bluuebunny/crossref_metadata_2025 huggingface dataset:
Imbedded singular continuous spectrum for Schrödinger operators
Authors: Kiselev Alexander
Published: May 2005

We construct examples of potentials

V
(
x
)

V(x)

satisfying

|

V
(
x
)

|

≤

h
(
x
)

1
+
x

,

|V(x)| \leq \frac {h(x)}{1+x},

where the function

h
(
x
)

h(x)

is growing arbitrarily slowly, such that the corresponding Schrödinger operator has an imbedded singular continuous spectrum. This solves one of the fifteen “twenty-first century" problems for Schrödinger operators posed by Barry Simon. The construction also provides the first example of a Schrödinger operator for which Möller wave operators exist but are not asymptotically complete due to the presence of a singular continuous spectrum. We also prove that if

|

V
(
x
)

|

≤

B

1
+
x

,

|V(x)| \leq \frac {B}{1+x},

the singular continuous spectrum is empty. Therefore our result is sharp.
Inferring protein–protein interactions through high-throughput interaction data from diverse organisms
Authors: Liu Yin , Liu Nianjun , Zhao Hongyu
Published: May 2005

Motivation: Identifying protein–protein interactions is critical for understanding cellular processes. Because protein domains represent binding modules and are responsible for the interactions between proteins, computational approaches have been proposed to predict protein interactions at the domain level. The fact that protein domains are likely evolutionarily conserved allows us to pool information from data across multiple organisms for the inference of domain–domain and protein–protein interaction probabilities.

Results: We use a likelihood approach to estimating domain–domain interaction probabilities by integrating large-scale protein interaction data from three organisms, Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster. The estimated domain–domain interaction probabilities are then used to predict protein–protein interactions in S.cerevisiae. Based on a thorough comparison of sensitivity and specificity, Gene Ontology term enrichment and gene expression profiles, we have demonstrated that it may be far more informative to predict protein–protein interactions from diverse organisms than from a single organism.

Availability: The program for computing the protein–protein interaction probabilities and supplementary material are available at http://bioinformatics.med.yale.edu/interaction

Contact:  hongyu.zhao@yale.edu
Semi-supervised protein classification using cluster kernels
Authors: Weston Jason , Leslie Christina , Ie Eugene , Zhou Dengyong , Elisseeff Andre , Noble William Stafford
Published: May 2005

Motivation: Building an accurate protein classification system depends critically upon choosing a good representation of the input sequences of amino acids. Recent work using string kernels for protein data has achieved state-of-the-art classification performance. However, such representations are based only on labeled data—examples with known 3D structures, organized into structural classes—whereas in practice, unlabeled data are far more plentiful.

Results: In this work, we develop simple and scalable cluster kernel techniques for incorporating unlabeled data into the representation of protein sequences. We show that our methods greatly improve the classification performance of string kernels and outperform standard approaches for using unlabeled data, such as adding close homologs of the positive examples to the training data. We achieve equal or superior performance to previously presented cluster kernel methods and at the same time achieving far greater computationalefficiency.

Availability: Source code is available at www.kyb.tuebingen.mpg.de/bs/people/weston/semiprot. The Spider matlab package is available at www.kyb.tuebingen.mpg.de/bs/people/spider

Contact:  jasonw@nec-labs.com

Supplementary information:  www.kyb.tuebingen.mpg.de/bs/people/weston/semiprot
Prediction error estimation: a comparison of resampling methods
Authors: Molinaro Annette M. , Simon Richard , Pfeiffer Ruth M.
Published: May 2005

Motivation: In genomic studies, thousands of features are collected on relatively few samples. One of the goals of these studies is to build classifiers to predict the outcome of future observations. There are three inherent steps to this process: feature selection, model selection and prediction assessment. With a focus on prediction assessment, we compare several methods for estimating the ‘true’ prediction error of a prediction model in the presence of feature selection.

Results: For small studies where features are selected from thousands of candidates, the resubstitution and simple split-sample estimates are seriously biased. In these small samples, leave-one-out cross-validation (LOOCV), 10-fold cross-validation (CV) and the .632+ bootstrap have the smallest bias for diagonal discriminant analysis, nearest neighbor and classification trees. LOOCV and 10-fold CV have the smallest bias for linear discriminant analysis. Additionally, LOOCV, 5- and 10-fold CV, and the .632+ bootstrap have the lowest mean square error. The .632+ bootstrap is quite biased in small sample sizes with strong signal-to-noise ratios. Differences in performance among resampling methods are reduced as the number of specimens available increase.

Contact:  annette.molinaro@yale.edu

Supplementary Information: A complete compilation of results and R code for simulations and analyses are available in Molinaro et al. (2005) (http://linus.nci.nih.gov/brb/TechReport.htm).
CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data
Authors: Margolin Adam A. , Greshock Joel , Naylor Tara L. , Mosse Yael , Maris John M. , Bignell Graham , Saeed Alexander I. , Quackenbush John , Weber Barbara L.
Published: May 2005

Summary: This synopsis provides an overview of array-based comparative genomic hybridization data display, abstraction and analysis using CGHAnalyzer, a software suite, designed specifically for this purpose. CGHAnalyzer can be used to simultaneously load copy number data from multiple platforms, query and describe large, heterogeneous datasets and export results. Additionally, CGHAnalyzer employs a host of algorithms for microarray analysis that include hierarchical clustering and class differentiation.

Availability: CGHAnalyzer, the accompanying manual, documentation and sample data are available for download at http://acgh.afcri.upenn.edu. This is a Java-based application built in the framework of the TIGR MeV that can run on Microsoft Windows, Macintosh OSX and a variety of Unix-based platforms. It requires the installation of the free Java Runtime Environment 1.4.1 (or more recent) (http://www.java.sun.com).

Contact:  weberb@mail.med.upenn.edu
MFAML: a standard data structure for representing and exchanging metabolic flux models
Authors: Yun Hongseok , Lee Dong-Yup , Jeong Joonwoo , Lee Seunghyun , Lee Sang Yup
Published: May 2005

Summary: MFAML is a standard data structure designed for the formal representation and effective exchange of metabolic flux models. It allows for the explicit description of stationary states of a metabolic system by defining environmental/genetic conditions of the system, e.g. flux measurements, balancing constraints and physiological objectives as well as basic information on metabolites and reactions. In addition, a library of MFAML comprising a model parser and a converter provides an open framework for establishing the pipeline from metabolic modeling to metabolic flux analysis.

Availability: MFAML (version 1) is fully described and available at http://mbel.kaist.ac.kr/mfaml/

Contact:  leesy@kaist.ac.kr
Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure
Authors: Jossinet Fabrice , Westhof Eric
Published: May 2005

Summary: Efficient RNA sequence manipulations (such as multiple alignments) need to be constrained by rules of RNA structure folding. The structural knowledge has increased dramatically in the last years with the accumulation of several large RNA structures similar to those of the bacterial ribosome subunits. However, no tool in the RNA community provides an easy way to link and integrate progress made at the sequence level using the available three-dimensional information. Sequence to Structure (S2S) proposes a framework in which an user can easily display, manipulate and interconnect heterogeneous RNA data, such as multiple sequence alignments, secondary and tertiary structures. S2S has been implemented using the Java language and has been developed and tested under UNIX systems, such as Linux and MacOSX.

Availability: S2S is available at http://bioinformatics.org/S2S/

Contact:  f.jossinet@ibmc.u-strasbg.fr
Exon–domain correlation and its corollaries
Authors: Liu Mingyi , Wu Shaoping , Walch Heiko , Grigoriev Andrei
Published: May 2005

Contact:  andrei.grigoriev@gpc-biotech.com
UB matrix implementation for inelastic neutron scattering experiments
Authors: Lumsden M. D. , Robertson J. L. , Yethiraj M.
Published: May 2005

The UB matrix approach has been extended to handle inelastic neutron scattering experiments with differing k_{\rm i} and k_{\rm f}. We have considered the typical goniometer employed on triple-axis and time-of-flight spectrometers. Expressions are derived to allow for calculation of the UB matrix and for converting from observables to Q-energy space. In addition, we have developed appropriate modes for calculation of angles for a specified Q-energy position.
Sample size: an important parameter in flash-cooling macromolecular crystallization solutions
Authors: Chinte U. , Shah B. , DeWitt K. , Kirschbaum K. , Pinkerton A. A. , Schall C.
Published: May 2005

The effect of sample size on flash-cooling was assessed using an assortment of Hampton Screen I solutions (Hampton Research). These were cryogenically cooled to ascertain the minimum glycerol concentration needed for vitrification of solutions. Solutions were `flash-cooled' in 1.0, 0.5 and 0.1 mm commercial cryoloops, using a 100 K nitrogen stream generated by an Oxford 600 Cryostream. The loops were visually examined and then X-ray diffraction data were collected and evaluated for ice formation. The glycerol concentration needed for vitrification was found to decrease significantly as sample size decreased; detailed key data are presented in tabular form. Glass transition temperatures, T
g, were measured for solutions leading to successful vitrification in the 1 mm cryoloop. The trends in the required concentration of glycerol and resultant T
g can be understood through a simplified heat-transfer analysis. This analysis points to a critical cooling time period for successful vitrification.
Structural analysis of single wool fibre by scanning microbeam SAXS
Authors: Kajiura Yoshio , Watanabe Shunichi , Itou Takashi , Iida Atsuo , Shinohara Yuya , Amemiya Yoshiyuki
Published: May 2005

The technique of scanning microbeam small-angle X-ray scattering (SAXS) has been applied to investigate the inhomogeneity in the nanostructure of a single bilateral wool fibre in relation to two types of cortices, the so-called orthocortex and paracortex, which are located at the outer side and the inner side of the curved fibre, respectively. On the basis of the equatorial scattering intensity profiles from both experiments and simulation, the inhomogeneity in the mean IF (intermediate filament)–IF distance, IF diameter and IF orientation, corresponding to the structural difference between the orthocortex and the paracortex in bilateral wool fibre, has been quantitatively obtained.
Correction for counting losses in X-ray diffractometry
Authors: Ida T. , Iwata Y.
Published: May 2005

Non-extended and extended dead-time models, a pulse-height analyser (PHA) windowing model, and a model intermediate between the non-extended and extended models for losses in counting methods are compared. The validities of the methods are examined by application to the analysis of powder diffraction peak intensity profiles measured by a foil method. The intermediate model including parameters for the dead-time and degree of extension can reproduce both the non-extended and the extended models and also intermediate dependence between the two models. A convenient approximate formula for the intermediate model, the maximum relative deviation of which is 0.0003, is also proposed. The determination of the parameters and a correction for the measured intensities can easily be achieved by applying the approximate model, because it provides simple formulae for the correction function expressed as a combination of elementary functions. Experimental and analytical methods for precise evaluation of the parameters to specify the counting losses are also presented. Systematic deviations of the observed dependence from the non-extended and extended dead-time models have been detected by the precise analyses of experimental data, while the PHA windowing model, intermediate model and its approximation have reproduced the observed dependence within the experimental errors.
Determining metal ion distributions using resonant scattering at very high-energy K-edges: Bi/Pb in Pb5Bi6Se14
Authors: Zhang Yuegang , Wilkinson Angus P. , Lee Peter L. , Shastri Sarvjit D. , Shu Deming , Chung Duck-Young , Kanatzidis Mercouri G.
Published: May 2005

Powder diffraction data collected at ∼86 keV, and just below both the Pb and the Bi K-edges, on an imaging plate detector using synchrotron radiation from the Advanced Photon Source have been used to examine the Pb/Bi distribution over the 11 crystallographically distinct sites in Pb5Bi6Se14 [space group P21/m, a = 16.0096 (2) Å, b = 4.20148 (4) Å, c = 21.5689 (3) Å and β = 97.537 (1)°]. The scattering factors needed for the analyses were determined both by Kramers–Kronig transformation of absorption spectra and by analyses of diffraction patterns from reference compounds. Even with the relatively low scattering contrast that is available at the K-edges, it was possible to determine the Pb/Bi distribution and probe the presence of cation site vacancies in the material. The current results indicate that resonant scattering measurements at high-energy K-edges are a viable, and perhaps preferable, route to site occupancies when absorption from the sample or sample environment/container is a major barrier to the acquisition of high-quality resonant scattering data at lower-energy edges.
Simulation of threading dislocation images in X-ray topographs of silicon carbide homo-epilayers
Authors: Vetter W. M. , Tsuchida H. , Kamata I. , Dudley M.
Published: May 2005

Three types of dislocation are seen in homo-epilayers of SiC grown on 4H-SiC wafers with an 8° surface offcut: axial screw dislocations, basal plane dislocations propagated into the epilayer at an 8° inclination and threading edge dislocations. These types may be imaged by monochromatic synchrotron X-ray topography in the grazing-incidence reflection geometry using the 11\overline 28 reflection. Equations needed to apply the ray-tracing method of computer simulating X-ray topographic defect images in this experimental geometry were derived and used to simulate images of all three. Simulations for axial screw dislocations appear as white circles surrounded by narrow dark rings, and those for basal plane dislocations as linear white streaks, both consistent with experimental topographs. Simulations of the threading edge dislocations showed 4 µm wide white ovals with narrow arcs of dark contrast at their ends, inclined relative to the g vector of the topograph according to the sign of their Burgers vector. These images resembled the experimental topographs inasmuch as was possible at the maximum resolution of X-ray topographs.
Study of point defects in as-grown and annealed bismuth germanate single crystals
Authors: Bhagavannarayana G. , Choubey A. , Shubin Yu. V. , Lal Krishan
Published: May 2005

Point defects and their clusters in bismuth germanate single crystals free from grain boundaries and having low density of dislocations were studied by high-resolution diffuse X-ray scattering measurements. Differences in defects in the colourless crystals (type A) and the crystals having yellow tinge (type B), which were grown with different raw materials, were investigated. In addition, interesting differences in defect structures in specimens from different regions of the same boule were investigated. Specimens with diffracting surfaces along (111), (112) and (100) planes were studied. A multicrystal X-ray diffractometer employing a well collimated and highly monochromated Mo Kα1 beam and set in (+,−,−,+) configuration was employed. The diffraction curves of all the samples were quite narrow with half-widths in the range 7–11 arcsec, which are close to the theoretically expected values, if instrumental broadenings are taken into account. The observed distribution of diffuse X-ray scattering (DXS) intensity showed that not all the point defects are isolated but a significant fraction are agglomerated into clusters. Experimental data of DXS intensity were analysed by using a phenomenological model for a small concentration of dislocation loops wherein the point defects are loosely clustered with weak interactions among them. From this analysis, the cluster radius R
cl, cluster volume A
cl, the number of point defects within a cluster N
cl and the relative concentration of the point-defect clusters among the samples were estimated. It was observed that cluster sizes do not vary from sample to sample. However, it was found that the concentration of clusters is approximately twice in the coloured sample compared with that of the colourless sample from the same boule. Annealing of the crystals at 1273 K produced an increase in point-defect clusters by a factor of ∼200. It was accompanied by a reduction in volume of clusters by a factor of ∼0.14.
A bound constrained conjugate gradient solution method as applied to crystallographic refinement problems
Authors: Coelho A. A.
Published: May 2005

Small modifications to the conjugate gradient method for solving symmetric positive definite systems have resulted in an increase in performance over LU decomposition by a factor of around 84 for solving a dense system of 1325 unknowns. Performance is further increased in the case of applying upper- and lower-bound parameter constraints. For structure solution employing simulated annealing and the Newton–Raphson method of non-linear least squares, the overall performance gain can be a factor of four, depending on the applied constraints. In addition, the new algorithm with bounding constraints often seeks out lower minima than would otherwise be attainable without constraints. The behaviour of the new algorithm has been tested against the crystallographic problems of Pawley refinement, rigid-body and general crystal structure refinement.
Quantitative texture analysis with the HIPPO neutron TOF diffractometer
Authors: Matthies S. , Pehl J. , Wenk H.-R. , Lutterotti L. , Vogel S. C.
Published: May 2005

One of the design goals of the neutron time-of-flight (TOF) diffractometer HIPPO (High Pressure–Preferred Orientation) at LANSCE (Los Alamos Neutron Science Center) was efficient quantitative texture analysis. In this paper, the effects of the HIPPO detector geometry and layout on texture analysis, particularly the shape and dimensions of the detector panels, are investigated in detail. An equal-channel angular-pressed (ECAP) aluminium sample with a strong texture was used to determine the methodological limitations of various methods of quantitative texture analysis. Several algorithms for extracting the orientation distribution function (ODF) from the TOF spectra are compared: discrete orientations at arbitrary positions, harmonic methods in Rietveld codes (MAUD and GSAS) and discrete methods in MAUD. Because of the detector geometry, the sharpest texture peaks that can be represented are 12–15° in width, resulting in an optimal texture resolution of 25–30°. Due to the limited resolution and incomplete pole-figure coverage, harmonic expansions beyond L = 12 (where L is the maximum degree of the harmonic expansion) introduce subsidiary oscillations, which are consistently identified as artifacts. Only discrete methods provide a quantitative representation of the texture. Harmonic methods are adequate for a qualitative description of the main texture component. The results of the analysis establish HIPPO as an efficient instrument to determine preferred orientations in relatively short measuring times.
Displacements induced by different nanoprecipitates: a SAXS and WAXS anomalous study on Cu–Ni–Fe and Cu–Ni–Co single crystals
Authors: Lyon O. , Guillon I. , Servant C. , Simon J. P.
Published: May 2005

Single crystals of different Cu–Ni–Co and Cu–Ni–Fe alloys, forming spheroid or plate-like precipitates during decomposition, have been studied by small-angle (SAXS) and wide-angle X-ray scattering (WAXS). The SAXS patterns gave information on the sizes and the organization of the precipitates, while the scattering near Bragg peaks allowed a determination of the distortions of the lattice created by these precipitates. The variations of the SAXS spectra with the atomic scattering factors of Co (or Fe) and Ni were used to determine the composition variation between matrix and precipitates (i.e. the `chemical' term), while those of the WAXS spectra enabled the determination of the displacements in the matrix and in the precipitates. The precipitates were found to be enriched in respectively Co and Ni, or Fe and Ni, inducing a local contraction of the lattice, while the matrix (mainly Cu) was of course depleted in the same elements, and its lattice was dilated. These precipitates are piled up along one of the three 〈100〉 `soft' directions. The variations of the deformation field with the precipitate sizes (along both directions parallel and orthogonal to the pile-up orientation), and with the distance between precipitates have been determined. From the knowledge of such variations, it was possible to modify the respective deformation fields in such a way that the respective precipitates have the same sizes, but with a different geometry, and then to isolate what was induced solely by the geometry of a precipitate. Moreover, these experiments yielded the determination of the secondary components of the displacement field (displacements orthogonal to the pile-up direction), which were found to be weak compared with the primary one (parallel to the same direction). Finally, from the variation of the aspect ratio of the precipitates with the aging duration, it was possible to estimate the surface energy of the precipitates, and a comparison between SAXS and WAXS results shows the applicability of this new approach to the decomposition process.
Resolution of small-angle neutron scattering with a refractive focusing optic
Authors: Mildner D. F. R.
Published: May 2005

A small-angle neutron scattering spectrometer that uses a refractive focusing optic can reach smaller values of the scattering vector, and with higher resolution, than that using pinhole collimation. The analytic expression for the resolution is independent of the sample size for one wavelength only, when the focusing lens images the source at the detector. At all other wavelengths the contribution from the sample size is non-zero. For a system that uses a range of wavelengths to increase the intensity without significantly degrading the instrumental performance, the contribution from the sample term is not zero, though it is small and less than that for the pinhole collimation system.
The use of gradient direction in pre-processing images from crystallization experiments
Authors: Wilson Julie , Berry Ian
Published: May 2005

Robots are now used routinely to perform crystallization experiments and many laboratories now have imaging systems to record the results. These images must be evaluated rapidly and the results fed back into optimization procedures. Software to analyse the images is being developed; described here are methods to restrict the area of the image to be analysed in order to speed up processing. Properties of the gradient of greyscale images are used to identify first the well and then the crystallization drop for various crystallization trays and different imaging systems. Methods are discussed to identify artefacts in the images that are not related to the experimental outcome, but can cause problems for the machine-learning algorithms used in classification and waste time during analysis. Gradient angles are exploited to eliminate faults in the crystallization trays, bubbles and splatter droplets prior to analysis.
An efficient routine for computing symmetric real spherical harmonics for high orders of expansion
Authors: Kudlicki Andrzej , Rowicka Małgorzata , Gilski Mirosław , Otwinowski Zbyszek
Published: May 2005

A numerically efficient method of constructing symmetric real spherical harmonics is presented. Symmetric spherical harmonics are real spherical harmonics with built-in invariance with respect to rotations or inversions. Such symmetry-invariant spherical harmonics are linear combinations of non-symmetric ones. They are obtained as eigenvectors of an appropriate operator, depending on symmetry. This approach allows for fast and stable computation up to very high order symmetric harmonic bases, which can be used in e.g. averaging of non-crystallographic symmetry in protein crystallography or refinement of large viruses in electron microscopy.
Determination of crystal orientation from micrographs using a MATLAB program
Authors: Gibson Ursula , Kou Yi
Published: May 2005

Crys.m is a MATLAB routine that combines a micrograph of a crystal with a scaleable, rotatable three-dimensional cage structure to determine the orientation of the crystal axes. The example presented here uses the morphology of tetragonal lysozyme. Rotation of the cage until it aligns with the crystal in the image yields the orientation of the c axis of the crystal relative to the image normal. This analysis can be used for quantitative determination of crystal orientation effects induced by electric, magnetic and/or gravitational fields.
Practical implementations for improving the throughput in a manual crystallization setup
Authors: Biertümpfel Christian , Basquin Jérôme , Suck Dietrich
Published: May 2005

For the past few years, the number of structural genomics projects has been growing enormously worldwide. All these projects are supported by substantial financial resources and therefore are able to employ robotics for setting up high-throughput platforms. This paper addresses a simple question: how can basic research laboratories draw profit from the efforts and innovations that have been made to establish high-throughput facilities? To answer this question, the implementations that have been made in the authors' laboratory to improve manual crystallization setup with very limited financial investments are presented. In combination with 96-well microplates, an advanced protocol has been introduced and several simple devices have been designed to speed up different aspects of the manual crystallization setup, from storage of solutions to the setting of drops. These implementations lead to the reduction of costs in terms of time and money without any loss of quality. In addition, the crystallization throughput in the manual setup has been significantly increased.
Interactive visualization of electron density slices
Authors: Maia Filipe R. N. C. , Szöke Abraham , DeLano Warren , van der Spoel David
Published: May 2005

A new tool has been developed to aid in the visualization of electron density in crystals or from quantum chemistry calculations. It displays the fine details of the electron density on a plane and the three-dimensional model of the molecule at the same time. The program enables the user to examine the details of weak or irregular features. Such features frequently occur in low-resolution maps, where they determine the correct tracing of a protein backbone. In high-resolution maps, solvent regions are difficult or impossible to observe using isosurfaces. The tool has been integrated into an existing molecular visualization package (PyMol) making it possible to observe and interact both with a structure model and the electron density slices freely, simultaneously and independently. This visualization model fills a gap in the visualization methods available to crystallographers and others who work with electron density maps.
The derivation of the cellulose microfibril angle by small-angle X-ray scattering from structurally characterized softwood cell-wall populations
Authors: Entwistle Kenneth M. , Eichhorn Stephen J. , Navaranjan Namasivayam
Published: May 2005

A method is presented for the measurement, using small-angle X-ray scattering (SAXS), of the microfibril angle and the associated standard deviation for the cellulose microfibrils in the S2 layer of the cell walls of softwood specimens. The length and orientation of over 1000 cell walls in the irradiated volume of the specimen are measured using quantitative image analysis. From these data are calculated the azimuthal variation of the scattered intensity. The calculated values are compared with the measured values. The undetermined parameters in the analysis are the microfibril angle (M) and the standard deviation (σΦ) of the intensity distribution arising from the wandering of the fibril orientation about the mean value. The two parameters are varied to give the best fit between the calculated and the measured values. Six separate pairs of values are determined for six different values of the angle of incidence of the X-ray beam relative to the normal to the radial direction in the specimen. The results show good agreement. The azimuthal distribution of scattered intensity for the real cell-wall structure is compared with that calculated for an assembly of rectangular cells with the same ratio of transverse to radial cell-wall lengths. Despite the existence of marked differences in the intensity distributions around the zero azimuth angle, the position of the extreme flanks of the distribution is very close for the real and the rectangular cells. This means that useful values of the microfibril angle can be obtained from the curve for the real cells using the Meylan parameter T derived by drawing tangents to the flanks of the intensity distribution and using M = kT. The value of k is M/(M + 2σΦ). Since both of these parameters are determined in the work now described, k is also determined. It is also demonstrated that for β = 45° (where β is the angle between the plane face of the wood specimens and the radial direction) the peaks in the azimuthal intensity distribution for the real and the rectangular cells coincide. If this peak position is Φ45, then the microfibril angle can be determined from the relation M = tan−1(tanΦ45/cos45°), which is precise for rectangular cells.
Advances in digital topography for characterizing imperfections in protein crystals
Authors: Lovelace Jeffrey J. , Murphy Cameron R. , Bellamy Henry D. , Brister Keith , Pahl Reinhard , Borgstahl Gloria E. O.
Published: May 2005

A system which joins digital topography with fine φ-sliced reflection profiling has been developed and applied to cryocrystallography. In this demonstration, fifteen fine φ-sliced reflection profiles with corresponding topographic sequences are evaluated: twelve reflections from a crystal at cryogenic temperatures and three reflections from a room-temperature crystal. The digitally collected data show results comparable with film, albeit at a lower resolution, but are acquired at a substantially higher rate. Additionally, anti-blooming circuitry in the CCD was tested and shown to provide useful data even when pixels were overloaded.
The LIESST state of [Fe(pic)3]Cl2.EtOH – the superstructure under continuous irradiation
Authors: Kusz Joachim , Schollmeyer Dieter , Spiering Hartmut , Gütlich Philipp
Published: May 2005

The superstructure recently discovered in [Fe(pic)3]Cl2.EtOH at temperatures inside the step region of the high-spin–low-spin transition curve sheds new light on the anomalous transition behaviour in spin crossover compounds. The structure of the metastable LIESST state of [Fe(pic)3]Cl2.EtOH at 10 K has been measured. The decay has been followed by X-ray diffraction using a CCD camera in order to detect reflections of the superstructure building up during the decay. No signal above the noise of the CCD camera was observed, so that even diffuse scattering could not be detected. This finding is in agreement with correlation lengths of pair correlations of molecules in the HS and LS states being very short, as was concluded earlier from the shape of the decay curves of the HS fraction by theoretical considerations [Romstedt et al. (1998). J. Phys. Chem. Solids, 59, 265–275]. The crystal structure inside the step at 118 K has also been studied under continuous irradiation. The temperature range of the superstructure and the degree of order could be changed by continuous irradiation with green laser light, indicating an increase of the lifetime of the HS excited state by several orders of magnitude compared with the temperature regions outside.
Absolute optical rotation of CsLiB6O10
Authors: Herreros-Cedrés Javier , Hernández-Rodriguez Cecilio , Kaminsky Werner
Published: May 2005

The optical rotation (OR) of CsLiB6O10 (CLBO, space group I\bar{4}2d) along the a axis has been determined by the HAUP method [Kobayashi & Uesu (1983). J Appl. Cryst.
16, 204–211] at a wavelength of 632.8 nm and by the TILTER method [Kaminsky & Glazer (1996). Ferroelectrics, 183, 133–141] at 532 nm and 650 nm. The respective rotatory powers were found to be 17 (1), 24 (2) and 19 (2)° mm−1. The absolute chirality has been established by comparing Bijvoet differences, {hkl} and {k\bar{h}l}, on the same crystal on which OR was measured. Atomic positions and electron density Fourier peak heights were exploited as input for semi-empirical calculations of refractive indices and OR, using WinOPTACT [Glazer (2002). J. Appl. Cryst.
35, 652] with only one free parameter fitted to match the average refractive index.
Intersect distributions of a `dead leaves' model with spherical primary grains
Authors: Gille Wilfried
Published: May 2005

This article analyses a tightly packed random two-phase system possessing spherical particles having the volume fraction of 1/8. For a three-dimensional hard-core `dead leaves' model of spheres of constant diameter, the chord length distribution density of typical chords m

i
of the connected phase (outside the hard particles) is investigated. The calculation starts from the second derivative of the small-angle scattering correlation function of the model and applies characteristic functions. The result fulfills Rosiwal's linear integration principle.
Cooler for obtaining crystals
Authors: Cabric B. , Pavlovic T.
Published: May 2005

A design for an air cooler (`air saw') with a series of movable teeth (`modular crystallization comb') installed in a laboratory chamber furnace is presented. The setup allows easy regulation of a series of different temperature gradients, shapes of crystallization fronts and rates, in crucible columns, with the purpose of obtaining crystals. This method can also be applied in crucible or tube furnaces.
Orientation relations between zincblende-, cinnabar- and NaCl-type phases of CdTe under high pressure
Authors: Sowa H.
Published: May 2005

The transition mechanisms of the pressure-induced phase transformations in CdTe below 4 GPa were studied with the aid of X-ray diffraction techniques. Distinct orientation relations between the zincblende-, the cinnabar- and the NaCl-type phase were observed. Some of the threefold axes of all three phases are oriented parallel to one another. In order to explain the results, three different transition pathways are discussed.
Glucose isomerase from Streptomyces rubiginosus – potential molecular weight standard for small-angle X-ray scattering
Authors: Kozak Maciej
Published: May 2005

Stability of solutions of glucose isomerase from Streptomyces rubiginosus on long-term storage and on exposure to synchrotron radiation has been studied by the small-angle X-ray scattering (SAXS) method. The values of the radii of gyration and forward scattering do not change significantly on storage and on exposure to synchrotron radiation. The mean value of the radius of gyration characterizing glucose isomerase is R
G = 3.27 ± 0.02 nm. For comparison, a SAXS study of monodispersive and aggregated bovine serum albumin (BSA) has been carried out. The results show that glucose isomerase could be a more stable molecular weight standard for SAXS than BSA.
WinXMorph: a computer program to draw crystal morphology, growth sectors and cross sections with export files in VRML V2.0 utf8-virtual reality format
Authors: Kaminsky Werner
Published: May 2005

A Microsoft Windows application for PC-users, WinXMorph, is introduced with which near reality crystal morphologies are made and exported as virtual reality files in the VRML V2.0 format.
A new approach to enhance the anticorrosive properties of treated Egyptian kaolin
Authors: Ahmed Nivin M.
Published: May 2005

Purpose

Kaolin (hydrated aluminum silicate) is one of few minerals that are found in nature in a relatively pure state which is abundant in many places of the world. In this research, a simple chemical treatment using traces of ammonium molybdate was carried out to enhance the anticorrosive properties of kaolin.

Design/methodology/approach

The steps of treatment of kaolin at 1,000°C were estimated. Characterization of three different combinations of aluminum oxide with iron oxide were studied using spectroscopic methods of analysis via X‐ray diffraction (XRD), transmission and scanning electron microscopy (TEM and SEM). Also, evaluation of the prepared pigments using (oil absorption, specific gravity, water‐soluble matter, and pH) international standard testing methods were estimated. Then these prepared pigments were incorporated in anticorrosive paint formulations based on medium oil alkyd resin as a binder, the physico‐mechanical and anticorrosive properties of paint films were detected by testing them in 3.5 percent NaCl solution for 28 days.

Findings

Introduction of small amounts of ammonium molybdate in kaolin promoted its physico‐mechanical and anticorrosive properties. Although, this process of treatment is economically feasible, treated kaolin can replace expensive commercial pigments found in markets with an almost near quality to their performance.

Originality/value

Treated kaolin can be applied in many industries beside pigment manufacture, and paint formulations, it can be applied as reinforcing filler in rubber, plastics, and ceramic composites. Also it is applied in paper filling, paper coatings, and electrical insulation.
Investigation of the performance of linings
Authors: Kalaoglu Fatma , Meric Binnaz
Published: May 2005

Purpose

To investigate the performance of linings in clothing.

Design/methodology/approach

A total of 24 lining fabrics were produced in different constructions. 150 denier 350 twist/cm filament polyester warp yarn was used for all of the fabrics. Two different weft yarns (textured, filament) were used to produce lining fabrics in three different densities.

Findings

In the garment sector, lining performance is highly important for the manufacture of proper quality garments. The main problem of linings during usage is seam slippage for some constructions.

Research limitations/implications

Fabric constructions were chosen as warp rips, weft rips, ripstop (rips both in warp and weft direction) and plain weave. Seam slippage, bending behaviour, crease recovery angle and comfort properties of the linings were measured and the results evaluated.

Originality/value

The paper contributes to understanding the performance of linings.
Uniformity and differentiation in fashion
Authors: Priest Ann
Published: May 2005

Purpose

The paper offers a general outline of four broad consumer categories or groups, in part distilled from the range of detailed and colourfully named descriptors used to differentiate fashion and clothing consumer groups, identify and recognize trends. The paper will offer the opportunity to look at the long‐term impact of external forces on fashion and clothing purchasing decisions.

Design/methodology/approach

The method of research was diverse, but largely drawn from observation; media analysis and industry intelligence. In the course of the work, it was possible to draw on a varied range of sources to categorize purchasing decisions (illustrating consumer categories) into four main drivers.

Findings

Thus to highlight some of the major forces that might drive the consumer.

Practical implications

In reducing the detailed forecasts usually prepared for fashion and related products, the paper might be of interest to those considering the long term impacts of society, culture and politics on the purchasing decisions of fashion and clothing customers.

Originality/value

An insight into the medium term future of fashion taking into consideration the consumer.
Clinical efficacy of the gonadotropin‐releasing hormone antagonist, ganirelix, in Korean women undergoing controlled ovarian hyperstimulation for in vitro fertilization and embryo transfer with recombinant follicle‐stimulating hormone
Authors: Moon Shin Yong , Ku Seung‐Yup , Kim Sun Mie , Jee Byung Chul , Suh Chang Suk , Choi Young Min , Kim Jung Gu , Kim Seok Hyun
Published: May 2005

Aim: To assess the clinical efficacy and safety of the gonadotropin‐releasing hormone (GnRH) antagonist, ganirelix (Orgalutran), treatment in women undergoing controlled ovarian hyperstimulation (COH) for in vitro fertilization and embryo transfer (IVF‐ET) in Korean women.

Methods: This was a non‐comparative, open‐label, single‐center trial carried out on 31 infertile Korean women. A daily dose of 0.25 mg of the GnRH antagonist, ganirelix, was given, beginning on the sixth day of recombinant follicle‐stimulating hormone (FSH) treatment. If the ovarian response was low, ganirelix treatment was delayed until the leading follicle reached a mean diameter of 14 mm. The ganirelix treatment was continued until the day of human chorionic gonadotropin (hCG) injection. Descriptive statistics were recorded for all parameters.

Results: The median duration of ganirelix treatment was 4 days (range: 2–6 days) and the median total recombinant FSH dose was 1350 IU (900–2350 IU). During ganirelix treatment, the incidence of luteinizing hormone (LH) rises (LH = 10 IU/L) was 3.2% (one of 31 cases). On the day ovulation was triggered by hCG, the mean number of follicles ≥11 mm in diameter was 12.4 ± 4.5, and the median of serum estradiol concentration was 4289.9 (1893.7–8268.5) pmol/L. The mean number of oocytes per retrieval was 10.9 ± 6.1. The fertilization rate was 61.5%, and the mean number of replaced embryos was 2.8 ± 0.6. The mean implantation rate was 10.0%, and the clinical pregnancy rate per transfer was 23.3% (seven of 30 cases) and the ongoing pregnancy rate per transfer was 20.0% (six of 30 cases).

Conclusion: The results of the present study support ganirelix as a safe, short, convenient and effective treatment for patients undergoing COH for IVF in Korean women.
Just‐in‐Time Evidence‐Based E‐mail “Reminders” in Home Health Care: Impact on Nurse Practices
Authors: Murtaugh Christopher M. , Pezzin Liliana E. , McDonald Margaret V. , Feldman Penny H. , Peng Timothy R.
Published: May 2005

Objective. To test the effectiveness of two interventions designed to improve the adoption of evidence‐based practices by home health nurses caring for heart failure (HF) patients.

Data Sources/Study Setting. Information on nurse practices was abstracted from the clinical records of patients admitted between June 2000 and November 2001 to the care of 354 study nurses at a large, urban, nonprofit home care agency.

Study Design. The study employed a randomized design with nurses assigned to usual care or one of two intervention groups upon identification of an eligible patient. The basic intervention was a one‐time e‐mail reminder highlighting six HF‐specific clinical recommendations. The augmented intervention consisted of the initial e‐mail reminder supplemented by provider prompts, patient education material, and clinical nurse specialist outreach.

Data Collection. At each home health visit provided by a study nurse to an eligible HF patient during the 45‐day follow‐up period, a structured chart abstraction tool was used to collect information on whether the nurse provided the care practices highlighted in the e‐mail reminder.

Principal Findings. Both the basic and the augmented interventions greatly increased the practice of evidence‐based care, according to patient records, in the areas of patient assessment and instructions about HF disease management. While not all results were statistically significant at conventional levels, intervention effects were positive in virtually all cases and effect magnitudes frequently were large.

Conclusions. The results of this randomized trial strongly support the efficacy of just‐in‐time evidence‐based reminders as a means of changing clinical practice among home health nurses who are geographically dispersed and spend much of their time in the field.
Just‐in‐Time Evidence‐Based E‐mail “Reminders” in Home Health Care: Impact on Patient Outcomes
Authors: Feldman Penny H. , Murtaugh Christopher M. , Pezzin Liliana E. , McDonald Margaret V. , Peng Timothy R.
Published: May 2005

Objective. To assess the impact and cost‐effectiveness of two information‐based provider reminder interventions designed to improve self‐care management and outcomes of heart failure (HF) patients.

Data Sources/Study Setting. Interview and agency administrative data on 628 home care patients with a primary diagnosis of HF.

Study Design. Patients were treated by nurses randomly assigned to usual care or one of two intervention groups. The basic intervention was an e‐mail to the patient's nurse highlighting six HF‐specific clinical recommendations. The augmented intervention supplemented the initial nurse reminder with additional clinician and patient resources.

Data Collection. Patient interviews were conducted 45 days post admission to measure self‐management behaviors, HF‐specific outcomes (Kansas City Cardiomyopathy Questionnaire‐KCCQ), health‐related quality of life (EuroQoL), and service use.

Principal Findings. Both interventions improved the mean KCCQ summary score (15.3 and 12.9 percent, respectively) relative to usual care (p≤.05). The basic intervention also yielded a higher EuroQoL score relative to usual care (p≤.05). In addition, the interventions had a positive impact on medication knowledge, diet, and weight monitoring. The basic intervention was more cost‐effective than the augmented intervention in improving clinical outcomes.

Conclusions. This study demonstrates the positive impact of targeting evidence‐based computer reminders to home health nurses to improve patient self‐care behaviors, knowledge, and clinical outcomes. It also advances the field's limited understanding of the cost‐effectiveness of selected strategies for translating research into practice.
Flexure Strength, Fracture Toughness, and Slow Crack Growth of YSZ/Alumina Composites at High Temperatures
Authors: Choi Sung R. , Bansal Narottam P.
Published: May 2005

Flexure strength and fracture toughness of zirconia–alumina composites, fabricated by hot pressing 10 mol% yttria‐stabilized zirconia (10‐YSZ) reinforced with 0–30 mol% alumina particulates or platelets, were determined as a function of alumina content at 1000°C in air. Both strength and fracture toughness of the two composite systems increased with increasing alumina content. For a given alumina content, flexure strength of the particulate composites was greater than that of the platelet composites at higher alumina contents (≥20 mol%); whereas, fracture toughness of the platelet composites was greater than that of the particulate counterparts, regardless of the alumina content. The susceptibility to slow crack growth (SCG), determined at 1000°C via constant stress‐rate testing, was greatest for 30 mol% particulate composite with SCG parameter n=5–8 and was least for 30 mol% platelet composite with n=33. Elastic modulus of both composite systems decreased below 400°C and then remained almost unchanged up to 1000°C, forming a unique transition around 400°C, irrespective of alumina content.