bluuebunny/crossref_metadata_2025 huggingface dataset:
Magnetic properties of composite Y-type hexagonal ferrites in a direct current magnetic field
Authors: Bai Yang , Zhou Ji , Yue Zhenxing , Gui Zhilun , Li Longtu
Published: September 2005

This study focuses on the structure and magnetic properties of Y-type hexagonal ferrite, especially the tunable permeability controlled by the direct current (dc) magnetic field. The composition of Ba2Zn1.2−xCoxCu0.8Fe12O22 (x varied from 0 to 1.2) is selected, where the changes in the amount of Zn and Co is to tailor the magnetic properties. The dependence of complex permeability (μ) in high frequency on the magnetic field was measured by a precision LCR meter with a bias current source. Magnetic permeability μ′ declined nonlinearly with the strengthening of a dc magnetic field generated by the bias current at a fixed test frequency. The permeability μ′ and its tunability reflect the magnetization process of ferrimagnet. And they both increase with the rise in the amount of Zn due to the decrease of magnetocrystalline anisotropy. Correlation existed between the microstructure, permeability μ′, and its tunability of the Y-type hexagonal ferrites. Increase of the permeability μ and its tunability was also observed as the sintering temperature rose, which was attributed to the increase of average grain size and decrease of porosity. The applied methods of magnetic field may also influence the permeability’s response to the external field. The ferrites’ nonlinear magnetic property provides a possibility for tunable inductive components in a wide frequency range.
Fast subnanometer particle localization by traveling-wave tracking
Authors: Busoni Lorenzo , Dornier Aurélie , Viovy Jean-Louis , Prost Jacques , Cappello Giovanni
Published: September 2005

Traveling-wave tracking (TWT) is a technique for the study of the motion of submicron-sized particles with a very high spatial and temporal resolutions: the particle can be localized with a subnanometer precision at the microsecond time scale. In this technique, a particle is moving through the traveling interference pattern, and measurements of the intensity and phase of the scattered light allow to precisely determine the particles position. In the present paper we describe the experimental setup and its performances. As an example of use of the TWT, we characterize the Brownian motion of a submicron-sized bead in a confined environment.
Sensitivity enhancement in thermoreflectance microscopy of semiconductor devices using suitable probe wavelengths
Authors: de Freitas L. R. , da Silva E. C. , Mansanares A. M. , Tessier G. , Fournier D.
Published: September 2005

In this paper we present an experimental and theoretical study of the thermoreflectance response as a function of the probe wavelength for layered microelectronics structures. The investigated sample consists of a polycrystalline silicon conducting track grown on a SiO2-coated Si substrate. Thermoreflectance measurements were carried out in the wavelength range from 450to750nm with the track biased in modulated regime. An oscillating pattern is observed in the spectral region where the upper layer is transparent. Such oscillations are due to the interference resulting from the multiple reflections at the interfaces. Using a thermo-optical model, we show that the optical constants (n and k) of the materials, which are wavelength dependent, as well as their temperature derivatives (dn∕dT and dk∕dT), strongly influence the thermoreflectance signal. The optical thicknesses of the layers, mainly determined by the real part of the refractive indices, define the period of oscillation. On the other hand, the imaginary part of the refractive indices establishes the cutoff wavelength of the oscillations. Below this cutoff wavelength, the probe light does not penetrate the material and the upper-surface reflectance dominates the signal.
Improving positioning accuracy of piezoelectric actuators by feedforward hysteresis compensation based on a new mathematical model
Authors: Ru Changhai , Sun Lining
Published: September 2005

The hysteresis characteristic of piezoelectric actuators is one of the major deficiencies in a wide variety of precise tracking positioning controls. This article proposes a control method for piezoelectric actuator based on a proportional integral differential (PID) feedback controller with a feedforward compensation. The hysteresis phenomenon of a piezoelectric actuator is described in the feedforward loop by using a new mathematical model. Finally, some tracking control experiments for a desired sinusoidal trajectory are performed according to the proposed control method. The experimental results demonstrate that the positioning precision is noticeably improved by adding the feedforward compensation based on the new hysteresis model. The maximum error in tracking the sinusoidal signal is lowered about one order of magnitude in comparison with a regular PID controller without any feedforward compensation.
Laser-launched flyer plates for shock physics experiments
Authors: Swift Damian C. , Niemczura Johnathan G. , Paisley Dennis L. , Johnson Randall P. , Luo Sheng-Nian , Tierney Thomas E.
Published: September 2005

The TRIDENT laser was used to launch Cu, Ga, and NiTi flyers from poly(methylmethacrylate) (PMMA) substrates, coated with thin (∼micron) layers to absorb the laser energy, confine the plasma, and insulate the flyer. The laser pulse was ∼600ns long, and the flyers were 50 to 250μm thick and 4 mm in diameter. With an energy of 10–20 J, speeds of several hundred meters per second were obtained. Simulations were performed of the flyer launch process, using different models. The simulations reproduced the magnitude of the flyer speed and qualitative variations with drive energy and design parameters, but systematically overpredicted the flyer speed. The most likely explanation is that some of the laser energy was deposited in the transparent substrate, reducing the amount available for acceleration. The deceleration of the flyer was measured on impact with a PMMA window. Given the equation of state and optical properties of PMMA, the deceleration allowed points to be deduced on the principal Hugoniot of Cu. The points deduced were in good agreement with the published equation of state for Cu, suggesting that there was no significant preheating of the flyer or other systematic effects which might reduce the accuracy of equation of state measurements.
Kirkpatrick-Baez type x-ray focusing mirror fabricated by the bent-polishing method
Authors: Takeuchi Akihisa , Suzuki Yoshio , Takano Hidekazu , Terada Yasuko
Published: September 2005

Microfocusing optics with total reflection mirrors has been constructed, and a performance test in the hard x-ray region has been carried out. The material of the mirror is fused quartz, and parabolic surface figures are fabricated by the bent-polishing method. The reflective surface is coated with platinum. By configuring two parabolic mirrors in the Kirkpatrick-Baez optics, a focused beam size of 150nm in the vertical direction ×110nm in the horizontal direction has been achieved at an x-ray energy of 12keV. A focused beam size of smaller than 300nm is obtained within an x-ray energy range of 8–28keV. In a performance test of the scanning microscope, fine periodic structures with a line pitch of 140nm are clearly resolved. Diffraction limit and modulation transfer function of these focusing optics are discussed.
Very high time-of-flight mobility in the columnar phases of a discotic liquid crystal
Authors: Iino Hiroaki , Hanna Jun-ichi , Bushby Richard J. , Movaghar Bijan , Whitaker Benjamin J. , Cook Michael J.
Published: September 2005

1,4,8,11,15,18,22,25-Octaoctylphthalocyanine shows the highest time-of-flight (“long-range”) hole mobility so far reported for the columnar phase of a discotic liquid crystal. Unlike most other high long-range mobility columnar discotics, there is no clear evidence from x-ray diffraction of high order.
Ion mass dependence of the etch yield of SrTiO3 films in reactive plasmas
Authors: Langlois O. , Stafford L. , Margot J. , Chaker M.
Published: September 2005

The influence of the positive ion composition on the ion-assisted chemical etch yield of SrTiO3 films in Ar∕SF6 plasmas is investigated using a parametric approach. The etch yield is found to decrease as the concentration fraction of molecular ions increases. Introducing the concept of effective mass for both ions and SrTiO3, these experimental results are quantitatively explained in the framework of a well-established model originally developed to describe the sputtering of single-atom materials by noble monoatomic ions.
A nuclear degradation pathway controls the abundance of normal mRNAs in
Saccharomyces cerevisiae
Authors: Kuai Letian , Das Biswadip , Sherman Fred
Published: September 2005

We previously demonstrated an increased degradation of mRNAs in mutants of
Saccharomyces cerevisiae
having blocks in nuclear export. The degradation activity, designated DRN (degradation of mRNA in the nucleus), requires Cbc1p, a nuclear cap-binding protein, and Rrp6p, a nuclear exosome component. Microarray procedures were used to determine the half-lives of mRNAs from normal and mutant strains, leading to the tentative identification of hundreds of normal mRNAs that were notably stabilized when either
CBC1
or
RRP6
were deleted. Northern blot analysis of representative mRNAs confirmed the diminished degradation. One representative of this group,
SKS1
mRNA, was also shown by a cytological procedure to be preferentially retained in the nucleus compared with typical mRNAs. We suggest that all normal mRNAs are subjected to degradation by DRN, but the degree of degradation is determined by the degree of nuclear retention. Furthermore, these mRNAs particularly susceptible to DRN were also diminished by overproduction of Cbc1p, demonstrating a regulatory role for
CBC1
. This conclusion was corroborated by finding an inverse relationship of the
CBC1
and
SKS1
mRNA levels in normal strains grown under different conditions.
RSIR: regularized sliced inverse regression for motif discovery
Authors: Zhong Wenxuan , Zeng Peng , Ma Ping , Liu Jun S. , Zhu Yu
Published: September 2005

Motivation: Identification of transcription factor binding motifs (TFBMs) is a crucial first step towards the understanding of regulatory circuitries controlling the expression of genes. In this paper, we propose a novel procedure called regularized sliced inverse regression (RSIR) for identifying TFBMs. RSIR follows a recent trend to combine information contained in both gene expression measurements and genes' promoter sequences. Compared with existing methods, RSIR is efficient in computation, very stable for data with high dimensionality and high collinearity, and improves motif detection sensitivities and specificities by avoiding inappropriate model specification.

Results: We compare RSIR with SIR and stepwise regression based on simulated data and find that RSIR has a lower false positive rate. We also demonstrate an excellent performance of RSIR by applying it to the yeast amino acid starvation data and cell cycle data.

Availability: Matlab programs are available upon request from the authors.

Contact:  jliu@stat.harvard.edu; yuzhu@stat.purdue.edu
Hematopoietic stem cell fate is established by the Notch–Runx pathway
Authors: Burns Caroline Erter , Traver David , Mayhall Elizabeth , Shepard Jennifer L. , Zon Leonard I.
Published: September 2005

Identifying the molecular pathways regulating hematopoietic stem cell (HSC) specification, self-renewal, and expansion remains a fundamental goal of both basic and clinical biology. Here, we analyzed the effects of Notch signaling on HSC number during zebrafish development and adulthood, defining a critical pathway for stem cell specification. The Notch signaling mutant mind bomb displays normal embryonic hematopoiesis but fails to specify adult HSCs. Surprisingly, transient Notch activation during embryogenesis via an inducible transgenic system led to a Runx1-dependent expansion of HSCs in the aorta-gonad-mesonephros (AGM) region. In irradiated adults, Notch activity induced runx1 gene expression and increased multilineage hematopoietic precursor cells approximately threefold in the marrow. This increase was followed by the accelerated recovery of all the mature blood cell lineages. These data define the Notch–Runx pathway as critical for the developmental specification of HSC fate and the subsequent homeostasis of HSC number, thus providing a mechanism for amplifying stem cells in vivo.
Mesodermally expressed Drosophila microRNA-1 is regulated by Twist and is required in muscles during larval growth
Authors: Sokol Nicholas S. , Ambros Victor
Published: September 2005

Although hundreds of evolutionarily conserved microRNAs have been discovered, the functions of most remain unknown. Here, we describe the embryonic spatiotemporal expression profile, transcriptional regulation, and loss-of-function phenotype of Drosophila miR-1 (DmiR-1). DmiR-1 RNA is highly expressed throughout the mesoderm of early embryos and subsequently in somatic, visceral, and pharyngeal muscles, and the dorsal vessel. The expression of DmiR-1 is controlled by the Twist and Mef2 transcription factors. DmiR-1KO mutants, generated using ends-in gene targeting, die as small, immobilized second instar larvae with severely deformed musculature. This lethality is rescued when a DmiR-1 transgene is expressed specifically in the mesoderm and muscle. Strikingly, feeding triggers DmiR-1KO-associated paralysis and death; starved first instar DmiR-1KO larvae are essentially normal. Thus, DmiR-1 is not required for the formation or physiological function of the larval musculature, but is required for the dramatic post-mitotic growth of larval muscle.
Cognitive performance is highly sensitive to prior experience in mice with a learning and memory deficit: Failure leads to more failure
Authors: Hebda-Bauer Elaine K. , Watson Stanley J. , Akil Huda
Published: September 2005

The impact of a previously successful or unsuccessful experience on the
subsequent acquisition of a related task is not well understood. The nature of
past experience may have even greater impact in individuals with learning
deficits, as their cognitive processes can be easily disrupted. Mice with a
targeted disruption of the α and δ isoforms of the cAMP-response
element-binding protein (CREB) gene (CREBαδ--deficient
mice) have a genetic vulnerability to impaired learning and memory that is
highly influenced by experimental conditions. Thus, we studied the impact of
prior successful and unsuccessful experiences on the degree to which
CREBαδ--deficient mice exhibit impaired spatial
learning and memory in the Morris water maze (MWM). In Experiment 1, we
replicated the cognitive deficit of CREBαδ--deficient
mice when given two trials per day with a 1-min intertrial interval (MWM2),
and labeled this experience as a “failure.” We rescued the deficit
using four trials per day with a 3- to 5-min intertrial interval (MWM4) and
labeled this experience a “success.” In Experiment 2, a new, naive
set of wild-type (WT) and CREBαδ--deficient mice were
randomly assigned to one of two sequence protocols to assess the influence of
a success or a failure on subsequent performance. In Group 1, mice were first
exposed to the MWM4 condition, followed by the more difficult MWM2 task. As
expected, CREBαδ--deficient mice performed well in the
MWM4; they also performed well during reversal testing (MWM4R) where the goal
location is changed. With this initial successful learning experience, the
CREBαδ--deficient mice then performed as well as WT
mice in the MWM2, the condition in which they are known to be impaired. In
contrast, CREBαδ--deficient mice in Group 2 had an
unsuccessful experience when first exposed to the MWM2 condition, and then
also showed impairment in the MWM4, the condition in which they would normally
perform well. This deficit was amplified when
CREBαδ--deficient mice were then tested in the reversal
test. Sex differences in learning among
CREBαδ--deficient mice were amplified upon exposure to
an unsuccessful learning experience. These data indicate that, under
conditions of cognitive impairment, past experience can—depending on its
nature—significantly facilitate or hinder future performance.
Protein synthesis underlies post-retrieval memory consolidation to a restricted degree only when updated information is obtained
Authors: Rodriguez-Ortiz Carlos J. , De la Cruz Vanesa , Gutiérrez Ranier , Bermudez-Rattoni Federico
Published: September 2005

Consolidation theory proposes that through the synthesis of new proteins
recently acquired memories are strengthened over time into a stable long-term
memory trace. However, evidence has accumulated suggesting that retrieved
memory is susceptible to disruption, seeming to consolidate again
(reconsolidate) to be retained in long-term storage. Here we show that
intracortical blockade of protein synthesis in the gustatory cortex after
retrieval of taste-recognition memory disrupts previously consolidated memory
to a restricted degree only if the experience is updated. Our results suggest
that retrieved memory can be modified as part of a mechanism for incorporating
updated information into previously consolidated memory.
A study on the role of the dorsal striatum and the nucleus accumbens in allocentric and egocentric spatial memory consolidation
Authors: De Leonibus Elvira , Oliverio Alberto , Mele Andrea
Published: September 2005

There is now accumulating evidence that the striatal complex in its two major components, the dorsal striatum and the nucleus accumbens, contributes to spatial memory. However, the possibility that different striatal subregions might modulate specific aspects of spatial navigation has not been completely elucidated. Therefore, in this study, two different learning procedures were used to determine whether the two striatal components could be distinguished on the basis of their involvement in spatial learning using different frames of reference: allocentric and egocentric. The task used involved the detection of a spatial change in the configuration of four objects placed in an arena, after the mice had had the opportunity to experience the objects in a constant position for three previous sessions. In the first part of the study we investigated whether changes in the place where the animals were introduced into the arena during habituation and testing could induce a preferential use of an egocentric or an allocentric frame of reference. In the second part of the study we performed focal injections of theN-methyl-d-aspartate (NMDA) receptors' antagonist, AP-5, within the two subregions immediately after training. The results indicate that using the two behavioral procedures, the animals rely on an egocentric and an allocentric spatial frame of reference. Furthermore, they demonstrate that AP-5 (37.5, 75, and 150 ng/side) injections into the dorsal striatum selectively impaired consolidation of spatial information in the egocentric but not in the allocentric procedure. Intra-accumbens AP-5 administration, instead, impaired animals trained using both procedures.
Spin-echo small-angle neutron scattering for dense systems of spheres
Authors: Kruglov Timofey
Published: September 2005

This paper presents (spin-echo) SANS correlation functions describing small-angle scattering on dense systems of spherical particles. (Spin-echo) small-angle correlation functions and associated correlation lengths for a single sphere, a dumbbell, excluded volume and structure are introduced. It is shown that the correlation length is proportional to the cumulative scattering probability. This approach is applied to a hard-sphere liquid.
Phase relations and equation of state of ZrO2to 100 GPa
Authors: Ohtaka Osamu , Andrault Denis , Bouvier Pierre , Schultz Emmanuelle , Mezouar Mohamed
Published: September 2005

The phase relations and equation of state of ZrO2were investigated up to 100 GPa by means ofin situobservation using laser heating in a diamond anvil cell and synchrotron radiation. A cotunnite (PbCl2)-type phase, which appears above 12.5 GPa, is stable to a pressure of 100 GPa and a temperature of 2500 K. No post-cotunnite phase was observed under the present experimental conditions. The unit-cell parameters and the volumes of the cotunnite-type ZrO2were determined as a function of pressure at room temperature using a laser-annealing technique. The cotunnite-type ZrO2shows rather isotropic compression. The bulk modulus calculated using the Birch–Murnaghan equations of state is 278 GPa, which suggests that high-density ZrO2is a candidate for potentially very hard materials.In situhigh-temperature experiments performed below 12.5 GPa revealed that a tetragonal fluorite (CaF2)-type phase is stable up to 3000 K, although a cubic fluorite-type phase has been assumed to exist in this high-temperature regime. The result suggests the possibility that stoichiometric ZrO2does not show the cubic structure up to the melting temperature.
Accurate charge density data collection in under a day with a home X-ray source
Authors: Zhurov Vladimir V. , Zhurova Elizabeth A. , Chen Yu-Sheng , Pinkerton A. Alan
Published: September 2005

Accurate charge density data for pentaerythritol were measured at 15 K in the laboratory in under a day using a Rigaku R-Axis Rapid high-power rotating-anode diffractometer with a curved image-plate detector, and open-flow liquid-helium cryostat. The experimental procedure and data treatment are briefly described, and data quality evaluated based on a number of criteria.
Rapid preparation of custom grid screens for crystal growth optimization
Authors: Senger Anne B. , Mueser Timothy C.
Published: September 2005

Initial crystallization conditions are typically discovered using commercially available sparse-matrix screens. Positive results are then refined using some type of expansion tray. For example, coarse and shallow gradients can be prepared which vary single chemical parameters around the initial conditions in a grid-screen format. Expansion trays are customarily formulated using numerous volume calculations and pipetting stock solutions into individual wells. This tedious process is plagued by pipetting errors, including differences in viscosity, small volumes with large dilutions, evaporation and poor mixing. Here we present a simple method to standardize expansion-tray formats. Instead of using independent well-volume calculations, the initial and final conditions are formulated and gradients (A/B gradients) are prepared using standardized pipetting maps. These step gradients can be prepared by adding decreasing amounts of the initial (A) solution to consecutive wells followed by the addition of the final (B) solution with increasing volume. This simple idea can be applied to both coarse and shallow grids where the pipetting errors are confined within the boundaries defined by the A and B solutions. Programmable electronic pipettes and robotic liquid handlers can be used to prepare the standardized A/B gradients rapidly, regardless of the components, eliminating reprogramming between trays.
Structural changes in titanium dioxide nanocrystals during plastic deformation
Authors: Gesenhues Ulrich
Published: September 2005

The polygonization of 200 nm rutile crystals during dry ball-milling at 10gwas monitored in detail by means of transmission electron microscopy (TEM) and X-ray diffraction (XRD). The TEM results showed how to modify the Williamson–Hall method for a successful evaluation of crystal size and microstrain from XRD profiles. Macrostrain development was determined from the minute shift of the most intense reflection. In addition, changes in pycnometrical density were monitored. Accordingly, the primary crystal is disintegrated during milling into a mosaic of 12–35 nm pieces where the grain boundaries induce up to 1.2% microstrain in a lower layer of 6 nm thickness. Macrostrain in the interior of the crystals rises to 0.03%. The pycnometrical density, reflecting the packing density of atoms in the grain boundary, decreases steadily by 1.1%. The results bear relevance to our understanding of plastic flow and the mechanism of phase transitions of metal oxides during high-energy milling.
A compact furnace for synchrotron powder diffraction measurements up to 1807 K
Authors: Yashima Masatomo , Tanaka Masahiko , Oh-uchi Kenjiro , Ida Takashi
Published: September 2005

A compact furnace has been designed and fabricated for measurements of high-resolution synchrotron radiation powder diffraction profiles from materials at high temperatures up to 1807 K in air, suitable for the multiple-detector system installed at the BL-4B2experimental station of the Photon Factory in Tsukuba, Japan. The whole powder pattern of the material at a high temperature can be scanned at a step interval of 0.004° in 2θ, with a counting time of 1.5 s step−1, in just 7 h.
Connection of segmented intensity data measured with a multiple-detector system for powder diffractometry
Authors: Ida T.
Published: September 2005

A Fourier method to connect segmented intensity data measured with a multiple-detector system (MDS) for powder diffractometry has been developed. Differences in sensitivity, slight shifts in peak positions and asymmetric instrumental broadening for different detectors are simultaneously adjusted by a Fourier-based deconvolution/convolution method. The Fourier transform of the adjustment function is evaluated as the ratio of the Fourier transforms of the intensity data sets in the overlapped region measured with the adjacent detectors. Even and odd polynomial functions with maximum order of 10 are separately fitted to the real and imaginary parts of the experimentally evaluated Fourier-transformed adjustment by a least-squares method applying an appropriate weighting for the Fourier-transformed data. The complex of the optimized polynomials is used to adjust the data measured with a detector in order to connect them with the data measured with an adjacent detector. The method is applied to connect the powder diffraction data of ZnO powder measured with the MDS on beamline BL4B2at the Photon Factory in Tsukuba. Slight differences in line width, asymmetry and sharpness detected in the observed diffraction peak profiles measured with the different detectors have successfully been removed by the Fourier-based adjustment procedures.
Rietveld refinement of LaB6: data from µXRD
Authors: Ning Guangrong , Flemming Roberta L.
Published: September 2005

The Rietveld method of crystal structure refinement was an important breakthrough, allowing crystal structural information to be obtained from powder diffraction data. One remaining challenge is to collect Rietveld-quality data for polycrystalline mineralsin situ, using laboratory-based micro X-ray diffraction (µXRD) techniques. Here a new data collection method is presented, called `multiframes', which produces high-quality data, suitable for Rietveld refinement, using the Bruker D8 DISCOVER micro X-ray diffractometer. 91 frames of two-dimensional X-ray diffraction data were collected for powdered NIST SRM 660 LaB6standard material, using a general area-detector diffraction system (GADDS), at intervals of 0.8° 2θ. For each frame, only the central 1° 2θ was integrated and merged to produce a diffraction profile from 17 to 90° 2θ. Rietveld refinement of this data usingTOPAS2gave a unit-cell parameter (ao) and atomic position of boron (x) for LaB6of 4.1549 (1) Å and 0.1991 (9), respectively (Rwp= 4.26,RBragg= 3.21). The corresponding La—B bond length was calculated to be 3.0522 Å. These parameters are in good agreement with the literature values for LaB6. These encouraging results suggest that Rietveld-quality micro X-ray diffraction data can be collected from the Bruker D8 DISCOVER diffractometer, provided that the GADDS detector is stepped in small increments, for each frame only the central 1° 2θ is integrated at constant arc length, and counting time is sufficient to yield adequate intensity (∼10 000 counts).
Structure of nanocrystalline MgFe2O4from X-ray diffraction, Rietveld and atomic pair distribution function analysis
Authors: Gateshki Milen , Petkov Valeri , Pradhan Swapan K. , Vogt Tom
Published: September 2005

The three-dimensional structure of nanocrystalline magnesium ferrite, MgFe2O4, prepared by ball milling, has been determined using synchrotron radiation powder diffraction and employing both Rietveld and atomic pair distribution function (PDF) analysis. The nanocrystalline ferrite exhibits a very limited structural coherence length and a high degree of structural disorder. Nevertheless, the nanoferrite possesses a very well defined local atomic ordering that may be described in terms of a spinel-type structure with Mg2+and Fe3+ions almost randomly distributed over its tetrahedral and octahedral sites. The new structural information helps explain the material's unusual magnetic properties.
Numerical conversion between the Pearson VII and pseudo-Voigt functions
Authors: Wang Hejing , Zhou Jian
Published: September 2005

The shape coefficient of a curve, which is defined as the ratio of its full width at half-maximum intensity to integral width, is a measure of variation in shape. From the definitions of the pseudo-Voigt, Pearson VII and Voigt functions used in X-ray diffractometry, three shape-converting formulae are deduced. Numerical solution helps to establish a numerical model for interconverting the shapes of the pseudo-Voigt, Pearson VII and Voigt functions. Assessment of the error level and some comments on the shape of the pseudo-Voigt and Pearson VII functions are thereby made.
High-order analytic translation matrix elements for real-space six-dimensional polar Fourier correlations
Authors: Ritchie David W.
Published: September 2005

Analytic expressions are presented for calculating translations of high-order three-dimensional expansions of orthonormal real spherical harmonic and Gaussian-type or exponential-type radial basis functions. When used with real spherical harmonic rotation matrices, the resulting translation matrices provide a fully analytic method of calculating six-dimensional real-space rotational–translational correlations. The correlation algorithm is demonstrated by using an exhaustive search to superpose the steric density functions of a pair of similar globular proteins in a matter of seconds on a contemporary personal computer. It is proposed that the techniques described could be used to accelerate the calculation ofe.g.real-space electron density correlations in molecular replacement, docking proteins into electron microscopy density maps, and searching the Protein Data Bank for structural homologues.
Muscle hypertrophy induced by the Ski protein: cyto‐architecture and ultrastructure
Authors: Bruusgaard J. C. , Brack A. S. , Hughes S. M. , Gundersen K.
Published: September 2005

Aim:  Transgenic mice overexpressing the c‐ski proto‐oncogene driven by the MSV promoter undergo muscle hypertrophy, most notably fast fibres of the lower limb. This hypertrophy is not accompanied by a correspondingly large increase in force, and individual skinned muscle fibres exhibit a 30% reduction in force per cross‐sectional area. In this respect, the MSV ski model is different from most other hypertrophy models and we here aim at describing the mechanisms for the reduced specific force.

Methods:  Cyoarchitecture and ultrastructure of muscle fibres from the fast extensor digitorum longus muscle of 2–3 months old MSV ski mice was studied. In addition to electron microscopy, we used in vivo intracellular injections of myonuclear dye to investigate nuclear number.

Results:  The number of nuclei did not increase in proportion to size, and consequently nuclear domains were increased compared with wild type. The fraction of the cytoplasm occupied by contractile material was reduced by 18%. In addition we observed poor intracellular alignment of Z‐discs. Such staggering has been reported to reduce force in desmin deficient mice, but the amount and distribution of desmin in the MSV ski mice seemed normal. The mitochondria of MSV ski mice showed irregularly spaced cristae that were frequently disrupted.

Conclusion:  The reduction in specific force observed in MSV ski mice could be explained by a reduced fraction of contractile material and reduced transversal mechanical coupling. The ultrastructural abnormalities could be related to an increase in nuclear domains.
Low sodium intake induces an increase in renal monoamine oxidase activity in the rat. Involvement of an angiotensin II dependent mechanism
Authors: De Luca Sarobe V. , Nowicki S. , Carranza A. , Levin G. , Barontini M. , Arrizurieta E. , Ibarra F. R.
Published: September 2005

Aims:  The interplay between natriuretic dopamine and antinatriuretic angiotensin II represents an important mechanism for the regulation of renal sodium and water excretion. Monoamine oxidase is the main metabolizing pathway for dopamine in the renal cortex. In this study, we have analysed the effect of low sodium feeding and AT1 receptor blockade on renal dopamine metabolism by monoamine oxidase.

Methods:  Four groups of rats were studied: 1, normal salt diet (NS); 2, low salt diet (LS); 3, NS receiving Losartan (Los, specific AT1 receptor antagonist, 20 mg kg−1 bwt day−1, NS + Los); 4, LS receiving Los (LS + Los).

Results:  Urinary dopamine excretion was lower in LS than in NS rats (543 ± 32 vs. 680 ± 34 ng day−1 100 g−1 bwt, P < 0.05). When treated with Los, DOPAC excretion and urinary DOPAC/dopamine ratio fell significantly in the LS + Los group as compared with the LS group (1199 ± 328 vs. 3081 ± 681 ng day−1 100 g−1 bwt and 1.90 ± 0.5 vs. 5.7 ± 1.2, respectively, both P < 0.02). Losartan increased hydroelectrolyte excretion in the LS group. No changes were found in the NS + Los group. Aromatic l‐amino acid decarboxylase activity in cortex was similar in NS and LS rats. Instead, monoamine oxidase activity was higher in cortical homogenates from LS rats (in nmol mg tissue−1 h−1: NS 7.66 ± 0.52; LS 9.82 ± 0.59, P < 0.05) and this difference was abolished in LS + Los rats (7.34 ± 0.49 nmol mg tissue−1 h−1, P < 0.01, vs. LS).

Conclusions:  We have concluded that low levels of dopamine in the urine of LS rats are because of an increase in the activity of renal monoamine oxidase and that angiotensin II mediates this increase through stimulation of AT1 receptors.
Countercurrent compartmental models describe hind limb skeletal muscle helium kinetics at resting and low blood flows in sheep
Authors: Doolette D. J. , Upton R. N. , Grant C.
Published: September 2005

Aims:  This study evaluated the relative importance of perfusion and diffusion mechanisms in compartmental models of blood : tissue helium exchange in a predominantly skeletal muscle tissue bed in the sheep hind limb. Helium has different physiochemical properties from previously studied gases and is a common diluent gas in underwater diving where decompression schedules are based on theoretical models of inert gas kinetics.

Methods:  Helium kinetics across skeletal muscle were determined during and after 20 min of helium inhalation, at separate resting and low steady‐states of femoral vein blood flow in six sheep under isoflurane anaesthesia. Helium concentrations in arterial and femoral vein blood were determined using gas chromatographic analysis and femoral vein blood flow was monitored continuously. Parameters and model selection criteria of various perfusion‐limited or perfusion‐diffusion compartmental models of skeletal muscle were estimated by simultaneous fitting of the models to the femoral vein helium concentrations for both blood flow states.

Results:  A model comprising two parallel perfusion‐limited compartment models fitted the data well but required a 51‐fold difference in relative compartment perfusion that did not seem physiologically plausible. Models that allowed a countercurrent diffusion exchange of helium between arterial and venous vessels outside of the tissue compartments provided better overall fit of the data and credible parameter estimates.

Conclusions:  These results suggest a role of arterial–venous diffusion in blood : tissue helium equilibration in skeletal muscle.
Accuracy of central venous pressure monitoring during simultaneous continuous infusion through the same catheter
Authors: Ho A. M.‐H. , Dion P. W. , Karmakar M. K. , Jenkins C. R.
Published: September 2005

Continuous central pressure monitoring and simultaneous continuous infusion via the same central venous catheter are sometimes necessary. Based on theoretical calculations and experimental measurements, we have determined that pressure monitoring is essentially unaffected if the continuous infusion rate is 50 ml.h−1 or less for an adult and a paediatric central catheter. At rates > 200 ml.h−1, the central venous pressure is exaggerated by up to 4 mmHg and 8 mmHg for the adult and paediatric catheters, respectively.
A serious case of failed extubation: difficulty removing a laser resistant tracheal tube in a 7‐year‐old child
Authors: Batas D. , Park C. , Hermon‐Taylor A. C.
Published: September 2005

A 7‐year‐old girl underwent laser ablation of tonsillar remnants. Following the procedure, which was surgically uncomplicated, the laser resistant tracheal tube used could not be removed; it was firmly lodged in the larynx, immediately below the glottic opening. This case highlights the importance of careful selection of laser resistant tracheal tubes for use in paediatric patients and challenges traditional concepts of paediatric upper airway anatomy.
Evaluation of femoral nerve blockade following inguinal paravascular block of Winnie: are there still lessons to be learnt?
Authors: Jochum D. , O'Neill T. , Jabbour H. , Diarra P. D. , Cuignet‐Pourel E. , Bouaziz H.
Published: September 2005

Lower limb peripheral nerve blocks are used to provide surgical anaesthesia or postoperative analgesia. Anatomical texts imply that femoral and saphenous nerve blocks be evaluated by sensory testing of the skin overlying the anterior aspect of the thigh, and the medial aspect of the foot, respectively. We have mapped the distribution of anaesthesia in 25 adults following femoral nerve blockade, performed using the inguinal paravascular technique of Winnie. There was substantial interindividual variation in the area of anaesthesia. Only the skin overlying the middle third of the medial thigh was consistently blocked in 100% of patients. The distribution of anaesthesia conformed to anatomical text descriptions in 24% of cases. We conclude that demonstration of complete quadriceps paralysis confirms femoral nerve blockade. Failing that, sensory evaluation of a femoral nerve block should involve testing the skin of the middle third of the medial aspect of the thigh. The skin overlying the anteromedial aspect of the middle third of the leg should be evaluated for saphenous nerve block.
Molecular evidence for hybridization of species in the genusGallusexcept forGallus varius
Authors: Nishibori M. , Shimogiri T. , Hayashi T. , Yasue H.
Published: September 2005

A phylogenetic tree for fowl including chicken in the genusGallusand based on mitochondrial D‐loop analysis further supports the hypothesis developed from morphology and progeny production that red junglefowl (RJF) is the direct ancestor of the chicken. The phylogenetic positions of the chicken and the other fowl species in the genusGallusare of great importance when considering maintenance and improvement of chicken breeds through introgression of genetic variation from wild‐type genomes. However, because the phylogenetic analysis based on the DNA sequences is not sufficient to conclude the phylogenetic positions of the fowls in the genus, in the present study, we have determined sequences of whole mitochondrial DNA (mtDNA) and two segments of the nuclear genome (intron 9 ofornithine carbamoyltransferase, and four chicken repeat 1 elements) for the species in the genusGallus. The phylogenetic analyses based on mtDNA sequences revealed that two grey junglefowls (GyJF) were clustered in a clade with RJFs and chicken, and that one GyJF was located in a remote position close to Ceylon junglefowl (CJF). The analyses based on the nuclear sequences revealed that alleles of GyJFs were alternatively clustered with those of CJF and with those of RJFs and chicken. Alternative clustering of RJF and chicken alleles were also observed. These findings taken together strongly indicate that inter‐species hybridizations have occurred between GyJF and RJF/chicken and between GyJF and CJF.
A genome scan with AFLPTM markers to detect fearfulness‐related QTLs in Japanese quail
Authors: Beaumont C. , Roussot O. , Feve K. , Vignoles F. , Leroux S. , Pitel F. , Faure J. M. , Mills A. D. , Guémené D. , Sellier N. , Mignon‐Grasteau S. , Le Roy P. , Vignal A.
Published: September 2005

A quantitative trait loci (QTL) study was undertaken to identify genome regions involved in the control of fearfulness in Japanese quail (Coturnix japonica). An F2 cross was made between two quail lines divergently selected over 29 generations on duration of tonic immobility (DTI), a catatonic‐like state of reduced responsiveness to a stressful stimulation. A total of 1065 animals were measured for the logarithm of DTI (LOGTI), the number of inductions (NI) necessary to induce the immobility reaction, open‐field behaviour including locomotor activity (MOVE), latency before first movement (LAT), number of jumps (JUMP), dejections (DEJ) and shouts (SHOUT), corticosterone level after a contention stress (LOGCORT) and body weight at 2 weeks of age (BW2). A total of 310 animals were included in a genome scan using selective genotyping with 248 AFLP markers. A total of 21 suggestive or genome‐wide significant QTL were observed. Two highly significant QTL were identified on linkage group 1 (GL1), one for LOGTI and one for NI. In the vicinity of the QTL for LOGTI, a nearly significant QTL for SHOUT and a suggestive QTL for LAT were also identified. On GL3, genome‐wide significant QTL were observed for JUMP and DEJ as well as suggestive QTL for LOGTI, MOVE, SHOUT and LAT. A significant QTL for BW2 was observed on GL2 and a nearly significant one on GL1. These results may be useful in the understanding of fearfulness in quail and related species provided that fearfulness has the same genetic basis.
Cloning and mapping of the porcine cytochrome‐p450 2E1 gene and its association with skatole levels in the domestic pig
Authors: Skinner T. M. , Doran E. , McGivan J. D. , Haley C. S. , Archibald A. L.
Published: September 2005

The porcine cytochrome‐p450 2E1 (CYP2E1) gene was isolated by screening a pig BAC library and partially sequenced. This sequence information was used to identify six single nucleotide polymorphisms (SNPs) within the CYP2E1 gene and its promoter. In addition, a microsatellite marker tightly linked to the CYP2E1 gene was subcloned from the BAC. One of these markers was used to map the CYP2E1 gene distal of SWC27 on SSC14, well outside reported quantitative trait loci on SSC14 for skatole, indole and taste test measures of boar taint. However, in a population of commercial pigs scored for backfat skatole levels, there was evidence of association between a SNP in the CYP2E1 promoter and skatole deposition, although there was no significant association between this SNP and skatole levels in the experimental cross.
No correlation between BRAFV600E mutation and clinicopathological features of papillary thyroid carcinomas in Taiwan
Authors: Liu Rue‐Tsuan , Chen Yi‐Ju , Chou Fong‐Fu , Li Chun‐Liang , Wu Wei‐Li , Tsai Po‐Chin , Huang Chao‐Cheng , Cheng Jiin‐Tsuey
Published: September 2005

Objective  Genetic alterations in four oncogenes, namely RAS point mutations, RET rearrangements (RET/PTC), NTRK1 rearrangements (TRK) and BRAF point mutations have been identified in human papillary thyroid carcinomas (PTCs). These oncogenes act along the RET/PTC(TRK)–RAS–BRAF–MEK–MAPK kinase pathway, mediating a number of cellular fates including growth, proliferation and survival in thyroid cells. In this study, we analysed mutations of BRAF in a cohort of PTCs.

Methods  To screen for BRAF mutations, the genomic DNA of 105 PTCs were amplified by polymerase chain reaction (PCR) with primers flanking exon 15 and PCR products were directly sequenced with an automatic sequencer. These results, together with data from our previous studies on RAS, RET rearrangements and NTRK1 rearrangements in the same tumours, were compared to determine their individual significance in the pathogenesis of PTCs in Taiwan.

Results  BRAF mutations were detected in 49 of 105 (47%) tumour samples. All mutations involved a thymine‐to‐adenine transversion at nucleotide 1799 and were heterozygous. There was no overlap between papillary carcinomas harbouring RET rearrangements, NTRK1 rearrangements and BRAF mutations. In this cohort, correlation between BRAF mutations and various clinicopathological parameters in 101 papillary carcinomas did not reveal any association with age at diagnosis, sex, tumour size, histological variants of PTC, multicentricity, cervical lymph node metastases, extrathyroidal invasion, distant metastases and clinical stage.

Conclusions  BRAFV600E mutation is the most prevalent oncogene in PTCs in Taiwan. Our data did not suggest that BRAFV600E mutation could be a potentially useful marker of prognosis in patients with papillary carcinomas in the population studied.
A method for the blind correction of the effects of attenuation and shading in light micrographs based upon moderated histogram equalization
Authors: ENTWISTLE A.
Published: September 2005

A means of correcting for the effects of attenuation and shading in multi‐dimensional, digital, light micrographs, blindly, i.e. without the need for additional control sets of image data that record these effects, is described. The method, termed trans‐elemental moderated histogram equalization (TEMHE), works with all three types of image that are collected in light microscopy: bright objects viewed against a dark background, bright and dark objects set against a grey background and darker objects set against a light background. In its most simple form TEMHE requires that the features of interest are distributed widely and evenly throughout the image data. If, however, the pattern of attenuation or shading is extracted, smoothed and the result used to correct the original set of image data, then the only restriction is that when different classes of feature are present the boundaries between them are not approximately parallel to the axes of one, or more, of the dimensions to be corrected. Moreover, when it is possible to formulate a simple model of the pattern of attenuation or shading this is no longer a constraint. The method does need to analyse a large number of elements of image data (pixels, voxels, etc.) to function correctly but it will correct shading in single frames of image data providing that they are quite large and the overall signal‐to‐noise ratio is relatively high.