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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)
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  • 2
    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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  • 3
    Publication Date: 2019-07-16
    Description: Petroleum systems located at passive continental margins received increasing attention in the last decade mainly because of deep- and ultra‐deep-water hydrocarbon exploration and production. The high risks associated with these settings originate mainly from the poor understanding of inherent geodynamic processes. The new priority program SAMPLE (South Atlantic Margin Processes and Links with onshore Evolution), established by the German Science Foundation in 2009 for a total duration of 6 years, addresses a number of open questions related to continental breakup and post‐breakup evolution of passive continental margins. 27 sub‐projects take advantage of the exceptional conditions of the South Atlantic as a prime “Geo‐archive.” The regional focus is set on the conjugate margins located east of Brazil and Argentina on one side and west of Angola, Namibia and South Africa on the other (Figure 1) as well as on the Walvis Ridge and the present‐day hotspot of Tristan da Cunha. The economic relevance of the program is demonstrated by support from several petroleum companies, but the main goal is research on fundamental processes behind the evolution of passive continental margins.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Book , peerRev
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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: 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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  • 6
    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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  • 7
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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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  • 8
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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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  • 9
    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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  • 10
    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
    Repository Name: Woods Hole Open Access Server
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  • 11
    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.).
    Repository Name: Woods Hole Open Access Server
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  • 12
    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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  • 13
    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
    Repository Name: Woods Hole Open Access Server
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  • 14
    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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  • 15
    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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  • 16
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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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  • 17
    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
    Repository Name: Woods Hole Open Access Server
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  • 18
    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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  • 19
    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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  • 20
    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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  • 21
    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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  • 22
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 1-7 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Short-range order parameters were obtained for a single crystal of 62Ni3Fe quenched from above Tc. These are the first absolute measurements of diffuse elastic neutron scattering complete enough to separate the effects of local order and atomic displacements (up to quadratic terms) and indicate that neutrons are ideally suited for such studies. The results are compared to those obtained with X-rays. The short-range order intensity of Ni3Fe is similar in shape to that for Cu3Au but in this alloy it is due to the plate-like nature of ordered domains, not the antiphase domain boundaries which are present in such regions in Cu3Au.
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 54-57 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: X-ray investigations of Eu2+-rich precipitates in NaCl single crystals have revealed the presence of two phases. Phase A of chemical formula EuCl2 with a CaF2-type structure and lattice parameter a = 6.969 (2) Å preserves strictly the orientation of the matrix lattice. Phase B with the lattice parameter a = 7.47 (1) Å and tentative formula EuCl2.2NaCl, containing Eu2+ ions and charge-compensating cation vacancies, is localized at subgrain boundaries and is thermally less stable than phase A.
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  • 24
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 68-74 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The present paper deals with the finding and the estimation of negative quartets. The use of symmetry is also discussed and the results obtained for four structures of increasing size are reported. Conditional probability distributions using magnitudes contained in the second representation of the quartets provides improved estimates of their phases.
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 116-122 
    ISSN: 1600-5724
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The concept of disorientation, previously used for studying the statistical distribution of the relative orientation of identical cubic crystals, is defined in this work for any two lattices. Using the proposed definition, an algorithm is presented, allowing all the known relative orientations between the two lattices to be conveniently classed. As an example, a unified classification of the numerous mutual orientations of the Al and CuAl2 crystals is suggested. The unit quaternion method used by Grimmer [Acta Cryst. (1974), A30, 685-688] for identical cubic lattices is here proved efficient for discussing the pair axis/angle disorientations in more complicated cases: cubic 1/cubic 2; tetragonal 1/tetragonal 2; hexagonal 1/hexagonal 2; cubic/tetragonal; cubic/orthorhombic and cubic/hexagonal. The general expressions of equivalent quaternions are given for any point group of lattice 1 or lattice 2.
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 122-126 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The controversial space-group problem of spinel, MgAl2O4, whether it is Fd3m or F{\bar 4}3m, was studied by electron diffraction. It was confirmed that the appearance of 'forbidden reflections' such as {200} was caused by the double reflection process of reflections with high indices on the non-zero-order Laue zone. Consequently, the space group of spinel is Fd3m, and the assignment of the space group to F{\bar 4}3m is ruled out. The change of space group from F{\bar 4}3m to Fd3m associated with a phase transition, proposed by Mishra & Thomas [Acta Cryst. (1977), A33, 678], can also be explained by double diffraction: the magnitudes of primary reflections with high indices rapidly decrease due to the increase of the Debye-Waller factors at elevated temperatures.
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 143-146 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: It is pointed out that there is some uncertainty as to the correct behaviour of the integrated reflectivity as a function of the degree of asymmetry for the scattering of X-rays from imperfect crystals in the extremely asymmetric Bragg case. Numerical calculations based on the Takagi-Taupin equations are exemplified and indicate that the integrated reflectivity for such crystals tends asymptotically to the perfect-crystal result in the asymmetric limits, the perfect-crystal result, in turn, tends to the kinematical value at these limits, as has been shown previously. In addition, comments are offered on the relevance of the present work to the study of highly imperfect crystals by section topography, and in particular to the study of the near-surface grain-boundary structure of crystals.
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 147-148 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The mean Debye-Waller parameter {\bar {\it B}}of TlCl has been determined by double- as well as triple-axis neutron diffraction for a powder sample. Thermal diffuse scattering (TDS) corrections have also been made to the intensity of the diffraction peaks obtained by these techniques. TDS was found negligible in the triple-axis diffraction pattern as expected. The {\bar {\it B}} values thus found are 3.08 ± 0.43 and 3.07 ± 0.22 Å2, respectively, for double- and triple-axis methods. These values are in good agreement with those found by recent X- ray diffraction measurements.
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 157-158 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 171-177 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Based on the new energy-transfer equations [Kato (1976). Acta Cryst. A32, 458-466; Kato (1979). Acta Cryst. A35, 9-16] the integrated intensities (II) are calculated. Since the energy-transfer equations have physical meanings different from the traditional ones originally given by Darwin [Philos. Mag. (1922), 43, 800-824] and extended by Hamilton [Acta Cryst. (1957), 10, 629-634], the method of calculating (II) must be modified, particularly in the case of a wide incident beam. Since the modified method does not include the angular integration, it is much simpler than the traditional method. Thus, the analytically rigorous expressions of (II) can be obtained for parallel-sided crystals including absorption, and for any diffraction conditions.
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 190-193 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: High-resolution electron microscopy can be used to differentiate between two structural models of long-period ordered alloys. These models differ in the nature of the disorder as seen in the stacking irregularities which can have planar boundaries as exemplified by Ag3Mg or wavy boundaries as in AuCu II. In the composition range 22-27 at.% Mg, Ag3Mg is built up with a regular arrangement of two kinds of structural layers, 1 or 2 L12 cells in thickness. Some stacking disorder exists, but this alloy can be locally described using a space-group notation and has the character of being an infinitely adaptative structure. High-resolution images have been used to show the perfect planarity of the boundaries in Ag3Mg, thus demonstrating the way in which disorder is accommodated in this alloy.
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 333-333 
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 334-334 
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 344-350 
    ISSN: 1600-5724
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Retention of known geometry, with regard to mean atomic positions, has proved useful in the refinement of macromolecules. In structures with a paucity of diffraction data and large displacements of the atoms from their mean positions, it is also of value to restrain the thermal factors to be consistent with known stereochemistry. This paper presents a technique for accomplishing this by restraining the variances of the interatomic distributions (which are functions of the mean atomic positions and the thermal parameters) to suitably small values. This procedure allows meaningful anisotropic refinement of macromolecules to be carried out with low-resolution diffraction data. Anisotropic thermal parameters obtained in this way should prove useful in understanding the dynamics of the biological functions of macromolecules.
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 353-356 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: From careful measurement and indexing of the powder diffraction patterns obtained for pure dicalcium silicate, unit-cell parameter vs temperature plots have been obtained covering the β and α' dicalcium silicate phases. It is found that these phases are all closely related, the temperature variations, for example, being gradual from 293 K (the β phase) and more discontinuous between 993 and 1043 K corresponding to the β = α'L transition. Our conclusions lead to a simplified dicalcium silicate transformation scheme which requires that there is no phase differentiation within the β-phase regime.
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    Acta crystallographica 36 (1980), S. 372-378 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The ordered domain structure present in the α-phase Cu-Al alloys investigated by Epperson, Ffirnrohr & Ortiz [Acta Cryst. (1978), A34, 667-681] is determined by an extension of the computer method developed recently by Epperson [J. Appl. Cryst. (1979), 12, 351-356] for analyzing a Gehlen-Cohen type simulated structure for a binary, f.c.c., locally ordered alloy in terms of nearest-neighbor atomic configurations. The dominant ordered feature of the more concentrated of these alloys is the existence of randomly dispersed Boric-Sparks tetrahedra; that is, four nearest-neighbor Al atoms arranged tetrahedrally about a Cu atom. The majority of these tetrahedra are isolated; however, as many as three or four are occasionally found to be joined in fragments of a Cu3Au-type antiphase-shift structure. This extended ordered structure also incorporates the Cu3Au-type ring configuration, another principal characteristic structural feature of these Cu-Al alloys. As a typical example, a Cu-14.76 at.% Al alloy quenched from 923 K and annealed for 1580 h at 423 K was found to contain 87 such locally ordered regions in an 8000-atom model. Of these 'domains', 74 were isolated tetrahedra and the remainder consisted of pairs of tetrahedra joined such that their central atoms were mutual second-nearest neighbors. For this alloy and heat treatment, the locally ordered regions of this type amount to about 14 volume % of the microstructure and contain 32% of the Al in the alloy. The average (spherical) domain size is only 3.4 Å. Not only are the locally ordered regions very small, but there are also perceptible imperfections in the packing sequence.
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 470-475 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A method of using quartets and quintets in the direct-methods program MULTAN is described with several successful applications.
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    Acta crystallographica 36 (1980), S. 330-330 
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    Acta crystallographica 36 (1980), S. 331-332 
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 334-334 
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 496-496 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: In Agarwal [Acta Cryst. (1978), A34, 791-809], equation (61) should read: c3 = 2Cm1 Cm2. All information is given in the Abstract.
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    Acta crystallographica 36 (1980), S. 499-500 
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    Acta crystallographica 36 (1980), S. 502-502 
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    Acta crystallographica 36 (1980), S. 520-530 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Above the 1300 K transition and in the defect fluorite phase, there is diffuse X-ray scattering which is similar for both Ca- and Y-stabilized zirconias. This is largely due to ionic displacements from the average structure, principally oxygen ions displaced locally in (100) directions. It has been proposed that some of this scattering is due to fine precipitates of ZrCa4O9 or ZrY4O9. The quantitative analysis of this diffuse scattering reported here does indeed indicate some similarities to this phase; in particular the stabilizing ions form rods in the ({\bar 3}{\bar 3}2) directions similar to those in the precipitate. However, in this compound the stabilizing ion is a second neighbor to an oxygen-ion vacancy, whereas the present results indicate that these tend to be first neighbors. This is the first direct evidence for this association in these materials. This probably occurs to reduce local distortions and to provide local charge balance. It is concluded that the diffuse intensity is from locally ordered regions, not precipitates.
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    Acta crystallographica 36 (1980), S. 573-578 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Some algorithms have been derived to calculate the expected values of one-phase seminvariants of first rank in space groups up to orthorhombic by a probabilistic approach [Giacovazzo (1978). Acta Cryst. A34, 562-576]. The method has been tested on several known structures. The results show how the method can secure a very reliable estimate for a limited number of one-phase seminvariants which can be used from the initial stages of phase determination. In addition, the estimated values can be used as a good figure of merit to select the correct K2 solution in a multisolution procedure.
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  • 46
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    Acta crystallographica 36 (1980), S. 600-604 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Extinction effects in white-beam X-ray and neutron diffraction are considered following the formulation developed for monochromatic-beam diffraction by Becker & Coppens [Acta Cryst. (1974), A30, 129-147]. In white-beam diffraction, a small deviation of the wavelength from the Bragg condition Δλ is a variable which represents the line profile of the diffraction peaks, so that by using the new parameter Δλ the theory is converted to one in white-beam diffraction. It is shown that for a convex crystal, primary extinction yp agrees with the results calculated already for monochromatic diffraction. The same relation is shown to hold in secondary extinction ys. It is concluded that extinction theory derived for monochromatic diffraction is applicable without any modification in white-beam diffraction.
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  • 47
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    Acta crystallographica 36 (1980), S. 620-624 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The minimum-variance weighting scheme for calculating the weighted mean of a quality for the following unusual case is analysed. The quantity is derived from the product of two independent quantities for each of the which a set of data is available. All the products between the two sets of data are taken into consideration. The application to measurements of the polarization state of X-radiation is outlined.
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  • 48
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    Acta crystallographica 36 (1980), S. 653-656 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Direct methods are applied to difference-structure factors for a structure containing one or more heavy atoms at known special or pseudo-special positions, such that the heavy atoms do not contribute to several reflection parity groups. Phases of reflections in these parity groups, represented by symbols, are analysed by the sign-correction method. Phases as well as amplitudes of the difference-structure factors are refined by the general DIRDIF procedure as described previously.
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  • 49
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    Acta crystallographica 36 (1980), S. 74-82 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A phase relationship involving triplet and quartet contributions is given. It is able to take account of the correlation between triplet and quartet relations. The information exploited by the formula is discussed and compared with that exploited by phase relationships arising from the properties of the Fourier transform of periodic positive functions. In particular, the information contained in a Karle-Hauptman determinant of low order is briefly considered.
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  • 50
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    Acta crystallographica 36 (1980), S. 57-67 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Two approximations that are commonly used to describe the scattering of high-energy electrons are the first Born approximation (kinematic approximation) and the closely related 'weak phase-object' approximation. The quantitative domains of validity for the use of these two scattering approximations for structural analysis of organic crystals are evaluated numerically in terms of resolution, crystal thickness and incident electron energy. The resulting calculations show how progressively important dynamical scattering effects lead to an increasingly large contribution to the R value in a structure factor analysis. Alternatively, the results show that an increasing dissimilarity is produced between the structure inferred from electron microscope images and the correct structure. The results also show that the actual images (and the structure inferred from the images) remain qualitatively similar to the projected Coulomb potential, even though dynamical scattering effects may lead to a large quantitative dissimilarity relative to the correct structure.
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  • 51
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    Acta crystallographica 36 (1980), S. 96-103 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The structure of sodium chloride has been studied by gas-phase electron diffraction using photographic plates designed for high-temperature work [Kakumoto, Ino, Kodera & Kakinoki (1977). J. Appl. Cryst. 10, 100-103]. The molecular structure at about 1130 K has been determined by an analysis based on the new complex scattering factors for Na+ and Cl- calculated recently by the present authors. The radial distribution function shows the existence of a considerable amount of dimer molecules in the vapor. The structures of the monomer and dimer have been analyzed by a least-squares method assuming that the dimer is of a planar diamond shape: for monomer ra(Na--Cl) = 2.392 ± 0.028, for dimer ra(Na-Cl) = 2.515 ± 0.017, ra(Cl-Cl) = 3.893 ± 0.021 Å, ∠ClNaCl = 101.4 ± 0.8°. The present study indicates that the Na--Cl distance of the dimer is longer than that of the monomer and the determined structure parameters differ appreciably from existing theoretical predictions.
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    Acta crystallographica 36 (1980), S. 741-746 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The cation distribution of the compounds (Fe0,5Ta0,5)O2 and (Fe0,45Nb0,53)O2 has been redetermined by the combined use of neutron and X-ray powder diffraction. Analysis of the powder patterns showed that the compounds are isostructural, their structure being of the rutile-type AO2. The cations are statistically distributed. There exists no partial ordering, neither of Fe and Ta nor of Fe and Nb. Neutron diffraction patterns taken at 4.2 K showed only one magnetic reflection, which is strongly broadened. The magnetic structure of (Fe0.5Ta0.5)O2 is of MnF2-type, whereas (Fe0.45Nb0.53)O2 orders in the BEY-structure. Profile analysis of these broadened reflections was carried out with the convolution integral of a Gaussian with a Lorentzian function, from which correlation lengths could be derived.
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    Acta crystallographica 36 (1980), S. 156-156 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The Abstract by Modlin & Rodgers [Acta Cryst. (1978), A34, S4, 381] was submitted without the knowledge of the present author, who was not aware of its content. Only preliminary discussions and work on certain aspects of a research programme had taken place at the time that the Abstract was submitted. The conclusions claimed in the last sentence had not been arrived at.
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    Acta crystallographica 36 (1980), S. 155-156 
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    Notes: The scattering factors of the 1s22s22p6 core for K+ and Cl- have been calculated from analytical wave functions and also with one-term Gaussian representations. These scattering factors, together with the experimental structure factors, have been used to obtain, by difference Fourier inversion, the valence-electron charge distributions of KCl in the [100], [110] and [111] directions. By comparison, a very simple one-term Gaussian representation has been shown to yield reliable results.
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    Acta crystallographica 36 (1980), S. 157-157 
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    Notes: In Bertaut & Dulac [Acta Cryst. (1972), 28, 580-588], for clerical reasons an error has crept in so that the numerical moment values of y and z components of Cr1 are to be interchanged. One should read in the Abstract and in relation (8.9): Sz(Cr1) = -0.73 (instead of -0.45); sy(Cr1) = 0.45 (instead of + 0.73).
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    Acta crystallographica 36 (1980), S. 819-826 
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    Notes: All geometric units in crystal structures of space groups P{\bar 4}3m, I{\bar 4}3m, Pn3m, F{\bar 4}3m and Fd3m possess point group {\bar 4}3m. These units may be vacant, or may contain one or more atoms. In units containing more atoms than one, the atoms form one or a collection of these polyhedra: tetrahedron, truncated tetrahedron, octahedron, cuboctahedron or truncated octahedron; the last two may be distorted. Therefore, a formula that lists the consecutive polyhedra starting from the center of the unit can be used for the tabulation of these crystal structures. Only structures of Cu2O type are known in Pn3m and typical structures of the other four space groups are tabulated.
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    Acta crystallographica 36 (1980), S. 830-830 
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    Notes: The equivalence relationships for general planes (or reflexions) in Laue class {\bar 3}1m are different from those for Laue class {\bar 3}m1. Table 3.5.1 of International Tables for X-ray Crystallography [(1969). Vol. I. Birmingham: Kynoch Press] makes no allowance for these differences. The necessary corrections are given.
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    Acta crystallographica 36 (1980), S. 834-834 
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    Acta crystallographica 36 (1980), S. 835-836 
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    Acta crystallographica 36 (1980), S. 836-836 
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    Acta crystallographica 36 (1980), S. 851-856 
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    Notes: New twin domains of thickness of the order of a few micrometres can be created in KClO3 crystals by applying a small uniaxial stress. The observed domain structure can be explained by postulating a hypothetical prototype phase of symmetry 4/mmm. The magnitude of spontaneous strain, σs, for the room-temperature monoclinic phase, computed on the basis of the postulated tetragonal prototype, has an exceptionally large value of 0.257. Further, σs varies linearly as the square root of temperature, implying a mean-field-like behaviour. However, presumably because of the very large spontaneous strain, attempts to move the domain walls back and forth by applying uniaxial stress (at room temperature) have not yet been successful, and the question asked in the title may be a matter of definition.
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    Acta crystallographica 36 (1980), S. 198-205 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A systematic theoretical analysis is made of the kinds of structural irregularity which occur in biological systems. The theoretical problems investigated were: (1) the precise meaning of the term 'paracrystal' when applied to biological systems such as tropomyosin tactoids, collagen fibrils, keratin and the myelin sheath of nerve; (2) the relationship between the paracrystal and liquid-theory descriptions of disorder which have recently been applied to the structure of collagen fibrils; (3) how structural irregularity affects the diffraction patterns (X-ray, neutron and electron) which are commonly used to investigate the structure of these systems experimentally. The conclusions are: (I) paracrystalline disorder of the first kind refers to a spatially disordered crystal but for biological systems it would generally be impracticable to distinguish this from thermal disorder; (2) paracrystalline disorder of the second kind provides a conceptually clumsy method for describing liquid-like systems; (3) paracrystal models are not strictly valid for finite systems; (4) modern liquid theory, as applied, for example, to the structure of the collagen fibrils, provides an elegant and economical alternative to paracrystal theory for disorder of the second kind; (5) the presence of peaks in diffraction patterns from biological systems does not necessarily imply that the system has very much regularity, i.e. it is not evidence for the existence of a lattice.
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    Acta crystallographica 36 (1980), S. 228-237 
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    Notes: Ternary oxides AMO2, A2MO3 and A5MO6 with monovalent A and tri-, tetra- or hepta-valent M metals can exhibit order/disorder transitions with about 20 superstructures of the NaC1 lattice. Some structures can be related to AM, A2M and A5M alloys with a larger distortion of the lattice due to stronger interactions between metal atoms. In ternary oxides about 30 short-range order configurations are selected for the first, second and third shell of metal atoms in applying Pauling's electrovalence rule. Stable configurations are characterized by the strength of Coulomb interactions and by a high point symmetry of the M atoms. Mainly disordered ternary oxides can vary stoichiometrically with a frequent occurrence of vacancies or with partial occupation of tetrahedral interstices by A atoms.
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    Acta crystallographica 36 (1980), S. 259-265 
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    Notes: A statistical distribution of ions M in lattices or partial lattices ∞[A1 - xMxLm] of mixed crystals being assumed, the probability functions PJ(V)(x) for single coordination polyhedra MLn (j = 1), pairs (j = 2) and larger clusters of MLn groups (j 〉 2) in 1D (v = 2) and v-connected 2D systems (v = 3, 4, 6) are calculated. On raising the connecting number v, increasing cluster probabilities are distinctly shifted to lower concentrations x of the foreign ion M. For a relation between the numerical values P(x) and experimental results, the mixed-crystal series (BaF)2[Zn1 - xCuxF4] of a four-connected 2D structure is given as an illustrative example.
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    Acta crystallographica 36 (1980), S. 282-287 
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    Notes: Oriented specimens of biomembranes give distinct X-ray diffraction patterns of circular symmetry along the equatorial plane. In order to interpret such a diffraction pattern, properties of the radial autocorrelation function were examined in detail in conjunction with electron-density distribution and applied. The radial autocorrelation function, which is the Fourier-Bessel transform of an intensity function with circular symmetry, is the radial projection of a two- dimensional autocorrelation function and can be interpreted in terms of Fourier components of electron-density projection along the membrane normal. Some useful information is obtainable on the structure of the scatterer: (i) the approximate size of the X-ray scatterer; (ii) judgement of crystalline or non-crystalline arrangement of molecules; (iii) the existence of a regular arrangement of the electron-density fluctuations in a projection along the membrane normal; (iv) the rotational symmetry element existing in the scatterer if any.
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    Acta crystallographica 36 (1980), S. 299-303 
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    Notes: The pressure dependence of the lattice parameters of PdZn having an L10-type structure has been measured up to 24 GPa (240 kbar) with a diamond-anvil-type cell and sodium chloride as an internal-pressure marker. The axial ratio c/a, which was originally 0.814 (1) [between the two extreme values 1.00 and 0.707 (= 1/ \sqrt{2}) for this type of structure], does not decrease but increases with increasing pressure and after reaching 0.822 at 10 GPa it remains almost constant on further compression. The equation of state has been derived for the L10-type structure assuming pairwise interactions between like atoms and between unlike atoms and comparison is made between the calculated and observed compression curves of the a and c axes. The anisotropy in the lattice compressibility leads to a considerably larger interatomic potential for the unlike atom pair than for the like atom pair.
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    Acta crystallographica 36 (1980), S. 442-450 
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    Notes: Formulas are derived extending several semi-empirical absorption-correction methods to diffractometers operating in Weissenberg geometries, with particular attention paid to flat-cone geometry. These formulas are useful for a variety of instruments using both area and linear position-sensitive detectors. While a complete data set can sometimes be corrected using a single absorption reflection, it was found that the best corrections are usually obtained by considering two absorption reflections rather than one. A discussion of the optimum choice of absorption correction when a crystal has at least a twofold symmetry axis is presented. The accuracy of the methods and the limits of applicability have been examined by computer simulations.
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    Acta crystallographica 36 (1980), S. 436-442 
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    Notes: Both real and imaginary components of the anomalous X-ray scattering were measured by single-crystal diffraction experiments with synchrotron radiation at wavelengths through the region of the three L absorption edges of cesium, the first such experiment for any element at the L edges. Near the L3 edge f' varies between -26.7 and -13.9 and f" between 4.0 and 16.1 electrons in a wavelength interval of 0.008 Å. Similar but smaller changes occur near the L2 edge, and still smaller ones at L1. Fine structure in the f" curve corresponds to that observed in an absorption curve and also, by a dispersion relation, to fine structure in the f' curve. These effects offer promise as a substitute for isomorphous replacement for solving the phase problem for macromolecular crystal structure. Similar experiments with cobalt near the K edge give f' values in agreement with measurements by other workers for nickel and copper by different methods at corresponding wavelengths; the lowest value observed is f' = -7.5 electrons.
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    Acta crystallographica 36 (1980), S. 1065-1070 
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    Notes: A systematic investigation of the effect of phase errors of different types on E maps is presented. Both random and systematic errors have been considered with distributions depending in different ways on the resolution of the data. Considerably large random errors can be tolerated without great loss of structural information in the E maps, while smaller systematic errors have greater destructive effects. These effects are explained by the introduction and analysis of a phase-error function.
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    Acta crystallographica 36 (1980), S. 1072-1088 
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    Acta crystallographica 36 (1980), S. 1093-1093 
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    Acta crystallographica 36 (1980), S. 1094-1094 
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    Acta crystallographica 36 (1980), S. 904-915 
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    Notes: Based on accurate X-ray diffraction intensity data collected from spherically shaped single crystals, net atomic charges and electron density distributions have been studied for MnO, Mn2SiO4, Mg2Si2O6, LiAlSi2O6 and CaMgSi2O6. Examination of various procedures for determining atomic charges in a given structure has led to the conclusion that the following approach appears to be most reliable. (1) For cations: the number of electrons in the sphere of radius ER, effective distribution radius, which is defined according to the characteristics of radial distribution functions or difference-Fourier maps, is calculated. (2) For oxygen atoms: with the cation charges fixed at the values obtained from the above procedure and the total charge of the crystal constrained to be neutral, oxygen charges are estimated from least-squares refinements using atomic scattering factors. The final charges of atoms examined are less ionic than the corresponding formal ones: those of Li, O, Mg, Al, Si, Ca and Mn are respectively + 0.7 (1), -1.1 to -1.5, + 1.4 (1) to + 1.8, + 2.4(1), + 2.2 (1) to + 2.6, + 1.4 (2) and + 1.2 (1) to + 1.6 e. Residual electron densities between Si and O have been clearly observed in difference-Fourier maps after charge refinements for crystals of LiAlSi2O6, CaMgSi2O6 and Mg2Si2O6.
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    Acta crystallographica 36 (1980), S. 937-944 
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    Notes: Beu, Musil & Whitney [Acta Cryst. (1962), 15, 1292-1301; Acta Cryst. (1963), 16, 1241-1242] proposed a maximum-likelihood method of estimating the lattice parameters of cubic, tetragonal and hexagonal crystals, and a method of testing the hypothesis that systematic errors had been satisfactorily accounted for. The use of maximum likelihood is unnecessary, and open to some objection. The argument is therefore rewritten in the more familiar least-squares form, and is generalized to cover the remaining crystal systems. Only if systematic errors are absent is it legitimate to estimate standard deviations of parameters from the differences of observed and calculated Bragg angles. With minor modifications the results are applicable to structural parameters also.
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    Acta crystallographica 36 (1980), S. 945-946 
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    Notes: If dispersive atoms are present the structure factor of a centrosymmetric crystal is not purely real, and the probability distribution of the modulus of the structure factor becomes P(F)dF = ( 2F/μ) exp (-ΣF2/μ2)I0(SF2/μ2)dF, where Io is the modified Bessel function of zero order, Σ is the sum of the squares of the moduli of the atomic scattering factors, S is the modulus of the sum of their squares, and μ is (Σ2 - S2)1/2. For a non-centrosymmetric crystal the form of the distribution is not altered, but Σ must be defined as in the preceding sentence.
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    Acta crystallographica 36 (1980), S. 975-978 
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    Notes: The comparison of molecular structures is facilitated by a combination of graphical and numerical techniques. Conversion to a molecular reference frame makes the linear relationships between the molecules or fragments easily visualized, and can be used to produce diagrams clearly displaying the molecular similarities and differences.
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    Acta crystallographica 36 (1980), S. 1002-1013 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The results of experiments in which an anomalous form of the Pendellösung fringes has been discovered together with a classical one are presented. The general theory of X-ray spherical-wave diffraction has been constructed taking into account the change of phase relationships for radiation propagating in vacuum. An explanation of the observed experimental results and classification of possible manifestations of the Pendellösung effect are given. New data concerning the previously discovered phenomenon of focusing are presented.
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  • 78
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 989-996 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The results of an investigation of the polarization coefficient of X-ray radiation diffracted in real crystals are given. The form of the angular dependence of the polarization coefficient in the range of the Bragg reflection is found to be qualitatively different in the cases of primary and secondary extinction. It allows the unambiguous identification of the type of extinction in the crystal. On the basis of the experimental data analysis of the polarization coefficients for silicon and germanium crystals with different dislocation densities, it is shown that the mosaic model of a crystal is suitable for describing X-ray scattering in real crystals if the dislocation density is higher than 104 mm-2 and in practice only primary extinction is present in mosaic crystals. An expression is given for the primary extinction factor for the mosaic crystal, obtained on the basis of the solution of the Takagi-Taupin equations for finite crystals. This expression was used for the analysis of the LiF and NaF structure factors measured by different authors. The effective size which was obtained for the domains appeared to be physically reasonable and to be directly connected with the value of the dislocation density in the crystal.
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  • 79
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 1025-1030 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Pendellösung intensity beats of white radiation diffracted from parallel-sided single-crystal wafers of silicon were measured by a solid-state detector. After a few corrections, the extremum positions in the beat were measured to evaluate the atomic scattering factors for various reflections. The scattering factor shows a dependence on wavelength, λ, which can be interpreted by the anomalous dispersion term, f', as calculated by Cromer [Acta Cryst. (1965), 18, 17-23]. The obtained values of the atomic scattering factor expressed as linear functions of wavelength are listed with those at λ = 0.5594 Å for comparison with the data so far obtained with Ag Kα1 and wedge crystals. The values for 111 and 220 reflections in the present experiment, 10.59 and 8.40, were almost the same as Tanemura & Kato's [Acta Cryst. (1972), A28, 69-80], 10.664 and 8.463, respectively.
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  • 80
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 1050-1057 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The direct-analysis formalism of Kurki-Suonio [e.g. Isr. J. Chem. (1977). 16, Nos. 2-3, 115-123, 132-136] is modified to apply to the calculation of nuclear distributional moments 〈xλyμzv〉, which are linear combinations of the multipole moments 〈rkylmp〉. They are integrated from the radical coefficients of the corresponding multipole terms through Gaussian and difference series procedures. An application to the thermal neutron diffraction structure factors of Merisalo & Larsen [Acta Cryst. (1977). A33, 351-354] on zinc indicates that the moment 〈x2〉 agrees with the anharmonic result of Merisalo & Larsen 〈z2〉 does not show discrepancy with the value based on harmonic assumption. The existence of the third-order component in the nuclear smearing function and, due to this, anharmonicity of thermal motion is well established, but the magnitude of 〈x3〉 is not accurately defined on the basis of the present data. The ratios of the fourth and second moments do not reveal deviation from harmonic thermal smearing.
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  • 81
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 1071-1071 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Corrections are given to §§ 4.3 and 4.4 of International Tables for X-ray Crystallography [Vol. I (1969), Birmingham: Kynoch Press].
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 1090-1091 
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 1091-1091 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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  • 84
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 1095-1095 
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  • 85
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 1096-1096 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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  • 86
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 37 (1981), S. 211-219 
    ISSN: 1600-5724
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: For explaining diamagnetic effects observed in condensed aromatic compounds, their molecular diamagnetic anisotropies must be known. A method is proposed which, on the basis of relatively accurate structural data and of two experimental crystal anisotropies, allows the determination of molecular anisotropies in the plane and perpendicular to it. For monoclinic compounds whose magnetic tensor has no revolution symmetry, it is necessary to correct to first order the orientation of the principal magnetic axes of the crystal with respect to revolution symmetry. The proposed method is applied and discussed in the case of ten condensed aromatic compounds which crystallize in the orthorhombic and monoclinic systems. It yields, in some cases, molecular anisotropies very different from those suggested by different authors. One very simplified model produces results which fit in with the molecular anisotropies obtained as long as the arrangement of the rings is not too complex.
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  • 87
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 37 (1981), S. 219-226 
    ISSN: 1600-5724
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Diffuse X-ray scattering in Li3N has been investigated in the range 293 to 880 K with monochromatic Mo Kα radiation. Crystal and film were fixed during the exposure. Diffuse intensity in the form of rods and discs was found. It increased with increasing temperature but without change of its features. The diffuse intensity distribution was calculated for various temperatures on the basis of an anisotropic shell model. Good agreement with the experimental results was achieved. The anharmonic effects detected in the difference electron density were studied taking into account split positions for the Li ions. This simulation leads to only minor changes in the calculated intensity distribution which indicates that the diffuse intensity of Li3N is mainly caused by harmonic lattice vibrations.
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  • 88
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 641-653 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Within certain good approximations the probability distribution function (p.d.f.) used to describe mosaic-block orientation in secondary-extinction models is exactly analogous to the p.d.f. for atomic thermal motion in the harmonic approximation. Use is made of this relationship to explain carefully, with the aid of several diagrams, certain distinctions and relationships common to both p.d.f.'s - which if not properly understood can lead (and have led) to some important confusions. For example, if the three-dimensional p.d.f. is Gaussian, surfaces of constant probability density are ellipsoidal (e.g. the thermal-vibration ellipsoid); but the scattering process 'sees' this p.d.f. as a one-dimensional projection, the half-width of which lies on a fourth-order surface (shaped, for example, like a peanut shell). For extinction it is shown explicitly that the form of this projected one-dimensional function is independent of experimental conditions (e.g. collimation), and that an earlier form [Coppens & Hamilton (1970), Acta Cryst. A26, 417-425], still commonly used and tested, is always incorrect. Apart from the intentional restriction of the detailed analysis of secondary extinction to type I extinction (in which mosaic-block orientation is the dominant effect), the approximations adopted are shown to have a wide range of validity. The (unusual) conditions under which the approximations may be sufficiently invalid to produce detectable effects are examined qualitatively in relation to the possibility of experimental investigations.
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  • 89
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 697-704 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A numerical method is developed for calculating the thermal diffuse scattering (TDS) correction from phonon inelastic scattering in a neutron diffraction pattern measured by the time-of-flight method. The correction is evaluated for a nickel powder spectrum at room temperature. It is shown to be more important than had been suggested previously. It gives rise to a reduction of the apparent Debye-Waller factor by about 10%. It may also lead to the appearance of the higher-order Debye-Waller factor previously ascribed to anharmonicity.
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  • 90
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 732-734 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A simple method is given for deriving the triclinic-cell parameters from three general reflections by vertical or horizontal measurements on upper-level films.
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  • 91
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 739-740 
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 740-740 
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  • 93
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 37 (1981), S. 267-268 
    ISSN: 1600-5724
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Recent experimental measurements have revealed systematic differences between measured values of f' and those calculated by the method of Cromer & Liberman [J. Chem. Phys. (1970), 53, 1891-1898] when the incident X-ray is near to and on the long-wavelength side of an edge. The source of the discrepancy has been identified and some previously published values of f' are corrected. These corrections also apply to Table 2.3.1 in International Tables for X-ray Crystallography, Vol. IV [(1974), Birmingham: Kynoch Press].
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  • 94
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 37 (1981), S. 269-269 
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  • 95
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 796-800 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Derivative lattices are related to one another by transformation matrices having rational elements. A simple algorithm for finding these matrices consists in testing if the scalar products of the vectors defining two arbitrary primitive cells of two lattices can be exactly or approximately related by equations with rational coefficients. A rational relationship indicates that two or more lattices have a number of geometrical features in common such as common superlattices, sublattices, etc. The algorithm can, therefore, be applied to a variety of crystallographic problems such as the study of twinning, the indexing of powder patterns, single-crystal diffractometry and the critical evaluation of crystal data. Five examples are discussed in detail.
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  • 96
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 916-921 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A neutron diffraction study of Debye-Waller factors has been performed on ThC and ThC0.77 powder samples at 4 and 250 K on the high-resolution diffractometers D1A and D1B of HFR (Grenoble); 25 diffraction lines were resolved and analysed with wavelength λ = 1.21 Å on D 1A, and 22 lines with λ = 1.28 Å on D1B. In the case of ThC, it is shown that the results (BTh = 0.07 ± 0.05 Å2 and BC = 0.40 ± 0.08 Å2 at 4 K; BTh = 0.32 ± 0.08 Å2 and BC = 0.68 ± 0.08 Å2 at 250 K) are mainly due to the thermal vibrations. For ThC0.77, we find BTh = 0.23 ± 0.03 Å2 and BC = 0.47 ± 0.05 Å2 at 4 K, and BTh = 0.48 ± 0.04 Å2 and BC = 0.69 ± 0.05 Å2 at 250 K. The enhancements of the Debye-Waller factors compared to the stoichiometric case are attributed to the static distortions induced by the presence of 23% vacancies in the carbon sublattice. The mean-square static displacements of thorium and carbon atoms are found to be about 1% of the lattice parameter \sqrt{\langle \Delta x^{2}\rangle _{\rm Th} = 0.08 ± 0.03 Å and \sqrt{\langle \Delta x^{2}\rangle _{\rm c}\simeq _{\rm Th} 0.05 ± 0.03 Å.
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  • 97
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 966-974 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: It has been observed that the reflectivity of the (110) planes of a quartz lamina can be increased by submitting it to a static or alternating electric field. Measurements have been performed on 2.5 and 6 mm thick plates using a curved-crystal spectrometer with DuMond geometry. Photon energies were in the range 50 to 300 keV. Under the proper conditions, the increase in reflectivity is accompanied by negligible loss in resolution. The effects are explained by the occurrence of a quasi-mosaicity.
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  • 98
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 996-1001 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Small-angle scattering experiments of horse-spleen ferritin solutions have been performed at various wavelengths near the K absorption edge of iron, using synchrotron radiation from the storage ring DORIS. The anomalous dispersion of the atomic form factor f as described by f' and if” has been monitored by the dependence of the radius of gyration R and the absorption coefficient μ respectively. There is a 4% increase of R at the absorption edge. The relative full half width of this peak of 0.0016 corresponding to 1 1 eV of the energy scale reflects the drastic variation of f' by 7 electrons. The predictable relation between R and has been verified by the Kramers-Kronig relation. As small-angle scattering is primarily influenced by f', best advantage from anomalous dispersion in small-angle scattering can be taken by measurements very near the absorption edges.
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  • 99
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 1017-1025 
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    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The theory of representations has been used to obtain probabilistic estimates of the two-phase variants and seminvariants for the non-centrosymmetric space groups up to orthorhombic. Some practical applications show that the phase estimations can be useful in direct procedures, mostly for those crystal structures in which the enantiomorph definition is difficult.
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  • 100
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    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 1041-1043 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: In MX2-type structures atoms are always in a sandwich form with an M atom surrounded by two X atoms. The orientation of the M atom is always determined by the two X atoms, e.g. an M atom with γ orientation will always have two X atoms in A and B (or B and A) orientations around it. Therefore, by representing both X atoms by one M atom, the calculation can be reduced to one third of the original since the summation in the structure-factor calculation over all atoms will reduce to the summation over M atoms only. How this can be done is examined in the paper.
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