bluuebunny/crossref_metadata_2025 huggingface dataset:
Development, validation and evaluation of a homogenous one-step reverse transcriptase-initiated PCR assay with competitive internal control for the detection of hepatitis C virus RNA
Authors: Mueller Jens , Gessner Matthias , Remberg Anja , Hoch Jochen , Zerlauth Gerold , Hanfland Peter
Published: August 2005

Nucleic acid amplification testing for hepatitis C virus (HCV) RNA has become an essential tool for the prevention and clinical management of hepatitis C. We describe the development, validation and evaluation of a homogenous reverse transcriptase-initiated HCV-PCR assay with competitive internal control that is applicable to both the quantitative detection of HCV genomes in single patient samples and the screening of blood donations by mini-pool testing. For the implementation of a positive run control, a HCV RNA-positive plasma sample was calibrated against an international HCV RNA standard preparation. For quantification purposes, an in vitro-transcribed RNA calibrator sequence was used. The detection limit of the assay (95% positive cut-off) was determined by probit analysis and was calculated as 114IU/mL. Comparable sensitivity to different HCV template sequences was verified for HCV genotypes 1–5. Quantitative test results correlated well with viral loads that had been previously determined by the Bayer VERSANT HCV RNA 3.0 bDNA assay (n=53, R=0.943, p<0.001). During more than 5years of blood donation testing, the specificity of the assay was found to be 99.51%. All assay components showed constant performance during this time period. In conclusion, we introduce a well-proven method that allows fast and reliable quantification of HCV genomes.
Preliminary evaluation of the performance of a new, highly sensitive commercial immunoassay for serum ferritin determination
Authors: Signò Paolo , Barassi Alessandra , Novario Raffaele , Melzi d'Eril Gian Vico
Published: August 2005

We evaluated the analytical performance of a new, commercial, fully automated immunoturbidimetric assay for the determination of ferritin [FER-Latex(X2)CN SEIKEN, Denka Seiken, Japan] in serum on the Olympus AU2700 analyzer. The new assay is a latex-enhanced turbidimetric immunoassay with an analysis time of 10min. The linearity of the assay was confirmed up to 2505pmol/L (R
Reconstruction of Chemically Burned Rat Corneal Surface by Bone Marrow–Derived Human Mesenchymal Stem Cells
Authors: Ma Yanling , Xu Yongsheng , Xiao Zhifeng , Yang Wei , Zhang Chun , Song E. , Du Yiqin , Li Lingsong
Published: August 2005

To examine whether transplantation of human mesenchymal stem cells (MSCs) could reconstruct the corneal damage and also whether grafted MSCs could differentiate into corneal epithelial cells, we isolated MSCs from healthy donors. After growth and expansion on amniotic membrane, cells were transplanted into rat corneas 7 days after chemical burns. Reconstruction of the damaged cornea and the rat vision were measured once a week by slit lamp and by an optokinetic head-tracking instrument, respectively. Corneas were then cut out, fixed, and imbedded for immunofluorescent study of the expression of keratin 3 and keratin-pan as epithelial cell markers. Expression of CD45, interleukin 2, and metalloproteinase-2 was also investigated for inflammation and inflammation-related angiogenesis. The data showed that transplantation of MSCs, like limbal epithelial stem cells, successfully reconstructed damaged rat corneal surface. Interestingly, the therapeutic effect of the transplantation may be associated with the inhibition of inflammation and angiogenesis after transplantation of MSCs rather than the epithelial differentiation from MSCs. This study provides the first line of evidence that MSCs can be used for reconstruction of damaged corneas, presenting a new source for autotransplantation in the treatment of corneal disorders.
The epidermal growth factor receptor family
Authors: Bazley L A , Gullick W J
Published: August 2005

The epidermal growth factor receptor family consists of four receptor genes and at least 11 ligands, several of which are produced in different protein forms. They create an interacting system that has the ability to receive and process information that results in multiple outputs. The family has an important role in directing and coordinating many normal processes, including growth and development, normal tissue turnover and wound healing. Its members are also aberrantly activated by overexpression or mutation in many common human tumour types and as such have been the target for anticancer drug development.
Overview of tyrosine kinase inhibitors in clinical breast cancer
Authors: Agrawal A , Gutteridge E , Gee J M W , Nicholson R I , Robertson J F R
Published: August 2005

Studies of cell models and profiling of clinical breast cancer material to reveal the mechanisms of resistance to anti-oestrogen therapy, and to tamoxifen in particular, have reported that this phenomenon can be associated with increased expression and signalling through erbB Type 1 growth factor receptors, notably the epidermal growth factor receptor (EGFR) and HER2. Further molecular studies have revealed an intricate interlinking between such growth factor receptor pathways and oestrogen receptor (ER) signalling. Inhibition of receptor tyrosine kinase activity involved in the EGFR signalling cascade forms the basis for the use of EGFR specific tyrosine kinase inhibitors exemplified by gefitinib (ZD1839, Iressa) and erlotinib (OSI-774, Tarceva). Such agents have proved promising in pre-clinical studies and are currently in clinical trials in breast cancer, where gefitinib has been studied more extensively to date. Here, we present an overview of the current development of gefitinib in clinical breast cancer. This includes results from our clinical breast cancer trial 1839IL/0057 that demonstrate the efficacy of gefitinib within ER-positive, tamoxifen-resistant patients with locally advanced/metastatic disease, where parallel decreases in EGFR signal transduction and the Ki67 (MIB1) proliferation marker can be detected as predicted from model system studies. We also consider trials examining combination treatment with gefitinib and anti-hormonal strategies that will begin to address the clinically important question of whether gefitinib can delay/prevent onset of anti-hormone resistance.
A family with X‐linked anophthalmia: Exclusion of SOX3 as a candidate gene
Authors: Slavotinek Anne , Lee Stephen S. , Hamilton Steven P.
Published: August 2005

We report on a four‐generation family with X‐linked anophthalmia in four affected males and show that this family has LOD scores consistent with linkage to Xq27, the third family reported to be linked to the ANOP1 locus. We sequenced the SOX3 gene at Xq27 as a candidate gene for the X‐linked anophthalmia based on the high homology of this gene to SOX2, a gene previously mutated in bilateral anophthlamia. However, no amino acid sequence alterations were identified in SOX3. We have improved the definition of the phenotype in males with anophthalmia linked to the ANOP1 locus, as microcephaly, ocular colobomas, and severe renal malformations have not been described in families linked to ANOP1. © 2005 Wiley‐Liss, Inc.
CH/π hydrogen bonds as evidenced in the substrate specificity of acetylcholine esterase
Authors: Umezawa Yoji , Nishio Motohiro
Published: August 2005

The crystal structure of acetylcholine esterase (AchE) in complex with various inhibitors, investigated as drugs for improvement of the cognitive ability of early stage Alzheimer's disease, has been analyzed with the use of our program CHPI. A number of CH/π hydrogen bonds have been disclosed in the binding of the inhibitors with Torpedo californica AchE. It has been demonstrated that, in order to be effective in the binding with AchE, C—H bonds in the inhibitor need not be polarized. © 2005 Wiley Periodicals, Inc. Biopolymers 79: 248–258, 2005

This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
The Chemistry of Wine Polyphenolic C‐Glycosidic Ellagitannins Targeting Human Topoisomerase II
Authors: Quideau Stéphane , Jourdes Michael , Lefeuvre Dorothée , Montaudon Danièle , Saucier Cédric , Glories Yves , Pardon Patrick , Pourquier Philippe
Published: August 2005

Polyphenolic nonahydroxyterphenoyl‐containing C‐glycosidic oak ellagitannins are found in wine as a result of the aging of this beverage in oak‐made barrels. Once in the slightly acidic wine (pH∼3–4), some of these complex natural products such as (−)‐vescalagin (1), but not its C‐1 epimer (−)‐castalagin (2), can capture grape‐derived nucleophilic entities such as ethanol, the flavanols catechin (10 a) and epicatechin (10 b), the anthocyanin oenin (13 b), and the thiolic glutathione (16) to furnish condensation products with retention of configuration at the C‐1 locus. A computer‐aided rationale of this high diastereoselectivity is given. These condensation products can contribute to the modulation of organoleptic properties of the wine, as evidenced by the 23 nm bathochromic shift color absorbance observed with the novel oenin‐based anthocyano‐ellagitannin (15 b). Hydrolysis of 1 under solvolytic conditions furnished another novel compound that we refer to as vescalene (21), in addition to the known (−)‐vescalin (18). Of pharmacological importance is the fact that most of these found‐in‐wine water‐soluble ellagitannin derivatives are much more potent than etoposide (VP‐16) at inhibiting top2‐mediated DNA decatenation in vitro (top2=topoisomerase II)). The known (−)‐vescalin (18) and the novel vescalene (21) fully inhibited top2 at 10 μM concentration!
Enantioselective binding to the human organic cation transporter‐1 (hOCT1) determined using an immobilized hOCT1 liquid chromatographic stationary phase
Authors: Moaddel R. , Patel S. , Jozwiak K. , Yamaguchi R. , Ho P.C. , Wainer I.W.
Published: August 2005

A liquid chromatography stationary phase containing immobilized membranes obtained from a cell line that expresses the human organic cation transporter (hOCT1–IAM) has been used to study the binding of the enantiomers of propranolol, atenolol, pseudoephedrine, and α‐methylbenzylamine to the immobilized hOCT1. Frontal displacement chromatography was used to determine the binding affinities (Kd values), and the data demonstrate that there was an enantioselective difference in the Kd values of the enantiomers of propranolol, atenolol, and pseudoephedrine, while α‐methylbenzylamine did not significantly bind to the transporter. Competitive inhibition studies with the cell line used to create the chromatographic column demonstrated that, for the enantiomers of propranolol, the ratio of the chromatographically determined Kd values [Kd (+)‐(R)‐propranolol/Kd (−)‐(S)‐propranolol = 2.98] reflected an enantioselective difference in the functional activity of the two enantiomers [IC50 (+)‐(R)‐propranolol/IC50 (−)‐(S)‐propranolol = 2.75]. The chromatographically determined Kd values were used to construct an initial pharmacophore which contains a hydrogen bond donating site that appears to be responsible for the observed enantioselectivity. Published 2005 Wiley‐Liss, Inc.† Chirality 17:501–506, 2005.
Purification and characterization of rat liver enzyme catalyzing stereoselective reduction of acetylpyridines
Authors: Uwai Koji , Konno Noboru , Kitamura Shigeyuki , Ohta Shigeru , Takeshita Mitsuhiro
Published: August 2005

Acetylpyridines (1–3) are known as aroma components of foods, perfumes, and smoking suppressants, showing several biological activities and constituting part of the structure of some important biologically active compounds. We purified and characterized an enzyme that catalyzes the stereoselective reduction of acetylpyridines so that we could clarify its function. The enzyme participating in the reductive metabolism of 4‐acetylpyridine (1) in the rat liver was purified by successively applying ammonium sulfate fractionation, anion‐exchange, gel filtration, and affinity chromatography, and it was definitively identified as 3α‐HSD. It preferentially reduced acetylpyridines (1–3) and acetophenone (7) to their corresponding (S)‐alcohols, with high enantioselectivity. Kinetic analyses of the compounds were performed, and the Vmax/Km values decreased in the order of 4‐, 2‐, and 3‐acetylpyridine (1, 3, 2), while acetophenone (7) showed almost the same value as 3‐acetylpyridine (2). These results suggested that the reduction of the substrates by 3α‐HSD is affected by the nitrogen atom in the aromatic ring. © 2005 Wiley‐Liss, Inc. Chirality 17:494–500, 2005.
Solvent and Protein Effects on the Structure and Dynamics of the Rhodopsin Chromophore
Authors: Röhrig Ute F. , Guidoni Leonardo , Rothlisberger Ursula
Published: August 2005

The structure and dynamics of the retinal chromophore of rhodopsin are investigated systematically in different environments (vacuum, methanol solution, and protein binding pocket) and with different computational approaches (classical, quantum, and hybrid quantum mechanics/molecular mechanics (QM/MM) descriptions). Finite temperature effects are taken into account by molecular dynamics simulations. The different components that determine the structure and dynamics of the chromophore in the protein are dissected, both in the dark state and in the early photointermediates. In vacuum and in solution the chromophore displays a very high flexibility, which is significantly reduced by the protein environment. In the 11‐cis chromophore, the bond‐length alternation, which is correlated with the dipole moment, is found to be similar in solution and in the protein, while it differs greatly with respect to minimum‐energy vacuum structures. In the model of the earliest protein photointermediate, the highly twisted chromophore shows a very reduced bond‐length alternation.
Facial recognition in primary focal dystonia
Authors: Rinnerthaler Martina , Benecke Cord , Bartha Lisa , Entner Tanja , Poewe Werner , Mueller Joerg
Published: August 2005

The basal ganglia seem to be involved in emotional processing. Primary dystonia is a movement disorder considered to result from basal ganglia dysfunction, and the aim of the present study was to investigate emotion recognition in patients with primary focal dystonia. Thirty‐two patients with primary cranial (n = 12) and cervical (n = 20) dystonia were compared to 32 healthy controls matched for age, sex, and educational level on the facially expressed emotion labeling (FEEL) test, a computer‐based tool measuring a person's ability to recognize facially expressed emotions. Patients with cognitive impairment or depression were excluded. None of the patients received medication with a possible cognitive side effect profile and only those with mild to moderate dystonia were included. Patients with primary dystonia showed isolated deficits in the recognition of disgust (P = 0.007), while no differences between patients and controls were found with regard to the other emotions (fear, happiness, surprise, sadness, and anger). The findings of the present study add further evidence to the conception that dystonia is not only a motor but a complex basal ganglia disorder including selective emotion recognition disturbances. © 2005 Movement Disorder Society
Poly‐(L‐alanine) expansions form core β‐sheets that nucleate amyloid assembly
Authors: Shinchuk Leonid M. , Sharma Deepak , Blondelle Sylvie E. , Reixach Natalia , Inouye Hideyo , Kirschner Daniel A.
Published: August 2005

Expansion to a total of 11–17 sequential alanine residues from the normal number of 10 in the polyadenine‐binding protein nuclear‐1 (PABPN1) results in formation of intranuclear, fibrillar inclusions in skeletal muscle and hypothalamic neurons in adult‐onset, dominantly inherited oculopharyngeal muscular dystrophy (OPMD). To understand the role that homopolymeric length may play in the protein misfolding that leads to the inclusions, we analyzed the self‐assembly of synthetic poly‐(L‐alanine) peptides having 3–20 residues. We found that the conformational transition and structure of polyalanine (polyAla) assemblies in solution are not only length‐dependent but also are determined by concentration, temperature, and incubation time. No β‐sheet complex was detected for those peptides characterized by n < 8, where n is number of alanine residues. A second group of peptides with 7 < n < 15 showed varying levels of complex formation, while for those peptides having n > 15, the interconversion process from the monomeric to the β‐sheet complex was complete under any of the tested experimental conditions. Unlike the typical tinctorial properties of amyloid fibrils, polyalanine fibrils did not show fluorescence with thioflavin T or apple‐green birefringence with Congo red; however, like amyloid, X‐ray diffraction showed that the peptide chains in these fibrils were oriented normal to the fibril axis (i.e., in the cross‐β arrangement). Neighboring β‐sheets are quarter‐staggered in the hydrogen‐bonding direction such that the alanine side‐chains were closely packed in the intersheet space. Strong van der Waals contacts between side‐chains in this arrangement likely account for the high stability of the macromolecular fibrillar complex in solution over a wide range of temperature (5–85°C), and pH (2–10.5), and its resistance to denaturant (< 8 M urea) and to proteases (protease K, trypsin). We postulate that a similar stabilization of an expanded polyalanine stretch could form a core β‐sheet structure that mediates the intermolecular association of mutant proteins into fibrillar inclusions in human pathologies. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Quantum computational analysis for drug resistance of HIV‐1 reverse transcriptase to nevirapine through point mutations
Authors: He Xiao , Mei Ye , Xiang Yun , Zhang Da W. , Zhang John Z.H.
Published: August 2005

Quantum chemical calculation has been carried out to analyze binding interactions of nevirapine to HIV‐1 reverse transcriptase (RT) and single point mutants Lys103 → Asn (K103N) and Tyr181→ Cys (Y181C). In this study, the entire system of HIV‐1 RT/nevirapine complex with over 15,000 atoms is explicitly treated by using a recently developed MFCC (molecular fractionation with conjugate caps) approach. Quantum calculation of protein–drug interaction energy is performed at Hartree‐Fock and DFT levels. The RT‐nevirapine interaction energies are computed at fixed geometries given by the crystal structures of the HIV‐1 RT/nevirapine complexes from protein data bank (PDB). The present calculation provides a quantum mechanical interaction spectrum that explicitly shows interaction energies between nevirapine and individual amino‐acid fragments of RT. Detailed interactions that are responsible for drug resistance of two major RT mutations are elucidated based on computational analysis in relation to the crystal structures of binding complexes. The present result provides a qualitative molecular understanding of HIV‐1 RT drug resistance to nevirapine and gives useful guidance in designing improved inhibitors with better resistance to RT mutation. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Database for three dimensional structures of pepsin‐like enzymes using the internal coordinate system
Authors: Russ A. , Pechik I. , Andreeva N.
Published: August 2005

A database for 3D structures of pepsin‐like enzymes has been created on the basis of a novel approach using the Internal Coordinate System (ICS). It allows rapid comparison of multiple structures of pepsin‐like enzymes without the need for preliminary calculations. Atomic displacements measured by this approach are very close to those estimated by the superposition procedures widely employed in comparing three‐dimensional structures of proteins. Any new structure of pepsin‐like enzyme converted to the ICS automatically becomes superimposed with all structures in a database. The ICS approach can be used for any class of enzymes and is especially efficient for families containing a large number of homologous structures. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Are tattooing and body piercing indicators of risk‐taking behaviours among high school students?
Authors: Deschesnes Marthe , Finès Philippe , Demers Stéphanie
Published: August 2005

Purpose

To date, studies pertaining to possible links between body modification and risk‐taking behaviours have been conducted mainly among targeted groups. The objective of this study is to examine the influence of a number of risk‐taking behaviours on the probability of being pierced or tattooed among a general adolescent population.

Methods

Data come from a cross‐sectional study conducted among a sample of 2180 students aged 12–18. Data were collected directly from students through a self‐report survey.

Results

Findings confirm the “risky” nature of these practices even though the tattooed and pierced subjects of this study were from a general adolescent population. Factors that contribute significantly to the likelihood of teenagers being tattooed or pierced, for both genders, are associated with “externalized risk behaviours” such as multiple drug use, illegal activities, gang affiliation, problem gambling, school truancy and rave attendance.

Conclusion

Nowadays, tattooing and body piercing are perceived by many as body decoration, increasingly belonging to the realm of generational conformity. Contrary to this view, our results suggest that these practices among adolescents are mostly adopted by those who are involved in various deviant or illegal activities, which are often interrelated.
Anaemia and coronary artery disease severity in patients with heart failure
Authors: Felker G. Michael , Stough Wendy Gattis , Shaw Linda K. , O'Connor Christopher M.
Published: August 2005

Background

Anaemia is common in heart failure (HF) and associated with higher mortality. Exacerbation of myocardial ischemia in patients with heart failure, coronary disease, and anaemia patients has been suggested as a potential mechanism underlying this association.

Aims

The aim of this study was to evaluate the hypothesis that greater CAD severity would exacerbate the adverse effects of anaemia in HF.

Methods

We examined data on patients with symptomatic heart failure (NYHA class ≥II) undergoing coronary angiography between 1995 and 2003 (n=4951). Patients with primary valvular or congenital heart disease were excluded. Cox proportional hazards modeling was used to evaluate the relationship between coronary disease severity (as defined by no. of diseased vessels) and hemoglobin concentration.

Results and conclusions

In patients with symptomatic HF undergoing coronary angiography, we found an interaction between hemoglobin and CAD severity (p=0.003 for interaction). Contrary to our hypothesis, the mortality hazard associated with anaemia was greatest in patients without CAD and progressively lower with increasing CAD severity. These data suggest that anaemia may exert its effect on HF outcomes through mechanisms beyond simply the exacerbation of myocardial ischemia.
Perlecan from human epithelial cells is a hybrid heparan/chondroitin/keratan sulfate proteoglycan
Authors: Knox S. , Fosang A.J. , Last K. , Melrose J. , Whitelock J.
Published: August 2005

Perlecan is a multidomain proteoglycan, usually substituted with heparan sulphate (HS), and sometimes substituted with both HS and chondroitin sulphate (CS). In this paper, we describe perlecan purified from HEK‐293 cells substituted with HS, CS and keratan sulphate (KS). KS substitution was confirmed by immunoreactivity with antibody 5D4, sensitivity to keratanase treatment, and fluorophore‐assisted carbohydrate electrophoresis. HEK‐293 perlecan failed to promote FGF‐dependent cell growth in an in vitro assay. This study is the first to report perlecan containing KS, and makes perlecan one of only a very few proteoglycans substituted with three distinct types of glycosaminoglycan chains.
Biochemical characterization of the HydE and HydG iron‐only hydrogenase maturation enzymes from Thermatoga maritima
Authors: Rubach Jon K. , Brazzolotto Xavier , Gaillard Jacques , Fontecave Marc
Published: August 2005

Fe‐only hydrogenases contain a di‐iron active site complex, in which the two Fe atoms have carbon monoxide and cyanide ligands and are linked together by a putative di(thiomethyl)amine molecule. We have cloned, purified and characterized the HydE and HydG proteins, thought to be involved in the biosynthesis of this peculiar metal site, from the thermophilic organism Thermotoga maritima. The HydE protein anaerobically reconstituted with iron and sulfide binds two [4Fe–4S] clusters, as characterized by UV and EPR spectroscopy. The HydG protein binds one [4Fe–4S] cluster, and probably an additional one. Both enzymes are able to reductively cleave S‐adenosylmethionine (SAM) when reduced by dithionite, confirming that they are Radical‐SAM enzymes.
Evidence for p62 aggregate formation: Role in cell survival
Authors: Paine Michael G. , Ramesh Babu J. , Seibenhener M. Lamar , Wooten Marie W.
Published: August 2005

The polyubiquitin‐binding protein p62 has been shown to localize in aggregates common to several types of diseases. Here, we report that p62 forms independent fibrillar aggregates in vitro in a time‐ and concentration‐dependent manner. FTIR spectra and ThT fluorescence assay of p62 reveals increased β‐sheet content as aggregates form compared to the native protein. The fibrillar nature of the aggregates was observed by transmission electron microscopy. Overexpression of p62 in HEK cells results in aggregate formation that may protect cells from apoptosis. Altogether, these results suggest that p62 fibrils may influence cell viability and indicates an important role for p62 in aggresome formation.
Vaginal misoprostol for cervical priming before hysteroscopy in perimenopausal and postmenopausal women
Authors: Barcaite E. , Bartusevicius A. , Railaite D.R. , Nadisauskiene R.
Published: August 2005

Objective: To evaluate the effectiveness and possible adverse effects of vaginal misoprostol for cervical priming before hysteroscopy in perimenopausal and postmenopausal women. Methods: A total of 105 women scheduled for hysteroscopy were randomly assigned to 2 groups. The study group (n = 51) received 400 μg of vaginal misoprostol at least 12 h before the procedure and the control group (n = 54) received no cervical priming agent. The primary outcome measure was the number of women who required cervical dilation. Secondary outcomes were cervical width (the largest size of Hegar dilator inserted without resistance) as well as complications and adverse effects. Results: In the misoprostol group 27 women (52.9%) required cervical dilation vs. 53 (98.1%) in the control group (P < 0.0001). The largest size of Hegar dilator inserted without resistance was 7.6 ± 1.4 mm in the misoprostol group vs. 5.0 ± 1.1 mm in the control group (P < 0.0001). A similar effect of misoprostol on cervical dilation was also found in the subgroup of treated postmenopausal women. Only 2 women (3.9%) experienced mild lower abdominal pain after misoprostol application. Conclusion: Vaginal misoprostol applied before hysteroscopy reduced cervical resistance and the need for cervical dilation in perimenopausal and postmenopausal women, with only mild adverse effects.
High Spatial Variation Tropospheric Model for GPS-Data Simulation
Authors: Farah Ashraf , Moore Terry , Hill Chris J
Published: August 2005

Precise GPS simulated data requires accurate simulation of the two major sources of error in GPS measurements, namely the ionospheric and tropospheric delays. The ionospheric delay modelling has been handled in a previous work (Farah, 2002). In this paper the simulation of the tropospheric delay is discussed. The suggested model should be accurate in estimating the tropospheric delay as well as capable of simulating high spatial variations of the troposphere resulting in more realistic simulated GPS data. In this paper, the EGNOS tropospheric correction model is considered as a possible tool for simulating the tropospheric delay in order to obtain more realistic simulated GPS data. Comparing the total tropospheric zenith delays from the EGNOS model with the CODE-tropospheric product has allowed the quality of the EGNOS model to be assessed. Four IGS-tracking stations have been selected for this study. Data from four non-consecutive weeks in different seasons over a period of one year were tested to assess the seasonal variation of the weather conditions. It is shown that the EGNOS model agrees well with the CODE-estimations with a mean zenith delay difference of approximately 2 cm. The maximum zenith delay difference between the EGNOS model and the CODE-estimations was in the range of 5 cm to 16 cm, which agrees well with previous studies. A second study has investigated the behaviour of the EGNOS model with other established tropospheric models such as the Saastamoinen, the Hopfield, the Marini and the Magnet model for three IGS-stations. It can be concluded from this study that the EGNOS model shows better agreement with the IGS estimations than the Magnet model and compares well with other models. The major shortcoming in the EGNOS model is its inability to simulate the variations in the troposphere over small regions. This shortcoming could be overcome by using the theory of Gaussian Random Fields, which has been previously used to model real life phenomena such as surface roughness (Chan, 1999). This paper was first presented at ION GPS 2003, the 16th Technical Meeting of the Satellite Division of the Institute of Navigation held at Portland Oregon, USA.
Albatross Long-Distance Navigation: Comparing Adults And Juveniles
Authors: Åkesson Susanne , Weimerskirch Henri
Published: August 2005

Albatrosses are known for their extreme navigation performance enabling them to locate isolated breeding islands after long-distance migrations across open seas. Little is known about the migration of young albatrosses and how they reach the adults' navigation and foraging skills during the period of immaturity lasting several years and spent permanently flying across the open ocean. We tracked by satellite telemetry the dispersal and migration of 13 juvenile wandering albatrosses from the Crozet Islands during their first year at sea. The young albatrosses covered an average distance of 184,000 km during the first year, restricting their dispersal movement to the unproductive and low wind subtropical Indian Ocean and Tasman Sea. The juveniles initiated the migration by an innate phase of rapid dispersal encoded as a fixed flight direction assisted by southerly winds towards north and northeast. Thereafter each individual restricted its movement to a particular zone of the ocean that will possibly be used until they start breeding 7–10 years later and return in contact with breeding adults. This dispersal in young birds corresponds well with movements observed for adult non-breeding wandering albatrosses. The results show clearly an inherited ability to navigate back to already visited areas in young wandering albatrosses. The juvenile dispersal behaviour and migration at sea suggest a genetically based migration program, encoding navigation to a destination area used throughout the life.
Epidemiological analysis of data for scrapie in Great Britain
Authors: HAGENAARS T. J. , DONNELLY C. A. , FERGUSON N. M.
Published: August 2005

In recent years, the control or eradication of scrapie and any other transmissible spongiform encephalopathies (TSEs) possibly circulating in the sheep population has become a priority in Britain and elsewhere in Europe. A better understanding of the epidemiology of scrapie would greatly aid the development and evaluation of control and eradication strategies. Here we bound the range of key epidemiological parameters using a combination of relatively detailed pathogenesis and demography data, more limited data on susceptibility and incubation times, and recent survey data on scrapie incidence in Great Britain. These data are simultaneously analysed using mathematical models describing scrapie transmission between sheep and between flocks. Our analysis suggests that occurrence of scrapie in a flock typically provokes changes in flock management that promote termination of the outbreak, such as the adoption of selective breeding, and that a large fraction of cases (possibly over 80%) goes undetected. We show that the data analysed are consistent with the within-flock reproduction number of scrapie lying in the range 1·5–6, consistent with previous epidemiological studies.
Coactivator functions in a stoichiometric complex with anaphase‐promoting complex/cyclosome to mediate substrate recognition
Authors: Passmore Lori A , Barford David
Published: August 2005

The anaphase‐promoting complex/cyclosome (APC/C) is a multisubunit E3 ligase required for ubiquitin‐dependent proteolysis of cell‐cycle‐regulatory proteins, including mitotic cyclins and securin/Pds1. Regulation of APC/C activity and substrate recognition, mediated by the coactivators Cdc20 and Cdh1, is fundamental to cell‐cycle control. However, the precise mechanism by which coactivators stimulate APC/C ubiquitylation activity and the nature of the substrate‐binding sites on the activated APC/C are not understood. Here, we show that the optimal interaction of substrate with APC/C is dependent specifically on the simultaneous association of coactivator. This is consistent with a model whereby both core APC/C subunits and coactivators contribute recognition sites for substrates, accounting for the bipartite nature (D and KEN boxes) of most APC/C degradation signals. A direct and stoichiometric function for the coactivators could explain how specific substrates are recognized by APC/C in a cell‐cycle‐specific manner, and how coactivator stimulates APC/C ubiquitylation activity.
Ablation of the spindle assembly checkpoint by a compound targeting Mps1
Authors: Schmidt Marc , Budirahardja Yemima , Klompmaker Rob , Medema René H
Published: August 2005

The spindle assembly checkpoint ensures accurate chromosome segregation by delaying anaphase initiation until all chromosomes are properly attached to the mitotic spindle. Here, we show that the previously reported c‐Jun amino‐terminal kinase (JNK) inhibitor SP600125 effectively disrupts spindle checkpoint function in a JNK‐independent fashion. SP600125 potently inhibits activity of the mitotic checkpoint kinase monopolar spindle 1 (Mps1) in vitro and triggers efficient progression through a mitotic arrest imposed by spindle poisons. Importantly, expression of an Mps1 mutant protein refractory to SP600125‐mediated inhibition restores spindle checkpoint function in the presence of SP600125, showing that its mitotic phenotype is induced by Mps1 inhibition in vivo. Remarkably, primary human cells are largely resistant to the checkpoint‐inactivating action of SP600125, suggesting the existence of Mps1‐independent checkpoint pathways that are compromised in tumour cells.
Bcr–Abl activates the AKT/FoxO3 signalling pathway to restrict transforming growth factor‐β‐mediated cytostatic signals
Authors: Atfi Azeddine , Abécassis Lucile , Bourgeade Marie‐Francoise
Published: August 2005

The fusion of Abl with either Bcr or Tel in human leukaemia leads to the constitutive activation of Abl tyrosine kinase, which in turn induces growth‐factor‐independent proliferation and cell survival. However, the mechanism by which Bcr–Abl induces cellular transformation has not yet been well characterized. Here, we show that Bcr–Abl‐expressing cells are resistant to growth inhibition and apoptosis mediated by transforming growth factor‐β (TGF‐β). Interestingly, we observed that the suppressive effects of Bcr–Abl on TGF‐β responses were not mediated by an impairment of Smad signalling, which is believed to act as the principal mediator of TGF‐β responses. In contrast, we found that Bcr–Abl can target the protein kinase AKT and the transcription factor FoxO3 to interfere with growth inhibition and apoptosis in response to TGF‐β. Our results show a novel mechanism of cellular transformation by the oncogenic fusion protein Bcr–Abl through suppression of the cytostatic actions of TGF‐β.
p75 neurotrophin receptor reduces ligand‐induced Trk receptor ubiquitination and delays Trk receptor internalization and degradation
Authors: Makkerh Joe P S , Ceni Claire , Auld Daniel S , Vaillancourt François , Dorval Genevieve , Barker Philip A
Published: August 2005

Target‐derived neurotrophins regulate neuronal survival and growth by interacting with cell‐surface tyrosine kinase receptors. The p75 neurotrophin receptor (p75NTR) is coexpressed with Trk receptors in long‐range projection neurons, in which it facilitates neurotrophin binding to Trk and enhances Trk activity. Here, we show that TrkA and TrkB receptors undergo robust ligand‐dependent ubiquitination that is dependent on activation of the endogenous Trk activity of the receptors. Coexpression of p75NTR attenuated ubiquitination of TrkA and TrkB and delayed nerve growth factor‐induced TrkA receptor internalization and receptor degradation. These results indicate that p75NTR may prolong cell‐surface Trk‐dependent signalling events by negatively regulating receptor ubiquitination.
Theoretical predictions of the initial decomposition steps of dimethylnitramine
Authors: Velardez Gustavo F. , Alavi Saman , Thompson Donald L.
Published: August 2005

The structures and energies of the reactants, products, and transition states of the initial steps in the gas-phase decomposition of dimethylnitramine (DMNA) have been determined by quantum chemical calculations at the B3LYP density-functional theory, MP2, and G2 levels. The pathways considered are NO2 elimination, HONO elimination, and nitro-nitrite rearrangement. The NO2 elimination is predicted to be the main channel of the gas-phase decomposition of DMNA in accord with experiment. The values of the Arrhenius parameters, logA=16.6±0.5 and Ea=40.0±0.6kcal∕mol, for the N–NO2 bond-fission reaction were obtained using a canonical variational theory with B3LYP energies and frequencies. The HONO-elimination channel has the next lowest activation energy of 44.7±0.5kcal∕mol (logA=13.6±0.5) and is characterized by a five-member transition-state configuration in which a hydrogen atom from one of the methyl groups is transferred to an oxygen atom of NO2. Tunneling contributions to the rate of this reaction have been estimated. The nitro-nitrite rearrangement reaction occurs via a transition state in which both oxygen atoms of NO2 are loosely bound to the central nitrogen atom, for which Rice-Ramsperger-Kassel-Marcus theory predicts logA=14.4±0.6 and Ea=54.1±0.8kcal∕mol.
Luminescence characteristics of pulsed-laser-ablated Y1.35Gd0.6O3:Eu3+ thin-film phosphors
Authors: Bae Jong Seong , Moon Byung Kee , Jeong Jung Hyun , Yi Soung Soo , Kim Jung Hwan
Published: August 2005

Y 2 O 3 : Eu 3 + and Y1.35Gd0.6O3:Eu3+ luminescent thin films were grown on Al2O3 (0001) and Si (100) substrates by a pulsed-laser deposition technique. Both films grown under different deposition conditions have been characterized using microstructural and luminescent measurements. The crystallinity, surface morphology, and photoluminescence of the films are highly dependent on the deposition conditions. The structural characterization carried out on the films grown on both substrates at the substrate temperature of 600°C and oxygen pressure of 200mTorr indicated that films were preferentially (222) oriented. In particular, the surface roughness of the thin films had a strong effect on the photoluminescence. The incorporation of Gd into the Y2O3 lattice induced a change of crystallinity, surface roughness, and a remarkable increase of photoluminescence. Due to a D05-F27 transition of Eu3+, the Y1.35Gd0.6O3:Eu3+ films emitted the radiation of red light with a 612-nm wavelength, whose brightness was increased by a factor of 3.1 in comparison with that of Y2O3:Eu3+ films.
Crystallographic and luminescent properties of orthorhombic BaAl2S4:Eu powder and thin films
Authors: Smet Philippe F. , Van Haecke Jo E. , Van Meirhaeghe Roland L. , Poelman Dirk
Published: August 2005

Ba Al 2 S 4 : Eu thin films were prepared from a multilayered BaS:Eu∕Al2S3 thin-film structure, deposited with electron-beam evaporation. Depending on the deposition and postdeposition annealing temperature, europium-doped BaAl2S4 thin films can show both an orthorhombic and the more common cubic crystal structure. The lattice constants of the orthorhombic BaAl2S4 are determined from powder-diffraction data. The photoluminescent properties of europium-doped orthorhombic and cubic BaAl2S4 powders are compared. The occurrence of both phases in thin films is discussed in terms of substrate and postdeposition annealing temperature. A temperature of 600°C is sufficient to obtain the orthorhombic phase, and annealing at 900°C leads to the cubic phase. The phase formation in the multilayered thin films is investigated by studying the crystallographic, optical, and photoluminescent properties.
Synthesis for semiconductor device design
Authors: Thalken Jason , Haas Stephan , Levi A. F. J.
Published: August 2005

Synthesis of semiconductor device design requires access to realistic physical models and adaptive algorithms. To demonstrate that such synthesis is feasible we design elements of a quantum-confined Stark-effect modulator. Optimization with respect to a target function is achieved using a genetic algorithm. It is then shown how automated searches of configuration space may be performed without the need to input a specific target function.
Enhancement of the magnetic properties in (Ga1−xMnx)N thin films due to Mn-delta doping
Authors: Jeon H. C. , Kang T. W. , Kim T. W. , Kang Joongoo , Chang K. J.
Published: August 2005

The effects of Mn delta-doping on the magnetic properties of (Ga1−xMnx)N thin films grown on GaN buffer layers by molecular-beam epitaxy were studied. The magnetization curve as a function of the magnetic field as 5K indicated that ferromagnetisms existed in the Mn delta-doped (Ga1−xMnx)N and (Ga1−xMnx)N thin films and that the magnetization in the Mn delta-doped (Ga1−xMnx)N thin film was significantly enhanced. The magnetization curve as a function of the temperature showed that the Curie temperature of the Mn delta-doped (Ga1−xMnx)N thin film was estimated to be above room temperature. The increase of the magnetization in the Mn delta-doped (Ga1−xMnx)N thin film in comparison with that in the (Ga1−xMnx)N thin film was attributed to the enhancement of the carrier-mediated ferromagnetism due to increased hole concentrations. The theoretical results showed that Ga vacancies near the Mn delta-doping layer were likely to cause p-type conductance, indicating that the enhancement of the magnetic properties in (Ga1−xMnx)N thin films originated from Mn delta doping.
Dielectric anomaly due to electrostatic coupling in ferroelectric-paraelectric bilayers and multilayers
Authors: Roytburd A. L. , Zhong S. , Alpay S. P.
Published: August 2005

A thermodynamic model is presented that describes the polarization and the dielectric response of ferroelectric-paraelectric bilayers and multilayers. It is shown that a strong electrostatic coupling between the layers results in the suppression of ferroelectricity at a critical paraelectric layer thickness. The bilayer is expected to have a gigantic dielectric response similar to the dielectric anomaly near Curie–Weiss temperature in homogeneous ferroelectrics at this critical thickness. A numerical analysis is carried out for a pseudomorphic (001) BaTiO3∕SrTiO3 heteroepitaxial bilayer on (001) SrTiO3 and a stress-free BaTiO3∕SrTiO3 bilayer. Complete polarization suppression and a dielectric peak are predicted to occur at approximately 66% and 14% of SrTiO3 in these two systems, respectively.
Plasma hydrogenation of strained Si∕SiGe∕Si heterostructure for layer transfer without ion implantation
Authors: Shao Lin , Lin Yuan , Lee J. K. , Jia Q. X. , Wang Yongqiang , Nastasi M. , Thompson Phillip E. , Theodore N. David , Chu Paul K. , Alford T. L. , Mayer J. W. , Chen Peng , Lau S. S.
Published: August 2005

We have developed an innovative approach without the use of ion implantation to transfer a high-quality thin Si layer for the fabrication of silicon-on-insulator wafers. The technique uses a buried strained SiGe layer, a few nanometers in thickness, to provide H trapping centers. In conjunction with H plasma hydrogenation, lift-off of the top Si layer can be realized with cleavage occurring at the depth of the strained SiGe layer. This technique avoids irradiation damage within the top Si layer that typically results from ion implantation used to create H trapping regions in the conventional ion-cut method. We explain the strain-facilitated layer transfer as being due to preferential vacancy aggregation within the strained layer and subsequent trapping of hydrogen, which lead to cracking in a well controlled manner.
Difference in electronic structure between tetragonal and cubic SrNbO2N
Authors: Borse Pramod H. , Kim Hyun G. , Lee Jae S.
Published: August 2005

We report here a comparative study of the electronic structure of earlier known cubic phase and the recently, reported correct tetragonal phase of SrNbO2N. We performed the calculations within the framework of density-functional theory (DFT) by using the WIEN97 code. The valence band consists of N 2p while the conduction band consists of Nb 4d in cubic system; on the contrary, these Nb 4d states show a strong interaction with anion p states in tetragonal system and indicate theoretically, a metallic behavior. The direct forbidden gap of tetragonal system was 0eV, whereas for cubic system was 0.2eV; the relative difference in the band gap of two systems is possibly attributed to the high covalency and is possibly acquired due to the presence of the shorter bond length of Nb–N than that of Nb–O in the tetragonal system. The results of electronic structures have been discussed in the light of optical applications of this oxynitride in solar energy conversion. The calculated optical-absorption coefficient I(w) from real and imaginary parts of dielectric function, further clarifies the suitability of the application.
Nanoscale mapping of the space charge layer of Au∕GaAs(110) contacts
Authors: Reusch T. C. G. , Wenderoth M. , Winking L. , Quaas N. , Ulbrich R. G.
Published: August 2005

We have investigated Au∕GaAs(110) Schottky contacts with scanning tunneling spectroscopy in cross-sectional configuration. The tunneling spectra show that both band edges are shifted and modified by the electrostatic potential of the space charge layer. The shifts were extracted and compared with simulations of the tunneling current including a local potential in the semiconductor. The resulting potential landscape is mapped on a near-atomic scale in the plane perpendicular to the metal-semiconductor interface.
Growth of high-quality ZnMgO epilayers and ZnO∕ZnMgO quantum well structures by radical-source molecular-beam epitaxy on sapphire
Authors: Sadofev S. , Blumstengel S. , Cui J. , Puls J. , Rogaschewski S. , Schäfer P. , Sadofyev Yu. G. , Henneberger F.
Published: August 2005

We report on a specific growth procedure combining low-temperature growth of ZnMgO and postgrowth annealing at intermediate temperatures. Despite the large lattice misfit induced by the sapphire substrate, layer-by-layer growth is accomplished up to the phase-separation limit found at a c-lattice constant of 0.5136nm and Mg mole fraction of 0.40. The procedure allows us to grow quantum wells with atomically smooth interfaces in a wide range of structural designs exhibiting prominent emission features up to room temperature.