bluuebunny/crossref_metadata_2025 huggingface dataset:
ASTRA– a program package for accurate structure analysis by the intermeasurement minimization method
Authors: Dudka Alexander
Published: May 2007

ASTRA2.0is a program package for single-crystal structure research using different experimental conditions and radiation of different types (X-rays, neutrons and electrons). The package includes programs for data collection optimization, data reduction, structural parameter refinement and electron density plotting. The expression that is responsible for minimization of the difference between reduced measurements is included in the goal function of the refinement program. The refinement program is based on an adaptive nonlinear least-squares method. The crystal structure is described by a detailed model for electron density analysis.ASTRAuses a multipole model up to eighth order for the aspherical electron density description, an anharmonic model up to sixth order for the description of atom displacement and a model of mixed atomic positions for the description of atomic replacement. Refinement of the structural parameters using data of precession electron diffraction and the Bloch-wave method to account for multiwave scattering is realized. Tools for refinement automation are included inASTRA.
IL MILIONE: a suite of computer programs for crystal structure solution of proteins
Authors: Burla Maria C. , Caliandro Rocco , Camalli Mercedes , Carrozzini Benedetta , Cascarano Giovanni L. , De Caro Liberato , Giacovazzo Carmelo , Polidori Giampiero , Siliqi Dritan , Spagna Riccardo
Published: May 2007

IL MILIONEis a suite of computer programs devoted to protein crystal structure determination by X-ray crystallography. It may be used in the following key activities. (a)Ab initiophasing,viaPatterson or direct methods. The program may succeed even with structures with up to 6000 non-H atoms in the asymmetric unit, provided that atomic resolution is available, and with data at quasi-atomic resolution (1.4–1.5 Å). (b) Single or multiple isomorphous replacement, single- or multiple-wavelength anomalous diffraction, and single or multiple isomorphous replacement with anomalous scattering techniques. In the first step the program finds the heavy-atom/anomalous scatterer substructure, then automatically uses the above information to phase protein reflections. Phase extension and refinement are performed by electron density modification techniques. (c) Molecular replacement. The orientation and the location of the protein molecules are foundviareciprocal space methods. Phase extension and refinement are performed by electron density modification techniques. All the programs integrated intoIL MILIONEare controlled by means of a user-friendly graphical user interface, which is used to input data and to monitor intermediate and final results by means of real-time updated messages, diagrams and histograms.
Electron density map using multiple scattering in grazing-incidence small-angle X-ray scattering
Authors: Lee Byeongdu , Park Insun , Park Haewoong , Lo Chieh-Tsung , Chang, Taihyun , Winans Randall E.
Published: May 2007

The electron density map of a block copolymer thin film having the hexagonally perforated layer (HPL) structure was directly obtained from the measured grazing-incidence small-angle X-ray scattering (GISAXS) pattern, exploiting the multiple-scattering phenomena present in GISAXS. It is shown that GISAXS is in principle equivalent to three-beam diffraction, which has been used to extract phases of diffraction peaks. In addition, X-ray reflectivity analysis has been performed which, when combined with the GISAXS results, provides full details of the HPL structure.
In situinvestigation of the non-linear optical crystal rubidium titanyl arsenate, RbTiOAsO4, under applied electric field using X-ray imaging
Authors: Walker D. , Thomas P. A. , Pernot-Rejmánková P. , Baruchel J.
Published: May 2007

Recent work on the non-linear optical single-crystal rubidium titanyl arsenate (RbTiOAsO4, RTA) has shown that it exhibits behaviour consistent with a ferroelectric semiconductor under large applied electric fields, with the development of a non-uniform field in the near-surface region. To confirm aspects of the proposed model, the behaviour of 001 slices of initially single-domain RTA, patterned with periodic Ag electrodes of spacing 38 µm, as for periodic poling in non-linear optics, were investigated using synchrotron X-ray section topography with the electric field appliedin situwhile under X-ray illumination at the ID19 topography beamline of the ESRF, Grenoble. The results of white-beam section topography as both a function of crystal to film distance, and under DC voltage are reported, confirming that there is a bending of the planes in the near-surface region. The strain in the near-surface region was examined directly using high-resolution monochromatic X-ray section topography. This revealed an extensive strain of 3 (±1) × 10−4at 1 kV, indicating that the electrostrictive coefficient, γ3333, in RTA is positive in sign.
Representation of orientation relationships in Rodrigues–Frank space for any two classes of lattice
Authors: He Youliang , Jonas John J.
Published: May 2007

The fundamental zones of Rodrigues–Frank (R-F) space applicable to misorientations between crystals of any two Laue groups are constructed by using a unified formulation in terms of quaternion algebra. Some of these regions are fully bounded by planes that are determined solely by the symmetries of the groups, while others have at least one unbounded direction. Each of the bounded fundamental zones falls into one of nine geometrically distinct configurations. The maximum symmetry-reduced angles and the corresponding Rodrigues–Frank vectors for these fundamental zones are evaluated. The use of Rodrigues–Frank space for the representation of orientation relationships between crystals of any two symmetry groups is also addressed. Examples concerning the transition of phases of the same symmetry group,i.e.from face-centered cubic to body-centered cubic, and of different groups,i.e.from body-centered cubic to hexagonal close-packed, are given to illustrate the usefulness of this space for representing orientation relationships during phase transformation or precipitation.
A mini-goniometer for X-ray diffraction studies down to 4 K on four-circle diffractometers equipped with two-dimensional detectors
Authors: Fertey Pierre , Argoud Roger , Bordet Pierre , Reymann Jacques , Palin Cyril , Bouchard Christophe , Bruyère Rémi , Wenger Emmanuel , Lecomte Claude
Published: May 2007

A `universal' low-temperature device for laboratory X-ray diffractometers equipped with two-dimensional detectors has been developed. Single-crystal data collections can be performed down to 4 K. Owing to its original design, the completeness of the data set is not affected by the limited number of accessible orientations of the sample. Classical structure analysis can therefore be performed as well as high-resolution (high-angle) studies for electron-density analysis. Derived from an idea of Argoud & Muller [J. Appl. Cryst.(1989),22, 584–591], the sample is mounted on a holder magnetically coupled to the diffractometer φ axis. The coupling is achieved by mounting a master magnet in place of the usual goniometer head. This magnet drives a slave magnet fixed on the crystal holder: a two-axis mini-goniometer. This low-temperature arrangement is adaptable to any kappa-geometry single-crystal diffractometer equipped with a two-dimensional detector, and can be placed into various types of cryostat. This paper reports the home-made mechanical design and the performance of this device.
Indirect two-trace method to determine a faceted low-energy interface between two crystallographically correlated crystals
Authors: Zhang Y. D. , Esling C. , Zhao X. , Zuo L.
Published: May 2007

An indirect two-trace method to determine interfaces between two crystals with a uniquely defined interface plane is proposed. It involves preparation of only one sample surface, instead of the two perpendicular sample surfaces required by the traditional two-trace method. By making use of two independent interface trace vectors from one uniquely defined interface and the orientations of their adjacent crystals, the interface plane normal and thus the interface plane in the two correlated crystal systems can be determined through numerical calculations concerning coordinate system change. The new method is widely applicable to identify any uniquely defined and reproducible interfaces between crystallographically correlated crystals, even slip systems, provided that they are microscopically visible and crystallographically of the same nature. It can simplify the experimental procedure, increase the determination accuracy and broaden the scope of interface studies.
Registering pole figures using an X-ray single-crystal diffractometer equipped with an area detector
Authors: Rodriguez-Navarro Alejandro B.
Published: May 2007

The orientation of crystals in a polycrystalline sample is adequately described using pole figures, displaying the three-dimensional distribution of specific crystallographic directions or poles. Registration of pole figures is necessary to characterize the preferred orientation of crystals and its influence on the anisotropy of properties in textured materials. It is also useful to understand the development of highly organized microstructures in polycrystalline materials. Pole figures can be registered efficiently using an area detector, available at most modern single-crystal diffractometers. This paper describes in detail the procedure of data collection and processing of pole figures using a single-crystal diffractometer equipped with an area detector. Specifically, a Bruker SMART APEX diffractometer was used, but this methodology can be readily adapted to other diffractometers.
Polarization-dependence of anomalous scattering in brominated DNA and RNA molecules, and importance of crystal orientation in single- and multiple-wavelength anomalous diffraction phasing
Authors: Sanishvili R. , Besnard C. , Camus F. , Fleurant M. , Pattison P. , Bricogne G. , Schiltz M.
Published: May 2007

In this paper the anisotropy of anomalous scattering at the BrK-absorption edge in brominated nucleotides is investigated, and it is shown that this effect can give rise to a marked directional dependence of the anomalous signal strength in X-ray diffraction data. This implies that choosing the correct orientation for crystals of such molecules can be a crucial determinant of success or failure when using single- and multiple-wavelength anomalous diffraction (SAD or MAD) methods to solve their structure. In particular, polarized absorption spectra on an oriented crystal of a brominated DNA molecule were measured, and were used to determine the orientation that yields a maximum anomalous signal in the diffraction data. Out of several SAD data sets, only those collected at or near that optimal orientation allowed interpretable electron density maps to be obtained. The findings of this study have implications for instrumental choices in experimental stations at synchrotron beamlines, as well as for the development of data collection strategy programs.
Pair distribution functions calculated from interatomic potential models using theGeneral Utility Lattice Program
Authors: Cope Elizabeth R. , Dove Martin T.
Published: May 2007

A new module has been developed for the widely usedGeneral Utility Lattice Program(GULP). The phonon-based theory developed by Chung & Thorpe [Phys. Rev. B(1999),59, 4807–4812] to calculate pair distribution function (PDF) peak widths has been utilized to give a selection of commonly used correlation functions. A numerical library of neutron scattering information is now available withinGULP, and is used to produce results that can be compared with neutron scattering experimental data. The influence of different phonon modes on the PDF can be assessed by excluding modes above or below a cut-off frequency. Results are presented for sample crystallographic systems, MgO, SrTiO3and α-cristobalite, as well as CaxSr1−xTiO3atx= 0.5, which makes use of the capability to handle partial occupancies to compare different Ca/Sr ordering arrangements with a disordered model in which every Ca/Sr site has 50% occupancy of both species.
Xpace: a Python class to store and analyse crystallization experiment data
Authors: Gutiérrez-Rodríguez Ángel , García-Granda Santiago
Published: May 2007

This document presents a Python script designed to store and analyse the outcome of the factorial designs of macromolecular crystallization experiments for X-ray diffraction. The resulting script comprises three classes with all the methods needed to perform the analysis.
A program for refinement of lattice parameters based on multiple convergent-beam electron diffraction patterns
Authors: Morawiec A.
Published: May 2007

A package of computer programs for refinement of lattice parameters based on convergent-beam electron diffraction (CBED) patterns has been developed. The package is intended to facilitate the measurement of local elastic strains. The strain or lattice parameters are determined by matching experimental and simulated central disks of CBED patterns. The kinematical simulation is used in the primary fitting. In some cases, further refinement by means of dynamical simulation can be applied. User-specified strain components, camera lengths and voltage can be fitted. The software is not limited to any particular material or structure. It is capable of simultaneous matching of multiple patterns originating from the same sample location. The use of a number of different strategies allows for the verification of results and for checking their reliability. Operation of the software is controlledviaa Windows user interface.
Wide-range three-dimensional reciprocal-space mapping: a novel approach applied to organic monodomain thin films
Authors: Resel R. , Lengyel O. , Haber T. , Werzer O. , Hardeman W. , de Leeuw D. M. , Wondergem H. J.
Published: May 2007

An X-ray method is presented to characterize thin films with unknown crystal structure with specific crystal orientations. The method maps large volumes of the reciprocal space by a series of pole-figure measurements using a standard texture goniometer. The data can be used for lattice indexing and texture evaluation and in subsequent steps for a complete structural thin-film characterization. The application of the method is demonstrated on an organic monodomain thin film consisting of uniaxially aligned crystallites.
MCE2005– a new version of a program for fast interactive visualization of electron and similar density maps optimized for small molecules
Authors: Rohlíček Jan , Hušák Michal
Published: May 2007

A new version ofMCEis described. This new version supports atom-position generation based on space groups and can display more unit cells around the basic unit cell. The display settings have been improved to allow the colors of the background, atoms and maps to be changed.
Orientation density function-controlled pole probability density function measurements: automated adaptive control of texture goniometers
Authors: Schaeben Helmut , Hielscher Ralf , Fundenberger Jean-Jacques , Potts Daniel , Prestin Jürgen
Published: May 2007

A novel control of a texture goniometer, which depends on the texture being measured itself, is suggested. In particular, it is suggested that the obsolete control with constant step sizes in both angles is replaced by an adaptive successive refinement of an initial coarse uniform grid to a locally refined grid, where the progressive refinement corresponds to the pattern of preferred crystallographic orientation. The prerequisites of this automated adaptive control is the fast inversion of pole intensities to orientation probabilities in the course of the measurements, and a mathematical method of inversion that does not require a raster of constant step sizes and applies to sharp textures.
Structures of stable and metastable Ge2Bi2Te5, an intermetallic compound in a GeTe–Bi2Te3 pseudobinary system
Authors: Matsunaga Toshiyuki , Kojima Rie , Yamada Noboru , Kifune Kouichi , Kubota Yoshiki , Takata Masaki
Published: May 2007

Ge2Bi2Te5 in the GeTe–Bi2Te3 pseudobinary system has two single-crystalline phases: a metastable phase with an NaCl-type structure and a stable phase with a nine-layer trigonal structure. In the metastable phase, the structure consists, in the hexagonal notation, of infinitely alternating stacks of Te and Ge/Bi layers at equal intervals along the c axis. On the other hand, in the stable phase those two layers are stacked alternately nine times to form an NaCl block. The blocks are then piled to construct a nine-layered trigonal structure with cubic close-packed stacking. Both ends of each block are covered with Te layers, contrary to the infinite alternation of Ge/Bi and Te layers in the structure of the metastable phase. The Ge/Bi layers in the metastable phase contain as much as 20 at. % vacancies; on the other hand, those in the stable phase are filled with atoms. These two crystalline phases in Ge2Bi2Te5 have identical atomic configurations to the two corresponding phases found in Ge2Sb2Te5.
Tautomerism and hydrogen bonding in guaninium phosphite and guaninium phosphate salts
Authors: Bendeif El-Eulmi , Dahaoui Slimane , Benali-Cherif Nourredine , Lecomte Claude
Published: May 2007

The crystal structures of three similar guaninium salts, guaninium monohydrogenphosphite monohydrate, C5H6N5O+·H2O3P−·H2O, guaninium monohydrogenphosphite dihydrate, C5H6N5O+·H2O3P−·2H2O, and guaninium dihydrogenmonophosphate monohydrate, C5H6N5O+·H2O4P−·H2O, are described and compared. The crystal structures have been determined from accurate single-crystal X-ray data sets collected at 100 (2) K. The two phosphite salts are monoclinic, space group P21/c, with different packing and the monophosphate salt is also monoclinic, space group P21/n. An investigation of the hydrogen-bond network in these guaninium salts reveals the existence of two ketoamine tautomers, the N9H form and an N7H form.
The application of cluster analysis to identify conformational preferences in enones and enimines from crystal structural data
Authors: Collins Anna , Barr Gordon , Dong Wei , Gilmore Christopher J. , Middlemiss Derek S. , Parkin Andrew , Wilson Chick C.
Published: May 2007

Cluster analysis can be an effective tool for analysing large quantities of data. Here it has been applied to the conformational analysis of enones and enimines in the crystalline solid state, using structural information mined from the Cambridge Structural Database. The forms that are common in the gaseous state and in solution are already known from spectroscopic studies. These forms are also found to be the most common conformations observed in the solid state; however, the clustering method highlights those structures that do not conform to the expected geometries. The study is supported by ab initio gas phase calculations on simple enone and enimine fragments.
LiNaSiB3O7(OH) – novel structure of the new borosilicate mineral jadarite determined from laboratory powder diffraction data
Authors: Whitfield Pamela S. , Le Page Yvon , Grice Joel D. , Stanley Chris J. , Jones Gary C. , Rumsey Michael S. , Blake Chris , Roberts Andrew C. , Stirling John A. R. , Carpenter Gordon J. C.
Published: May 2007

The structure of a new mineral jadarite, LiNaSiB3O7(OH) (IMA mineral 2006–36), has been determined by simulated annealing and Rietveld refinement of laboratory X-ray powder diffraction data. The structure contains a layer of corner-sharing, tetrahedrally coordinated Li, Si and B forming an unbranched vierer single layer, which is decorated with triangular BO3 groups. The Na ion is situated between the tetrahedral layers in a distorted octahedral site. As the very high boron content in this mineral makes obtaining neutron diffraction data very problematic, ab initio optimization using VASP was used to validate the structure and to better localize the H atom. The H atom is located on the apex of the triangular BO3 group and is involved in a weak intralayer hydrogen bond. The final Rietveld refinement agrees with the ab initio optimization with regard to a hydrogen bond between the H atom and one of the tetrahedral corner O atoms. The refined structure seems to be of a remarkably high quality given the complexity of the structure, the high proportion of very light elements and the fact that it was determined from relatively low-resolution laboratory data over a limited 2θ range (10–90° 2θ).
Electron diffraction and microscopy study of the structure and microstructure of the hexagonal perovskite Ba3Ti2MnO9
Authors: Maunders Christian , Whitfield Harold J. , Hay David G. , Etheridge Joanne
Published: May 2007

This paper reports a structural and microstructural investigation of the hexagonal perovskite Ba3Ti2MnO9 using electron microscopy and diffraction. Convergent-beam electron diffraction (CBED) revealed the structure has the non-centrosymmetric space group P63
mc (186) at room temperature and at ∼ 110 K. Compared with the centrosymmetric parent structure BaTiO3, with space group P63/mmc, this represents a break in mirror symmetry normal to the c axis. This implies the Ti and Mn atoms are ordered on alternate octahedral sites along the 〈0001〉 direction in Ba3Ti2MnO9. Using high-resolution electron microscopy (HREM), we observed occasional 6H/12R interfaces on (0001) planes, however, no antiphase boundaries were observed, as were seen in Ba3Ti2RuO9. Using powder X-ray Rietveld refinement we have measured the lattice parameters from polycrystalline samples to be a = 5.6880 ± 0.0005, c = 13.9223 ± 0.0015 Å at room temperature.
Superspace crystal symmetry of thermoelectric misfit cobalt oxides and predicted structural models
Authors: Grebille D. , Muguerra H. , Pérez O. , Guilmeau E. , Rousselière H. , Funahashi R.
Published: May 2007

Single crystals of thermoelectric misfit lamellar cobalt oxide phases in the Bi–Ca–Co–O and I–Bi–Ca–Co–O systems were synthesized. They are characterized by aperiodic structures involving two partially independent sublattices: a CdI2-type pseudohexagonal CoO2 layer and a rocksalt-type BiCaO2 slab allowing the intercalation of iodine. The crystal symmetry of these structures is discussed using the four-dimensional superspace formalism. The superspace Laue classes of the iodine-free and the intercalated compounds are P2/m(0δ½) (a
1 = 4.901, b
1 = 4.730, b
2 = 2.80, c
1 = 14.66 Å, β = 93.49°) and A2/m(0δ1) (a_1^{\prime} = 4.903, b_1^{\prime} = 4.742, c_1^{\prime} = 36.51 Å, β = 87.30°), respectively. A comparison is given with the related Bi–Sr–Co–O misfit compounds. The present structures are compatible with the presence of an intrinsic modulation with a wavelength matching the misfit aperiodicity in the b direction. Preliminary partial structure refinements confirm the layer stacking of the structure and the intercalation of I between the Bi—O layers for the second phase. A comparison with other cobalt oxide phases, as well as symmetry and metric considerations allow us to predict average structures for these new phases and to describe the common structural features assumed for all these lamellar misfit cobalt oxides.
Rapid structure determination of the hydrogen-containing compound Cs2C2O4·H2O by joint single-crystal X-ray and powder neutron diffraction
Authors: Weller Mark T. , Henry Paul F. , Light Mark E.
Published: May 2007

The structure determination of caesium oxalate monohydrate using single-crystal X-ray diffraction, powder neutron diffraction data and a combination of both has been undertaken. Results show that even for hydrogen-containing materials data collected rapidly on a high-flux neutron diffractometer improve the refinement such that accurate positional and thermal displacement parameters can be extracted for all atom types. This contrasts with structural models extracted from either data set alone that demonstrate the inherent limitations of the individual diffraction methods. The rapidity with which useful neutron diffraction data has been collected from hydrogen-containing compounds, 10 min in this study, indicates that the technique should be widely applicable allowing the facile and accurate extraction of hydrogen positions for many compounds.
Investigation of hydrogen-bond network in bis(glycinium) oxalate using single-crystal neutron diffraction and spectroscopic studies
Authors: Chitra R. , Choudhury R. R
Published: May 2007

Single-crystal neutron diffraction investigation of bis(glycinium) oxalate was undertaken in order to study its hydrogen-bonding network, particularly the very short hydrogen bond between the glycinum and oxalate ions, indicated by the X-ray diffraction study. The non-existence of any phase transition in these crystals was attributed to the fact that the short hydrogen bond in bis(glycinium) oxalate is asymmetric in nature, with no hydrogen disorder. The potential energy landscape for the above-mentioned H atom was found to have a single minimum closer to the glycinium ion. IR and Raman investigations of the title complex supported the above result.
Isostructuralism among `bridge-flipped' isomeric benzylideneanilines and phenylhydrazones
Authors: Ojala William H. , Smieja Jonathan M. , Spude Jill M. , Arola Trina M. , Kuspa Marika K. , Herrera Nell , Ojala Charles R.
Published: May 2007

`Bridge-flipped' isomers may be defined as pairs of molecules related by a reversal of a bridge of atoms connecting two major parts of the individual molecules. This kind of isomerism is commonly found among benzylideneanilines and phenylhydrazones. Isostructural pairs might be suitable for co-crystallization and are thus useful in the preparation of new solid materials. Although most of the examples of bridge-flipped isomeric benzylideneanilines and phenylhydrazones in the crystallographic literature are not isostructural, a small number of isostructural pairs have been reported by previous workers. This paper describes the molecular and crystal structures of four pairs of bridge-flipped isomers: two isostructural phenylhydrazones, (E)-2-bromobenzaldehyde 4-cyanophenylhydrazone (I) and (E)-4-cyanobenzaldehyde 2-bromophenylhydrazone (II); two pairs of isostructural benzylideneanilines, N-(2-trifluoromethylbenzylidene)-2-methylaniline (III) and N-(2-methylbenzylidene)-2-trifluoromethylaniline (IV), and N-(2-bromobenzylidene)-2-methylaniline (V) and N-(2-methylbenzylidene)-2-bromoaniline (VI); and a pair of benzylideneanilines with closely similar unit-cell dimensions but different packing arrangements, N-(4-methylbenzylidene)-4-cyanoaniline (VII) and N-(4-cyanobenzylidene)-4-methylaniline (VIII). The structure of (V) is disordered. The packing arrangement of (VIII) resembles that of the chloro-/methyl-substituted benzylideneanilines MBZCLA/MBZCLB [N-(4-methylbenzylidene)-4-chloroaniline and N-(4-chlorobenzylidene)-4-methylaniline]. Although intermolecular hydrogen bonding plays a part in the isostructuralism of the two phenylhydrazones, the other examples of isostructuralism occur in the absence of similar, relatively strong intermolecular interactions.
Pseudoatoms and preferred skeletons in crystals
Authors: Vegas Angel , García-Baonza Valentín
Published: May 2007

The generalization of the Zintl–Klemm concept provides a universal formulation of a crystal structure in terms of universal building skeletons formed by Klemm's pseudoatoms: atoms that behave structurally according to their formal total electron charge. An important difference in this novel view is that charge is considered to be transferred, in the strict Zintl's sense, from the donor cations to the building skeleton as a whole, not specifically to a given atom or ion. Although application is restricted to (IV)–(IV) compounds (group 14 structures), the principle seems to be universal and can be applied to understand, to relate and to predict the structure of complex compounds on the basis of more simple structures, e.g. a given AB skeleton provides the building block for A
2
B, AB
2, ABX

m

etc. compounds of a very different nature. The application of such a principle only requires information on the constituent atoms and on the existing phases of the p-block elements (observed under ambient and high-pressure and/or high-temperature conditions). The ideas introduced here demonstrate, for the first time, that a generalization of the Zintl–Klemm concept is possible and that such a generalization helps to establish a univocal link between chemical composition (in terms of pseudoatoms) and the crystalline structures observed experimentally.
Update on the Interaction of Rifampin and Warfarin
Authors: Kim Karissa Y. , Epplen Kelly , Foruhari Farzin , Alexandropoulos Hattie
Published: May 2007

A 79‐year‐old man with a history of deep vein thrombosis and pulmonary embolism received anticoagulation therapy with warfarin 5 mg daily for 8 months. He was diagnosed with osteomyelitis and underwent partial metatarsal resection of his right foot. After surgery, antibiotics were initiated including ertapenem sodium 1 g intravenously every 24 hours, vancomycin 1400 mg intravenously every 24 hours, and rifampin 300 mg by mouth twice daily. Achieving a therapeutic level of anticoagulation was difficult despite escalating doses of warfarin, because of the interaction with rifampin. A 5‐ to 6‐fold increase in warfarin dose was prescribed to reach therapeutic international normalized ratios (INRs), but even these increases were insufficient to maintain his INR in the therapeutic range. After rifampin was discontinued, warfarin doses were gradually reduced over the next 2 months. When concurrent warfarin‐rifampin therapy is necessary, vigilant monitoring is imperative and significant increases in warfarin doses are likely.
Resuspension of algal cells by benthivorous fish boosts phytoplankton biomass and alters community structure in shallow lakes
Authors: ROOZEN FRANK C. J. M. , LÜRLING MIQUEL , VLEK HANNEKE , VAN DER POUW KRAAN EDWIN A. J. , IBELINGS BAS W. , SCHEFFER MARTEN
Published: May 2007

1. Positive effects of fish on algal biomass have variously been attributed to cascading top‐down effects and to nutrient enrichment by fish excretion.

2. Here, we used a combination of field and laboratory approaches to test an additional hypothesis, namely that the physical resuspension of settled algal cells by fish enhances algal biomass and alters community composition.

3. A multi‐lake survey showed that phytoplankton biomass and the fraction of motile algae increased with the concentration of inorganic suspended solids. This correlation could not be explained by wind‐induced resuspension because of the small size of the lakes.

4. In an enclosure experiment, chlorophyll‐a concentration, phytoplankton abundance and inorganic suspended solids increased significantly in the presence of Cyprinus carpio (common carp), but only if the fish had access to the sediment. No such effects were seen when a net prevented carp reaching the sediment.

5. The effects of enhanced nutrients and reduced zooplankton grazing as a result of fish feeding could not (fully) explain these observations, suggesting that the resuspension by carp of settled algae from a surface film on the sediment was the major factor in the outcome of the experiment.

6. An increase in diatoms and green algae (organisms with a relatively large sedimentation velocity) only in enclosures where carp could reach the sediment supported this view.

7. Several lines of evidence indicate that fish‐induced resuspension of algal cells from the sediment is an important mechanism that affects phytoplankton biomass and community composition in shallow lakes.
Use of Shields stress to reconstruct and forecast changes in river metabolism
Authors: CRONIN GREG , MCCUTCHAN JAMES H. , PITLICK JOHN , LEWIS WILLIAM M.
Published: May 2007

1. Discharge patterns of streams and rivers may be substantially affected by changes in water management, land use, or climate. Such hydrological alterations are likely to influence biotic processes, including overall ecosystem metabolism (photosynthesis and respiration). One regulator of aquatic ecosystem metabolism directly tied to hydrology is movement of bed sediments.

2. We propose that ecosystem metabolism can be reconstructed or predicted for any suite of hydrological conditions through the use of quantitative relationships between discharge, bed movement and metabolism. We tested this concept on a plains reach of the South Platte River in Colorado.

3. Movement of bed sediments was predicted from river discharge and the Shields stress, a ratio of velocity‐induced stress to sediment grain size. Quantitative relationships were established empirically between metabolic response to bed movement and recovery from bed movement, thus linking metabolism to hydrology.

4. The linkage of metabolism to hydrology allowed us to reconstruct daily photosynthesis and respiration over the 70‐year period for which discharge is known at our study site on the South Platte River. The reconstruction shows major ecological change caused by hydrological manipulation: the river has lost two‐thirds of its photosynthetic potential, and the ratio of photosynthesis to respiration is now much lower than it was prior to 1960.

5. The same approach could be used to anticipate ecological responses to proposed hydrological manipulations, to quantify benefits of hydrological restoration, or to illustrate potential effects of change in climate or land use on flowing‐water ecosystems.
Wide‐angle linear forward modelling of synthetic seismograms
Authors: Dey A. , Gisolf A.
Published: May 2007

We address the issue of linearity and scale dependence in forward modelling of seismic data from well logs, for large ray parameters, wide angles or large offsets. We present a forward model, within the context of seismic‐to‐well matching, that is linearized in the elastic properties of the earth. This model preserves linearity at large ray parameters and can handle fine‐layering effects such as induced anisotropy. Starting from a low‐contrast small‐ray‐parameter model, we extend it to a large‐ray‐parameter model by fully linearizing the elastic‐property contrasts. Overall linearity of the forward model is extended by partitioning the compressional‐wave and shear‐wave velocity fields into two fundamental scales: a kinematic scale that governs wavefield propagation effects and a dynamic scale that governs wavefield scattering effects. This analysis reveals that the standard practice in forward modelling of strongly filtering the ratio of compressional‐wave velocity to shear‐wave velocity is well founded in the underlying physics. The partitioning of the velocity fields also leads naturally to forward modelling that accounts fully for stretch effects, to resolution of the angle‐of‐incidence versus ray‐parameter dichotomy in seismic‐amplitude analysis, and to full accounting for induced anisotropy and dispersion effects due to fine‐layering of isotropic media. With the onset of routine long‐offset acquisition and the compelling need to optimize asset management in order to maximize reserve recovery, this forward model recognizes the physics of seismic wave propagation and enables a more complete exploitation of amplitude information in pre‐critical seismic data.
Genomic and evolutionary analyses of Tango transposons in Aedes aegypti, Anopheles gambiae and other mosquito species
Authors: Coy M. R. , Tu Z.
Published: May 2007

Tango is a transposon of the Tc1 family and was originally discovered in the African malaria mosquito, Anopheles gambiae. Here we report a systematic analysis of the genome sequence of the yellow fever mosquito, Aedes aegypti, which uncovered three distinct Tango transposons. We name the only An. gambiae Tango transposon AgTango1 and the three Ae. aegypti Tango elements AeTango1–3. Like AgTango1, AeTango1 and AeTango2 elements both have members that retain characteristics of autonomous elements such as intact open reading frames and terminal inverted repeats (TIRs). AeTango3 is a degenerate transposon with no full‐length members. All full‐length Tango transposons contain subterminal direct repeats within their TIRs. AgTango1 and AeTango1–3 form a single clade among other Tc1 transposons. Within this clade, AgTango1 and AeTango1 are closely related and share approximately 80% identity at the amino acid level, which exceeds the level of similarity of the majority of host genes in the two species. A survey of Tango in other mosquito species was carried out using degenerate PCR. Tango was isolated and sequenced in all members of the An. gambiae species complex, Aedes albopictus and Ochlerotatus atropalpus. Oc. atropalpus contains a rich diversity of Tango elements, while Tango elements in Ae. albopictus and the An. gambiae species complex all belong to Tango1. No Tango was detected in Culex pipiens quinquefasciatus, Anopheles stephensi, Anopheles dirus, Anopheles farauti or Anopheles albimanus using degenerate PCR. Bioinformatic searches of the Cx. p. quinquefasciatus (~10 × coverage) and An. stephensi (0.33 × coverage) databases also failed to uncover any Tango elements. Although other evolutionary scenarios cannot be ruled out, there are indications that Tango1 underwent horizontal transfer among divergent mosquito species.
Empirical evaluation of non‐invasive capture–mark–recapture estimation of population size based on a single sampling session
Authors: PUECHMAILLE SEBASTIEN J , PETIT ERIC J
Published: May 2007

Non‐invasive genetic data analysed with capture–mark–recapture (CMR) models can be used to estimate population size, particularly for elusive and endangered species. Data generated from non‐invasive genetic sampling are different, however, from conventional CMR data because individuals can be contacted several times within a single sampling session. Two methods have been proposed recently to accommodate this type of data, but no study has attempted to compare their estimates and evaluate their reliability compared with independent estimates of population size.

We investigated the reliability and accuracy of estimating the abundance of lesser horseshoe batsRhinolophus hipposiderosby genotyping DNA from droppings collected non‐invasively at three colonies over 2 consecutive years. The number of times that each individual was ‘contacted’ (i.e. the number of droppings per individual) was used to estimate population size with two different published methods: a maximum likelihood and a Bayesian estimator.

Among the 586 samples extracted, 534 provided a complete genotype at six to eight microsatellite loci, which enabled a reliable discrimination of 165 individuals. Statistical estimates of colony sizes often included independent estimates obtained from visual counts, validating the method. Discrepancies appeared when capture heterogeneity was not taken into account while it occurred.

Synthesis and applications.We have taken a first step towards improving methods of estimating numbers of bats by demonstrating that genetic data produced from bat faecal DNA are of high quality and can provide accurate estimates of population size even when samples are taken during only one sampling session. Such protocols provide valuable management tools for elusive and rare species in general. The method is relatively easy and cost‐efficient because only one sampling session is required.
Repeatedly out of Beringia:Cassiope tetragonaembraces the Arctic
Authors: Eidesen Pernille Bronken , Carlsen Tor , Molau Ulf , Brochmann Christian
Published: May 2007

Aim Eric Hultén hypothesized that most arctic plants initially radiated from Beringia in the Late Tertiary and persisted in this unglaciated area during the Pleistocene glaciations, while their distribution ranges were repeatedly fragmented and reformed elsewhere. Whereas taxonomic and fossil evidence suggest thatCassiope tetragonaoriginated in Beringia and expanded into the circumarctic area before the onset of the glaciations, lack of chloroplast DNA (cpDNA) variation may suggest that colonization was more recent. We address these contradictory scenarios using high‐resolution nuclear markers.

Location Circumpolar Arctic.

Methods The main analysis was by amplified fragment‐length polymorphism (AFLP), while sequences of chloroplast DNA verified the use ofCassiope mertensianaas an outgroup forC. tetragona.Data were analysed using Bayesian clustering, principal coordinates analyses, parsimony and neighbour‐joining, and measures of diversity and differentiation were calculated.

Results The circumpolarC. tetragonassp.tetragonawas well separated from the North AmericanC. tetragonassp.saximontana. The genetic structure in ssp.tetragonashowed a strong east–west trend, with the Beringian populations in an intermediate position. The highest level of diversity was in Beringia, while the strongest differentiation in the data set was found between the populations from the Siberian Arctic west of Beringia and the remainder.

Main conclusions The results are consistent with a Beringian origin of the species, but the levels and geographical patterns of differentiation and gene diversity suggest that the latest expansion from Beringia into the circumarctic was recent, possibly during the current interglacial. The results are in accordance with a recent leading‐edge mode of colonization, particularly towards the east throughout Canada/Greenland and across the North Atlantic into Scandinavia and Svalbard. As fossils demonstrate the presence of the species in North Greenland 2.5–2.0 Ma, as well as in the previous interglacial, we conclude thatC. tetragonaexpanded eastwards from Beringia several times and that the earlier emigrants of this woody species became extinct. The last major westward expansion from Beringia seems older, and the data suggest a separate Siberian refugium during at least one glaciation.
Asynchronous forest–stream coupling in a fire‐prone boreal landscape: insights from woody debris
Authors: ARSENEAULT DOMINIQUE , BOUCHER ÉTIENNE , BOUCHON ÉLODIE
Published: May 2007

We used dendrochronology to reconstruct the transfer of coarse woody debris across a forest–stream interface in a fire‐prone boreal landscape. A sequence of regulating factors was considered from source to sink of in‐stream woody debris (SWD), including fire history at the landscape scale, patterns of post‐fire recovery of riparian forest and inputs of SWD at the scale of a stream reach and its associated floodplain, and burial of SWD at an excavated site.

Fires occurred repeatedly in the studied landscape (at least in 1708, 1733, 1791, 1811, c. 1838, c. 1850, 1882, 1941 and 1998), and were generally patchy on the floodplain because of the firebreak effect of the riparian corridor. Unburned forest remnants were regularly generated at the stream margin, thus permitting temporally continuous but spatially localized transfer of woody material across the forest–stream interface. These remaining forest patches also increased forest resilience by dispersing seeds and promoting conifer re‐establishment in burned areas.

Because of higher severity compared with previous fires, the 1941 fire burned almost everywhere on the floodplain, creating only a few widely isolated unburned forest remnants. Consequently, following an abrupt post‐fire increase, SWD inputs almost completely ceased. In addition, post‐fire recovery of the riparian wood source is slow because of the spatially restricted seed source.

In this alluvial stream, wood burial is faster than decay and largely determines the residence time of SWD. Because the residence time is about 150 years, the current density of SWD is high and contrasts sharply with the very low tree density at the stream margin. Although this long residence time helps maintain stream integrity while the forest is recovering from the 1941 fire, it is unlikely that SWD inputs would resume extensively before burial of the current SWD pool.

Our research exemplifies the potentially complex impacts of disturbances on material transfer between a source and a sink ecosystem. We conclude that when certain components of ecosystems are coupled by unidirectional flow, those components will behave asynchronously if a disturbance impact at the source ecosystem does not propagate rapidly to the sink and the source and the sink recover at different rates.
Flexible observation: guidelines versus reality
Authors: KETTLES A. M. , PATERSON K.
Published: May 2007

This paper reports a small‐scale pilot study to introduce flexible observation of patients in an acute psychiatric clinical area where nurses have increased autonomy to make such decisions. The Clinical Resource and Audit Group document ‘Engaging People: Observation of People with Acute Mental Health Problems: A Good Practice Statement’ outlines very clearly the observation levels that should be used in acute psychiatric areas in Scotland. It also states clearly who is responsible for conducting different parts of the observation process and how such observation procedures should be conducted. The available literature recommends three observation levels with engagement and considers that intermittent or time period checks are unsafe. A small‐scale action research pilot study was conducted over a period of 6 months with individual incidents (n = 57) of patients requiring increased or decreased observation levels being included in the study. There were no exclusion criteria and this was a total sample in one clinical area. The results were analysed using the Statistical Package for the Social Sciences v.14.0 using non‐parametric statistics and chi square. The results indicated there has been a shift away from doctors deciding on the levels of observation towards multidisciplinary or nursing decisions regarding this aspect of care. During the pilot, there was a gradual shift away from high levels of observation. Those that were placed on increased levels of observation were on them for a much shorter time than previously and staff generally found the new recording system to be more practical. There were a number of ‘sub‐levels’ of general and constant observation in use. Over the years, recording has suffered from incomplete information and this pilot is no different with 56% (n = 34) of the recording sheets had at least one section of clinical information incomplete or not filled in at all. Despite the guidelines and the subsequent training of staff in the clinical area, some nursing staff were not participating as fully as they might in the decision‐making process. Fewer patients were being placed on increased observation levels. Those that were placed on observation were on them for a much shorter time than previously and staff generally found the new recording system to be more practical.
The immigration experience among elderly Korean immigrants
Authors: LEE Y.‐M.
Published: May 2007

The purpose of this preliminary, qualitative study was to describe elderly Korean immigrants' perception of stressors they experienced through immigration and the acculturation process. The methodology used was naturalistic inquiry, a descriptive approach used to elicit the elderly immigrants' own perception of their immigration and acculturation experiences. The six elderly Korean immigrants were interviewed via a semi‐structured, open‐ended interview guide. The main stressors identified by the subjects as a result of adjusting to life in the United States were language barriers, isolation and loneliness, fear of dependence upon their children, fear of being a burden, financial problems, transportation problems, discrimination, and fear of death. These Korean elders also perceived changes in the traditional family values of respect for elders and support for the aged. The results of this research help to provide an understanding of the immigration and acculturation experiences of elderly Korean immigrants.