bluuebunny/crossref_metadata_2025 huggingface dataset:
The oceanic tides in the South Atlantic Ocean
Authors: Genco M. L. , Lyard F. , Le Provost C.
Published: April 2005

Abstract. The finite element ocean tide model of Le Provost and Vincent (1986) has been applied to the simulation of the M2 and K1 components over the South Atlantic Ocean. The discretisation of the domain, of the order of 200 km over the deep ocean, is refined down to 15 km along the coasts, such refinement enables wave propagation and damping over the continental shelves to be correctly solved. The marine boundary conditions, from Dakar to Natal, through the Drake passage and from South Africa to Antarctica, are deduced from in situ data and from Schwiderski's solution and then optimised following a procedure previously developed by the authors. The solutions presented are in very good agreement with in situ data: the root mean square deviations from a standard subset of 13 pelagic stations are 1.4 cm for M2 and 0.45 cm for K1, which is significantly better overall than solutions published to date in the literature. Zooms of the M2 solution are presented for the Falkland Archipelago, the Weddell Sea and the Patagonian Shelf. The first zoom allows detailing of the tidal structure around the Falklands and its interpretation in terms of a stationary trapped Kelvin wave system. The second zoom, over the Weddell Sea, reveals for the first time what must be the tidal signal under the permanent ice shelf and gives a solution over that sea which is generally in agreement with observations. The third zoom is over the complex Patagonian Shelf. This zoom illustrates the ability of the model to simulate the tides, even over this area, with a surprising level of realism, following purely hydrodynamic modelling procedures, within a global ocean tide model. Maps of maximum associated tidal currents are also given, as a first illustration of a by-product of these simulations.
A numerical study of contrail development
Authors: Boin M. , Levkov L.
Published: April 2005

Abstract. In this study, the formation of a contrail from an aircraft flying near the tropopause is simulated using a three-dimensional mesoscale atmospheric model including a very complex scheme of parameterized cloud microphysical processes. Two different primary ice nucleation parameterizations for deposition nucleation, condensation freezing, and contact freezing are applied. The model-predicted ice concentrations are compared to data measured during the International Cirrus Experiment (ICE), 1989.
SABRE observations of structured ionospheric flows during substorm expansion phase onset
Authors: Bradshaw E. G. , Lester M. , Jones T. B.
Published: April 2005

Abstract. The irregularity velocity patterns observed by the SABRE coherent radar at substorm expansion phase onset, which is identified by magnetometer observations of Pi2 pulsations, are occasionally highly structured. In all the examples of structured velocity patterns examined, the SABRE viewing area is located at longitudes within the inferred substorm current wedge. Three types of structured velocity regime are apparent depending on the level of magnetic activity and the position of the radar viewing area relative to the substorm enhanced currents and the Pi2 pulsation generation region. Firstly, vortex-like velocity patterns are observed and these may be caused by the field-aligned currents associated with the substorm current wedge. Secondly, regions of equatorward velocity are also observed at times of substorm expansion phase onset moving longitudinally across the SABRE viewing area. The longitudinal movement is usually westward although an example of eastward motion has been observed. The phase velocity of these regions of equatorward flow is typically 1-3 km s-1. The observed equatorward velocities occur at the poleward edge or poleward of the background convection velocities observed by SABRE. These equatorward velocities may be related to the westward travelling surge and to the expansion (eastwards as well as westwards) of the brightening arc region at substorm onset. Thirdly, the flow rotates equatorward within the field of view but does not then appear to move longitudinally. These equatorward velocities may relate to the earthward surge of plasma from the magnetotail at substorm onset.
Mean thermospheric winds observed from Halley, Antarctica
Authors: Crickmore R. I.
Published: April 2005

Abstract. Thermospheric winds on a total of 237 nights have been studied for the effects due to geomagnetic activity, solar flux, and season. The observations have been made from 1988 to 1992 by a Fabry-Perot interferometer (FPI) operating at Halley (75.5°S, 26.6°W), Antarctica. This is the first statistical study of thermospheric winds near the southern auroral zone. The main factor affecting the wind velocities is the geomagnetic activity. Increases in activity cause an increase in the maximum equatorward wind, and cause the zonal wind in the evening to become more westward. Smaller changes in the mean wind occur with variations in season and solar flux. The small variation with solar flux is more akin to the situation found at mid-latitudes than at high latitudes. Since the geomagnetic latitude of Halley is only 61°, it suggests that the variability of the wind with solar flux may depend more on geomagnetic than geographic latitude. These observations are in good agreement with the empirical Horizontal Wind Model (HWM90). However, comparisons with predictions of the Vector Spherical Harmonic Model (VSH) show that for low geomagnetic activity the predicted phases of the two components of the wind closely resemble the observations but the modelled amplitudes are too small by a factor of two. At high geomagnetic activity the major differences are that modelled zonal velocity is too westward in the evening and too eastward after 04 UT. The modelled ion densities at the F-region peak are a factor of up to 9 too large, whilst the predicted mean value and diurnal variation of the altitude of the peak are significantly lower than those observed. It is suggested that these differences result from the ion loss rate being too low, and an inaccurate model of the magnetic field.
Note on the dependence of Pc3-4 activity on the solar wind velocity
Authors: Guglielmi A. V. , Potapov A. S.
Published: April 2005

Abstract. Various models that describe the dependence of pulsation amplitude A on the solar wind velocity V are discussed. Phenomenological considerations and experimental data count in favour of a model of the form A/A0=(V/V0) exp (-V0/V). The linear model A=a+bV which is common in the literature gives negative values of amplitude as V->0, which is strange from the physical point of view. The possibility of modifying the linear model by including critical phenomena is discussed.
Movement disorders: Classifications
Authors: Klein C.
Published: April 2005

Movement disorders (ataxia, dystonic disorders, gait disorders, Huntington disease, myoclonus, parkinsonism, spasticity, tardive dyskinesia, tics and tremor) are clinically, pathologically and genetically heterogeneous and are characterized by impairment of the planning, control or execution of movement. Current classifications of these disorders have inherent shortcomings due to the complex nature of movement disorders and the lack of diagnostic tests for the majority. Undiscriminating terminology, as well as the clinical, pathological and genetic heterogeneity, further complicate the development of comprehensive categorizations. Modern classification schemes tend to focus on clinical, pathological or genetic/molecular criteria, but more recent attempts have been made to integrate across these levels. From a historical perspective, two ‘golden ages’ have shaped the current and evolving classification schemes: (1) the definition of clinical pathological entities in the early twentieth century and (2) the application of molecular neurogenetics in the past 10–15 years. However, the classification of movement disorders on clinical grounds (according to age at onset, distribution of symptoms, disease course, provoking factors and therapeutic response) remains one of the most useful modes of categorization. Postmortem criteria have been employed to distinguish between degenerative and nondegenerative disorders, and specific hallmarks may be required to establish or confirm a diagnosis. Genetic features used for classification purposes include mode of inheritance and molecular genetic data, such as linkage to a known gene locus or identification of a specific genetic defect. A final classification scheme is based on alterations in molecular mechanisms (e.g. trinucleotide expansions) or protein function (e.g. channelopathies). Despite recent advances, it may not be possible to develop the ‘ultimate’ classification of movement disorders, and different patterns of lumping and splitting may be useful for the clinician, the pathologist or the geneticist/molecular biologist. Furthermore, certain individual cases with unique features may not fit into any particular category. Continued research by both clinicians and basic scientists is necessary in order to refine and redefine classification schemes of movement disorders.
Treatment strategies in movement disorders
Authors: Speelman J. D.
Published: April 2005

Strategies in treatment of movement disorders are discussed with the illustration of three patients with dystonia. Pharmacotherapy can be applied in two ways: (1) a precise directed therapy, or (2) a ‘shotgun’ approach. Botulinum toxin is successfully injected in focal and segmental forms of movement disorders. Stereotactic neurosurgery can be considered in pharmacotherapy‐resistant dystonias, but also in other forms of movement disorders. Intrathecal baclophen treatment by continuous infusion is only indicated in severe forms of spasticity.
ST PETERSBURG AND MOSCOW, AUTUMN 2004
Authors: McBurney Gerard
Published: April 2005

Between 22 September and 4 October last year, Gerard McBurney made a short research and lecturing trip to St Petersburg and Moscow. On his return he circulated a private, informal account of his activities and impressions of the current state of musical life in Russia to a number of interested parties and friends. Among these was the Editor of Tempo, who considered that parts of the report were of such interest that they merited wider circulation. At his request, Gerard McBurney has prepared this edited version of his report for publication.
John Foulds
Authors: Head Raymond
Published: April 2005

FOULDS: Three Mantras op. 61b3; Lyra Celtica, Concerto for voice and orchestra op. 501; Apotheosis (Elegy) for violin and orchestra op. 182; Mirage op. 20. 1Susan Bickley (mezzo), 2Daniel Hope (vln), 3City of Birmingham Youth Chorus, City of Birmingham Symphony Orchestra c. Sakari Oramo. Warner Classics 2564 61525-2.
Amsterdam: Hungarian State Opera at Het Muziektheater in Szókolay's ‘Blood Wedding’
Authors: Dunnett Roderic
Published: April 2005

Blood Wedding is the first opera by the Hungarian composer Sándor Szókolay, (b.1931), who being three years older than Birtwistle and Maxwell Davies is, with Emil Petróvics (whose Kafka-like one-acter C'est la Guerre coexists with Blood Wedding in the Hungarian State Opera's regular repertoire), arguably the leading modernist among Hungarian opera composers.
Forced obliquity variations of Mercury
Authors: Bills Bruce G. , Comstock Robert L.
Published: April 2005

The spin pole of Mercury is very nearly, but not quite, aligned with its orbit pole. Tidal dissipation has driven the free obliquity to very small values, and the high rate of spin pole precession allows the forced obliquity variations to remain small despite significant variations in orbital inclination and eccentricity. We present calculations of the obliquity for a 10 million year time span, centered on the present. The obliquity remains small, with typical values of 2–4 minutes of arc. The dominant period of obliquity oscillations is 895 kyr, which is also the main period at which the orbital inclination varies. If the orbit pole precession rate were uniform, dissipation would have driven Mercury into a Cassini state, in which the spin pole and orbit pole remain coplanar with the invariable pole, as the spin pole precesses about the moving orbit pole. However, due to the nonuniform orbit precession rate, this simple coplanar configuration is not maintained, except on a mode‐by‐mode basis. That is, when the orbit pole motion is represented as a sum of normal modes of the coupled oscillations of the planetary system, the spin pole coprecesses with the orbit pole at each modal frequency. This is a generalization of Cassini's second and third laws of lunar rotation to the case of nonuniform orbit precession. We compare results of a linearized obliquity model with a numerical integration of the equations of motion. The two solutions agree at the level of a few seconds of arc.
High quality seismological recordings from the SN‐1 deep seafloor observatory in the Mt. Etna region
Authors: Monna Stephen , Frugoni Francesco , Montuori Caterina , Beranzoli Laura , Favali Paolo
Published: April 2005

We show over 4 months of 3‐component broadband seismometer data from the SN‐1 seafloor multidisciplinary observatory, deployed offshore of Eastern Sicily (Italy) at 2105 m b.s.l. The SN‐1 spectra show background noise levels above 0.1 Hz similar to levels at a nearby ground station. An important noise source below 0.1 Hz is caused by tilt of the sensor induced by sea currents. Seismic noise levels above 0.01 Hz are strongly dependent on Etna volcanic activity. In spite of these intense noise sources, SN‐1 recorded many local, regional and global events. The quality of seismic recordings confirms the validity of the installation procedure and good ground coupling of the 3‐component broadband sensor, suggesting that SN‐1 can be proposed as permanent observatory in this high seismic and volcanic hazard area.
Measurements of HO2 uptake to aqueous aerosol: Mass accommodation coefficients and net reactive loss
Authors: Thornton Joel , Abbatt Jonathan P. D.
Published: April 2005

We present room temperature measurements of HO2 uptake to aqueous submicron aerosol obtained with an entrained aerosol flow tube coupled to a chemical ionization mass spectrometer. Two aqueous aerosol types were examined, H2SO4 at 35–40% relative humidity (RH) and (NH4)2SO4 at 40–45% RH. By doping the aerosol with Cu(II) (∼0.1 M in aerosol) to create an efficient aerosol sink, we determine lower limits to the mass accommodation coefficient, αHO2, to be 0.8 ± 0.3 for H2SO4 and 0.5 ± 0.1 for (NH4)2SO4 particles. In the absence of Cu(II), net reactive loss of HO2 on H2SO4 aerosol was slow, and we measured a reaction probability, γHO2, less than 0.01. In contrast, loss of HO2 to (NH4)2SO4 aerosol, buffered to pH = 5.1 but without Cu(II), was efficient in our experiment. For this system, aerosol‐induced loss of gas‐phase HO2 was observed to follow second‐order kinetics, and we infer from our measurements a second‐order aqueous phase reaction rate coefficient of 1 ± 0.25 × 107M−1 s−1 in good agreement with an estimate of 2 ± 1 × 107M−1 s−1 based on literature values of HO2 aqueous‐phase chemical parameters. These results imply that heterogeneous loss of HO2 to submicron aqueous sulfate aerosol will be strongly temperature dependent with negligible contribution to odd hydrogen radical (HOx) removal rates at temperatures warmer than ∼270 K, but potentially large contributions to HOx loss (e.g., >50% of total HOx loss) in colder regions of the troposphere depending on the available aqueous aerosol volume.
Naturally occurring scour pits in nearshore sands
Authors: Hay Alex E. , Speller Rachel
Published: April 2005

Depressions 10–50 cm in diameter and O(10) cm deep were observed in rotary acoustic imagery of the seafloor during SandyDuck97. The rotary sonar record spans a 77 day period and 13 storm events. The depressions occurred during both the wave growth and the wave decay phases of each storm and over a relatively narrow range of wave energies (urms = 0.32 cm/s ± 0.05 cm/s standard deviation) and grain roughness Shields parameters(=0.7 ± 0.2). The observations are mainly from the outer surf zone in ≈3 m mean water depth at two stations separated by 40 m cross‐shore distance. Depressions were 6.5 times more frequent at the inner station (N = 485) than at the outer (N = 75). Areal densities were small: O(0.1) m−2. Depressions were also observed in the inner surf zone at a third station, for which the data record is less complete. The probability distribution of the locations of depression first occurrences is nonrandom (i.e., non‐Poisson) due to 50% reoccurrence in roughly the same positions from storm to storm. The geometry and temporal development of the depressions are similar to scour pits formed by cylindrical piles and other objects. On the basis of these similarities, and the clustering of first occurrence locations, we conclude that the likely origin of the depressions is scour about compact semimobile obstacles on or embedded within the sandy seafloor. Possible candidate obstacles include pebbles, large shells or large shell fragments, and the chimney structures left by burrowing organisms. Importantly, 13 of the pits evolved into meter‐scale lunate megaripples, indicating that these features can act as megaripple precursors.
The first cysteine-rich domain of the receptor GFRα1 stabilizes the binding of GDNF
Authors: VIRTANEN Heidi , YANG Jianmin , BESPALOV Maxim M. , HILTUNEN Jukka O. , LEPPÄNEN Veli-Matti , KALKKINEN Nisse , GOLDMAN Adrian , SAARMA Mart , RUNEBERG-ROOS Pia
Published: April 2005

The GDNF (glial cell line-derived neurotrophic factor)-binding receptor GFRα1 (GDNF family receptor α1) is attached to the membrane by a GPI (glycosylphosphatidylinositol) anchor and consists of three cysteine-rich domains. The region corresponding to the second and third domains has been shown previously to participate in ligand binding, and to interact with the transmembrane tyrosine kinase receptor RET. No function has so far been found for the N-terminal, first domain (D1). Here we show that the GPI-anchored full-length receptor binds 125I-GDNF two times more tightly than does a GPI-anchored truncated receptor lacking D1. Scintillation proximity assays with purified receptor proteins also show that the GDNF-binding capacity of the soluble full-length GFRα1 is two times higher than the GDNF-binding capacity of the soluble D1-truncated GFRα1. As RET stabilizes the binding of GDNF equally well to the full-length and truncated receptors, D1 seems not to be involved in the interaction between GFRα1 and RET. Moreover, soluble full-length GFRα1 mediates GDNF-promoted neurite outgrowth in PC6-3 cells more efficiently than the soluble truncated GFRα1 protein. At low concentrations, the soluble fulllength receptor mediates the phosphorylation of RET more efficiently than the soluble truncated receptor. However, when the receptors are overexpressed on the cell surface as GPI-anchored proteins, or added to the growth medium at high concentrations as soluble proteins, full-length and truncated GFRα1 are indistinguishable in GDNF-dependent RET-phosphorylation assays. High levels of the receptors can thus mask a slightly impaired function in the phosphorylation assay. Based on assays with both GPI-anchored and soluble receptors, we therefore conclude that D1 contributes to the optimal function of GFRα1 by stabilizing the interaction between GFRα1 and GDNF.
Misfolded BiP is degraded by a proteasome-independent endoplasmic-reticulum-associated degradation pathway
Authors: DONOSO Gerda , HERZOG Volker , SCHMITZ Anton
Published: April 2005

Misfolded proteins are removed from the ER (endoplasmic reticulum) by retrotranslocation to the cytosol and degradation by the ubiquitin–proteasome system in a process designated ERAD (ER-associated degradation). Analysing the turnover of a misfolded form of the ER-resident chaperone BiP (heavy-chain binding protein) (BiPΔA), we found that the degradation of BiPΔA did not follow this general ERAD pathway. In transfected cells, BiPΔA was degraded, although proteasome-dependent ERAD was inactivated either by proteasome inhibitors or by ATP depletion. In semi-permeabilized cells, which did not support the degradation of the proteasomal substrate α1-antitrypsin, the degradation of BiPΔA was still functional, excluding the Golgi apparatus or lysosomes as the degradative compartment. The degradation of BiPΔA was recapitulated in biosynthetically loaded brain microsomes and in an extract of luminal ER proteins. In contrast with proteasome-dependent ERAD, degradation fragments were detectable inside the microsomes and in the extract, and the degradation was prevented by a serine protease inhibitor. These results show that the degradation of BiPΔA was initiated in the ER lumen by a serine protease, and support the view that proteasome-independent ERAD pathways exist.
Parametrization of an anharmonic Kirkwood–Keating potential for AlxGa1−xAs alloys
Authors: Sim Eunji , Beckers Joost , de Leeuw Simon , Thorpe Michael , Ratner Mark A.
Published: April 2005

We introduce a simple semiempirical anharmonic Kirkwood–Keating potential to model AxB1−xC-type semiconductors. The potential consists of the Morse strain energy and Coulomb interaction terms. The optical constants of pure components, AB and BC, were employed to fit the potential parameters such as bond-stretching and -bending force constants, dimensionless anharmonicity parameter, and charges. We applied the potential to finite temperature molecular-dynamics simulations on AlxGa1−xAs for which there is no lattice mismatch. The results were compared with experimental data and those of harmonic Kirkwood–Keating model and of equation-of-motion molecular-dynamics technique. Since the Morse strain potential effectively describes finite temperature damping, we have been able to numerically reproduce experimentally obtained optical properties such as dielectric functions and reflectance. This potential model can be readily generalized for strained alloys.
Molecular dynamics integration and molecular vibrational theory. I. New symplectic integrators
Authors: Janežič Dušanka , Praprotnik Matej , Merzel Franci
Published: April 2005

New symplectic integrators have been developed by combining molecular dynamics integration with the standard theory of molecular vibrations to solve the Hamiltonian equations of motion. The presented integrators analytically resolve the internal high-frequency molecular vibrations by introducing a translating and rotating internal coordinate system of a molecule and calculating normal modes of an isolated molecule only. The translation and rotation of a molecule are treated as vibrational motions with the vibrational frequency zero. All types of motion are thus described in terms of the normal coordinates. The method’s time reversibility requirement was used to determine the equations of motion for internal coordinate system of a molecule. The calculation of long-range forces is performed numerically within the generalized second-order leap-frog scheme, in the same way as in standard second-order symplectic methods. The new methods for integrating classical equations of motion using normal mode analysis allow us to use a long integration step and are applicable to any system of molecules with one equilibrium configuration.
Saturated Kochen–Specker-type configuration of 120 projective lines in eight-dimensional space and its group of symmetry
Authors: Ruuge Artur E. , van Oystaeyen Freddy
Published: April 2005

There exists an example of a set of 40 projective lines in eight-dimensional Hilbert space producing a Kochen–Specker-type contradiction. This set corresponds to a known no-hidden variables argument due to Mermin. In the present paper it is proved that this set admits a finite saturation, i.e., an extension up to a finite set with the following property: every subset of pairwise orthogonal projective lines has a completion, i.e., is contained in at least one subset of eight pairwise orthogonal projective lines. An explicit description of such an extension consisting of 120 projective lines is given. The idea to saturate the set of projective lines related to Mermin’s example together with the possibility to have a finite saturation allow to find the corresponding group of symmetry. This group is described explicitely and is shown to be generated by reflections. The natural action of the mentioned group on the set of all subsets of pairwise orthogonal projective lines of the mentioned extension is investigated. In particular, the restriction of this action to complete subsets is shown to have only four orbits, which have a natural characterization in terms of the construction of the saturation.
Efficient radiative recombination and potential profile fluctuations in low-dislocation InGaN∕GaN multiple quantum wells on bulk GaN substrates
Authors: Franssen G. , Grzanka S. , Czernecki R. , Suski T. , Marona L. , Riemann T. , Christen J. , Teisseyre H. , Valvin P. , Lefebvre P. , Perlin P. , Leszczyński M. , Grzegory I.
Published: April 2005

We investigated the relation between structural properties and carrier recombination processes in InGaN∕GaN multiple quantum well (MQW) structures with quantum well widths of 3 and 9nm, grown by metal-organic chemical-vapor deposition on bulk GaN crystals. Quantum barriers of the samples are heavily n-type doped in order to effectively screen the large polarization-induced electric fields which commonly occur in hexagonal InGaN∕GaN quantum structures. High thermal stability in these structures, reflected by strong photoluminescence (PL) even above 400K, is attributed to a combination of low-dislocation densities and potential profile fluctuations in the InGaN∕GaN quantum wells. The role of potential profile fluctuations is further investigated by time-resolved photoluminescence and cathodoluminescence (CL) mapping. Comparison of both samples shows that the sample with 3-nm-wide QWs exhibits (i) a larger width of the PL peak in the temperature range of 8–420K, (ii) a higher amplitude of potential profile fluctuations as measured by CL mapping, and (iii) higher radiative and nonradiative PL recombination times. At the same time a much weaker drop of PL intensity with temperature is recorded on the sample with 9-nm-wide QWs. Our results show that, contrary to intuitive expectation, a decrease of the potential profile fluctuation amplitude can be helpful in enhancing the radiative recombination efficiency, particularly at high temperatures.
Magnetostrictive and magnetoelectric behavior of Fe–20at.% Ga∕Pb(Zr,Ti)O3 laminates
Authors: Dong Shuxiang , Zhai Junyi , Bai Feiming , Li JieFang , Viehland D. , Lograsso T. A.
Published: April 2005

The magnetostrictive and magnetoelectric (ME) properties of laminate composites of Fe–20at.%Ga and Pb(Zr,Ti)O3 (PZT) have been studied for laminates of different geometries. The results show that (i) a long-type magnetostrictive Fe–20at.%Ga crystal plate oriented along ⟨001⟩c and magnetized in its longitudinal (or length) direction has higher magnetostriction than a disk-type one; and consequently (ii) a long-type Fe–20at.%Ga∕PZT laminate has a giant ME effect, and is sensitive to low-level magnetic fields.
Structural and optical investigation of plasma deposited silicon carbon alloys: Insights on Si-C bond configuration using spectroscopic ellipsometry
Authors: Losurdo Maria , Giangregorio Maria , Capezzuto Pio , Bruno Giovanni , Giorgis Fabrizio
Published: April 2005

Amorphous (a–Si1−xCx:H) and microcrystalline (μc–Si1−xCx:H) thin films have been deposited by plasma-enhanced chemical-vapor deposition using SiF4–CH4−H2 rf plasmas. Gas flow rates have been varied to deposit films with different carbon content and microstructure. The microstructure and optical properties have been investigated by IR/Raman spectroscopy and by spectroscopic ellipsometry in the energy range of 1.5–5.0 eV. Ellipsometric spectra have been analyzed in terms of the tetrahedron model combined with the Bruggeman effective-medium approximation to determine the film microstructure and silicon–carbon-bond configurations. Correlation between Si–C bond configurations and optical properties of films has been studied as a function of carbon content and microstructure. It is found that the optical properties and the band gap value depend not only on the carbon content, but also on the Si–C bond configuration and microcrystallinity. The films consist of Si-centered Si–Si4−vCv(v=0–3) Si-centered tetrahedra with segregation of μc–Si. The amorphous matrix changes from Si–Si3C to Si–SiC3 with the increase of the μc–Si phase. The optical gap is found to increase with both carbon content and microcrystallinity.
Genotyping of human neutrophil antigen‐5a (Ond)
Authors: Sachs U. J. H. , Reil A. , Bauer C. , Bux J. , Bein G. , Santoso S.
Published: April 2005

summary.  Antibodies to human neutrophil alloantigens (HNA) can cause immune‐mediated neutropenias and transfusion complications. The diagnosis of antibodies to the HNA‐5a (Ond) isoform of the αLβ2 integrin is hampered by the lack of reliable methods for HNA‐5a antigen typing. We have devised a polymerase chain reaction sequence‐specific primer method (PCR‐SSP) and used it to determine the HNA‐5a gene frequencies in 320 individuals from different ethnicities. 15·3% were found to be HNA‐5a negative, with no significant deviation between the populations. Results of HNA‐5a genotyping were in accordance with phenotyping. Availability of HNA‐5a PCR‐SSP will facilitate the diagnosis of Ond antibody‐mediated clinical conditions.
Prevention of transfusion‐transmitted hepatitis E by donor‐initiated self exclusion
Authors: Lee C. K. , Chau T. N. , Lim W. , Tsoi W. C. , Lai S. T. , Lin C. K.
Published: April 2005

summary.  Safety in blood transfusion has all along been focused on blood borne viruses like HIV, hepatitis B and C. However, infective agents that are not usually transmitted through blood may also pose risk to transfusion if the donor gives blood in the early‐viraemic phase. A case report of potential transfusion‐transmitted hepatitis E (HEV) is described. It shows the virus can be transmissible via blood because of the presence of HEV RNA in the blood donated. Pre‐donation health screening was unable to exclude this asymptomatic donor. But donor‐initiated call back system which acts as an additional safety net prevented the release of the potential infective blood products.
Bootstrap methods for statistical inference from stereological estimates of volume fraction
Authors: MATTFELDT T. , FLEISCHER F.
Published: April 2005

We suggest the use of bootstrap methods for inference from stereological estimates of volume fraction. An informal introduction to stereological estimation of volume fraction and to principles of bootstrap techniques is given. The bootstrap method is a robust computer‐intensive resampling technique, based on independent random sampling from a data set with replacement. Bootstrap methods were used to estimate confidence intervals for volume fractions, and to test for a significant difference between estimated volume fractions from two samples. Two sampling designs are considered: independent replicated samples (visual fields) from a single object, and estimates of volume fraction from multiple independent objects. The methods are presented as worked examples on real data sets obtained from tumour pathology (mammary cancer, pancreatic cancer). The volume fraction of glandular lumina per total volume of the epithelial phase was chosen as target parameter. It indicates the degree of glandular differentiation in adenocarcinomas and is estimated as a ratio‐of‐means statistic with variable denominator within cases. The confidence intervals of the volume fraction estimated by the bootstrap method were slightly narrower than the parametrically calculated confidence intervals for all data sets. The outcomes of significance tests based on the bootstrap technique were unchanged as compared with classical tests based on the assumptions of normality and homoscedasticity of the data. Special attention was paid to the reproducibility of the bootstrap technique in replicated trials on the same data.
Crystallographic analysis of thin specimens
Authors: SIVEL V. G. M. , TICHELAAR F. D. , MOHDADI H. , ALKEMADE P. F. A. , ZANDBERGEN H. W.
Published: April 2005

Electron backscattering diffraction (EBSD) is commonly used on bulk samples for crystallographic material characterization. In this work, the technique was applied on transmission electron microscopy (TEM)‐type thin specimens, prepared with a focused ion beam. Orientation maps were successfully collected on specimens made of a Cu3Au copper–gold alloy. As compared to EBSD analysis on a bulk specimen, an improved pattern quality and a high spatial resolution (well below 10 nm) were obtained. Furthermore, a clear improvement of the signal‐to‐noise ratio with decreasing sample thickness was observed.
SEM examination of human erythrocytes in uncoated bloodstains on stone: use of conventional as environmental‐like SEM in a soft biological tissue (and hard inorganic material)
Authors: HORTOLÀ P.
Published: April 2005

Although nowadays the so‐called environmental scanning electron microscopes (ESEMs) allow the observation of the samples without metal or carbon coating, many conventional scanning electron microscopes (SEMs) are still in use. On the other hand, the presence of erythrocytes (red blood cells, RBCs) in a smear is considered a blood confirmation. Such a presence has been previously reported even in Lower Stone Age implements. In previous works, I have reported several studies dealing with cytomorphology of RBCs in bloodstains using scanning electron microscopy with standard specimen preparation procedures, i.e. via coating the samples before SEM analysis. In order to explore the potential of conventional SEM as environmental‐like SEM in haemotaphonomical studies, two alkaline (limestone) and two acid (flint) rock fragments were smeared with human blood from a male and a female. The bloodstains obtained in this way were then air dried indoors and stored into a non‐hermetic plastic box. Afterwards, the smears and their rock substrates were examined directly without coating, via secondary electrons, using a JEOL JSM‐6400 scanning electron microscope. Satisfactory results reveal the capability of a conventional SEM to work in secondary‐electron mode as an environmental‐like SEM on these kinds of biological and inorganic materials, and probably in many other biological and non‐biological samples.
Automated alignment and pattern recognition of single‐molecule force spectroscopy data
Authors: KUHN M. , JANOVJAK H. , HUBAIN M. , MÜLLER D. J.
Published: April 2005

Recently, direct measurements of forces stabilizing single proteins or individual receptor–ligand bonds became possible with ultra‐sensitive force probe methods like the atomic force microscope (AFM). In force spectroscopy experiments using AFM, a single molecule or receptor–ligand pair is tethered between the tip of a micromachined cantilever and a supporting surface. While the molecule is stretched, forces are measured by the deflection of the cantilever and plotted against extension, yielding a force spectrum characteristic for each biomolecular system. In order to obtain statistically relevant results, several hundred to thousand single‐molecule experiments have to be performed, each resulting in a unique force spectrum. We developed software and algorithms to analyse large numbers of force spectra. Our algorithms include the fitting polymer extension models to force peaks as well as the automatic alignment of spectra. The aligned spectra allowed recognition of patterns of peaks across different spectra. We demonstrate the capabilities of our software by analysing force spectra that were recorded by unfolding single transmembrane proteins such as bacteriorhodopsin and NhaA. Different unfolding pathways were detected by classifying peak patterns. Deviant spectra, e.g. those with no attachment or erratic peaks, can be easily identified. The software is based on the programming language C++, the GNU Scientific Library (GSL), the software WaveMetrics IGOR Pro and available open‐source at http://bioinformatics.org/fskit/.
Refinement of the chromosome 16 locus for benign familial infantile convulsions
Authors: Callenbach PMC , Van Den Boogerd EH , De Coo RFM , Ten Houten R , Oosterwijk JC , Hageman G , Frants RR , Brouwer OF , Van Den Maagdenberg AMJM
Published: April 2005

Benign familial infantile convulsions (BFIC) is an autosomal dominantly inherited partial epilepsy syndrome of early childhood with remission before the age of 3 years. The syndrome has been linked to loci on chromosomes 1q23, 2q24, 16p12‐q12, and 19q in various families. The aim of this study was to identify the responsible locus in four unrelated Dutch families with BFIC. Two of the tested families had pure BFIC; in one family, affected individuals had BFIC followed by paroxysmal kinesigenic dyskinesias at later age, and in one family, BFIC was accompanied by later‐onset focal epilepsy in older generations. Linkage analysis was performed for the known loci on chromosomes 1q23, 2q24, 16p12‐q12, and 19q. The two families with pure BFIC were linked to chromosome 16p12‐q12. Using recombinants from these and other published families, the chromosome 16‐candidate gene region was reduced from 21.4 Mb (4.3 cm) to 2.7 Mb (0.0 cm). For the other two families, linkage to any of the known loci was unlikely. In conclusion, we confirm the linkage of pure BFIC to chromosome 16p12‐q12, with further refinement of the locus. Furthermore, the lack of involvement of the known loci in two of the families indicates further genetic heterogeneity for BFIC.
Psychological and genetic counseling implications for adolescent daughters of mothers with breast cancer
Authors: Cappelli M. , Verma S. , Korneluk Y. , Hunter A. , Tomiak E. , Allanson J. , DeGrasse C. , Corsini L. , Humphreys L.
Published: April 2005

Adolescent daughters of women with breast cancer (BC) are themselves at risk for heritable BC. Although some preliminary evidence suggests this group is at an increased risk for emotional problems, evidence is limited to studies with small samples and no comparison groups. This study examined psychological and family functioning, health attitudes and beliefs about genetic risks in adolescent females. A case‐comparison design was used to compare 55 mother – daughter pairs in which the mother had been treated for BC (BC group) to 55 families from the general population (GP). Participants completed an assessment battery measuring perceptions of personal risk for BC and attitudes about gene testing for BC susceptibility, family functioning, and adolescent psychological adjustment. Based on manova, no significant differences were found between the two groups on measures of the psychological functioning. However, BC group adolescents reported significant (p < 0.01) worries about their future health and genetic risk for BC. About 68% of BC adolescents compared with 12% of GP adolescents reported being moderately to greatly concerned about their susceptibility to genetic mutations. Further, 85% of BC group adolescents believed they were susceptible to BC compared with 10% of GP adolescents. The results indicated no evidence of emotional, behavioral, or familial distress in these families. However, BC adolescents have significant worries about their future health. The results of this study demonstrate the need to develop a comprehensive model of care where accurate information about genetics and health risks can be provided. The adolescents also need support to help them cope and communicate with their mothers their worries about BC.
Effect of carbon and nitrogen assimilation on chlorophyll fluorescence emission by the cyanobacterium Anacystis nidulans
Authors: Romero José M. , Lara Catalina , Sivak Mirta N.
Published: April 2005

O2 evolution and chlorophyll a fluorescence emission have been monitored in intact cells of the cyanobacterium Anacystic nidulans 1402–1 to stdy the influence of carbon and nitrogen assimilation on the operation of the photosynthetic apparatus. The pattern of fluorescence induction in dark‐adapted cyanobacterial cells was different from that of higher plants. Cyanobacteria undergo large, rapid state transitions upon illumination, which lead to marked changes in the fluorescence yield, complicating the estimation of quenching coefficients. The Kautsky effect was not evident, although it could be masked by a state II–state I transition, upon illumination with actinic light. The use of inhibitors of carbon assimilation such as D,L‐glyceraldehyde or iodoacetamide allowed us to relate changes in variable fluorescence to active CO2 fixation. Ammonium, but not nitrate, induced non‐photochemical fluorescence quenching, in agreement with a previous report on green algae, indicative of an ammonium‐induced state I transition.
Variations in the evaluation of colorectal cancer risk
Authors: Hodder R. J. , Ballal M. , Selvachandran S. N. , Cade D.
Published: April 2005

Objectives  To test the variability in estimating cancer risk and demonstrate the consequences that subjectivity has on patient care.

Subjects and methods  Forty‐three clinicians were each asked to assess 40 symptomatic colorectal referrals. Each clinician was provided with a comprehensive history on the 40 patients. The clinicians graded the referral according to a malignancy risk score, decided on the required first line investigation and the priority of that investigation. The main outcome measures used was accuracy in cancer detection and appropriateness of investigations selected.

Results  There was a wide degree of variation among all clinicians grading both benign and malignant disease with the overall correct classification of 54% (P‐value of <0.001). On average, the clinicians correctly diagnosed 71.3% of the cancer patients as compared to 44% of the benign patients. Of the cancer patients, 47% were correctly classified as an urgent referral whilst 52% of the benign patients were over classified and graded as an urgent referral. The mean number chosen by clinicians to have a flexible sigmoidoscopy as the appropriate first investigation was 13 (of 40 patients); this was despite the diagnosis being possible in all cases with a flexible sigmoidoscopy. The choice to use full colonic investigation was seen throughout all disciplines. Junior doctors demonstrated the highest tendency choosing full colonic investigation in 92.3%. Consultants and senior grades showed the least tendency to choose full colonic imaging although even here colonoscopy or barium enema represented 48.5%.

Conclusion  Subjective assessment of cancer referrals is a significant problem that needs to be confronted. Improvements are needed to resolve the inherent problems of subjectivity and operator bias if uniform quality of patient care and best use of resources is to be achieved.
Unreasonable expectations in emergency colorectal cancer surgery
Authors: Metcalfe M S. , Norwood M. G. A. , Miller A. S. , Hemingway D.
Published: April 2005

Objectives  The recently published ACPGBI colorectal cancer (ACPGBI CRC) scoring system for predicting operative mortality has been suggested as an instrument to improve patient consent procedures and to compare results between centres. This study compares the results of a surgical unit against the standards set by the ACPGBI colorectal cancer model and for emergency surgery, against the p‐POSSUM instrument.

Methods  Data for the ACPGBI CRC model were collected prospectively through 2003 at the Leicester Royal Infirmary. Additional data needed for the p‐POSSUM was retrospectively collected from case records. The actual mortality was compared with that predicted by the models.

Results  Seventy‐two colorectal cancer operations were performed during the study period. The observed operative mortality in elective cases was lower, and in emergency cases higher, than predicted by the ACPGBI CRC model. With emergency cases the predicted mortality using P‐POSSUM was significantly higher than that using the ACPGBI CRC model, particularly in the presence of faecal contamination.

Conclusion  The ACPGBI CRC model may be accurate for elective cases, but appears to significantly underestimate predicted mortality in the emergency setting, both actual and predicted by p‐POSSUM. This may be due to a failure to incorporate adequate weighting for faecal peritonitis and the associated systemic insult into the ACPGBI model.
Progressive and extensive hypomelanosis and extensive pityriasis alba: same disease, different names?
Authors: Di Lernia Vi , Ricci C
Published: April 2005

We report the cases of five female patients with high skin phototype affected by relapsing, hypochromic, non‐scaling macules occurring after the summer on the back and spreading over large areas of skin. Histological features disclosed decreased epidermal melanin. Psoralen plus ultraviolet A (PUVA) treatment proved to be beneficial, but new relapses were noted after stopping treatment. Clinical and histological features were consistent with the diagnosis of ‘progressive and extensive hypomelanosis’ described by Guillet in persons of mixed racial background. We discuss the differential diagnosis of the latter entity with respect to the other idiopathic acquired primitive hypomelanosis and hypothesize an overlapping with the so‐called extensive pityriasis alba (EPA).
Persistent serpentine supravenous hyperpigmented eruption associated with docetaxel
Authors: Aydogan I , Kavak A , Parlak AH , Alper M , Annakkaya AN , Erbas M
Published: April 2005

Various mucocutaneous reactions have been reported with the use of systemic docetaxel. We describe a 47‐year‐old man who developed a persistent serpentine supravenous hyperpigmented eruption (PSSHE), beginning at the site of docetaxel injection and spreading along the superficial venous network in the anterior aspect of the right forearm and distal arm. The eruption occurred after the first infusion of docetaxel following insufficient venous washing. A second infusion was administered through a vein in the other forearm, but this time, abundant venous washing was performed and a similar eruption did not occur. To our knowledge, this is the second report of docetaxel‐induced supravenous discoloration and we discussed the terminology and mechanism of this unique reaction.
Misregulation of poly(ADP‐ribose) polymerase‐1 activity and cell type‐specific loss of poly(ADP‐ribose) synthesis in the cerebellum of aged rats
Authors: Malanga M. , Romano M. , Ferone A. , Petrella A. , Monti G. , Jones R. , Limatola E. , Farina B.
Published: April 2005

Protein modification by ADP‐ribose polymers is a common regulatory mechanism in eukaryotic cells and is involved in several aspects of brain physiology and physiopathology, including neurotransmission, memory formation, neurotoxicity, ageing and age‐associated diseases. Here we show age‐related misregulation of poly(ADP‐ribose) synthesis in rat cerebellum as revealed by: (i) reduced poly(ADP‐ribose) polymerase‐1 (PARP‐1) activation in response to enzymatic DNA cleavage, (ii) altered protein poly(ADP‐ribosyl)ation profiles in isolated nuclei, and (iii) cell type‐specific loss of poly(ADP‐ribosyl)ation capacity in granule cell layer and Purkinje cells in vivo. In particular, although PARP‐1 could be detected in virtually all granule cells, only a fraction of them appeared to be actively engaged in poly(ADP‐ribose) synthesis and this fraction was reduced in old rat cerebellum. NAD+, quantified in tissue homogenates, was essentially the same in the cerebellum of young and old rats suggesting that in vivo factors other than PARP‐1 content and/or NAD+ levels may be responsible for the age‐associated lowering of poly(ADP‐ribose) synthesis. Moreover, PARP‐1 expression was substantially down‐regulated in Purkinje cells of senescent rats.