bluuebunny/crossref_metadata_2025 huggingface dataset:
Haemolytic anaemia and alterations in hepatic iron metabolism in aged mice lacking Cu,Zn-superoxide dismutase
Authors: Starzyński Rafał R. , Canonne-Hergaux François , Willemetz Alexandra , Gralak Mikołaj A. , Woliński Jarosław , Styś Agnieszka , Olszak Jarosław , Lipiński Paweł
Published: March 2009

The continuous recycling of haem iron following phagocytosis and catabolism of senescent and damaged red blood cells by macrophages is a crucial process in the maintenance of systemic iron homoeostasis. However, little is known about macrophage iron handling in haemolytic states resulting from a deficiency in antioxidant defences. Our observations indicate that the recently described chronic, but moderate regenerative, haemolytic anaemia of aged SOD1 (superoxide dismutase 1)-knockout mice is associated with red blood cell modifications and sensitivity to both intra- and extra-vascular haemolysis. In the present study, we have characterized the molecular pathways of iron turnover in the liver of Sod1-deficient mice. Despite iron accumulation in liver macrophages, namely Kupffer cells, we did not measure any significant change in non-haem liver iron. Interestingly, in Kupffer cells, expression of the rate-limiting enzyme in haem degradation, haem oxygenase-1, and expression of the iron exporter ferroportin were both up-regulated, whereas the hepcidin mRNA level in the liver was decreased in Sod1−/− mice. These results suggest that concerted changes in the hepatic expression of iron- and haem-related genes in response to haemolytic anaemia in Sod1−/− mice act to reduce toxic iron accumulation in the liver and respond to the needs of erythropoiesis.
Controlled oxidation of FeCo magnetic nanoparticles to produce faceted FeCo/ferrite nanocomposites for rf heating applications
Authors: Collier K. N. , Jones N. J. , Miller K. J. , Qin Y. L. , Laughlin D. E. , McHenry M. E.
Published: March 2009

We report the oxidation products and qualitative rates for polydisperse FeCo magnetic nanoparticles (MNPs) synthesized using an induction plasma torch. X-ray diffraction (XRD) and TEM showed MNPs to have a thin ferrite shell. Nanopowders were isochronally annealed to promote oxidation and XRD was used to follow the evolution of the FeCo core and the Fe3O4 and FeO oxide shells. Isothermal anneals were used to follow oxidation kinetics at 350 and 500°C. High resolution transmission electron microscopy (HRTEM) revealed faceted morphologies terminated at (100) and (110) FeCo faces with (110)FeCo∥(111)oxide and (100)FeCo∥(100)oxide, and [010]FeCo∥[011]oxide orientation relationships between the FeCo core and oxide shell. We show HRTEM images of MNP chaining and compare the rf heating of samples of aqueous ferrofluids similarly loaded with as synthesized and oxidized MNPs.
Room temperature ferromagnetic ordering in indium substituted nano-nickel-zinc ferrite
Authors: Thakur Sangeeta , Katyal S. C. , Gupta A. , Reddy V. R. , Singh M.
Published: March 2009

Nano-nickel-zinc-indium ferrite (NZIFO)(Ni0.58Zn0.42InxFe2−xO4) with varied quantities of indium (x=0,0.1,0.2) have been synthesized via reverse micelle technique. X-ray diffraction and transmission electron microscopy confirmed the size, structure, and morphology of the nanoferrites. The addition of indium in nickel-zinc ferrite (NZFO) has been shown to play a crucial role in enhancing the magnetic properties. Room temperature Mössbauer spectra revealed that the nano-NZFO ferrite exhibit collective magnetic excitations, while indium doped NZFO samples have the ferromagnetic phase. The dependence of Mössbauer parameters, viz. isomer shift, quadrupole splitting, linewidth, and hyperfine magnetic field, on In3+ concentration has been studied. Mössbauer study on these nanosystems shows that the cation distribution not only depends on the particle size but also on the preparation route. Mössbauer results are also supported by magnetization data. Well defined sextets and appearance of hysteresis at room temperature indicate the existence of ferromagnetic couplings which makes nano-NZIFO ferrite suitable for magnetic storage data.
Mapping a magnetization switching field in Ga0.98Mn0.02As microbars with a scanning laser magneto-optical microscope
Authors: Aoyama J. , Hashimoto Y. , Kobayashi S. , Munekata H.
Published: March 2009

Local information on 90° magnetization switching in ferromagnetic Ga0.98Mn0.02As microbars with in-plane magnetization was obtained successfully by a homemade scanning laser magneto-optical microscopy. The switching occurs from the edge regions that include edges whose directions are perpendicular to the initial magnetization direction. The local switching field depends strongly on the direction of initial magnetization. The observed results suggest that demagnetization is one of the important factors for magnetization switching in micron-scale (Ga,Mn)As structures.
Self-similar bandgap structure and spin-polarized transport in quasiperiodic cascade junctions of ferromagnet and semiconductor
Authors: Li Jia , Zhang R. L. , Peng R. W. , Wu Xin , Li De , Hu Qing , Qiu Yan , Wang Mu
Published: March 2009

We theoretically investigate spin-dependent transport in quasiperiodic cascade junctions of a ferromagnetic metal (FM) and semiconductor (SC), where FM and SC are arranged in the Fibonacci sequence. It is shown that spin-up and spin-down electrons possess different bandgap structures against the Rashba spin-orbit wave vector. The spin-dependent bandgap structure has the hierarchical characteristic and present self-similarity. Due to the quasiperiodicity, multiple resonant transmissions for spin-up or spin-down electrons can be observed within the bandgap; thereafter, spin polarization has multiple reversals. And it is also found that the electrical conductance can come from one kind of spin electrons around the resonant wave vector. These investigations may provide a unique way to design the devices such as spin filters and spin switches.
Temperature stability of the half-metallic CrO2 (110) and (001) surfaces in ultrahigh vacuum
Authors: Ivanov P. G. , Bussmann K. M.
Published: March 2009

CrO 2 has the highest measured spin transport polarization (P), yet produces low values of magnetoresistance (MR) in spin valves. This work tests the limits of CrO2 surface stability as a culprit of spin loss in magnetoresistive devices. Epitaxial CrO2 films are grown on TiO2 single-crystal substrates from Cr8O21 precursor in flowing oxygen and transferred directly to UHV without exposure to air. The surface structure is observed by low-energy electron diffraction as a function of temperature. The main result is that it is possible under specific conditions to stabilize the CrO2 (001) and (110) surfaces for growth of multilayer devices. Under UHV conditions CrO2 (110) is stable to ∼99 °C while (001) is stable to ∼150 °C with evidence of faceting. In some cases well ordered CrO2 surface can be recovered by annealing in oxygen.
Experimental verification and analytical approach to influence stator skew on electromagnetic performance of permanent magnet generators with multipole rotor
Authors: Choi Jang-Young , Jang Seok-Myeong , Ko Kyoung-Jin
Published: March 2009

This paper deals with experimental verification and analytical approach to influence stator skew on electromagnetic performance of a permanent magnet generator (PMG) with multipole rotor. The analytical expressions for magnetic field distributions are due to permanent magnets and the two-dimensional permeance function considering skew effects are established. On the basis of these analytical solutions, the analytical solutions for cogging torque and back-emf considering skew effects are also derived. Then, by applying estimated electrical parameters to a simple equivalent circuit of one phase for the PMG, output performances of the PMG with/without a skewed stator are investigated. Finally, by confirming that all analytical results are validated extensively by nonlinear finite element calculations and measurements, the validity of analysis methods presented in this paper is verified, and the influence stator skew on cogging torque, back-emf, and output performances of the PMG is also clearly described.
Manipulation of the crystal structures and the consequent FMR behaviors in GaAs/Ag/Fe system with an ultrathin Fe seeding layer
Authors: Yu C. C. , Teng Y. H. , Tsai C. S. , Yao Y. D. , Liou Y.
Published: March 2009

The crystal structures, magnetic properties, and the behaviors of ferromagnetic resonance of the GaAs(001)/Fe/Ag/Fe multilayers with different thicknesses of the Fe seeding layer are investigated. For the first time, a transformation from polycrystal into nearly bcc (001) single-crystal structure is observed in the top Fe layer while the thickness of the Fe seeding layer increases. The frequency of ferromagnetic resonance in Fe/Ag/Fe multilayers can be tuned by varying the strength of the external magnetic field and the thickness of the Fe seeding layer. Also it can be well fitted by the resonance equation. The correlation between crystal structures and ferromagnetic resonance manifests itself.
Homogeneous nucleation of nitrogen
Authors: Iland Kristina , Wedekind Jan , Wölk Judith , Strey Reinhard
Published: March 2009

We investigated the homogeneous nucleation of nitrogen in a cryogenic expansion chamber [A. Fladerer and R. Strey, J. Chem. Phys. 124, 164710 (2006)]. Gas mixtures of nitrogen and helium as carrier gas were adiabatically expanded and cooled down from an initial temperature of 83 K until nucleation occurred. This onset was detected by constant angle light scattering at nitrogen vapor pressures of 1.3–14.2 kPa and temperatures of 42–54 K. An analytical fit function well describes the experimental onset pressures with an error of ±15%. We estimate the size of the critical nucleus with the Gibbs–Thomson equation yielding critical sizes of about 50 molecules at the lowest and 70 molecules at the highest temperature. In addition, we estimate the nucleation rate and compare it with nucleation theories. The predictions of classical nucleation theory (CNT) are 9 to 19 orders of magnitude below the experimental results and show a stronger temperature dependence. The Reguera–Reiss theory [Phys. Rev. Lett. 93, 165701 (2004)] predicts the correct temperature dependence at low temperatures and decreases the absolute deviation to 7–13 orders of magnitude. We present an empirical correction function to CNT describing our experimental results. These correction parameters are remarkably close to the ones of argon [Iland et al., J. Chem. Phys. 127, 154506 (2007)] and even those of water [J. Wölk and R. Strey, J. Phys. Chem. B 105, 11683 (2001)].
A MinMax self-consistent-field approach for auxiliary density functional theory
Authors: Köster Andreas M. , del Campo Jorge M. , Janetzko Florian , Zuniga-Gutierrez Bernardo
Published: March 2009

A MinMax self-consistent-field (SCF) approach is derived in the framework of auxiliary density functional theory. It is shown that the SCF convergence can be guided by the fitting coefficients that arise from the variational fitting of the Coulomb potential. An in-core direct inversion of the iterative subspace (DIIS) algorithm is presented. Due to its reduced memory demand this new in-core DIIS method can be applied without overhead to very large systems with tens of thousands of basis and auxiliary functions. Due to the new DIIS error definition systems with fractional occupation numbers can be treated, too.
Pulsed plasma electron sources
Authors: Krasik Ya. E. , Yarmolich D. , Gleizer J. Z. , Vekselman V. , Hadas Y. , Gurovich V. Tz. , Felsteiner J.
Published: March 2009

There is a continuous interest in research of electron sources which can be used for generation of uniform electron beams produced at E≤105 V/cm and duration ≤10−5 s. In this review, several types of plasma electron sources will be considered, namely, passive (metal ceramic, velvet and carbon fiber with and without CsI coating, and multicapillary and multislot cathodes) and active (ferroelectric and hollow anodes) plasma sources. The operation of passive sources is governed by the formation of flashover plasma whose parameters depend on the amplitude and rise time of the accelerating electric field. In the case of ferroelectric and hollow-anode plasma sources the plasma parameters are controlled by the driving pulse and discharge current, respectively. Using different time- and space-resolved electrical, optical, spectroscopical, Thomson scattering and x-ray diagnostics, the parameters of the plasma and generated electron beam were characterized.
Mean field theory of ionic free energy using scaled binding energies
Authors: Bhattacharya Chandrani , Menon S. V. G.
Published: March 2009

A mean field model for ionic free energy is developed using the scaled binding energy formula. The model is evaluated using experimental data on Hugoniot, phase diagrams, melting curves, and other thermodynamic parameters of several solids. Predictions of the model are also compared with the Debye–Gruneisen theory, which is also based on the same binding energy formula. The binding energy formulation employs just four parameters, all corresponding to ambient condition—density, bulk modulus, its pressure derivative, and cohesive energy. These are obtained either from experiments or electronic structure theory. The Debye–Gruneisen theory compares better with available data for the phase diagrams of iron, zirconium, and titanium. However, the Hugoniot and melting curves obtained using both models yield similar results.
Observation of stacking faults formed during homoepitaxial growth of p-type 4H-SiC
Authors: Song Ho Keun , Moon Jeong Hyun , Kim Hyeong Joon , Mehregany Mehran
Published: March 2009

Threading dislocations and their transformation into stacking faults (SFs) are observed in p-type 4H-SiC epitaxial layers by high voltage transmission electron microscope. Homoepitaxial growth and in situ aluminum doping of 4H-SiC epitaxial layers are carried out using the organosilicon precursor bistrimethylsilylmethane (C7H20Si2 and the metal-organic precursor trimethylaluminum (C3H9Al), and the free hole concentration of the most heavily aluminum-doped epitaxial layers is >1021 cm−3. Threading dislocations are formed at the interface between the epitaxial layer and the substrate. However, the density of these threading dislocations decreases toward the epitaxial layer surface with their transformations to SFs.
Topology-based potentials and the study of the competition between protein folding and aggregation
Authors: Prieto Lidia , Rey Antonio
Published: March 2009

Topology-based or Gō-type potentials have been shown to be very useful in the understanding of the relations between the structure of the native state of a protein and some of its folding characteristics. A different question is whether they can also make such a contribution when the aggregation process of misfolded or partially folded structures is under study. In this work, in spite of the obvious trend of these simulation models toward the native state, we show that there are some aspects about aggregation that can be addressed by topology-based potentials: the role of the thermodynamic characteristics of the transition on preventing the aggregation process, or the larger propensity of highly symmetric protein structures to form domain swapped dimers. In a second part of this work, we use the possibilities of computer simulation as a design of numerical experiments to analyze the fundamental role of intermediate states in the aggregation process of globular proteins.
Magnetic and half-metallic properties of MPo (M=Ti, V, Cr, Mn, Fe) compounds
Authors: Kahal L. , Zaoui A. , Ferhat M.
Published: March 2009

In this paper, we present a theoretical study of magnetic properties of MPo (M=Ti, V, Cr, Mn, Fe) compounds in the zinc-blend structure using full-potential linear augmented plane wave method. Our calculation indicates that MnPo and FePo are antiferromagnetic, whereas TiPo, VPo, and CrPo are magnetic. The ferromagnetic phase is enhanced with decreasing lattice constant and increasing atomic number along the sequence TiPo→VPo→CrPo. TiPo, VPo, and CrPo are predicted to be half-metal ferromagnetic with magnetic moments of 2.0μB, 3.0μB, and 4.0μB, respectively, which is confirmed from the calculated minority (majority) spin channel band structure showing the semiconducting (metallic) behavior of these compounds. The magnetism comes essentially from the d orbital of Ti, V, and Cr atoms. In addition, we have found that half-metallicity can be maintained even when spin-orbit interaction is included for TiPo and VPo. However spin-orbit effect destroys magnetism in CrPo.
Defect-related light emission in the 1.4–1.7 μm range from Si layers at room temperature
Authors: Shklyaev A. A. , Nakamura Y. , Dultsev F. N. , Ichikawa M.
Published: March 2009

High density of crystal defects is formed in Si layers during their growth on the nanostructured surface composed of dense arrays of Ge islands grown on oxidized Si substrates. Although these defect-rich Si layers exhibit intense photoluminescence only at low temperatures, the forward-biased diodes with the Si layers located in the region of the p-i-n+ junction can emit light at room temperature. The difference suggests that the influence of thermal emission of carriers from defect states on the light emission intensity is essentially reduced when the spatial distribution of carrier density is governed by the bias voltage and band bending. The results show that Si layers emitting light in the 1.4–1.7 μm range at room temperature can be prepared by means of growth.
Time reversal of continuous-wave, steady-state signals in elastic media
Authors: Anderson Brian E. , Guyer Robert A. , Ulrich Timothy J. , Johnson Paul A.
Published: March 2009

Experimental observations of spatial focusing of continuous-wave, steady-state elastic waves in a reverberant elastic cavity using time reversal are reported here. Spatially localized focusing is achieved when multiple channels are employed, while a single channel does not yield such focusing. The amplitude of the energy at the focal location increases as the square of the number of channels used, while the amplitude elsewhere in the medium increases proportionally with the number of channels used. The observation is important in the context of imaging in solid laboratory samples as well as problems involving continuous-wave signals in Earth.
Carrier mobility in a polar semiconductor measured by an optical pump-probe technique
Authors: Hase Muneaki
Published: March 2009

Ultrafast dephasing of the plasmonlike longitudinal optical phonon-plasmon coupled (LOPC) mode in highly doped n-GaAs has been investigated by using a femtosecond optical pump-probe technique with 40 THz bandwidth as a function of photodoping levels. The direct measurement of plasmon damping with the help of a wavelet analysis enables us to extract carrier (electron) mobility, which decreases with increasing the photodoping levels. It is found that the mobility is suppressed at high photodoping levels due to electron-hole scattering, while it is enhanced near a critical density, being plausibly attributed to the strong coherent coupling of the LO phonon with the plasmon.
Binocular Vision: Defining the Historical Directions
Authors: Ono Hiroshi , Wade Nicholas J , Lillakas Linda
Published: March 2009

Ever since Kepler described the image-forming properties of the eye (400 years ago) there has been a widespread belief, which remains to this day, that an object seen with one eye is always seen where it is. Predictions made by Ptolemy in the first century, Alhazen in the eleventh, and Wells in the eighteenth, and supported by Towne, Hering, and LeConte in the nineteenth century, however, are contrary to this claimed veridicality. We discuss how among eighteenth-and nineteenth-century British researchers, particularly Porterfield, Brewster, and Wheatstone, the erroneous idea continued and also why observations made by Wells were neither understood nor appreciated. Finally, we discuss recent data, obtained with a new method, that further support Wells's predictions and which show that a distinction between headcentric and relative direction tasks is needed to appreciate the predictions.
Francis Joseph's Fatal Mistake: The Consequences of Rejecting Kremsier/Kroměříž
Authors: Reifowitz Ian
Published: March 2009

Since 1918, much historical debate on Austria–Hungary has revolved around the supposed inevitability of its demise. Most historians of recent decades have rejected this inevitability. Nevertheless, one can argue that although Austria–Hungary could have survived well into the twentieth century, there were certainly key factors and decisions that made its dissolution much more likely.
Novel transition complexes of Co(II), Ni(II), Cu(II), and Zn(II) derived from 3-[p-(5-substituted salicylidinehydrazinocarbonyI)]phenylsydnone
Authors: Phaniband Mohammedshafi A. , Dhumwad Shreedhar D. , Jogul Johnson J. , Avaji Prakash Gouda
Published: March 2009

Schiff bases derived from 5-substituted salicylidine 3-[p-(5-substituted salicylidinehydrazinocarbonyl)]phenylsydnones and their transition metal complexes with Co(II), Ni(II), Cu(II), and Zn(II) have been synthesized and characterized by elemental analysis, molar conductance, magnetic susceptibilities, electronic, infrared, Proton Magnetic Resonance (PMR) (1H NMR), Fast Atomic Bombardment-(FAB)-mass spectra, Electron Spin Resonance (ESR), and thermal studies. From the above spectral studies, it is concluded that the ligands viz., 3-[p-(salicylidinehydrazinocarbonyl)]phenylsydnone (L1); p-(vanillidine hydrazinocarbonyl)]phenylsydnone (L2); and 3-[p-(5′chlorosalicylicdinehydrazinecarbonyl)]phenylsydnones (L3) act as bidentate molecules coordinating through azomethine nitrogen and phenolic oxygen. The ligands and their metal complexes have been screened in vitro for antibacterial, antifungal, and antitumor activities. The results indicate that the biological activity has increased on complexation. The Cu(II) complexes of the above-said ligands have proven to be antitumor agents toward the P388/s tumor cells at lower concentrations.
Acid-catalyzed synthesis of zinc imidazolates and related bimetallic metal-organic framework compounds
Authors: Schubert David M. , Visi Mandana Z. , Knobler Carolyn B.
Published: March 2009

A convenient method involving acid catalysis is described for the preparation of zinc imidazolate metal organic framework compounds of the type ZnIm2 (Im = imidazolate,1,3-N2C3H3) and C-substituted derivatives, including 2-Me-, 2-Et- and benzimidazolates. This method also applies to synthesis of analogous copper and cobalt imidazolates, copper–zinc bimetallic imidazolates, (CuaZnbIm2(a+b)), heterometal-doped zinc imidazolates (MxZn(1–x)Im2), and multimetallic imidazolates. An unusual copper(1)-containing crystalline bimetallic imidazolate framework compound Cu2ZnIm4 was prepared in high yield and structurally characterized (P421c, a = b = 10.9623 (3), c = 6.3231 (4) Å, α = β = γ = 90°, V = 759.86 (6) Å3, Z = 2). Crystal structure redeterminations were also made for tetragonal zinc imidazolate framework solid and monomeric zinc diimidazole diacetate.
Prm3p Is a Pheromone-induced Peripheral Nuclear Envelope Protein Required for Yeast Nuclear Fusion
Authors: Shen Shu , Tobery Cynthia E. , Rose Mark D.
Published: March 2009

Nuclear membrane fusion is the last step in the mating pathway of the yeast Saccharomyces cerevisiae. We adapted a bioinformatics approach to identify putative pheromone-induced membrane proteins potentially required for nuclear membrane fusion. One protein, Prm3p, was found to be required for nuclear membrane fusion; disruption of PRM3 caused a strong bilateral defect, in which nuclear congression was completed but fusion did not occur. Prm3p was localized to the nuclear envelope in pheromone-responding cells, with significant colocalization with the spindle pole body in zygotes. A previous report, using a truncated protein, claimed that Prm3p is localized to the inner nuclear envelope. Based on biochemistry, immunoelectron microscopy and live cell microscopy, we find that functional Prm3p is a peripheral membrane protein exposed on the cytoplasmic face of the outer nuclear envelope. In support of this, mutations in a putative nuclear localization sequence had no effect on full-length protein function or localization. In contrast, point mutations and deletions in the highly conserved hydrophobic carboxy-terminal domain disrupted both protein function and localization. Genetic analysis, colocalization, and biochemical experiments indicate that Prm3p interacts directly with Kar5p, suggesting that nuclear membrane fusion is mediated by a protein complex.
6 Politics and Aesthetics
Authors: Rotman Andy
Published: March 2009

Chapter 6 discusses the aesthetics and erotics of prasāda and how these help to explain the compelling power that prasāda exerts, both in objects and in people, and its apparent naturalism. The seemingly automatic and spontaneous nature of prasāda-initiated giving has important implications for a sociology of prasāda and, perhaps, the politics behind it. The chapter also considers the various connections between giving, karmic status, and social status, and the insights this might offer into the prestige economy of Buddhism. Lastly, the chapter considers the stages of faith in the Buddhist path and how the discourse of prasāda may have been a refuge for the dispossessed.
Artefacts and biases affecting the evaluation of scoring functions on decoy sets for protein structure prediction
Authors: Handl Julia , Knowles Joshua , Lovell Simon C.
Published: March 2009

Motivation: Decoy datasets, consisting of a solved protein structure and numerous alternative native-like structures, are in common use for the evaluation of scoring functions in protein structure prediction. Several pitfalls with the use of these datasets have been identified in the literature, as well as useful guidelines for generating more effective decoy datasets. We contribute to this ongoing discussion an empirical assessment of several decoy datasets commonly used in experimental studies.

Results: We find that artefacts and sampling issues in the large majority of these data make it trivial to discriminate the native structure. This underlines that evaluation based on the rank/z-score of the native is a weak test of scoring function performance. Moreover, sampling biases present in the way decoy sets are generated or used can strongly affect other types of evaluation measures such as the correlation between score and root mean squared deviation (RMSD) to the native. We demonstrate how, depending on type of bias and evaluation context, sampling biases may lead to both over- or under-estimation of the quality of scoring terms, functions or methods.

Availability: Links to the software and data used in this study are available at http://dbkgroup.org/handl/decoy_sets.

Contact:  simon.lovell@manchester.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System
Authors: Messina David N. , Sonnhammer Erik L. L.
Published: March 2009

Summary: The rise in biological sequence data has led to a proliferation of separate, specialized databases. While there is great value in having many independent annotations, it is critical that there be a way to integrate them in one combined view. The Distributed Annotation System (DAS) was developed for that very purpose. There are currently no DAS clients that are open source, specialized for aggregating and comparing protein sequence annotation, and that can run as a self-contained application outside of a web browser. The speed, flexibility and extensibility that come with a stand-alone application motivated us to create DASher, an open-source Java DAS client. Given a UniProt sequence identifier, DASher automatically queries DAS-supporting servers worldwide for any information on that sequence and then displays the annotations in an interactive viewer for easy comparison. DASher is a fast, Java-based DAS client optimized for viewing protein sequence annotation and compliant with the latest DAS protocol specification 1.53E.

Availability: DASher is available for direct use and download at http://dasher.sbc.su.se including examples and source code under the GPLv3 licence. Java version 6 or higher is required.

Contact:  erik.sonnhammer@sbc.su.se

Supplementary information:  Supplementary data and all figures in color are available at Bioinformatics online.
Testing different methods of incorporating climate data into the assessment of US West Coast sablefish
Authors: Schirripa Michael J. , Goodyear C. Phillip , Methot Richard M.
Published: March 2009

Schirripa, M. J., Goodyear, C. P., and Methot, R. M. 2009. Testing different methods of incorporating climate data into the assessment of US West Coast sablefish. – ICES Journal of Marine Science, 66: 1605–1613. The objective of this investigation was to evaluate different methods of including environmental variability directly into stock assessments and to demonstrate how this inclusion affects the estimation of recruitment parameters, stock status, and the conservation benchmarks used to manage a stock. Variations on two methods of incorporating environmental effects were tested. The first method (“model” method) utilizes a structural change in the stock–recruitment function to adjust the annual expected number of recruits by a value, either positive or negative, equal to that year's anomaly in the environmental variable. The second method (“data” method) allows for observation error in the environmental data and uses the time-series as an index to tune the vector of estimates of annual recruitment deviations. Simulation techniques were utilized to produce datasets of known quantities that were subsequently analysed with a widely used stock assessment platform. Under the circumstances simulated in this study, neither method could be said to have performed significantly better than the other in all situations. Because the two approaches handle years of missing data differently, the best approach is dictated by the available data, rather than a more appropriate method.
Gene divergence and pathway duplication in the metabolic network of yeast and digital organisms
Authors: Gerlee P. , Lundh T. , Zhang B. , Anderson A. R. A.
Published: March 2009

We have studied the metabolic gene–function network in yeast and digital organisms evolved in the artificial life platform A
vida
. The gene–function network is a bipartite network in which a link exists between a gene and a function (pathway) if that function depends on that gene, and can also be viewed as a decomposition of the more traditional functional gene networks, where two genes are linked if they share any function. We show that the gene–function network exhibits two distinct degree distributions: the gene degree distribution is scale-free while the pathway distribution is exponential. This is true for both yeast and digital organisms, which suggests that this is a general property of evolving systems, and we propose that the scale-free gene degree distribution is due to pathway duplication, i.e. the development of a new pathway where the original function is still retained. Pathway duplication would serve as preferential attachment for the genes, and the experiments with A
vida
revealed precisely this; genes involved in many pathways are more likely to increase their connectivity. Measuring the overlap between different pathways, in terms of the genes that constitute them, showed that pathway duplication also is a likely mechanism in yeast evolution. This analysis sheds new light on the evolution of genes and functionality, and suggests that function duplication could be an important mechanism in evolution.
Chlamydia trachomatis detection in cervical PreservCyt specimens from an Irish urban female population
Authors: Keegan H. , Ryan F. , Malkin A. , Griffin M. , Lambkin H.
Published: March 2009

Objective:  The aim of this study was to determine the prevalence of cervical Chlamydia trachomatis infection by polymerase chain reaction (PCR) in urban women undergoing routine cervical cytological screening and to investigate the relationship with age, cytology, smoking status and concurrent human papillomavirus (HPV) infection.

Methods:  A total of 996 women (age range 16–69 years) attending general practitioners for routine liquid‐based cervical smear screening in the Dublin area were recruited in the study of prevalence of C. trachomatis. Informed consent was obtained and liquid‐based cytology (LBC) specimens were sent for cytological screening. DNA was extracted from residual LBC and tested for C. trachomatis by PCR using the highly sensitive C. trachomatis plasmid (CTP) primers and for HPV infection using the MY09/11 primers directed to the HPV L1 gene in a multiplex format.

Results:  The overall prevalence of C. trachomatis was 5.4%. Prevalence was highest in the <25 years age group (10%). Coinfection with HPV and C. trachomatis occurred in 1% of the screening population. A higher rate of smoking was observed in women positive for C. trachomatis, HPV infections or those with abnormal cervical cytology. Chlamydia trachomatis infection was not associated with abnormal cytology.

Conclusions:  Women (5.4%) presenting for routine cervical screening are infected with C. trachomatis. Opportunistic screening for C. trachomatis from PreservCyt sample taken at the time of cervical cytological screening may be a possible strategy to screen for C. trachomatis in the Irish female population.
Head and neck cancer in the UK: what is expected of cytopathology?
Authors: Kocjan G. , Ramsay A. , Beale T. , O’Flynn P.
Published: March 2009

Objective:  This review highlights the role of cytopathology in cancer management within UK Head and Neck Cancer Networks and informs on the issues raised by recent UK Department of Health documents and other UK professional guidance. UK guidance requires the formal involvement of cytopathologists within multidisciplinary cancer teams, with medical and non‐medical cytopathology staff setting up and running rapid access lump clinics, and support for image‐guided fine needle aspiration cytology (FNAC) services. UK guidance also makes recommendations for training, resources and quality control. This review also highlights the resource gap between best practice evidence‐based guidance for head and neck (HN) cancer services and existing UK provision for cytopathology, as evidenced by lack of availability of experienced staff and adequacy of training and quality control (QC). Finally, it stresses the importance in the UK of the Royal College of Pathologists’ guidance, which defines the need for training, the experience needed for new consultants, the requirements for audit and QC. The implications for the additional resources required for HN cancer cytopathology services are discussed. Recent professional guidance specifying the provision of HN cancer services in the UK includes a cytopathology service for cancer networks, such as rapid access FNAC clinics. Although these clinics already operate in some institutions, there are many institutions where they do not and where the provision of cytopathology services would have to be restructured. This would need the support of local cancer networks and their acceptance of the detailed requirements for cytopathology, including resources, training and QC. The standards are not defined locally, as Strategic Health Authorities and Primary Care Trusts have been instructed by the Department of Health to support, invest and implement them.
Structure and stability in exploited marine fish communities: quantifying critical transitions
Authors: PETRIE BRIAN , FRANK KENNETH T. , SHACKELL NANCY L. , LEGGETT WILLIAM C.
Published: March 2009

Correlations between time series of the abundance of predator and prey fish species in heavily exploited western North Atlantic marine fisheries vary temporally but are generally positive in southern, warmer waters and negative in northern, colder ones. The correlations provide an index of trophic structure and dynamics. We construct a framework to quantify critical thresholds between states in which the predator–prey correlations are positive or negative. We do so by developing a quantitative model of the distribution of the correlations between predator (15 species) and prey (8 species) functional groups based on the annual predator depletion rates and bottom temperatures (or alternatively species richness). The model accounts for 58% of the variance of the correlations with a root mean square error of 0.3. This index of trophic structure indicates that warmer, species‐rich, southern fish populations resist transformation from positive to negative predator–prey correlations at exploitation rates that can be double those in the colder, relatively species‐poor, northern areas. The model can be used to set limits for exploitation rates that preserve the functional relationships between predator–prey groups in emerging fisheries, and to assess the potential for and measures required to achieve recovery of degraded fish communities.
Expression of c‐MET, low‐molecular‐weight cytokeratin, matrix metalloproteinases‐1 and ‐2 in spinal chordoma
Authors: Naka Takahiko , Boltze Carsten , Samii Amir , Samii Madjid , Herold Christian , Ostertag Helmut , Iwamoto Yukihide , Oda Yoshinao , Tsuneyoshi Masazumi , Kuester Doerthe , Roessner Albert
Published: March 2009

Aims:  In skull base chordoma, c‐MET expression has been reported to correlate with younger patient age and favourable prognosis; however, it also contributes to tumour invasiveness, especially in recurrent lesions, suggesting variable roles for c‐MET according to clinical status. The aim of this study was to investigate the significance of c‐MET expression in spinal chordoma, which affects patients who are 10–20 years older than those with skull base chordoma.

Methods and results:  Using immunohistochemical techniques, the expression of c‐MET and its ligand, hepatocyte growth factor (HGF) was investigated in 34 primary spinal chordomas and compared with other clinicopathological parameters. Expression of c‐MET and HGF was observed in 85.3 and 21.7% of lesions, respectively. c‐MET expression correlated with the expression of an epithelial marker, low‐molecular‐weight cytokeratin (CAM5.2). Lesions with higher c‐MET expression showed significantly stronger expression of proteinases, including matrix metalloproteinase (MMP)‐1 and MMP‐2. However, c‐MET expression was not associated with patient age, proliferative ability estimated by MIB‐1 labelling index, or prognosis.

Conclusions:  c‐MET expression was observed in most spinal chordomas and correlated with the expression of CAM5.2, suggesting a relationship to an epithelial phenotype.
Validation of a perceptions of care adjective checklist
Authors: Redshaw Maggie , Martin Colin R.
Published: March 2009

Background  This study describes the psychometric characteristics, validity and reliability of the revised version of the perceptions of care adjective checklist (PCACL‐R) with women who had recently given birth. Data were collected from a national survey of women's experiences of maternity care (n = 2960).

Methods  Internal consistency, predictive validity, convergent validity, discriminant validity and confirmatory factor analyses were applied to the data.

Results  Confirmatory factor analysis revealed an excellent fit to a bi‐dimensional structure entirely consistent with the negative and positive valencing of adjectives in the measure, supporting the use of the instrument as a two subscale tool comprising positive and negative subscales. The PCACL‐R revealed good convergent validity against measures of satisfaction with care and excellent divergent validity characteristics assessed against duration of labour. Discriminant validity was assessed against measures of area‐based maternal deprivation, partner status and type of delivery. These analyses revealed commendable discriminant validity of the PCACL‐R. Internal consistency characteristics of the positive and negative subscales of the PCACL‐R were acceptable. The predictive validity of the PCACL‐R was also found to be excellent.

Conclusion  The PCACL‐R is consequently recommended as a valid, reliable, respondent acceptable and easy to administer instrument to assess women's experiences of their care during labour and childbirth. The measurement characteristics of the PCACL‐R suggest that the tool could be incorporated into both clinical and research contexts with confidence. The checklist terms used are applicable to other phases of maternity care and indeed to a wide range of health care contexts. Exploratory use in with other user groups is recommended.
Knowledge about cervical cancer screening among family physicians: cross‐sectional survey
Authors: Del Refugio Gonzalez‐Losa Maria , Gongora‐Marfil Glendy K. , Puerto‐Solis Marylin
Published: March 2009

Background  Cervical cancer (CC) is an important public health problem worldwide. In Mexico, there has been a National Cervical Cancer Screening Program (NCCSP) since 1974. Mexican Social Security Institute attended Mexican workers and family physicians are responsible of the primary care of patients.

Objective  To evaluate knowledge about the aetiology and prevention of CC among family physicians working in Yucatan, Mexico, at Mexican Social Security Institute.

Methods  A questionnaire was applied to 187 family doctors. Self‐administer questionnaire with 10 item previously used by ours and other researchers, was used for the evaluation. Each correctly answered item was given a point. The maximum grade was 10 and the minimum 0.

Results  The knowledge mean was 6.93 points. Fewer than 50% knew what to do with women who are human papillomavirus (HPV) positive without a precancerous cervical lesion and the appropriate age range for Pap smears. A total of 61.1% identified CC as an important health problem in Mexico; however, 95.1% identified CC as a preventive cause of deaths among Mexican women and recognized that HPV is the main CC aetiological agent, and 90.3% mentioned the Pap smear as the main method of diagnosis of CC.

Conclusion  The family doctors need to have an adequate knowledge of the practical elements of the NCCSP to give an efficient attention to their patients.
Mirror, mirror on the wall: placebo effects that exist only in the eye of the beholder
Authors: Kelley John M. , Boulos Patrick R. , Rubin Peter A.D. , Kaptchuk Ted J.
Published: March 2009

Rationale The extent to which placebo effects can be driven exclusively by subjective impressions of improvement in the absence of any independent corroboration is unclear.

Methods Thirty‐six self‐referred patients were treated with a light therapy device intended to rejuvenate facial skin. At each of eight weekly treatments, participants' facial skin was exposed for 40 seconds to pulses of multispectral LED‐generated light in the range of 588 nm wavelength at 0.1 J cm−2. Outcomes were assessed by participants as well as by the treating doctor and by blinded, expert raters.

Results Patients reported robust and statistically significant improvements in seven facial features at the conclusion of the 8‐week treatment regimen as well as at 1‐month follow‐up (for all comparisons,P ≤ 0.003, mediand = 1.14). In sharp contrast, both the treating doctor and blinded, expert raters were unable to detect any improvement whatsoever (for all comparisons,P > 0.05). Moreover, effect sizes were close to zero and in theoppositedirection from improvement (mediand = −0.06 for doctor ratings; and for observer ratings, there was only a 46% success rate at identifying post‐treatment as compared with pre‐treatment photographs).

Conclusion The robust placebo responses documented in this trial were confined to the subjective impressions of the patients. Neither the treating doctor nor blinded, expert raters could detect any improvement. Thus, patients can perceive improvement in medical interventions in the absence of any independent corroboration that improvement has occurred. This result is used a heuristic to more clearly define the components of the placebo response.
Closing the safety loop: evaluation of the National Patient Safety Agency's guidance regarding wristband identification of hospital inpatients
Authors: Sevdalis Nick , Norris Beverley , Ranger Chris , Bothwell Sue ,   the Wristband Project Team
Published: March 2009

Rationale, aims and objectives  Wristbands are essential for accurate patient identification. Some evidence suggests that missing wristbands is not an infrequent occurrence in acute hospitals. The National Patient Safety Agency (NPSA) has developed guidance on patient identification for hospitals in England and Wales. Here we report an evaluation of the uptake of the guidance.

Method  The evaluation was designed as a ‘pre–post’ intervention survey. Fifty hospitals (response rate 67%) responded to the ‘pre‐guidance’ part and 40 hospitals (response rate 43%) responded to the ‘post‐guidance’ part.

Results  The majority of the hospitals use wristbands to identify inpatients. Fifty‐eight per cent of the hospitals in the ‘pre‐guidance’ survey and 50% of them in the ‘post‐guidance’ survey reported not having a patient identification policy before receiving the guidance. Only one hospital reported not having developed such a policy in the ‘post‐guidance’ survey. Ninety‐eight per cent of the hospitals reported that their policies are consistent with the guidance. Relevant training to staff is provided in about a quarter of the organizations, both before and after the guidance. Problems in implementing the guidance were reported by 23% of the hospitals, and included difficulties with staff or patient attitudes, or with the guidance itself, or difficulty to identify a lead staff member.

Conclusion  Overall, implementation of NPSA guidance regarding inpatient identification was satisfactory. The reported problems should be taken into account, as they likely apply to a range of patient safety interventions. Limitations of evaluating intervention uptake, rather than efficacy, and relying on self‐report are discussed.
Do landscape processes predict phylogeographic patterns in the wood frog?
Authors: LEE‐YAW JULIE A. , DAVIDSON ANDREW , MCRAE BRAD H. , GREEN DAVID M.
Published: March 2009

Understanding factors that influence population connectivity and the spatial distribution of genetic variation is a major goal in molecular ecology. Improvements in the availability of high‐resolution geographic data have made it increasingly possible to quantify the effects of landscape features on dispersal and genetic structure. However, most studies examining such landscape effects have been conducted at very fine (e.g. landscape genetics) or broad (e.g. phylogeography) spatial scales. Thus, the extent to which processes operating at fine spatial scales are linked to patterns at larger scales remains unclear. Here, we test whether factors impacting wood frog dispersal at fine spatial scales are correlated with genetic structure at regional scales. Using recently developed methods borrowed from electrical circuit theory, we generated landscape resistance matrices among wood frog populations in eastern North America based on slope, a wetness index, land cover and absolute barriers to wood frog dispersal. We then determined whether these matrices are correlated with genetic structure based on six microsatellite markers and whether such correlations outperform a landscape‐free model of isolation by resistance. We observed significant genetic structure at regional spatial scales. However, topography and landscape variables associated with the intervening habitat between sites provide little explanation for patterns of genetic structure. Instead, absolute dispersal barriers appear to be the best predictor of regional genetic structure in this species. Our results suggest that landscape variables that influence dispersal, microhabitat selection and population structure at fine spatial scales do not necessarily explain patterns of genetic structure at broader scales.