bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prenatal testing for a novel EBP missense mutation causing X‐linked dominant chondrodysplasia punctata
Authors: Tysoe Carolyn , Law Caroline J. , Caswell Richard , Clayton Peter , Ellard Sian 
Published: April 2008

AbstractObjectiveTo determine the pathogenicity of a novel conserved missense mutation, p.Ser98Phe, in the emopamil binding protein (EBP) gene in order to perform a prenatal diagnostic test for X‐linked dominant chondrodysplasia punctata (CDPX2) in a male foetus at 50% risk.MethodsFamily members were tested for p.Ser98Phe using PCR and sequence analysis of leucocyte or buccal cell DNA. Haplotype analysis was employed to identify the grandparental chromosome on which p.Ser98Phe had arisen. In silico protein analyses were used to predict whether p.Ser98Phe significantly altered the EBP protein structure.ResultsThe mutation was detected in the proband and her affected mother but not in the maternal grandmother, who was thought to be mildly affected. However, haplotype analysis showed that p.Ser98Phe had arisen de novo on the grandpaternal X chromosome. Protein secondary structure predictions suggested that p.Ser98Phe alters the properties of the helix within which it is located.ConclusionWe concluded that p.Ser98Phe is likely to be pathogenic and proceeded with prenatal testing. The male foetus had not inherited p.Ser98Phe and his unaffected status was confirmed at birth. This family demonstrates some of the difficulties in interpreting the significance of novel missense mutations, particularly when results are needed urgently for prenatal diagnosis. Copyright © 2008 John Wiley & Sons, Ltd.
Inhibin A measurement using an automated assay platform
Authors: Lambert‐Messerlian G. M. , Palomaki G. E. , Canick J. A. 
Published: April 2008

AbstractBackgroundSecond–trimester measurement of maternal serum inhibin A is widely used for Down syndrome screening. To date, only a manual enzyme‐linked immunosorbent assay (ELISA) produced by Diagnostic Systems Laboratories, Inc (DSL) has been available. The objective of this study was to compare the DSL assay with a new automated assay produced by Beckman Coulter, Inc (Access).MethodsResidual serum samples from 570 women, who were receiving routine screening for Down syndrome, were retrieved from storage. The Access assay sensitivity, linearity and reproducibility were determined and a method comparison was performed. Inhibin A levels were measured using both assays. Twenty samples from women with confirmed Down syndrome pregnancy were also tested.ResultsThe Access assay had coefficients of variation of less than 10% across the range of values tested, and a sensitivity below 1 pg/mL. The DSL and Access inhibin A assay values were highly correlated (r = 0.961, r2 = 0.923), with no apparent outliers. Inhibin A values from the Access assay were a constant 23% lower (95% CI 1–41%) than corresponding values from the DSL assay. Median values from 15 to 20 completed weeks' gestation were computed and found to be consistent with expectations. The weight‐adjusted multiples of the median (MoM) levels in the unaffected pregnancies fit a log Gaussian distribution well between at least the 5th and 95th percentiles with corresponding log standard deviations of 0.1960 and 0.1919 for DSL and Access, respectively.ConclusionsWith median inhibin A levels appropriately calculated for the Access assay, Down syndrome screening performance is expected to be comparable to that obtained with the manual DSL assay. Copyright © 2008 John Wiley & Sons, Ltd.
Refined fluorescent STR quantification of cell‐free fetal DNA during pregnancy in physiological and Down syndrome fetuses
Authors: Vodicka Radek , Vrtel Radek , Dusek Ladislav , Prochazka Martin , Schneiderova Eva , Vrbicka Dita , Krejcirikova Eva , Dhaifalah Ishraq , Santava Alena , Santavy Jiri 
Published: April 2008

AbstractBackgroundCell‐free fetal (cff) DNA analysis by short tandem repeats (STR) has the advantage of better recognizing the different genotypes. However, quantitative examination by quantitative fluorescent (QF) polymerase chain reaction (PCR) by STRs is limited to only a rough approximation. This project focuses on a more precise calculation of the relative cff DNA amount tested in the STRs' loci.MethodsThe cff DNA was analyzed in 363 samples from 258 pregnant women with physiological fetuses in different stages of pregnancy (from 4–37 gestational weeks) separately in three STRs [D21S1435, D21S1446 and PentaD (pD)] and also by gonosomal sequences amelogenin gene, X/Y‐linked/testis specific protein, Y‐linked (AMELX/Y/TSPY). Seventeen samples of cff DNA from fetuses with Down syndrome (DS) were compared. We optimized the refined quantitative fluorescent (RQF) PCR for STRs in a particular locus.Results and ConclusionsThe cff DNA detection rate was 74% in at least one of the STRs. The efficiency decreased from shorter to longer PCR fragments. All three STR and gonosomal loci proved an increase in cff DNA during pregnancy. The stutter variability rate is greatest in short STR fragments and decreases as the STR fragments increase in length. Results showed that DS samples had a significantly higher amount of cff DNA. Copyright © 2008 John Wiley & Sons, Ltd.
Staining efficiency of specific proteins depends on the staining method: Wheat gluten proteins
Authors: van den Broeck Hetty C. , America Antoine H. P. , Smulders Marinus J. M. , Gilissen Ludovicus J. W. J. , van der Meer Ingrid M. 
Published: April 2008

AbstractTo analyze gluten proteins involved in celiac disease (CD) by proteomic analysis, prolamins extracted from hexaploid wheat varieties were analyzed by SDS‐PAGE and 2‐DE. Differences between staining methods (CBB, silver nitrate, SYPRO Ruby, and CyDye) were analyzed in comparison to immunoblotting. Staining efficiency varied per protein across methods, and complete staining of all gluten proteins could not be achieved by one of these methods. Care should be taken in the selection of staining method especially if one wants to relate the results to data obtained by immunoblotting.
Post‐translational modification of cellular proteins during Leishmania donovani differentiation
Authors: Rosenzweig Doron , Smith Derek , Myler Peter J. , Olafson Robert W. , Zilberstein Dan 
Published: April 2008

AbstractThe pathogenic intracellular parasites Leishmania donovani cycle between sand fly gut and the human macrophage phagolysosome, differentiating from extracellular promastigotes to intracellular amastigote forms. Using isobaric tagging for relative and absolute quantifications (iTRAQ/LC‐MS/MS) proteomic methodology, we recently described the ordered gene expression changes during this process. While protein abundance changes in Leishmania were documented, little is known about their PTMs. Here we used iTRAQ to detect protein phosphorylation, methylation, acetylation, and glycosylation sites throughout differentiation. We found methylation of arginines, aspartic acids, glutamic acids, asparagines, and histidines. Detected acetylation sites included serines and protein N‐terminal acetylations on methionines, serines, alanines, and threonines. Phosphorylations were detected on serines and threonines, but not tyrosines. iTRAQ identified novel fucosylation sites as well as hexosylations. We observed quantity changes in some modifications during differentiation, suggesting a role in L. donovani intracellular development. This study is the first high‐throughput analysis of PTM sites dynamics during an intracellular parasitic development.
Thermodynamics of dark energy
Authors: Bilić N. 
Published: April 2008

AbstractThermodynamic properties of dark energy are discussed assuming that dark energy is described in terms of a selfinteracting complex scalar. We first show that, under certain assumptions, selfinteracting complex scalar field theories are equivalent to purely kinetic k‐essence models. Then we analazie the themal properties of k‐essence and in particular we show that dark‐energy in the phantom regime does not necesserely yield negative entropy.
Coset space dimensional reduction of Einstein–Yang–Mills theory
Authors: Chatzistavrakidis A. , Manousselis P. , Prezas N. , Zoupanos G. 
Published: April 2008

AbstractIn the present contribution we extend our previous work by considering the coset space dimensional reduction of higher‐dimensional Einstein–Yang–Mills theories including scalar fluctuations as well as Kaluza–Klein excitations of the compactification metric and we describe the gravity‐modified rules for the reduction of non‐abelian gauge theories.
Non‐topological non‐commutativity in string theory
Authors: Guttenberg S. , Herbst M. , Kreuzer M. , Rashkov R. 
Published: April 2008

AbstractQuantization of coordinates leads to the non‐commutative product of deformation quantization, but is also at the roots of string theory, for which space‐time coordinates become the dynamical fields of a two‐dimensional conformal quantum field theory. Appositely, open string diagrams provided the inspiration for Kontsevich's solution of the long‐standing problem of quantization of Poisson geometry by virtue of his formality theorem. In the context of D‐brane physics non‐commutativity is not limited, however, to the topolocial sector. We show that non‐commutative effective actions still make sense when associativity is lost and establish a generalized Connes‐Flato‐Sternheimer condition through second order in a derivative expansion. The measure in general curved backgrounds is naturally provided by the Born–Infeld action and reduces to the symplectic measure in the topological limit, but remains non‐singular even for degenerate Poisson structures. Analogous superspace deformations by RR–fields are also discussed.
Observational effects of strong gravity in vicinity of supermassive black holes
Authors: Jovanović P. , Popović L.Č. 
Published: April 2008

AbstractHere we discuss the effects of strong gravity that can be observed in electromagnetic spectra of active galactic nuclei (AGN). According to the unification model of an AGN, there is a supermassive black hole (107 ‐ 109 MȮ) in its center, surrounded by an accretion disk that radiates in the X‐ray band. Accretion disks could have different forms, dimensions, and emission, depending on the type of central black hole (BH), whether it is rotating (Kerr metric) or nonrotating (Schwarzschild metric). We modeled the emission of an accretion disk around supermassive BH using numerical simulations based on a ray‐tracing method in the Kerr metric. A broad emission line Fe Kα at 6.4 keV with asymmetric profile (narrow bright blue peak and a wide faint red wing) has been observed in a number of type 1 AGN. The effects of strong gravitational field are investigated by comparison between the modeled and observed iron Kα line profiles. The results of our modeling show that the parameters of the Fe Kα line emitting region have significant influence on the line profile and thus, allow us to determine the space‐time geometry (metric) in vicinity of the central BH of AGN, and also can give us information about the plasma conditions in these regions.
Masses of tetraquark candidates D
Authors: Borka Jovanović V. 
Published: April 2008

AbstractUsing the Glozman‐Riska (flavor‐spin) interaction Hamiltonian and the SU(3) flavor symmetry breaking, we perform a schematic study of the masses of the scalar charmed tetraquarks in the following representations: $\overline{15}_\mathrm{S}$, $\bar{3}_\mathrm{S}$, $6_\mathrm{A}$ and$\bar{3}_\mathrm{A}$. Obtained pattern indicates that Ds+(2317) is a four‐quark state in the SU(3)F $\bar{3}_\mathrm{A}$ representation. Ds+(2632) is identified with a state from mixing of the $\overline{15}_\mathrm{S}$ and $\bar{3}_\mathrm{S}$ representations. There are 27 different tetraquarks composed of a charm quark c and of the three light flavors u, d, s: 11 cryptoexotic (3 Ds+, 4 D+, 4 D0) and 16 explicit exotic states. The identification of Ds+(2317) and Ds+(2632) with two cryptoexotic states in tetraquark spectrum is possible when including Glozman‐Riska hyperfine interaction. We also compare Glozman‐Riska and Fermi‐Breit contributions to the tetraquark masses and analyze the corresponding tetaraquark mass spectra.
Giant magnons on γ deformed AdS5 × S5
Authors: Rashkov R.C. , Stoilov N.M. 
Published: April 2008

AbstractIn this short note we report on the dispersion relation of a new magnon type string solution in γ deformed AdS5 × S5 background. Our magnon solution has one spin in AdS5 part and two in S5 part of the background.
R4 in type II superstrings
Authors: Tsimpis D. 
Published: April 2008

AbstractWe review the result, given in [1], of the complete four‐point effective action of both type II superstrings to all orders in α′, at tree level in string loops. We find that, in the quartic‐field approximation, the supergravity Lagrangian can be thought of as the tensor product of two copies of the super Yang‐Mills Lagrangian in ten dimensions.
Interaction of the particle with the string in pole‐dipole approximation
Authors: Vasilić M. , Vojinović M. 
Published: April 2008

AbstractWithin the framework of generalized Papapetrou method, we derive the effective equations of motion for a string with two particles attached to its ends, along with appropriate boundary conditions. The equations of motion are the usual Nambu‐Goto‐like equations, while boundary conditions turn out to be equations of motion for the particles at the string ends. The form of those equations is discussed, and they are explicitly solved for a particular case of a straight‐line string rotating around its center. From this solution we obtain the correction terms to the J ∝ E2 law describing Regge trajectories, due to nonzero angular momenta of the particles.
Perturbative quantum corrections and flux compactifications
Authors: Berg M. , Haack M. , Pajer E. 
Published: April 2008

AbstractWe review the results of arxiv:0704.0730, a string theory test of the phenomenologically interesting large volume scenario (LVS) of Balasubramanian et al. In particular, we consider whether the LVS expansion of the string effective action is consistent when the open string one‐loop corrections due to D‐branes and O‐planes are taken into account. The result is that LVS is surprisingly robust. We also review the computation of soft supersymmetry breaking terms, which is only modified at subleading order.
Expression profiling of CD133+ and CD133— epithelial cells from human prostate
Authors: Shepherd Christopher J. , Rizzo Siân , Ledaki Ioanna , Davies Melissa , Brewer Daniel , Attard Gerhardt , de Bono Johann , Hudson David L. 
Published: April 2008

AbstractBACKGROUNDRecent evidence suggests that prostate stem cells in benign and tumor tissue express the cell surface marker CD133, but these cells have not been well characterized. The aim of our study was to gene expression profile CD133‐expressing cells.METHODSWe analyzed CD133‐positive (CD133+) and ‐negative (CD133−) sub‐populations of high‐integrin expressing epithelial cells isolated from benign human prostate tissue and hormone‐refractory prostate cancer (HRPC).RESULTSCD133+ cells freshly isolated from benign prostate tissue exhibited an expression profile characteristic of a putative stem/progenitor cell population, with transcripts involved in biological processes ranging from development and ion homeostasis to cell communication. The profile of CD133− cells was consistent with that of a transit amplifying population, suggesting up‐regulated proliferation and metabolism. Comparison of benign populations to those from HRPC showed some similarities between CD133+ profiles but also revealed significant differences that provide a tumor‐specific pattern, which included evidence of increased metabolic activity and active proliferation. Subsequently, we demonstrated protein expression of a number of candidate genes in these cell populations and in benign tissue. In a novel observation we also found expression of some of these markers in prostate tumors, including the oligodendrocyte lineage transcription factor OLIG1.CONCLUSIONSThis study provides a unique genome‐wide molecular signature of CD133+ and CD133− human prostate epithelial cells. This will provide a valuable resource for prostate stem cell biology research and the identification of novel therapeutic targets for the treatment of prostate cancer. Prostate 68:1007–1024, 2008. © 2008 Wiley‐Liss, Inc.
Analysis of the sequence and structural features of the left‐handed β‐helical fold
Authors: Choi Jay H. , Govaerts Cedric , May Barnaby C. H. , Cohen Fred E. 
Published: April 2008

AbstractThe left‐handed parallel β‐helix (LβH) is a structurally repetitive, highly regular, and symmetrical fold formed by coiling of elongated β‐sheets into helical “rungs.” This canonical fold has recently received interest as a possible solution to the fibril structure of amyloid and as a building block of self‐assembled nanotubular structures. In light of this interest, we aimed to understand the structural requirements of the LβH fold. We first sought to determine the sequence characteristics of the repeats by analyzing known structures to identify positional preferences of specific residues types. We then used molecular dynamics simulations to demonstrate the stabilizing effect of successive rungs and the hydrophobic core of the LβH. We show that a two‐rung structure is the minimally stable LβH structure. In addition, we defined the structure‐based sequence preference of the LβH and undertook a genome‐wide sequence search to determine the prevalence of this unique protein fold. This profile‐based LβH search algorithm predicted a large fraction of LβH proteins from microbial origins. However, the relative number of predicted LβH proteins per specie was approximately equal across the genomes from prokaryotes to eukaryotes. Proteins 2008. © 2008 Wiley‐Liss, Inc.
A monitoring programme for 1,3‐dichloropropene and metabolites in groundwater in five EU countries
Authors: Terry Adrian S , Carter Andrée D , Humphrey Rebecca L , Capri Ettore , Grua Bruno , Panagopoulous Andreas C , Pulido‐Bosch Antonio , Kennedy Stephen H 
Published: April 2008

AbstractBACKGROUND: 1,3 Dichloropropene (1,3‐D) is a preplanting soil fumigant for the control of cyst and free‐living nematodes and is currently undergoing a resubmission under Annex 1 listing of Directive 91/414/EEC. The characteristics of 1,3‐D are such that the risk of it or its soil metabolites leaching through the soil profile cannot be excluded. As such, groundwater monitoring programmes were established in five EU countries representing a wide range of agricultural, climatic and hydrogeological situations, covering a range of groundwater vulnerability scenarios. All monitoring was conducted in areas where there has been historical use of 1,3‐D.RESULTS: Over 5000 groundwater samples were analysed for the presence of 1,3‐D and its metabolites over a 2 year period. Almost all analyses (for parent and metabolites) yielded concentrations of < 0.1 µg L−1. There were just two detections of > 0.1 µg L−1 (0.12 µg L−1 and 0.4 µg L−1) for the 3‐chloroacrylic acid metabolite in shallow groundwater samples of the alluvial gravels of the River Tiétar in the Caceres region of Spain.CONCLUSION: Groundwater monitoring programmes have been conducted in the EU in five countries. These have demonstrated that there is negligible contamination of groundwater with 1,3‐D or its metabolites across a range of agroclimatic regions where 1,3‐D is known to have been used for a number of years. Local scientific knowledge of geological features, hydrology, agricultural practice and specific local issues was essential to the conduct of the study. Copyright © 2008 Society of Chemical Industry
Controlling charge‐transfer at the gate interface of organic field‐effect transistors
Authors: Mühlenen Adrian von , Castellani Mauro , Schaer Michel , Zuppiroli Libero 
Published: April 2008

AbstractThe performance and charge transport characteristics of pentacene transistors with oxide gates such as SiO2 and Al2O3 have been recently shown to largely depend on the density of residual carriers due to electron acceptor defects at the oxide surface. The threshold field in particular is strongly connected to the density of these surface states. We demonstrate that by vapor deposition of self‐assembled monolayers on the oxide gate prior to pentacene growth this charge transfer process is inhibited, the residual charge concentration is decreased by up to two orders of magnitude, and the field‐effect mobility increases by up to a factor of four. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Exponential series representation for heat capacities of semiconductors and wide‐bandgap materials
Authors: Pässler Roland 
Published: April 2008

AbstractThe Thirring series expansion is used as the starting point for the design of a structurally novel, dispersion‐related analytical model for descriptions of the temperature dependences of harmonic parts of isochoric heat capacities, CVh (T). The notorious problem of slow convergence of this conventional series expansion is satisfactorily resolved here by its transformation into an associated exponential series representation, which shows up markedly better convergence properties than the original Thirring expansion. Combining this unprecedented analytical CVh (T) model in a physically adequate way with the recently introduced power series expansion for contributions of lattice expansion and anharmonicity effects to the observable isobaric heat capacities, we get a novel effective tool for numerical simulations and analyses of corresponding Cp (T) data sets, which is suitable for applications to the practically important regions of intermediate to high temperatures. This model is usable, among other things, as a physically consistent substitution for various types of ad hoc chosen polynomials that are hitherto still frequently used, especially in the field of thermochemistry. In order to illustrate the considerable usefulness of the novel analytical tool, especially for the technologically important class of wide‐bandgap materials, we perform simultaneous least‐mean‐square fittings of combined sets of available high‐ and low‐temperature Cp (T) data for diamond, SiC‐3C, the III‐nitrides BN, AlN, and GaN, and the zinc chalcogenides ZnO, ZnS, and ZnSe. For a comparison with results obtained recently for Si and Ge on the basis of a three‐oscillator model, we have re‐examined the respective Cp (T) data sets. As interesting byproducts of present fittings we evaluate several even‐order moments of the respective phonon density of states spectral functions. The discussion of numerical results reveals, among other things, the basic physical cause of the obvious inappropriateness of the conventional Debye model with respect to the majority of the materials under study. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Theoretical studies of the spin Hamiltonian parameters and the local structure for the orthorhombic V4+ in CaYAlO4
Authors: Fu Chuan‐Ji , Wu Shao‐Yi , Wei Li‐Hua , Zhang Zhi‐Hong , Hu Yue‐Xia 
Published: April 2008

AbstractThe spin Hamiltonian parameters (g ‐factors and the hyperfine structure constants) and the local structure for the orthorhombic V4+ in CaYAlO4 are theoretically studied from the perturbation formulas of these parameters for a 3d1 ion in orthorhombically distorted octahedra. Based on the present studies, this center is explicitly assigned to V4+ occupying the Al3+ site, associated with one next‐nearest‐neighbor Mg2+ replacing the host Al3+ (i.e. MgAl) in the ab ‐plane due to the charge compensation. Since the effective charge of the compensator is negative (−e), the ligand O2− intervening in the impurity V4+ and the MgAl would undergo a small displacement (≈0.08 Å) towards the central ion because of the electrostatic repulsion. The local structure of this center can be described as elongation of the oxygen octahedron along the c‐ axis and the slight orthorhombic distortion in the perpendicular direction. The theoretical spin Hamiltonian parameters and the optical transitions based on the above local structure show reasonable agreement with the experimental data. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)