bluuebunny/crossref_metadata_2025 huggingface dataset:
Salivary gland manifestations of sinus histiocytosis with massive lymphadenopathy: Fine‐needle aspiration cytology findings. A case report
Authors: Panikar Nirupma , Agarwal Sarla
Published: August 2005

Sinus histiocytosis with massive lymphadenopathy (SHML or Rosai–Dorfman disease) is a nonneoplastic, usually self‐limiting disease. Alhough it affects all age groups, it is more commonly seen in young males in their first or second decades. The disease primarily manifests as painless lymphadenopathy of cervical region, but other nodal groups and extranodal sites may also be affected. Seldom SHML may involve the salivary glands. We present the cytologic features and differential diagnoses of one such case.

A 45‐yr‐old woman presented with an enlarged submandibular gland on the left side with ipsilateral cervical lymphadenopathy that had been persisting for 1 mo. The gland and the two enlarged nodes measured 2.5 × 2.5 cm2 each and were firm in consistency. Clinically, tumor of the salivary glands was suspected. Fine‐needle aspiration (FNA) smears showed moderate cellularity, with large histiocytes dispersed in the background of intense lymphoplasmacytic infiltrate. These histiocytes showed lymphophagocytosis. Isolated stromal fragments consisting of fibrocytes were seen separate from salivary acinar clusters on repeat aspirations. The diagnosis of SHML involving left submandibular gland and ipsilateral lymph nodes was returned.

When analyzed in the context of clinical findings (laboratory data), the cytologic features of SHML involving salivary gland could be differentiated from those of malignancies and other benign lesions, especially Kuttner's tumor of the submandibular gland, which mimics neoplasm clinically. Diagn. Cytopathol. 2005;33:187–190. © 2005 Wiley‐Liss, Inc.
Atypical repair on Pap smears: Clinicopathologic correlates in 647 cases
Authors: Levine Pascale Hummel , Elgert Paul A. , Sun Paranee , Simsir Aylin
Published: August 2005

The Bethesda system separates atypical reparative changes (ARC) from “typical” repair and places it into the atypical squamous cells of undetermined significance (ASC‐US) category. The cytologic diagnosis of ARC represents both diagnostic and management challenges because its clinical significance is controversial and has not been fully investigated. On the basis of scant literature on follow‐up of women with ARC on Papanicolaou (Pap) test, we reviewed data from our patient population, which consists of a mixture of low‐ and high‐risk women. Six hundred forty‐seven patients with ARC on their Pap tests were identified in a 7‐yr period. Of this, 189 (29%) women were lost to follow‐up. Of the 458 women with follow‐up, 31% had cervical biopsies and 69% were followed by repeated Pap tests. The age ranged from 16 to 86 (mean 47 yr). The incidence of squamous intraepithelial lesion was 5.2% (5% low‐grade and 0.2% high‐grade). Most women (62%) with ARC on Pap test had a benign condition on follow‐up. For some women, the immediate cause was not known and the Pap abnormality resolved spontaneously. Our study questions the validity of reporting ARC within the ASC‐US category. Diagn. Cytopathol. 2005;33:214–217. © 2005 Wiley‐Liss, Inc.
Background features of endometrial carcinoma on ThinPrep® cytology
Authors: Selvaggi Suzanne M.
Published: August 2005

Conventional smear screening has had little impact on the detection of endometrial carcinoma. Recent studies on liquid‐based preparations show promise with increased detection rates of endometrial lesions. The purpose of this 2‐yr retrospective study (February 1, 2002–February 29, 2004) was to evaluate the background features on ThinPrep® slide preparations from endometrial carcinomas. During this period, 20 (0.06%) cases were diagnosed as adenocarcinoma, of which 15 (75%) showed endometrial carcinoma on cervical or vaginal biopsy. Classic tumor diathesis was present on the slides in 8 (53%) of the cases, the majority of which were from high‐grade tumors. In 1 (7%) case, the tumor diathesis consisted of precipitated protein in a watery background. Tumor diathesis was absent in 6 (40%) of the cases, the majority of which were low‐grade lesions. Background features on ThinPrep® Pap tests™ from patients with endometrial features range from classic tumor diathesis to clean; findings dependent on the histologic type and grade of the tumor and the extent of the disease process. Diagn. Cytopathol. 2005;33:162–165 © 2005 Wiley‐Liss, Inc.
Fourth‐ and tenth‐order compact finite difference solutions of perturbed circular vortex flows
Authors: Ferreira de Sousa P. J. S. A. , Pereira J. C. F.
Published: August 2005

In this study, high‐order compact finite difference calculations are reported for 2D unsteady incompressible circular vortex flow in primitive variable formulation. The fourth‐order Runge–Kutta temporal discretization is used together with fourth‐ or tenth‐order compact spatial discretization. Dependent on the perturbation initially imposed, the solutions display a tripole, triangular or square vortex. The comparison of the predictions with the detailed spectral calculations of Kloosterziel and Carnevale (J. Fluid Mech. 1999; 388:217–257) shows that the vorticity fields are very well captured. The spectral resolution of the present method was quantified from the decomposition of the vorticity distribution in its azimuthal components and compared with reported spectral results. Using identical grid resolution to the reference results yields negligible differences in the main features of the flow. The perturbation amplitude and its first harmonic are virtually identical to the reference results for both fourth‐ or tenth‐order spatial discretization, as theoretically expected but seldom a posteriori verified. The differences between the two spatial discretizations appear only for coarser grids, favouring the tenth‐order discretization. Copyright © 2005 John Wiley & Sons, Ltd.
A semi‐Lagrangian level set method for incompressible Navier–Stokes equations with free surface
Authors: Gutiérrez Leo Miguel González , Bermejo Rodolfo
Published: August 2005

In this paper, we formulate a level set method in the framework of finite elements‐semi‐Lagrangian methods to compute the solution of the incompressible Navier–Stokes equations with free surface. In our formulation, we use a quasi‐monotone semi‐Lagrangian scheme, which is both unconditionally stable and essentially non oscillatory, to compute the advective terms in the Navier–Stokes equations, the transport equation and the equation of the reinitialization stage for the level set function. The method we propose is quite robust and flexible with regard to the mesh and the geometry of the domain, as well as the magnitude of the Reynolds number. We illustrate the performance of the method in several examples, which range from a benchmark problem to test the volume conservation property of the method to the flow past a NACA0012 foil at high Reynolds number. Copyright © 2005 John Wiley & Sons, Ltd.
Simulation of daily discharges for the upper Durance catchment (French Alps) using subgrid parameterization for topography and a forest canopy climate model
Authors: Strasser Ulrich , Etchevers Pierre
Published: August 2005

This study describes the application of the coupled SAFRAN (meteorological variables), ISBA (soil–vegetation–atmosphere transfer) and CROCUS (snow cover evolution) models to simulate daily discharges for the upper Durance catchment (French Alps) from 1981 to 1994. The results are validated by comparison with measurements at three gauging stations located in the watershed. Previous investigations have shown a remarkable overestimation of the spring flood peak generated by the modelled snowmelt. It could be significantly improved by increasing the model resolution from 8 km to 1 km, thus more precisely considering the elevation‐dependent snowmelt process. However, it is also possible to use subgrid parameterizations at the coarse grid resolution to improve simulations. This paper investigates the influence of a subgrid parameterization for topography, a subgrid parameterization for the snow cover in a forest canopy and a combination of the two on the simulated spring flood peak. Results show a significant improvement in the simulations by both subgrid parameterizations, in particular by their combination: the Nash–Sutcliffe efficiency of the daily discharges is improved from 0·73 (original experiment) to 0·77 (subgrid topography), to 0·75 (forest) and to 0·78 (combination of subgrid topography and forest). Copyright © 2005 John Wiley & Sons, Ltd.
The role of social capital in the promotion of conservation farming: the case of ‘landcare’ in the Southern Philippines
Authors: Cramb R. A.
Published: August 2005

‘Social capital’ refers to the relationships of trust, communication, and cooperation that facilitate collective action in a community. It is particularly relevant to soil conservation in developing countries, which requires collective efforts to raise awareness of soil degradation, provide effective training in soil conservation practices, and implement soil conservation measures on individual farms. The Landcare Program in the Southern Philippines promotes simple conservation practices in upland environments through establishing and supporting community landcare groups and municipal landcare associations, thus augmenting the social capital of farmers in these locations. An evaluation of the Landcare Program in Barangay Ned, South Cotabato, based on a survey of 313 farm households and case studies of nine landcare groups, shows that, despite extreme isolation and difficult working conditions, farmers responded by rapidly forming landcare groups and a landcare association, and adopting contour barriers on their maize farms. They utilized the bonding social capital inhering in their local communities to build stocks of bridging social capital, linking them to information, training and resources from outside their immediate locality. A logistic regression model of the factors affecting adoption of contour barriers shows that farmers who had undergone the practical, farmer‐based training provided by the Landcare Program, and who were members of a landcare group, were significantly more likely to adopt conservation measures. These results confirm the value of investing in social capital to promote soil conservation. Copyright © 2005 John Wiley & Sons, Ltd.
Two cardinals models with gap one revisited
Authors: Shelah Saharon
Published: August 2005

We succeed to say something on the identities of (μ+, μ) when μ > θ > cf(μ) with μ strong limit θ‐compact or even μ is limit of compact cardinals. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The Necessary Maximality Principle for c. c. c. forcing is equiconsistent with a weakly compact cardinal
Authors: Hamkins Joel D. , Hugh Woodin W.
Published: August 2005

The Necessary Maximality Principle for c. c. c. forcing with real parameters is equiconsistent with the existence of a weakly compact cardinal. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Gas‐Phase Assisted Surface Polymerization Behavior of β‐Propiolactone on Inorganic and Organic Substrates and Consequent Composite Production
Authors: Nishida Haruo , Yamashita Mitsuhiro , Andou Yoshito , Jeong Jae‐Mun , Endo Takeshi
Published: August 2005

Summary: Gas‐phase assisted surface polymerization (GASP) of β‐propiolactone (βPL) was investigated using substrate‐supported anionic initiators to produce a strongly bonded poly(β‐propiolactone) (PPL)/CaO composite and a novel PPL crystalline deposit with a high melting point value on Al plates. The polymerization of βPL smoothly proceeded in the gas phase to give high‐molecular‐weight PPLs having high PDI values. An almost linear relationship between $\overline M _{\rm n}$ value and incremental increase in the deposit suggested the living nature of the GASP of βPL. The obtained polymer‐coated substrates, especially PPL/CaO composite, showed strong interaction at the organic/inorganic interface. Moreover, the thermal and structural analyses of deposits revealed that some specific conformations were formed on CaO powder and Al plate surfaces to give highly crystallized deposits. These results demonstrate that the GASP is an effective method for coating any substrate that has a complex shape and a surface morphology.

Accumulation process of poly(β‐propiolactone) on CaO as substrate‐supported initiator during GASP.

magnified image

Accumulation process of poly(β‐propiolactone) on CaO as substrate‐supported initiator during GASP.
Case report: Severe acute Parkinsonism associated with streptococcal infection and antibasal ganglia antibodies
Authors: McKee D.H. , Sussman J.D.
Published: August 2005

We report the case of a young man who presented with a severe acute akinetic–rigid disorder 2 weeks after complete recovery from an episode of pharyngitis. Magnetic resonance imaging scan abnormalities strikingly localized to the basal ganglia were accompanied by serological evidence of recent streptococcal infection and the presence of anti‐basal ganglia antibodies in the serum. The case represents an unusually clear example in the spectrum of inflammatory neurological disorders associated with streptococcal infection, an etiology that should be considered in the differential diagnosis of all acute onset movement disorders. © 2005 Movement Disorder Society
Unbiased contribution of the first two blastomeres to mouse blastocyst development
Authors: Alarcón Vernadeth B. , Marikawa Yusuke
Published: August 2005

Several recent studies have proposed a model that the organization of the mouse blastocyst is determined by the pattern of early cleavages: the plane of first cleavage divides the two‐cell embryo into embryonic (Em) and abembryonic (Ab) halves, while the timing of the second cleavages specifies which blastomere becomes the Em half. This model is still controversial because of conflicting observations in various studies. Here, we investigated the possibility that the difference between mouse strains contributed to the discrepancy of the findings of different experiments regarding the relationship between the first two cleavages and the blastocyst axial pattern. First, we showed by using a lipophilic, fluorescent tracer that the plane of the first cleavage bears no consistent spatial relationship to the Em‐Ab axis of the blastocyst regardless of the genotypic background. Secondly, the order of the second cleavage does not correlate with the Em‐Ab polarity of the blastocyst. This was demonstrated by tracing the lineage of the early‐ and later‐dividing two‐cell stage blastomeres in the whole embryo as well as by comparing the developmental potential of isolated early‐ and later‐dividing blastomeres and chimeras made entirely of early‐ or later‐dividing blastomeres. These results suggest that contrary to recent studies, the differences between the early‐ and later‐dividing blastomeres of the two‐cell embryo are not functionally evident and do not define the Em‐Ab polarity of the blastocyst. The significance of these findings is discussed in relation to human assisted reproduction and preimplantation genetic diagnosis. Mol. Reprod. Dev. © 2005 Wiley‐Liss, Inc.
Knockdown of the Dnmt1s transcript using small interfering RNA in primary murine and bovine fibroblast cells
Authors: Adams A.M. , Pratt S.L. , Stice S.L.
Published: August 2005

RNA interference (RNAi) has rapidly developed into one of the most widely applied technologies in molecular and cellular research, and although young, is now an essential experimental tool. The versatility of RNAi, especially in mammalian species, lends to its potential applications in a wide array of fields. Without having to genetically manipulate the genome, the ability to selectively reduce the level of a specific transcript using small interfering RNA (siRNA) molecules has great appeal in studying reprogramming issues in somatic cell nuclear transfer (SCNT) embryos. In such embryos, the aberrant expression of the somatic isoform of Dnmt1 (Dnmt1s), the enzyme responsible for maintaining DNA methylation in all somatic cells, has been implicated as one factor in the improper reprogramming of the donor genome. In the present study, the ability to develop a method allowing for the knockdown, or reduction, of Dnmt1s in primary fibroblast cells, like those commonly used as karyoplast donors in SCNT studies, was investigated in primary murine and bovine fibroblast cells as well as in a compromised cell line (NIH/3T3). Two Dnmt1s‐specific siRNA candidates were designed and tested. Using optimized conditions, these siRNAs were transiently transfected into the cells with total RNA and nuclear protein being collected. A 56.5% knockdown in Dnmt1s was achieved in the compromised and primary murine cells whereas Dnmt1s was reduced by 15.4% in the primary bovine cells. A reduction in Dnmt1s mRNA did not correspond to a reduction in protein as determined by immunodetection of Western blots. Overall, this study demonstrated the ability of siRNA to knockdown Dnmt1s mRNA in primary fibroblast donor cells. In order to substantially increase the efficiency while decreasing the anomalies seen in SCNT, novel techniques, like the one proposed, are needed to assist the oocyte's ability to reprogram a differentiated genome. Mol. Reprod. Dev. © 2005 Wiley‐Liss, Inc.
Novel thermally latent self‐crosslinkable copolymers bearing oxetane and hemiacetal ester moieties: The synthesis, self‐crosslinking behavior, and thermal properties
Authors: Komatsu Hiroyuki , Hino Tetsuo , Endo Takeshi
Published: August 2005

Novel thermally latent self‐crosslinkable copolymers (14 and 15) containing hemiacetal ester and oxetane moieties were synthesized by the radical copolymerizations of 1‐propoxyethyl methacrylate, 3‐ethyl‐3‐methacryloyloxymethyl oxetane, and/or n‐butyl methacrylate at 60 °C in the presence of 2,2′‐azoisobutylonitrile as an initiator. The obtained copolymers showed good solubility for common organic solvents such as tetrahydrofuran, chloroform, and dimethyl sulfoxide (DMSO). The thermal crosslinking behaviors were examined with several Lewis acid catalysts (6). In particular, the treatment with aluminum‐2‐ethylhexanate triethanolamine complex (6c) at 160 °C was found to efficiently yield the corresponding self‐crosslinked polymers (14′ and 15′). Incidentally, the resulting products were hardly insoluble in various organic solvents, including DMSO. The thermal properties of the obtained self‐crosslinked polymers 14′ and 15′ were estimated by thermogravimetric analysis and differential scanning calorimetry. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 4260–4270, 2005
Mass spectrometry identification of NASP binding partners in HeLa cells
Authors: Alekseev Oleg M. , Richardson Richard T. , Pope Marshall R. , O'Rand Michael G.
Published: August 2005

Nuclear autoantigenic sperm protein (NASP) is a linker histone binding protein that is cell‐cycle regulated. Synchronized HeLa cells are delayed in progression through the G1/S border when transiently transfected to overexpress full‐length NASP, but not the histone‐binding site (HBS) deletion mutant (NASP–ΔHBS). The purpose of the current study was to identify possible NASP‐associated proteins in HeLa cell nuclei that could elucidate NASP's influence on the cell cycle and chromatin remodeling. For this purpose, we employed a new approach: mass spectrometry identification of initially cross‐linked proteins after their separation in a second dimension by reducing SDS‐polyacrylamide gel electrophoresis (SDS‐PAGE). Of the twelve proteins identified, three appear to be relevant to NASP's function: heat shock protein 90 (HSP90), DNA‐activated protein kinase, and ATP‐dependent DNA helicase II (70‐kDa subunit). Individual protein–protein interactions were tested by immunoprecipitation techniques. This new method can be used for expedited identification of binding partners of different proteins in enriched fractions and as a complementary or alternative strategy to the yeast two‐hybrid system and immunoprecipitation methods. Proteins 2005. © 2005 Wiley‐Liss, Inc.
A comparative study of the semantics and pragmatics of enfin and finalement, in synchrony and diachrony
Authors: HANSEN MAJ-BRITT MOSEGAARD
Published: August 2005

This article compares and contrasts two related adverbs, enfin and finalement, in synchrony and diachrony. Both are polysemous in contemporary French, and largely intersubstitutable in many contexts. However, the functional range of enfin is much greater than that of finalement. Evidence is presented for the existence of a division of labour, such that speakers seem to favour finalement for more ‘literal’ functions, i.e. for the expression of temporal sequence, whereas enfin is preferred for more abstract, non-propositional functions. This is attributed to the respective formal properties and degree of grammaticalisation of the two expressions, which can also explain why enfin has developed a vastly greater range of abstract, non-propositional functions than finalement. The argument is supported by diachronic evidence that the functional extension of enfin has gone hand in hand with significant changes in the formal status of the expression, while functional extension of finalement stops at approximately the time when enfin begins to expand its range.
Locating adverbials in discourse
Authors: VIEU LAURE , BRAS MYRIAM , ASHER NICHOLAS , AURNAGUE MICHEL
Published: August 2005

This article analyses Locating Adverbials (LAs) such as un peu plus tard, ce matin, deux kilomètres plus loin (‘a little later’, ‘this morning’, ‘two kilometers further’) when they are dislocated to the left of the sentence (IP Adjuncts cases). Although not discourse connectives, in such a position, they seem to play an important part in structuring discourse. It is this contribution of LAs to discourse that we tackle, providing a descriptive analysis and a formal account grounded on Segmented Discourse Representation Theory. In particular, we deal with the frame introducer role of the LAs and with spatio-temporal interpretations of these markers occurring in trajectory descriptions.
Nest-site selection and nesting success of three hornbill species in Arunachal Pradesh, north-east India: Great Hornbill Buceros bicornis, Wreathed Hornbill Aceros undulatus and Oriental Pied Hornbill Anthracoceros albirostris
Authors: DATTA APARAJITA , RAWAT G. S.
Published: August 2005

Nest-site selection by the sympatric Great Hornbill Buceros bicornis, Wreathed Hornbill Aceros undulatus and Oriental Pied Hornbill Anthracoceros albirostris was investigated in a lowland tropical forest in Arunachal Pradesh, north-east India during 1997–2000. Information on two nests of Rufous-necked Hornbill Aceros nipalensis in higher-elevation forests is also presented. All species nested in live trees of three tree genera, 83% (n = 36) in Tetrameles nudiflora, an emergent deciduous softwood, relatively common in lowland foothill forests. No difference was recorded in nest-tree species or nesting habitats of sympatric hornbills, but there were a few differences in structural characteristics of nest-trees. Cavity size was the main variable separating the three species. Great Hornbills used larger cavities while Oriental Pied Hornbills used smaller cavities closer to riverine areas. Nesting was attempted at 64% of known sites and successful fledging of chicks was 80% overall (n = 72 nests, pooled over 4 years). Nest-trees in disturbed habitats near human habitation were used but were often abandoned or unsuccessful and 50% of all nest-trees were inactive by the end of the study. Potential large nest-trees had a density of 5.9/ha, that of the two most used species was 1.3/ha, and minimum nest densities of all three species was about 1 pair/km2. Interference competition for nest-sites was not observed, despite similarity in nest-tree characteristics, low nest density and high loss of nest-trees. Nest-site availability may naturally limit hornbill populations in the area, and additional loss of nesting habitat to human activities may exacerbate limited availability of breeding sites.
A numerical study of turbulent mixing in eruption clouds using a three‐dimensional fluid dynamics model
Authors: Suzuki Yujiro J. , Koyaguchi Takehiro , Ogawa Masaki , Hachisu Izumi
Published: August 2005

The dynamics of eruption clouds in explosive volcanic eruptions are governed by entrainment of ambient air into eruption clouds by turbulent mixing. We develop a new numerical pseudo gas model of an eruption cloud by employing three‐dimensional coordinates, a third‐order accuracy scheme, and a fine grid size in order to investigate the behavior of entrainment due to turbulent mixing. The quantitative features of entrainment are measured by a proportionality constant relating the inflow velocity at the edge of the flow to the average vertical velocity (i.e., the entrainment coefficient). Our model has successfully reproduced the quantitative features of entrainment observed in the laboratory experiments as well as fundamental features of the dynamics of eruption clouds, such as the generation of eruption columns and/or pyroclastic flows. The value of the entrainment coefficient for eruption clouds is estimated from the column height and critical condition for column collapse by comparing results of our model with those of previous one‐dimensional models. It is suggested that the value of the entrainment coefficient for an eruption cloud is approximately constant, although the value estimated from the critical condition for column collapse (k ∼ 0.07) is slightly smaller than that based on the column height (k ∼ 0.1). This difference reflects the vertical change of flow structure in the eruption cloud. The eruption cloud in the upper region exhibits a meandering instability, which leads to efficient mixing, whereas the cloud near the vent maintains a concentric structure with an inner dense core surrounded by an outer shear region. Our model is consistent with previous one‐dimensional models for steady eruption clouds supported by the laboratory experiments, and it is also applicable to unsteady and transient features of actual eruption clouds.
40Ar/39Ar dating of Apollo 12 impact spherules
Authors: Levine Jonathan , Becker Timothy A. , Muller Richard A. , Renne Paul R.
Published: August 2005

We have used the 40Ar/39Ar isochron technique to determine ages of 81 lunar spherules from Apollo 12 soil sample 12023. Most spherules are created in meteoroid impacts, and their ages correspond to the timing of the impacts that formed them. Of the 81 impacts we have dated, most occurred in the last 500 million years. The abundance of spherules from the most recent ∼10% of the history of the Moon is consistent with an increase in the meteoroid bombardment of the inner Solar System, but does not require this explanation. The soil sample from which we extracted our spherules was from the ejecta of a recent impact; our spherule age measurements support models of lunar soil mechanics and impact cratering in which ejecta are stratified and inverted relative to the stratigraphy that was present before the impact.
Molecular chaperones as therapeutic targets in amyotrophic lateral sclerosis
Authors: Kalmar B. , Kieran D. , Greensmith L.
Published: August 2005

Neurodegenerative diseases are characterized by a number of common hallmarks, such as the presence of intracellular aggregates and activation of the apoptotic cell-death pathway. Intracellular chaperones, responsible for protein integrity and structural repair, may play a crucial role in the progression of a disease. In this paper, we aim to summarize our understanding of the role and potential of a particular family of chaperones, the heat-shock proteins, in neurodegeneration, by focusing our discussion on models of motoneuron death.
Disease modifying strategies for the treatment of Alzheimer's disease targeted at modulating levels of the β-amyloid peptide
Authors: Pangalos M.N. , Jacobsen S.J. , Reinhart P.H.
Published: August 2005

AD (Alzheimer's disease) is characterized neuropathologically by the presence of amyloid plaques, neurofibrillary tangles and profound grey matter loss. The ‘amyloid’ hypothesis postulates that the toxic Aβ (amyloid β) peptide, enzymatically derived from the proteolytic processing of a larger protein called APP (amyloid precursor protein), is one of the principal causative factors of neuronal cell death in the brains of AD patients. As such, methods for lowering Aβ levels in the brain are of significant interest with regard to identifying novel disease modifying therapies for the treatment of AD. In this review, we will review a variety of approaches and mechanisms capable of modulating levels of Aβ.
Phenotype associated with recessively inherited mutations in DNA mismatch repair (MMR) genes
Authors: de Vos M. , Hayward B. , Bonthron D.T. , Sheridan E.
Published: August 2005

The MMR (DNA mismatch repair) system helps to maintain the integrity of the genome. This involves eliminating base–base mismatches and insertion/deletion loops, which can lead to microsatellite instability, as seen in tumour cells. Hereditary non-polyposis colon cancer is the result of dominant mutations in MMR genes, such as MLH1, MSH2 and MSH6. More recently there have been case reports of biallelic mutations in the MMR genes MLH1, MSH2 and PMS2. These result in a distinct autosomal recessive cancer predisposition syndrome. The syndrome is characterized by childhood haematological malignancies, brain tumours and the presence of café au lait patches. Second primaries occur frequently in this condition, and survival into adulthood is rare.
Flavocytochrome P450 BM3: an update on structure and mechanism of a biotechnologically important enzyme
Authors: Warman A.J. , Roitel O. , Neeli R. , Girvan H.M. , Seward H.E. , Murray S.A. , McLean K.J. , Joyce M.G. , Toogood H. , Holt R.A. , Leys D. , Scrutton N.S. , Munro A.W.
Published: August 2005

Since its discovery in the 1980s, the fatty acid hydroxylase flavocytochrome P450 (cytochrome P450) BM3 (CYP102A1) from Bacillus megaterium has been adopted as a paradigm for the understanding of structure and mechanism in the P450 superfamily of enzymes. P450 BM3 was the first P450 discovered as a fusion to its redox partner – a eukaryotic-like diflavin reductase. This fact fuelled the interest in soluble P450 BM3 as a model for the mammalian hepatic P450 enzymes, which operate a similar electron transport chain using separate, membrane-embedded P450 and reductase enzymes. Structures of each of the component domains of P450 BM3 have now been resolved and detailed protein engineering and molecular enzymology studies have established roles for several amino acids in, e.g. substrate binding, coenzyme selectivity and catalysis. The potential of P450 BM3 for biotechnological applications has also been recognized, with variants capable of industrially important transformations generated using rational mutagenesis and forced evolution techniques. This paper focuses on recent developments in our understanding of structure and mechanism of this important enzyme and highlights important problems still to be resolved.
Flavoenzyme catalysed oxidation of amines: roles for flavin and protein-based radicals
Authors: Rigby S.E. , Basran J. , Combe J.P. , Mohsen A.W. , Toogood H. , van Thiel A. , Sutcliffe M.J. , Leys D. , Munro A.W. , Scrutton N.S.
Published: August 2005

Amines are a carbon source for the growth of a number of bacterial species and they also play key roles in neurotransmission, cell growth and differentiation, and neoplastic cell proliferation. Enzymes have evolved to catalyse these reactions and these oxidoreductases can be grouped into the flavoprotein and quinoprotein families. The mechanism of amine oxidation catalysed by the quinoprotein amine oxidases is understood reasonably well and occurs through the formation of enzyme–substrate covalent adducts with TPQ (topaquinone), TTQ (tryptophan tryptophylquinone), CTQ (cysteine tryptophylquinone) and LTQ (lysine tyrosyl quinone) redox centres. Oxidation of amines by flavoenzymes is less well understood. The role of protein-based radicals and flavin semiquinone radicals in the oxidation of amines is discussed.
Anaerobic synthesis of vitamin B12: characterization of the early steps in the pathway
Authors: Frank S. , Brindley A.A. , Deery E. , Heathcote P. , Lawrence A.D. , Leech H.K. , Pickersgill R.W. , Warren M.J.
Published: August 2005

The anaerobic biosynthesis of vitamin B12 is slowly being unravelled. Recent work has shown that the first committed step along the anaerobic route involves the sirohydrochlorin (chelation of cobalt into factor II). The following enzyme in the pathway, CbiL, methylates cobalt-factor II to give cobalt-factor III. Recent progress on the molecular characterization of this enzyme has given a greater insight into its mode of action and specificity. Structural studies are being used to provide insights into how aspects of this highly complex biosynthetic pathway may have evolved. Between cobalt-factor III and cobyrinic acid, only one further intermediate has been identified. A combination of molecular genetics, recombinant DNA technology and bioorganic chemistry has led to some recent advances in assigning functions to the enzymes of the anaerobic pathway.
Biotin synthase mechanism: an overview
Authors: Lotierzo M. , Tse Sum Bui B. , Florentin D. , Escalettes F. , Marquet A.
Published: August 2005

Biotin synthase, a member of the ‘radical SAM’ (S-adenosylmethionine) family, converts DTB (dethiobiotin) into biotin. The active form of the Escherichia coli enzyme contains two (Fe-S) centres, a (4Fe-4S) and a (2Fe-2S). The (4Fe-4S)2+/+ mediates the electron transfer required for the reductive cleavage of SAM into methionine and a DOA• (deoxyadenosyl radical). Two DOA•, i.e. two SAM molecules, are consumed to activate the positions 6 and 9 of DTB. A direct transfer of isotope from the labelled substrate into DOAH (deoxyadenosine) has been observed with 2H, although not quantitatively, but not with tritium. The source of the sulphur introduced to form biotin is still under debate. We have shown that the (2Fe-2S)2+ cluster can be reconstituted in the apoenzyme with S2− and Fe2+. When S2− was replaced by [34S2−], [35S2−] or Se2−, biotin containing mostly the sulphur isotopes or selenium was obtained. This leads us to favour the hypothesis that the (2Fe-2S) centre is the sulphur donor, which may explain the absence of turnover of the enzyme. DTBSH (9-mercaptodethiobiotin), which already contains the sulphur atom of biotin, was shown to be an alternative substrate of biotin synthase both in vivo and with a crude extract. When this compound was tested with a well-defined in vitro system, the same turnover of one and similar reaction rates were observed for DTB and DTBSH. We postulate that the same intermediate is formed from both substrates.
Ubiquinone reduction in the photosynthetic reaction centre of Rhodobacter sphaeroides: interplay between electron transfer, proton binding and flips of the quinone ring
Authors: Mulkidjanian A.Y. , Kozlova M.A. , Cherepanov D.A.
Published: August 2005

This review is focused on reactions that gate (control) the electron transfer between the primary quinone QA and secondary quinone QB in the photosynthetic reaction centre of Rhodobacter sphaeroides. The results on electron and proton transfer are discussed in relation to structural information and to the steered molecular dynamics simulations of the QB ring flip in its binding pocket. Depending on the initial position of QB in the pocket and on certain conditions, the rate of electron transfer is suggested to be limited either by the quinone ring flip or by the charge-compensating proton equilibration between the surface and the buried QB site.
Optical emission from individual InGaAs quantum dots in single-defect photonic crystal nanocavity
Authors: Chang W.-H. , Chen W.-Y. , Chang H.-S. , Hsu T. M. , Hsieh T.-P. , Chyi J.-I.
Published: August 2005

Collective and individual emissions from In0.5Ga0.5As quantum dots (QDs) in single-defect photonic crystal nanocavities are investigated. When the cavity mode is collectively excited by the QD ensemble, a pair of dipolelike modes with definite linear polarizations is shown. Under low excitations, single-exciton emission lines are resolved. The power dependence of individual QD emissions reveals a nearly tenfold light enhancement for on-resonance QDs. The polarization state of each individual QD is also investigated. It is found that an individual dot could excite either a pure dipole mode or a mixture of both dipole modes. This behavior can be attributed to the random distribution of QDs in the nanocavity.
Resonant excitation of plasma oscillations in a partially gated two-dimensional electron layer
Authors: Popov V. V. , Polischuk O. V. , Shur M. S.
Published: August 2005

We have solved the problem of diffraction of terahertz radiation on a perfectly conductive gate strip that partially screens a two-dimensional (2D) electron layer located at some distance from the gate. Scattering and absorption spectra of such a structure reveal the fundamental plasma resonance excited under the gate. We have shown that the absorption enhancement factor at plasma resonance may reach very high values (up to 60). However, for narrow gate strips (with the width less than 100nm) the resonant scattering length of such a scatterer is shorter than its resonant absorption length by four orders of magnitude, which means that the gated plasmons in this case weakly couple to the terahertz radiation. We discuss the effects of interaction between plasma oscillations in gated and ungated regions of 2D electron layer and provide a qualitative explanation of the rather intensive terahertz emission from unstable gated plasmons in a 60-nm gate field-effect transistor observed recently.
The mechanism of linear and nonlinear optical effects in fluoride crystals
Authors: Tong Yongzai , Meng X. Y. , Wang Z. Z. , Chen Chuangtian , Lee Ming-Hsien
Published: August 2005

Electronic structure calculations of Na2SbF5, BaMgF4, and BaZnF4 are performed from first principles based on a plane-wave pseudopotential method. The linear optical properties and the static second-harmonic generation coefficients are also calculated. Furthermore, a real-space atom-cutting method is employed to analyze the respective contributions of the anionic groups and cations in Na2SbF5 to the optical response. The results show that the anionic groups (SbF5)2− in the crystal are quite favorable for producing larger microscopic second-order susceptibilities.
Growth and characterization of Si1−xMnx alloys on Si(100)
Authors: Zhang Yangting , Jiang Qian , Smith David J. , Drucker Jeff
Published: August 2005

Si 1 − x Mn x alloy films of 50 nm thickness with 0.005⩽x⩽0.035 were grown by low-temperature molecular-beam epitaxy onto Si(100) substrates held at temperatures T in the range of 150°C⩽T⩽350°C. All films exhibit surface roughness with ∼20-nm-lateral and ∼1-nm-vertical length scales. This roughness is random for films with small x grown at the lower end of the temperature range. Films with larger x grown at higher T exhibit roughness organized into ⟨110⟩-oriented cluster arrays centered on shallow surface depressions. This organized roughness correlates with the formation of subsurface complexes of four {111} planar defects or “funnel” defects. Mn-rich, nanometer-sized nodules form near the bottom of the Si1−xMnx film and seed the formation of vertical, amorphous nanopipes. For growth of small x films at the lower end of the temperature range, these vertical nanopipes extend to the surface. In contrast, films with larger x grown at higher T form funnel defects which appear to emanate from the vertical nanopipes. Regardless of growth conditions, the Mn-rich nodules appear crystalline and do not correlate to any known Si–Mn phase. Ion channeling indicates that up to 90% of the Mn is substitutionally incorporated for samples with x=0.005. Although the substitutional fraction decreases with increasing x, the substitutional content increases. Our results indicate that Mn may be substitutionally incorporated in epitaxial thin films at concentrations of several orders of magnitude greater than its equilibrium solubility.
Criterion for the occurrence of the gas-liquid phase transition
Authors: Wang Xian-Zhi
Published: August 2005

Using Yang-Lee theory of phase transition and our extension, it is found that for a real fluid, both the singularity of canonical partition function and the critical point of the gas-liquid phase transition occur precisely at the temperature when all the cluster integrals become positive. The critical temperature is determined by the limit of the first zeros of the cluster integrals.
Investigation of laser beam-induced current techniques for heterojunction photodiode characterization
Authors: Redfern D. A. , Fang W. , Ito K. , Bahir G. , Musca C. A. , Dell J. M. , Faraone L.
Published: August 2005

A reduced model is developed that has significant advantages over the full drift-diffusion model for the simulation of laser beam-induced current (LBIC) signals in the presence of heterojunctions. The model determines the contribution to the LBIC signal that would occur from photogeneration at any position within the semiconductor, and is particularly useful for heterostructures where judicious choice of illumination wavelength can result in photogeneration at different depths within the device structure. The reduced model is used to examine the basic features of LBIC as applied to two types of planar P-n HgCdTe heterojunction photodiode structures. In particular, the question of correctly identifying erroneous device structures formed during the fabrication process is addressed, and experimental measurements are presented to support the simulation results.
Donor-acceptor pair emission enhancement in mass-transport-grown GaN
Authors: Paskova T. , Arnaudov B. , Paskov P. P. , Goldys E. M. , Hautakangas S. , Saarinen K. , Södervall U. , Monemar B.
Published: August 2005

A dominating donor-acceptor pair (DAP) emission at about 3.27eV is observed in the photoluminescence and cathodoluminescence spectra of intentionally undoped mass-transport (MT)-grown GaN, while only a weak presence of the DAP emission is recorded in the as-grown hydride vapor phase epitaxial GaN. A comparative study of impurity and native defect incorporation in the as-grown and MT GaN was performed, showing a significant increase of oxygen and empty clusters involving Ga vacancy and oxygen in the MT GaN. Based on the observed results as well as on doping analysis of the structure and kinetic analysis of the emission intensities, we propose an acceptorlike complex, creating a state as a semiclassical potential well near the valence-band top due to the local tensile strain caused by the empty clusters to be responsible for the dominating behavior of the DAP emission.
Current density and poloidal magnetic field for toroidal elliptic plasmas with triangularity
Authors: Martín P. , Haines M. G. , Castro E.
Published: August 2005

Changes in the poloidal magnetic field around a tokamak magnetic surface due to different values of triangularity and ellipticity are analyzed in this paper. The treatment here presented allows the determination of the poloidal magnetic field from knowledge of the toroidal current density. Different profiles of these currents are studied. Improvements in the analytic forms of the magnetic surfaces have also been found. The treatment has been performed using a recent published system of coordinates. Suitable analytic equations have been used for the elliptic magnetic surfaces with triangularity and Shafranov shift.
Study of CoFeSiB glass-covered amorphous microwires under applied stress
Authors: Carara M. , Sossmeier K. D. , Viegas A. D. C. , Geshev J. , Chiriac H. , Sommer R. L.
Published: August 2005

Magnetoimpedance-based ferromagnetic resonance (FMR) studies of annealed Co68.15Fe4.35Si12.5B15 glass-covered amorphous microwires under stress are reported. The applied stress modifies the anisotropy and the domain structure present in each sample, in such a way that it can be studied through magnetoimpedance measurements and FMR dispersion relations extracted from them. From the fitting of the FMR dispersion relations, the magnitude and the orientation of the transverse anisotropy field, as well as an insight on the micromagnetic structure of glass-covered microwires, were obtained. From these studies, it can be concluded that a longitudinal anisotropy dominates the microwire behavior under zero stress. By applying an increasing stress to the microwires, an inner core with a longitudinal anisotropy surrounded by an outer shell with a circumferential anisotropy develops and dominates its magnetic behavior.
The magnitude of sawtooth crash events in multiple and quasi-single helicity states in a reversed-field-pinch plasma
Authors: Yagi Y. , Frassinetti L. , Hirano Y. , Koguchi H. , Sakakita H.
Published: August 2005

Factors affecting the magnitude of sawtooth crashes in soft x-ray (SXR) signals (ISXR) have been studied using data from high-Θ (pinch parameter) discharges in the toroidal pinch experiment TPE-1RM20 reversed-field pinch device [Y. Yagi et al., J. Plasma Fusion Research 69, 700 (1993)]. In TPE-1RM20, discharges with a high Θ that are free of large sawteeth (improved high-Θ mode discharges), spontaneously appeared [Y. Hirano et al., Nucl. Fusion 36, 721 (1996)] among typical conventional discharges exhibiting large sawtooth crashes. The reason for the spontaneous appearance of sawtooth-free discharges has been unclear. It is shown that the normalized magnitude of the SXR crashes, [Δ(ISXR)∕ISXR], is well correlated with the m(poloidalmodenumber)=0 mode amplitude in the postcrash phase. It is also shown that Δ(ISXR)∕ISXR is smaller when the quasi-single helicity state precedes the crash rather than when the multiple-helicity state precedes the crash, and Δ(ISXR)∕ISXR is smaller when E‖ (the parallel electric field at the plasma surface) is approximately zero in the precrash phase rather than E‖ being negative.
Neoclassical reversed-field pinch equilibrium with dominant self-induced plasma current
Authors: Shiina S. , Nagamine Y. , Taguchi M. , Aizawa M. , Osanai Y. , Yagi Y. , Hirano Y. , Ashida H. , Koguchi H. , Saito K. , Sakakita H. , Sugimoto H. , Watanabe M.
Published: August 2005

The neoclassical magnetohydrodynamic equilibrium of reversed-field pinch (RFP) is self-consistently solved considering the self-induced plasma current IϕSI in a reactor relevant parameter regime. The current IϕSI consists of bootstrap currents due to α particles as well as the bulk plasma, where the conventional neoclassical transport theory is applied without considering the finite banana-width effect, Pfirsch–Schluter current, and diamagnetic current. The neoclassical effect enhances IϕSI in a low-aspect-ratio RFP (aspect ratio A=2), when β is high. An IϕSI as high as 94.4% of the plasma current in the equilibrium with ellipticity κ=1.4 and triangularity δ=0.4 is obtained with a flat pressure profile, which provides a toroidal β of βt=63% (volume-averaged β, ⟨β⟩=66%) stable against both the ideal kink mode and Mercier mode. This dominant self-induced current makes the steady-state approach feasible. Its hollow current profile gives a strong magnetic shear and a high-stability β.
Diffraction-limited two-dimensional hard-x-ray focusing at the 100nm level using a Kirkpatrick-Baez mirror arrangement
Authors: Matsuyama S. , Mimura H. , Yumoto H. , Yamamura K. , Sano Y. , Endo K. , Mori Y. , Nishino Y. , Tamasaku K. , Ishikawa T. , Yabashi M. , Yamauchi K.
Published: August 2005

The spatial resolution of scanning x-ray microscopy depends on the beam size of focused x rays. Recently, nearly diffraction-limited line focusing has been achieved using elliptical mirror optics at the 100nm level. To realize such focusing two-dimensionally in a Kirkpatrick-Baez system, the required accuracies of the mirror aligners in this system were estimated using optical simulators based on geometrical or wave-optical theories. A focusing unit fulfilling the required adjustment accuracies was constructed. The relationships between alignment errors and focused beam profiles were quantitatively examined at the 1km long beamline (BL29XUL) of SPring-8 to be in good agreement with the simulation results.