bluuebunny/crossref_metadata_2025 huggingface dataset:
Management of Psychosexual Problems in Primary Care
Authors: Rolfe Alexandra , Henderson Patricia
Published: February 2010

Sexual health can be described as enjoying and fulfilling sexual desires without causing harm, physical or psychological, to oneself or others. Psychosexual problems affect about 40% of the population and sexual functioning is an important part of a patient's health and well-being. Patients often present late due to embarrassment and commonly with an alternative problem. Learning to recognize and act upon both verbal and non-verbal clues, with empathy, is essential in their management. This article aims to give an overview of common psychosexual problems, specific circumstances where they present more frequently and management options.
Infectious Hepatitis
Authors: Mahida Nikunj A , Nicum Sonal , Simon Chantal
Published: February 2010

Infectious hepatitis is a systemic infection predominantly affecting the liver. Most cases resolve spontaneously, but some progress to chronic hepatitis. Infectious hepatitis has a number of causes but this article will focus on hepatitis A, B and C. Diagnosis is made using liver function tests and serological tests to identify the virus. Depending on the specific virus, treatment and vaccination can be offered to patients and close contacts.
Air-breathing adaptation in a marine Devonian lungfish
Authors: Clement Alice M. , Long John A.
Published: February 2010

Recent discoveries of tetrapod trackways in 395 Myr old tidal zone deposits of Poland (Niedźwiedzki
et al
. 2010
Nature
463
, 43–48 (
doi:10.1038/nature.08623
)) indicate that vertebrates had already ventured out of the water and might already have developed some air-breathing capacity by the Middle Devonian. Air-breathing in lungfishes is not considered to be a shared specialization with tetrapods, but evolved independently. Air-breathing in lungfishes has been postulated as starting in Middle Devonian times (
ca
385 Ma) in freshwater habitats, based on a set of skeletal characters involved in air-breathing in extant lungfishes. New discoveries described herein of the lungfish
Rhinodipterus
from marine limestones of Australia identifies the node in dipnoan phylogeny where air-breathing begins, and confirms that lungfishes living in marine habitats had also developed specializations to breathe air by the start of the Late Devonian (
ca
375 Ma). While invasion of freshwater habitats from the marine realm was previously suggested to be the prime cause of aerial respiration developing in lungfishes, we believe that global decline in oxygen levels during the Middle Devonian combined with higher metabolic costs is a more likely driver of air-breathing ability, which developed in both marine and freshwater lungfishes and tetrapodomorph fishes such as
Gogonasus
.
Development of the pseudothumb in frogs
Authors: Tokita Masayoshi , Iwai Noriko
Published: February 2010

Frogs have highly conserved hand and foot morphology, possessing four fingers and five toes. As an exception, two Japanese ranid frog species, the Otton frogBabina subasperaand the dagger frogBabina holsti, possess a unique thumb-like structure (the pseudothumb) in the forelimb, giving an appearance of a total of five fingers on the hand. To obtain insights into the developmental mechanisms that generate this novel character, we investigated the hand morphogenesis of the Otton frog. The unique morphological pattern of the pseudothumb was already established in juveniles. Surprisingly, the bud-like structure, which is similar to the area of inductive activity (e.g. feather buds in birds and the carapacial ridge in turtles), was detected over the site where the future prepollex develops in larvae. By contrast, this bud-like structure was not found in larvae of other ranid species. We discuss possible scenarios that would favour the evolution of this very unusual trait in frogs.
Utilization of granular solidification during terrestrial locomotion of hatchling sea turtles
Authors: Mazouchova Nicole , Gravish Nick , Savu Andrei , Goldman Daniel I.
Published: February 2010

Biological terrestrial locomotion occurs on substrate materials with a range of rheological behaviour, which can affect limb-ground interaction, locomotor mode and performance. Surfaces like sand, a granular medium, can display solid or fluid-like behaviour in response to stress. Based on our previous experiments and models of a robot moving on granular media, we hypothesize that solidification properties of granular media allow organisms to achieve performance on sand comparable to that on hard ground. We test this hypothesis by performing a field study examining locomotor performance (average speed) of an animal that can both swim aquatically and move on land, the hatchling Loggerhead sea turtle (Caretta caretta). Hatchlings were challenged to traverse a trackway with two surface treatments: hard ground (sandpaper) and loosely packed sand. On hard ground, the claw use enables no-slip locomotion. Comparable performance on sand was achieved by creation of a solid region behind the flipper that prevents slipping. Yielding forces measured in laboratory drag experiments were sufficient to support the inertial forces at each step, consistent with our solidification hypothesis.
Protocols for sampling viral sequences to study epidemic dynamics
Authors: Stack J. Conrad , Welch J. David , Ferrari Matt J. , Shapiro Beth U. , Grenfell Bryan T.
Published: February 2010

With more emphasis being put on global infectious disease monitoring, viral genetic data are being collected at an astounding rate, both within and without the context of a long-term disease surveillance plan. Concurrent with this increase have come improvements to the sophisticated and generalized statistical techniques used for extracting population-level information from genetic sequence data. However, little research has been done on how the collection of these viral sequence data can or does affect the efficacy of the phylogenetic algorithms used to analyse and interpret them. In this study, we use epidemic simulations to consider how the collection of viral sequence data clarifies or distorts the picture, provided by the phylogenetic algorithms, of the underlying population dynamics of the simulated viral infection over many epidemic cycles. We find that sampling protocols purposefully designed to capture sequences at specific points in the epidemic cycle, such as is done for seasonal influenza surveillance, lead to a significantly better view of the underlying population dynamics than do less-focused collection protocols. Our results suggest that the temporal distribution of samples can have a significant effect on what can be inferred from genetic data, and thus highlight the importance of considering this distribution when designing or evaluating protocols and analysing the data collected thereunder.
The Shannon entropy of Sudoku matrices
Authors: Newton Paul K. , DeSalvo Stephen A.
Published: February 2010

We study properties of an ensemble of Sudoku matrices (a special type of doubly stochastic matrix when normalized) using their statistically averaged singular values. The determinants are very nearly Cauchy distributed about the origin. The largest singular value is

, while the others decrease approximately linearly. The normalized singular values (obtained by dividing each singular value by the sum of all nine singular values) are then used to calculate the average Shannon entropy of the ensemble, a measure of the distribution of ‘energy’ among the singular modes and interpreted as a measure of the disorder of a typical matrix. We show the Shannon entropy of the ensemble to be 1.7331±0.0002, which is slightly lower than an ensemble of 9×9 Latin squares, but higher than a certain collection of 9×9 random matrices used for comparison. Using the notion of
relative entropy
or
Kullback–Leibler divergence
, which gives a measure of how one distribution differs from another, we show that the relative entropy between the ensemble of Sudoku matrices and Latin squares is of the order of 10
−5
. By contrast, the relative entropy between Sudoku matrices and the collection of random matrices has the much higher value, being of the order of 10
−3
, with the Shannon entropy of the Sudoku matrices having better distribution among the modes. We finish by ‘reconstituting’ the ‘average’ Sudoku matrix from its averaged singular components.
Piezoelectric effect on the velocities of waves in an anisotropic piezo-poroelastic medium
Authors: Sharma M. D.
Published: February 2010

A mathematical model for mechanical and electrical dynamics in an anisotropic piezo-poroelastic (hereafter referred to as APP) medium is solved for three-dimensional propagation of harmonic plane waves. A system of modified Christoffel equations is derived to explain the existence and propagation of four waves in the medium of arbitrary anisotropy. This system is solved to calculate the phase velocities of four waves in an unbounded APP medium. Directional derivatives of phase velocity are derived analytically and are used to calculate the components of the ray velocity vector. A hypothetical numerical model is considered to compute the phase velocity for given (arbitrary) phase direction and then the ray velocity vector. Surfaces are plotted for the phase velocity and ray velocity of each wave in a saturated poroelastic medium in the absence/presence of piezoelectricity. The contributions of the piezoelectric activeness of the solid frame and pore-fluid to the phase and ray velocities are identified and analysed for each of the four waves in the medium.
Sub-wavelength plasmonic crystals: dispersion relations and effective properties
Authors: Fortes Santiago P. , Lipton Robert P. , Shipman Stephen P.
Published: February 2010

We obtain a convergent power series expansion for the first branch of the dispersion relation for sub-wavelength plasmonic crystals consisting of plasmonic rods with frequency-dependent dielectric permittivity embedded in a host medium with unit permittivity. The expansion parameter is
η
=
kd
=2
πd
/
λ
, where
k
is the norm of a fixed wavevector,
d
is the period of the crystal and
λ
is the wavelength, and the plasma frequency scales inversely to
d
, making the dielectric permittivity in the rods large and negative. The expressions for the series coefficients (also called dynamic correctors) and the radius of convergence in
η
are explicitly related to the solutions of higher order cell problems and the geometry of the rods. Within the radius of convergence, we are able to compute the dispersion relation and the fields and define dynamic effective properties in a mathematically rigorous manner. Explicit error estimates show that a good approximation to the true dispersion relation is obtained using only a few terms of the expansion. The convergence proof requires the use of properties of the Catalan numbers to show that the series coefficients are exponentially bounded in the
H
1
Sobolev norm.
Colour appearance and compensation in the near periphery
Authors: Webster Michael A. , Halen Kimberley , Meyers Andrew J. , Winkler Patricia , Werner John S.
Published: February 2010

The spectral sensitivity of the visual system varies markedly between the fovea and surrounding periphery owing in part to the rapid fall in macular pigment density with eccentricity. We examined how colour appearance changes between the fovea and near periphery (8°) by measuring achromatic loci and the loci of unique and binary hues. Chosen colours remained much more similar at the two locations than predicted by the change in spectral sensitivity. Compensation for white may reflect long-term gain changes within the cones that equate sensitivity for the local average stimulus in the fovea and periphery. However, adjusting only to the average stimulus cannot correct for all of the effects of a spectral sensitivity change, and predicts differences in colour percepts between the fovea and periphery that were not observed. The similarities in hue percepts at 0 and 8° thus suggest that additional processes help compensate colour appearance to maintain constancy in the near periphery. We model the results of previous studies to show that similar adjustments are implied by age-related changes in lens pigment, and to show that these adjustments are consistent with previous measurements of peripheral colour appearance based on hue cancellation.
Species interactions–area relationships: biological invasions and network structure in relation to island area
Authors: Sugiura Shinji
Published: February 2010

The relationship between species number and island area is a fundamental rule in ecology. However, the extent to which interactions with exotic species and how the structure of species interactions is related to island area remain unexplored. Here, I document the relationship between island area and (i) interactions with exotic species and (ii) network structure of species interactions in the context of mutualistic interactions between ants and extrafloral nectary-bearing plants on the oceanic Ogasawara (Bonin) Islands, Japan. Pooled data contained 122 interactions among 19 plant (including five exotic) and 23 ant (including 20 exotic) species. Of the observed interactions, 82.8 per cent involved at least one exotic species, ranging from 68.2 to 86.4 per cent among islands. The number of links including exotic species increased in proportion to island area, although the number of links excluding exotic species did not. These results indicate that the number of interactions with exotic species increased in proportion to island area. Connectance, or the proportion of interactions actually observed among all possible interactions, decreased with island area. Nestedness, an asymmetry index in the species interaction network, also decreased with island area. Therefore, island area affects both the number of interactions with exotic species and the network structure.
Experimental cooling during incubation leads to reduced innate immunity and body condition in nestling tree swallows
Authors: Ardia Daniel R. , Pérez Jonathan H. , Clotfelter Ethan D.
Published: February 2010

Nest microclimate can have strong effects that can carry over to later life-history stages. We experimentally cooled the nests of tree swallows (Tachycineta bicolor). Females incubating in cooled nests reduced incubation time and allowed egg temperatures to drop, leading to extended incubation periods. We partially cross-fostered nestlings to test carry-over effects of cooling during incubation on nestling innate constitutive immunity, assessed through bacteria killing ability (BKA) of blood. Nestlings that had been cooled as eggs showed a lower ability to kill bacteria than control nestlings, regardless of the treatment of their foster mother. However, there was no effect of treatment of rearing females on nestling BKA in control nestlings, even though cooled females made significantly fewer feeding visits than did control females. This suggests that the effect of cooling occurred during incubation and was not due to carry-over effects on nestling condition. Nestlings that were exposed to experimental cooling as embryos had lower residual body mass and absolute body mass at all four ages measured. Our results indicate that environmental conditions and trade-offs experienced during one stage of development can have important carry-over effects on later life-history stages.
Heterogeneity in chronic myeloid leukaemia dynamics during imatinib treatment: role of immune responses
Authors: Wodarz Dominik
Published: February 2010

Previous studies have shown that during imatinib therapy, the decline of chronic myeloid leukaemia BCR-ABL transcript numbers involves a fast phase followed by a slow phase in averaged datasets. Drug resistance leads to regrowth. In this paper, variation of treatment responses between patients is examined. A significant positive correlation is found between slopes of the fast and the slow phase of decline. A significant negative correlation is found between slopes of the slow phase of decline and the regrowth phase. No correlation is found between slopes of the fast phase of decline and the regrowth phase. A mathematical model that is successfully fitted to diverse clinical profiles explains these correlations by invoking the immune response as a key determinant of tumour decline during treatment. Boosting immunity during drug therapy could enhance the response to treatment in patients.
Nectar yeasts warm the flowers of a winter-blooming plant
Authors: Herrera Carlos M. , Pozo María I.
Published: February 2010

Yeasts are ubiquitous in terrestrial and aquatic microbiota, yet their ecological functionality remains relatively unexplored in comparison with other micro-organisms. This paper formulates and tests the novel hypothesis that heat produced by the sugar catabolism of yeast populations inhabiting floral nectar can increase the temperature of floral nectar and, more generally, modify the within-flower thermal microenvironment. Two field experiments were designed to test this hypothesis for the winter-blooming herb
Helleborus foetidus
(Ranunculaceae). In experiment 1, the effect of yeasts on the within-flower thermal environment was tested by excluding them from flowers, while in experiment 2 the test involved artificial inoculation of virgin flowers with yeasts. Nectary temperature (
T
nect
), within-flower air temperature (
T
flow
) and external air temperature (
T
air
) were measured on experimental and control flowers in both experiments. Experimental exclusion of yeasts from the nectaries significantly reduced, and experimental addition of yeasts significantly increased, the temperature excess of nectaries (
Δ
T
nect
=
T
nect
−
T
air
) and the air space inside flowers in relation to the air just outside the flowers. In non-experimental flowers exposed to natural pollinator visitation,
Δ
T
nect
was linearly related to log yeast cell density in nectar, and reached +6°C in nectaries with the densest yeast populations. The warming effect of nectar-dwelling yeasts documented in this study suggests novel ecological mechanisms potentially linking nectarivorous microbes with winter-blooming plants and their insect pollinators.
Semi-automated protein crystal mounting device for the sulfur single-wavelength anomalous diffraction method
Authors: Kitago Yu , Watanabe Nobuhisa , Tanaka Isao
Published: February 2010

Use of longer-wavelength X-rays has advantages for the detection of small anomalous signals from light atoms, such as sulfur, in protein molecules. However, the accuracy of the measured diffraction data decreases at longer wavelengths because of the greater X-ray absorption. The capillary-top mounting method (formerly the loopless mounting method) makes it possible to eliminate frozen solution around the protein crystal and reduces systematic errors in the evaluation of small anomalous differences. However, use of this method requires custom-made tools and a large amount of skill. Here, the development of a device that can freeze the protein crystal semi-automatically using the capillary-top mounting method is described. This device can pick up the protein crystal from the crystallization drop using a micro-manipulator, and further procedures, such as withdrawal of the solution around the crystal by suction and subsequent flash freezing of the protein crystal, are carried out automatically. This device makes it easy for structural biologists to use the capillary-top mounting method for sulfur single-wavelength anomalous diffraction phasing using longer-wavelength X-rays.
Local atomic structure in tetragonal pure ZrO2nanopowders
Authors: Acuña Leandro M. , Lamas Diego G. , Fuentes Rodolfo O. , Fábregas Ismael O. , Fantini Márcia C. A. , Craievich Aldo F. , Prado Rogério J.
Published: February 2010

The local atomic structures around the Zr atom of pure (undoped) ZrO2nanopowders with different average crystallite sizes, ranging from 7 to 40 nm, have been investigated. The nanopowders were synthesized by different wet-chemical routes, but all exhibit the high-temperature tetragonal phase stabilized at room temperature, as established by synchrotron radiation X-ray diffraction. The extended X-ray absorption fine structure (EXAFS) technique was applied to analyze the local structure around the Zr atoms. Several authors have studied this system using the EXAFS technique without obtaining a good agreement between crystallographic and EXAFS data. In this work, it is shown that the local structure of ZrO2nanopowders can be described by a model consisting of two oxygen subshells (4 + 4 atoms) with different Zr—O distances, in agreement with those independently determined by X-ray diffraction. However, the EXAFS study shows that the second oxygen subshell exhibits a Debye–Waller (DW) parameter much higher than that of the first oxygen subshell, a result that cannot be explained by the crystallographic model accepted for the tetragonal phase of zirconia-based materials. However, as proposed by other authors, the difference in the DW parameters between the two oxygen subshells around the Zr atoms can be explained by the existence of oxygen displacements perpendicular to thezdirection; these mainly affect the second oxygen subshell because of the directional character of the EXAFS DW parameter, in contradiction to the crystallographic value. It is also established that this model is similar to another model having three oxygen subshells, with a 4 + 2 + 2 distribution of atoms, with only one DW parameter for all oxygen subshells. Both models are in good agreement with the crystal structure determined by X-ray diffraction experiments.
Critical region and metal–nonmetal transition in expanded fluid mercury: advanced evaluation of small-angle X-ray scattering data
Authors: Ruland Wilhelm , Hensel Friedrich
Published: February 2010

The small-angle X-ray scattering data of expanded fluid mercury published in the literature were evaluated using a modified form of the Teubner–Strey equation for microemulsions together with the general treatment of two-phase systems according to Porod. The parameters obtained in the critical region and the metal–nonmetal (M–NM) transition are evidence of a nanoemulsion composed of M and NM domains. The structure of this emulsion is characterized by density, volume fraction and size parameters (average chord length, polydispersity) of the domains. On the basis of these parameters, a structural model for fluid mercury in the liquid–vapour critical region and the M–NM transition is developed. Analysis of the relationship between the volume fraction of the M domains and the electrical conductivity reveals that a percolation transition occurs, with a threshold located near the liquid–vapour critical density. This observation is consistent with recent theoretical developments.
Quality control of protein standards for molecular mass determinations by small-angle X-ray scattering
Authors: Akiyama Shuji
Published: February 2010

Small-angle X-ray scattering (SAXS) is a powerful technique with which to evaluate the size and shape of biological macromolecules in solution. Forward scattering intensity normalized relative to the particle concentration,I(0)/c, is useful as a good measure of molecular mass. A general method for deducing the molecular mass from SAXS data is to determine the ratio ofI(0)/cof a target protein to that of a standard protein with known molecular mass. The accuracy of this interprotein calibration is affected considerably by the monodispersity of the prepared standard, as well as by the precision in estimating its concentration. In the present study, chromatographic fractionation followed by hydrodynamic characterization is proposed as an effective procedure by which to prepare a series of monodispersed protein standards. The estimation of molecular mass within an average deviation of 8% is demonstrated using monodispersed bovine serum albumin as a standard. The present results demonstrate the importance of protein standard quality control in order to take full advantage of interprotein calibration.
Getting the best out of long-wavelength X-rays:de novochlorine/sulfur SAD phasing of a structural protein from ATV
Authors: Goulet Adeline , Vestergaard Gisle , Felisberto-Rodrigues Catarina , Campanacci Valérie , Garrett Roger A. , Cambillau Christian , Ortiz-Lombardía Miguel
Published: February 2010

The structure of a 14 kDa structural protein fromAcidianustwo-tailed virus (ATV) was solved by single-wavelength anomalous diffraction (SAD) phasing using X-ray data collected at 2.0 Å wavelength. Although the anomalous signal from methionine sulfurs was expected to suffice to solve the structure, one chloride ion turned out to be essential to achieve phasing. The minimal data requirements and the relative contributions of the Cl and S atoms to phasing are discussed. This work supports the feasibility of a systematic approach for the solution of protein crystal structures by SAD based on intrinsic protein light atoms along with associated chloride ions from the solvent. In such cases, data collection at long wavelengths may be a time-efficient alternative to selenomethionine substitution and heavy-atom derivatization.
Structure determination using poorly diffracting membrane-protein crystals: the H+-ATPase and Na+,K+-ATPase case history
Authors: Pedersen Bjørn P. , Morth J. Preben , Nissen Poul
Published: February 2010

An approach is presented for the structure determination of membrane proteins on the basis of poorly diffracting crystals which exploits molecular replacement for heavy-atom site identification at 6–9 Å maximum resolution and improvement of the heavy-atom-derived phases by multi-crystal averaging using quasi-isomorphous data sets. The multi-crystal averaging procedure allows real-space density averaging followed by phase combination between non-isomorphous native data sets to exploit crystal-to-crystal nonisomorphism despite the crystals belonging to the same space group. This approach has been used in the structure determination of H+-ATPase and Na+,K+-ATPase using Ca2+-ATPase models and its successful application to the Mhp1 symporter using LeuT as a search model is demonstrated.
Direct inter-subdomain interactions switch between the closed and open forms of the Hsp70 nucleotide-binding domain in the nucleotide-free state
Authors: Shida Meiri , Arakawa Akihiko , Ishii Ryohei , Kishishita Seiichiro , Takagi Tetsuo , Kukimoto-Niino Mutsuko , Sugano Sumio , Tanaka Akiko , Shirouzu Mikako , Yokoyama Shigeyuki
Published: February 2010

The 70 kDa heat-shock proteins (Hsp70s) are highly conserved chaperones that are involved in several cellular processes, such as protein folding, disaggregation and translocation. In this study, the crystal structures of the human Hsp70 nucleotide-binding domain (NBD) fragment were determined in the nucleotide-free state and in complex with adenosine 5′-(β,γ-imido)triphosphate (AMPPNP). The structure of the nucleotide-free NBD fragment is similar to that of the AMPPNP-bound NBD fragment and is designated as the `closed form'. In the nucleotide-free NBD fragment the closed form is intrinsically supported through interactions between Tyr15, Lys56 and Glu268 which connect subdomains IA, IB and IIB at the centre of the protein. Interaction with the substrate-binding domain (SBD) of Hsp70 or the BAG domain of BAG1 impairs this subdomain connection and triggers the rotation of subdomain IIA around a hydrophobic helix from subdomain IA. The subdomain rotation is limited by Asp199 and Asp206 from subdomain IIA and clearly defines the open form of the NBD. The open form is further stabilized by a new interaction between Gly230 from subdomain IIB and Ser340 from subdomain IIA. The structure of the NBD in the nucleotide-free state is determined by switching of the inter-subdomain interactions.
Structure of the unbound form of HIV-1 subtype A protease: comparison with unbound forms of proteases from other HIV subtypes
Authors: Robbins Arthur H. , Coman Roxana M. , Bracho-Sanchez Edith , Fernandez Marty A. , Gilliland C. Taylor , Li Mi , Agbandje-McKenna Mavis , Wlodawer Alexander , Dunn Ben M. , McKenna Robert
Published: February 2010

The crystal structure of the unbound form of HIV-1 subtype A protease (PR) has been determined to 1.7 Å resolution and refined as a homodimer in the hexagonal space groupP61to anRcrystof 20.5%. The structure is similar in overall shape and fold to the previously determined subtype B, C and F PRs. The major differences lie in the conformation of the flap region. The flaps in the crystal structures of the unbound subtype B and C PRs, which were crystallized in tetragonal space groups, are either semi-open or wide open. In the present structure of subtype A PR the flaps are found in the closed position, a conformation that would be more anticipated in the structure of HIV protease complexed with an inhibitor. The amino-acid differences between the subtypes and their respective crystal space groups are discussed in terms of the differences in the flap conformations.
Rapid chain tracing of polypeptide backbones in electron-density maps
Authors: Terwilliger Thomas C.
Published: February 2010

A method for the rapid tracing of polypeptide backbones has been developed. The method creates an approximate chain tracing that is useful for visual evaluation of whether a structure has been solved and for use in scoring the quality of electron-density maps. The essence of the method is to (i) sample candidate Cαpositions at spacings of approximately 0.6 Å along ridgelines of high electron density, (ii) list all possible nonapeptides that satisfy simple geometric and density criteria using these candidate Cαpositions, (iii) score the nonapeptides and choose the highest scoring ones, and (iv) find the longest chains that can be made by connecting nonamers. An indexing and storage scheme that allows a single calculation of most distances and density values is used to speed up the process. The method was applied to 42 density-modified electron-density maps at resolutions from 1.5 to 3.8 Å. A total of 21 428 residues in these maps were traced in 24 CPU min with an overall r.m.s.d. of 1.61 Å for Cαatoms compared with the known refined structures. The method appears to be suitable for rapid evaluation of electron-density map quality.
Structural insights into the assembly of the human and archaeal signal recognition particles
Authors: Wild Klemens , Bange Gert , Bozkurt Gunes , Segnitz Bernd , Hendricks Astrid , Sinning Irmgard
Published: February 2010

The signal recognition particle (SRP) is a conserved ribonucleoprotein (RNP) complex that co-translationally targets membrane and secretory proteins to membranes. The assembly of the particle depends on the proper folding of the SRP RNA, which in mammalia and archaea involves an induced-fit mechanism within helices 6 and 8 in the S domain of SRP. The two helices are juxtaposed and clamped together upon binding of the SRP19 protein to their apices. In the current assembly paradigm, archaeal SRP19 causes the asymmetric loop of helix 8 to bulge out and expose the binding platform for the key player SRP54. Based on a heterologous archaeal SRP19–human SRP RNA structure, mammalian SRP19 was thought not to be able to induce this change, thus explaining the different requirements of SRP19 for SRP54 recruitment. In contrast, the crystal structures of a crenarchaeal and the all-human SRP19–SRP RNA binary complexes presented here show that the asymmetric loop is bulged out in both binary complexes. Differences in SRP assembly between mammalia and archaea are therefore independent of SRP19 and are based on differences in SRP RNA itself. A new SRP-assembly scheme is presented.
ScotlandsPlaces XML: bespoke XML or XML mapping?
Authors: Beamer Ashley , Gillick Mark
Published: February 2010

Purpose

The purpose of this paper is to investigate web services (in the form of parameterised URLs), specifically in the context of the ScotlandsPlaces project. This involves cross‐domain querying, data retrieval and display via the development of a bespoke XML standard rather than existing XML formats and mapping between them.

Design/methodology/approach

In looking at the different heritage domain datasets as well as the metadata formats used for storage and data exchange, the ScotlandsPlaces XML format is revealed as the most appropriate for this type of project. The nature of the project itself and the need for dynamic web services are in turn explored.

Findings

It was found that, due to the nature of the project, the combination of a bespoke ScotlandsPlaces XML format and a set of matching web services was the best choice in terms of the retrieval of different domain datasets, as well as the desired extensible nature of the project.

Research limitations/implications

It may have proven useful to investigate the datasets of more ScotlandsPlaces partners, but as yet only a limited number of first phase partners' datasets could be studied, as the second phase of the project has yet to begin.

Originality/value

Rather than an information portal, the ScotlandsPlaces web site aggregates disparate types of record, whether site records, archival or otherwise, into a single web site and makes these records discoverable via geographical searching. Aggregated data are accessed through web service queries (using a bespoke XML format developed specifically for the project for data return) and allow partner organisations to add their datasets regardless of the organisational domain. The service also allows spatially referenced records to be plotted on to a geo‐browser via a KML file, which in turn lets users evaluate the results based on geographical location.
Developing a web tool for searching and viewing collections of high‐quality cultural images
Authors: Lazarinis Fotis
Published: February 2010

Purpose

Searching for information and viewing visual representations of products in e‐organisations is a common activity of the e‐visitors to these organisations. For example, in e‐museums, users are shown images or other visual information of the existing objects. The aim of this paper is to present a tool which supports the effective searching for images in e‐organisations. The tool also supports the effective presentation of high‐quality images with zooming facilities. The tool is used in searching for and viewing high‐resolution cultural images in order to test its usefulness.

Design/methodology/approach

Initially, the problems of finding and effectively viewing high‐quality images in e‐organisations are discussed. Then, a review of the literature on zoomable browsers, which discuss effective ways of depicting large quantities of visual data on small screens or in a fast mode, through the web, is presented. Concept‐based image retrieval and the image‐browsing modules of the proposed tool are described. Finally, the system is evaluated with the aid of real users in viewing high‐quality cultural images downloaded from the web. The opinions of the users are presented, along with other statistics, and future research plans are discussed.

Findings

The emphasis of the evaluation was on the zoomable image viewer of the presented web tool. The evaluation showed that the zooming viewer is easy to use and reduces significantly the data that need to be downloaded for viewing high‐quality images.

Originality/value

The integrated searching and viewing application could be used in e‐organisations for searching for and viewing detailed images of their products and exhibits. Further, the zoomable image browser could be used for viewing libraries of high‐quality image collections in a time‐ and network‐efficient mode.
The Bookshelf: digitisation and access to copyright items in Norway
Authors: Moe Skarstein Vigdis
Published: February 2010

Purpose

The purpose of this paper is to provide an overview of the challenges faced in digitising copyright‐protected books and other materials within the National Library of Norway.

Design/methodology/approach

Following a description of Bokhylla, or The Bookshelf, the paper outlines the strategies adopted within the National Library of Norway for digitising a range of materials, including books.

Findings

The National Library of Norway has negotiated a contract with Kopinor, an organisation that represents rights‐holders from about 30 different organisations, and this will enable users to access some 50,000 copyright‐protected books within the next three years.

Originality/value

Copyright presents challenges in any digitisation project. Norway has adopted a unique solution for enabling its citizens to gain digital access to materials deposited within the National Library.
Peer reference redefined: new uses for undergraduate students
Authors: Faix Allison I. , Bates Margaret H. , Hartman Lisa A. , Hughes Jennifer H. , Schacher Casey N. , Elliot Brooke J. , Woods Alexander D.
Published: February 2010

Purpose

This paper aims to redefine the peer reference model – using student assistants to staff the reference desk – by expanding it to include upper‐level undergraduate students from various disciplines providing full reference service with minimal supervision as well as performing paraprofessional‐level duties.

Design/methodology/approach

Set within a backdrop of budget cuts, severe time and staffing limitations, and increasing demands for library services, the paper assesses the processes and results of implementing this new model of peer reference at a medium‐sized academic library.

Findings

The findings suggest that undergraduate students are not only capable but perhaps optimal at providing high‐quality reference service to their peers.

Originality/value

This paper redefines the peer reference model, using a case study carried out in a US university library.
Critically divided?
Authors: Tregear Angela , Dobson Suzanne , Brennan Mary , Kuznesof Sharron
Published: February 2010

Purpose

“Theory versus practice” and “rigour versus relevance” debates have long been a feature of the discipline of marketing, not least within the sub‐field of marketing education, where authors have increasingly called for the adoption of more critical approaches as a means to enhance undergraduate degrees. To date, however, little is actually known about how undergraduate programmes are perceived by those who deliver them. The aim of this research is to investigate educators' views of the primary purpose of undergraduate degrees, and their perceptions and experiences of critical approaches.

Design/methodology/approach

A series of 23 exploratory interviews was conducted, followed by a national survey of UK marketing educators. For the main phase of data analysis, multivariate techniques were employed.

Findings

Respondents generally agreed that intellectual rigour is a priority in marketing education. However, significant differences in opinion were identified on the extent to which degrees actually provide this, the extent to which students should be treated as customers, and whether curricula should be driven by industry. In terms of critical approaches, the majority of staff rated such approaches as important to undergraduate programmes, and most had introduced at least one type in their own teaching. There were no significant differences in ratings and experiences of critical approaches between those respondents who emphasised industry relevance in marketing education and the rest.

Originality/value

The divergence of views revealed by the research raises important questions about how marketing is currently positioned to different stakeholders, and how the discipline may evolve in future.
High Court considers whether FSA disclosures are exempt from freedom of information requests
Authors: Gray Joanna
Published: February 2010

Purpose

The purpose of this paper is to report and comment on the High Court ruling on whether Financial Services Authority (FSA) disclosures are exempt from freedom of information requests.

Design/methodology/approach

The paper outlines the facts surrounding the case and comments on the decision.

Findings

The High Court allowed the FSA's appeal in respect of the Owen appeal and the second part of the Lewis appeal (that the names of the seven firms investigated by the FSA as a result of the mystery shopping should not be disclosed) but agreed with the Tribunal on the first part of the Lewis appeal, that the names of the firms subject to the mystery shopping exercise could be disclosed.

Originality/value

This appeal shows how two very differently motivated, yet equally well‐intentioned, regulatory regimes can come into conflict.
Portfolio optimisation and bootstrapping
Authors: Srivatsa Rahul , Smith Andrew , Lekander Jon
Published: February 2010

Purpose

The purpose of this paper is to develop a more robust methodology for asset allocation for the property investment market which takes into account inherent valuation and data issues.

Design/methodology/approach

The methodology applied is that of a bootstrap, borrowed from Carlstein, and is applied to an investment universe consisting of UK equities, gilts and property. The bootstrap selectively re‐samples the return time series by maintaining the economic cycle. The resulting return series is then used in the standard mean‐variance optimisation (MVO) on an unconstrained basis. Finally, a “sanity” test is applied on the correlation matrix to ensure that spurious instances do not skew the results.

Findings

The bootstrapped optimisation provides a range within which the portfolio weights can be manoeuvred instead of a static point under the standard MVO. It provides a more robust methodology for asset allocation and without giving any undue significance to one year of extreme result.

Research limitations/implications

The current analysis is based on unconstrained portfolio optimisation, with a very limited investment universe. Additionally, by conforming with the MVO methodology, normality of asset returns is implicitly assumed, which is clearly not the case in the data used. Future work will also focus on an all‐property portfolio.

Practical implications

The proposed methodology will prove to be useful for making asset allocation decisions, particularly in turbulent financial markets.

Originality/value

The paper focuses solely on bootstrapping with the IPD UK annual index and is particularly significant after one year of extremely poor performance of UK property. The results will be of use to fund managers and portfolio analysts.
Inhibition of ErbB2 by Herceptin reduces survivin expression via the ErbB2–β‐catenin/TCF4‐survivin pathway in ErbB2‐overexpressed breast cancer cells
Authors: Zhu Hongxia , Zhang Guo , Wang Yan , Xu Ninghong , He Shun , Zhang Wei , Chen Meigui , Liu Mei , Quan Lanping , Bai Jingfeng , Xu Ningzhi
Published: February 2010

Overexpression of ErbB2 is associated with poor prognosis in breast cancer. Targeting of ErbB2 is a very common therapeutic strategy in ErbB2‐overexpressed breast cancer. Herceptin is the first approved and most widely used agent for ErbB2‐targeting therapy in breast cancer. Even though the clinical application has been performed for more than 10 years, the exact mechanism underlying how Herceptin exhibits its effects has not been fully elucidated. In this study, we found that Herceptin could inhibit the expression of survivin in ErbB2‐overexpressed cell lines. Overexpression of survivin could abrogate the inhibition of cell growth induced by Herceptin. Herceptin could reduce survivin expression at the transcriptional level. The β‐catenin/T‐cell factor (TCF) pathway played a very crucial role in this cascade. We found that Herceptin could reduce tyrosine phosphorylation levels of ErbB2 and β‐catenin. Herceptin treatment induced degradation of β‐catenin protein, resulting in reduced binding affinity of β‐catenin/TCF4 to the promoter region of survivin. When we cross‐mutated the TCF4 binding sites in the promoter region of survivin, the reduction of survivin promoter activity almost diminished. Taken together, we showed that Herceptin could inhibit survivin expression through the ErbB2–β‐catenin/TCF4‐survivin pathway in ErbB2‐overexpressed breast cancer cells. This indicates that there may be a new cascade axis from ErbB2 to survivin.

(Cancer Sci 2010; 101: 1156–1162)
Overexpression of Necl‐5 correlates with unfavorable prognosis in patients with lung adenocarcinoma
Authors: Nakai Reiko , Maniwa Yoshimasa , Tanaka Yugo , Nishio Wataru , Yoshimura Masahiro , Okita Yutaka , Ohbayashi Chiho , Satoh Naoyuki , Ogita Hisakazu , Takai Yoshimi , Hayashi Yoshitake
Published: February 2010

Nectin‐like molecule‐5 (Necl‐5) is an immunoglobulin (Ig)‐like molecule that is up‐regulated in many types of cancer cells. It was shown experimentally that Necl‐5 enhances cell migration, proliferation, and metastasis, but its clinical significance has not been documented. The aim of this study was to observe the expression of Necl‐5 in surgically resected primary lung adenocarcinomas and to investigate its clinical significance. A total of 63 surgically resected primary pulmonary adenocarcinoma tissues were investigated by immunohistochemistry for the expression of Necl‐5. The relationship between expression of Necl‐5 and clinicopathological features was analyzed, and the influence of Necl‐5 expression on outcomes in these patients was assessed. A strong expression of Necl‐5 by cancer cells was observed in 43 of the 63 tumors. The overexpression of Necl‐5 by cancer cells was significantly associated with lymph node metastasis (P = 0.0398), TNM staging (P = 0.0367), and the bronchioloalveolar carcinoma ratio of tumors (P = 0.0423). Furthermore, the disease‐free survival rate in patients with positive Necl‐5 overexpression was significantly lower than that in patients with negative Necl‐5 overexpression (P = 0.0004). Multivariate survival analysis revealed Necl‐5 expression to be an independent risk factor for an unfavorable outcome (P = 0.0294). Additionally, an analysis including only the stage I cases revealed that the disease‐free survival rate of the Necl‐5‐positive group was significantly lower than that of the Necl‐5‐negative group (P = 0.0192). These results indicate that Necl‐5 plays a role in mediating tumor cell invasion and that the overexpression of Necl‐5 in cancer cells has clinical significance for prognostic evaluation of patients with primary pulmonary adenocarcinoma.

(Cancer Sci 2010; 101: 1326–1330)
The effects of mild induced hypothermia on the myocardium: a systematic review
Authors: Kelly F. E. , Nolan J. P.
Published: February 2010

Mild induced hypothermia improves neurological outcome and reduces mortality among initially comatose survivors of out‐of‐hospital cardiac arrest. Similar pathological processes occur in the heart and the brain, namely ischaemia followed by reperfusion injury. Animal data indicate that mild induced hypothermia results in improved myocardial salvage, reduced infarct size, reduced left ventricular remodelling and better long‐term left ventricular function. Several small human studies suggest that infarct size may be reduced by mild induced hypothermia, although this has not reached significance in any human study to date. There are variable reports of harm to the myocardium caused by mild induced hypothermia, including reduced myocardial contractility and cardiac output, electrocardiographic changes and arrhythmias, especially bradycardia. These harmful effects are reversible with rewarming.