bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic analysis of Mrr1p‐ and Tac1p‐associated differential protein expression in azole‐resistant clinical isolates of Candida albicans
Authors: Hoehamer Christopher F. , Cummings Edwin D. , Hilliard George M. , Morschhäuser Joachim , Rogers P. David 
Published: August 2009

AbstractAzole resistance in Candida albicans is frequently caused by the overexpression of multi‐drug efflux pump genes MDR1, CDR1, and CDR2 due to gain‐of‐function mutations in the zinc cluster transcription factors Mrr1p and Tac1p. In this study, we performed a comparative proteomic analysis to identify proteins whose expression level is influenced by these transcription factors. Both 2‐DE and PMF were used to examine the expression profiles of six pairs of matched C. albicans isolates carrying gain‐of‐function mutations in either MRR1 or TAC1 resulting in the overexpression of either MDR1 or CDR1 and CDR2. Using this approach, 17 differentially expressed proteins were identified in the MDR1‐overexpressing isolates, while 14 were identified in the isolates that overexpress CDR1 and CDR2. Furthermore, we found that the expression of many of these proteins was increased in a wild‐type strain of C. albicans after the introduction of a gain‐of‐function allele of MRR1 or TAC1. Moreover, disruption of MRR1 and TAC1 in isolates carrying gain‐of‐function mutations resulted in decreased expression of these proteins, confirming their regulation by Mrr1p or Tac1p. Several proteins involved in heat shock and carbohydrate metabolism were differentially expressed in all clinical isolate sets, but these proteins were not dependent upon either Tac1p or Mrr1p.
Urine collected from diapers can be used for 2‐D PAGE in infants and young children
Authors: Kennedy Mary Jayne , Griffin Angela , Su Ruifeng , Merchant Michael , Klein Jon 
Published: August 2009

AbstractUrinary proteomic profiling has potential to identify candidate biomarkers of renal injury in infants provided an adequate urine sample can be obtained. Although diapers are used to obtain urine for clinical evaluation, their use for proteomic analysis has not been investigated. We therefore performed feasibility studies on the use of diaper‐extracted urine for 2‐D PAGE. Pediatric waste urine (2–20 mL) was applied to gel‐containing, non‐gel and cotton‐gauze diapers and then mechanically expressed. Urine volume and total protein were measured pre‐ and post‐extraction. Proteins were separated via 2‐D PAGE following application of urine (20–40 mL) to each matrix. 2‐D PAGE was also performed on clinical specimens collected using each diaper type. Differences in the adsorption and retention of urine volume and protein were noted between matrices. Non‐gel and cotton‐gauze diapers provided the best protein/volume recovery and the lowest interference with the Bradford assay. 2‐D PAGE was also successfully completed using urine samples from both cotton fiber matrices. Conversely, samples from low‐gel diapers demonstrated poor protein separation and reproducibility. Diapers containing cotton–fiber matrices appear adequate for 2‐D PAGE. Qualitative and quantitative analyses of resolved proteins using replicate, high‐resolution gels will be required, however, before diaper‐extracted urine can be applied in proteomic profiling.
Elucidation of the stability and functional regions of the human coronavirus OC43 nucleocapsid protein
Authors: Huang Chun‐Yu , Hsu Yen‐Lan , Chiang Wan‐Ling , Hou Ming‐Hon 
Published: August 2009

AbstractHuman coronavirus OC43 (HCoV‐OC43) is one of the causes of the “common cold” in human during seasons of cold weather. The primary function of the HCoV‐OC43 nucleocapsid protein (N protein) is to recognize viral genomic RNA, which leads to ribonucleocapsid formation. Here, we characterized the stability and identified the functional regions of the recombinant HCoV‐OC43 N protein. Circular dichroism and fluorescence measurements revealed that the HCoV‐OC43 N protein is more highly ordered and stabler than the SARS‐CoV N protein previously studied. Surface plasmon resonance (SPR) experiments showed that the affinity of HCoV‐OC43 N protein for RNA was approximately fivefold higher than that of N protein for DNA. Moreover, we found that the HCoV‐OC43 N protein contains three RNA‐binding regions in its N‐terminal region (residues 1–173) and central‐linker region (residues 174–232 and 233–300). The binding affinities of the truncated N proteins and RNA follow the order: residues 1–173–residues 233–300 > residues 174–232. SPR experiments demonstrated that the C‐terminal region (residues 301–448) of HCoV‐OC43 N protein lacks RNA‐binding activity, while crosslinking and gel filtration analyses revealed that the C‐terminal region is mainly involved in the oligomerization of the HCoV‐OC43 N protein. This study may benefit the understanding of the mechanism of HCoV‐OC43 nucleocapsid formation.
Crystallographic structure of the tetratricopeptide repeat domain of Plasmodium falciparum FKBP35 and its molecular interaction with Hsp90 C‐terminal pentapeptide
Authors: Alag Reema , Bharatham Nagakumar , Dong Aiping , Hills Tanya , Harikishore Amaravadhi , Widjaja Anissa Anindya , Shochat Susana Geifman , Hui Raymond , Yoon Ho Sup 
Published: August 2009

AbstractPlasmodium falciparum FK506‐binding protein 35 (PfFKBP35) that binds to FK506 contains a conserved tetratricopeptide repeat (TPR) domain. Several known TPR domains such as Hop, PPP5, CHIP, and FKBP52 are structurally conserved and are able to interact with molecular chaperones such as Hsp70/Hsp90. Here, we present the crystal structure of PfFKBP35‐TPR and demonstrate its interaction with Hsp90 C‐terminal pentapeptide (MEEVD) by surface plasmon resonance and nuclear magnetic resonance spectroscopy‐based binding studies. Our sequence and structural analyses reveal that PfFKBP35 is similar to Hop and PPP5 in possessing all the conserved residues which are important for carboxylate clamping with Hsp90. Mutational studies were carried out on positively charged clamp residues that are crucial for binding to carboxylate groups of aspartate, showing that all the mutated residues are important for Hsp90 binding. Molecular docking and electrostatic calculations demonstrated that the MEEVD peptide of Hsp90 can form aspartate clamp unlike FKBP52. Our results provide insightful information and structural basis about the molecular interaction between PfFKBP35‐TPR and Hsp90.
Fabrication of nano‐structured diamond films for SAOS‐2 cell cultivation
Authors: Babchenko Oleg , Kromka Alexander , Hruska Karel , Kalbacova Marie , Broz Antonin , Vanecek Milan 
Published: August 2009

AbstractThe present work reports on application of gold, nickel, and diamond nano‐particles as a masking material for realization of diamond 3D nano‐structures after a low power (100 W) plasma etching process in a gas mixture of CF4/O2. Obtained 3D structures strongly depend on the masking material. Application of the Ni mask results in diamond nano‐rods, whereas the Au mask leads to homogenous “ultra” nano‐cone structures. The diamond powder application results in irregular nano‐cone structures. The present procedure uses a strategy where no lithographic steps are implemented. Prepared samples are tested as the substrates for human osteoblast‐like cells cultivation. Obtained results exhibit a distinctive behavior in cell adhesion on used surface morphologies, as demonstrated by immunofluorescent staining of vinculin (a structural protein of focal adhesion).
Effect of the abnormal electric field induced by the passive layer on imprint failures of ferroelectric capacitors
Authors: Zheng X. J. , Yin W. , Zhang T. , Chen Y. Q. , Tang M. H. , Sun J. 
Published: August 2009

AbstractThe polarization and electric field versus time (P –t and E –t) curves of ferroelectric and passive layers were simulated for different thickness ratios based on the Landau–Khalatnikov theory, and the corresponding hysteresis loops of the ferroelectric capacitor placed in a Sawyer–Tower circuit were obtained via the polarization and electric fields at each time point on the P –t and E –t curves. The results show that the larger the thickness ratio is, the more remarkable the abnormal electric field in the ferroelectric layer and the horizontal shift of hysteresis loops are. The imprint failure may be attributed to the abnormal electric field induced by the passive layer. It is expected to predicate the imprint failure of ferroelectric thin films in a metal–ferroelectric–metal structure. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Advanced tilt correction from flow distortion effects on turbulent CO2 fluxes in complex environments using large eddy simulation
Authors: Griessbaum F. , Schmidt A. 
Published: August 2009

AbstractMeasurement of the turbulent fluxes of gases, momentum and heat can be biased by obstacles such as buildings or instrument platforms distorting the flow of air to the flux instruments. Standard methods have long been used to account for non‐horizontal mean flows. Here we demonstrate a novel approach to correct for the effects of flow distortion which combines numerical flow modelling with eddy covariance measurements of the fluxes. This approach applies a flow distortion correction to the data prior to the application of the standard planar‐fit and double‐rotation methods. This new direction‐dependent flow correction allows the determination of the correct orthogonal wind vector components and hence the vertical turbulent fluxes. We applied the method to a 10 Hz dataset of 3D wind components, temperature, and the concentrations of carbon dioxide and water vapour, as measured on top of a military tower above the city of Münster in northwest Germany during spring and summer 2007. Significant differences appeared between the fluxes that were calculated with the standard rotation methods alone and those that underwent flow distortion correction prior to the application of the rotation methods. The highest deviations of 27% were obtained for the momentum flux. Pronounced differences of 15% and 8% were found for the diurnal net fluxes of carbon dioxide and water vapour, respectively. The flow distortion correction for the carbon dioxide fluxes yielded the same magnitude as the WPL (Webb–Pearman–Leuning) correction for density fluctuations. Copyright © 2009 Royal Meteorological Society
Swarm intelligence based key generation for stream cipher
Authors: Sreelaja N. K. , Vijayalakshmi Pai G. A. 
Published: August 2009

AbstractEncryption of data traffic in a network is essential since it is vulnerable to eavesdropping. The security of data traffic becomes important since the communications over open network occur frequently. This paper focuses on encryption of plain text using a stream cipher method. However, the keys for encryption are generated using a swarm intelligence approach. Swarm intelligence is the emergent collective intelligence of groups of simple autonomous agents. The Ant Colony Optimization key Generation Algorithm (AKGA) is a novel approach to generate keystream for encrypting the plain text. The advantage of this approach is that it reduces the number of keys to be distributed. Experimental results demonstrating AKGA's encrypting plain text of different lengths and the comparison of its performance with other stream cipher methods are presented. Copyright © 2009 John Wiley & Sons, Ltd.
Estimating regional centile curves from mixed data sources and countries
Authors: van Buuren Stef , Hayes Daniel J. , Stasinopoulos D. Mikis , Rigby Robert A. , ter Kuile Feiko O. , Terlouw Dianne J. 
Published: August 2009

AbstractRegional or national growth distributions can provide vital information on the health status of populations. In most resource poor countries, however, the required anthropometric data from purpose‐designed growth surveys are not readily available. We propose a practical method for estimating regional (multi‐country) age‐conditional weight distributions based on existing survey data from different countries. We developed a two‐step method by which one is able to model data with widely different age ranges and sample sizes. The method produces references both at the country level and at the regional (multi‐country) level. The first step models country‐specific centile curves by Box–Cox t and Box–Cox power exponential distributions implemented in generalized additive model for location, scale and shape through a common model. Individual countries may vary in location and spread. The second step defines the regional reference from a finite mixture of the country distributions, weighted by population size. To demonstrate the method we fitted the weight‐for‐age distribution of 12 countries in South East Asia and the Western Pacific, based on 273 270 observations. We modeled both the raw body weight and the corresponding Z score, and obtained a good fit between the final models and the original data for both solutions. We briefly discuss an application of the generated regional references to obtain appropriate, region specific, age‐based dosing regimens of drugs used in the tropics. The method is an affordable and efficient strategy to estimate regional growth distributions where the standard costly alternatives are not an option. Copyright © 2009 John Wiley & Sons, Ltd.
Fully specified bootstrap confidence intervals for the difference of two independent binomial proportions based on the median unbiased estimator
Authors: Lin Yan , Newcombe Robert G. , Lipsitz Stuart , Carter Rickey E. 
Published: August 2009

AbstractIn studies in which a binary response for each subject is observed, the success probability and functions of this quantity are of interest. The use of confidence intervals has been increasingly encouraged as complementary to, and indeed preferable to, p‐values as the primary expression of the impact of sampling uncertainty on the findings. The asymptotic confidence interval, based on a normal approximation, is often considered, but this interval can have poor statistical properties when the sample size is small and/or when the success probability is near 0 or 1. In this paper, an estimate of the risk difference based on median unbiased estimates (MUEs) of the two group probabilities is proposed. A corresponding confidence interval is derived using a fully specified bootstrap sample space. The proposed method is compared with Chen's quasi‐exact method, Wald intervals and Agresti and Caffo's method with regard to mean square error and coverage probability. For a variety of settings, the MUE‐based estimate of risk difference has mean square error uniformly smaller than maximum likelihood estimate within a certain range of risk difference. The fully specified bootstrap had better coverage probability in the tail area than Chen's quasi‐exact method, Wald intervals and Agresti and Caffo's intervals. Copyright © 2009 John Wiley & Sons, Ltd.
Efficient experimental design for binary matched pairs data
Authors: Lennox Kristin P. , Sherman Michael 
Published: August 2009

AbstractThe analysis of data from matched pairs binary experiments, often performed with McNemar's test, presents a unique experimental design challenge in dealing with the effect of the discordance probability, p. Most approaches for determining size and power use point estimates or maximization, but this fails to account for the considerable variability across values of the nuisance parameter that occur for all common tests. We recommend viewing the size and power functions across the full range of possible discordance probability values, which gives a complete picture of the behavior of a test for any given sample size. This method also allows us to compare the behavior of different hypothesis tests. We present exact power and size functions for several tests, including the original McNemar's test and its most common variants, and compare their properties. This analysis reveals that, in general, McNemar's test comes closest to the nominal size and has the highest power. We also demonstrate our technique using the transmission/disequilibrium test (TDT) to check for linkage between schizophrenia and a locus related to the D3 dopamine receptor, and on a hypnosis pain management data set. Copyright © 2009 John Wiley & Sons, Ltd.
Efficient interval estimation of a ratio of marginal probabilities in matched‐pair data: Non‐iterative method
Authors: Nam Jun‐Mo 
Published: August 2009

AbstractMatched‐pair designs have been commonly employed in diagnostic, epidemiologic and laboratory studies. For estimation of a ratio of two marginal probabilities in matched‐pair data, a Wald‐type logarithmic method is computationally simple, but an actual coverage rate is known to be smaller than a nominal one and a length of the confidence interval is shorter than it should be. The Fieller‐type method based on constrained maximum likelihood (CML) estimators possesses asymptotically optimum statistical properties and a coverage rate is close to a nominal one. However, hitherto the limits have been obtained by numerical iterations. In this paper, we derive the efficient confidence limits based on CML as analytical solutions of a quartic equation and present the confidence limits in a closed form. Published in 2009 by John Wiley & Sons, Ltd.
Detecting SNP‐expression associations: A comparison of mutual information and median test with standard statistical approaches
Authors: Szymczak S. , Igl B.‐W. , Ziegler A. 
Published: August 2009

AbstractSingle nucleotide polymorphism‐gene expression associations have received increasing interest. The aim of these studies is discovering a difference in the location parameters of gene expressions given genotype. Because gene expressions often are highly skewed, heavy‐tailed or data of different genotypes vary in dispersion, the median is the most appropriate measure of location. In this case, model assumptions of standard statistical methods for comparing locations such as the analysis of variance (ANOVA) or the Kruskal–Wallis (KW) test are violated. Alternatives that might be more appropriate are the median test (MED) and tests based on mutual information (MI). In simulation studies these approaches and a novel MI test are compared with ANOVA and KW. Location, dispersion and skewness parameters of the gene expression distributions given genotypes are varied as well as genotype frequencies. The MED test and the novel MI‐based method keep the nominal significance levels for comparing medians if gene expression data are non‐normally distributed. ANOVA and KW have substantially inflated type I errors. They are, however, optimal if standard model assumptions are fulfilled. The MED test generally has larger power than MI and is therefore recommended if model assumptions of standard procedures are violated. A 300 kb region on chromosome 9p21.3, which is associated with coronary artery disease, was analyzed using the HapMap data. Only the alternative approaches were able to identify three genes (ADM, FCGR3B and ADORA1) as promising candidates to clarify the molecular mechanism of the genetic association. Copyright © 2009 John Wiley & Sons, Ltd.
Simultaneous confidence intervals using ordinal effect measures for ordered categorical outcomes
Authors: Ryu Euijung 
Published: August 2009

AbstractWhen outcomes are ordered categorical, a model using an ordinal effect size measure is a good alternative of the cumulative logit model to compare several independent group differences. We present a method of constructing simultaneous confidence intervals for the ordinal effect size measures, using the studentized range distribution with the score test statistic. A simulation study shows that the proposed method performs well in terms of coverage probability, and it seems better than the method using a Bonferroni correction for Wald‐type statistics and methods that account for the dependencies among pairwise ordinal effect size measures using the multivariate normal distribution (or the multivariate t‐distribution for small samples). Copyright © 2009 John Wiley & Sons, Ltd.
Optimal Kα XRF detection geometry of arsenic in skin using an extended fundamental parameter method
Authors: Gherase Mihai Raul , Fleming David 
Published: August 2009

AbstractThe fundamental parameter (FP) method was extended to account for the geometrical details of experimental x‐ray fluorescence (XRF) detection. In the traditional FP method the primary fluorescence photons have parallel pathways towards the detector. In the new approach the primary fluorescence photons can travel in any direction which allows them to reach the detector if not absorbed or scattered. The derived XRF signal equation explicitly depends on the length of the collimator in front of the detector, the detector size, position and orientation. An algorithm which numerically calculates the XRF signal for any set of parameters was developed and implemented for the Kα XRF signal of arsenic in skin. Optimal positions and orientations of the detector and collimator ensemble which maximize the XRF signal were found. Results and limitations of the method were also discussed. Copyright © 2009 John Wiley & Sons, Ltd.
Stannyl‐substituted Disilenes and a Disilastannirane
Authors: Abersfelder Kai , Nguyen Thi‐loan , Scheschkewitz David 
Published: August 2009

AbstractThe reaction of disilenide Tip2Si=Si(Tip)Li (1, Tip = 2,4,6‐iPr3C6H2) with chlorostannanes R3SnCl quantitatively affords the first stannyl‐substituted disilenes Tip2Si=Si(Tip)SnR3 (2a: R = Me, 2b: R = Bu, 2c: R = Ph). The Sn‐functional derivative Tip2Si=Si(Tip)SntBu2Cl (3) is accessible in good yield from 1 and tBu2SnCl2. Additionally, the first heavy analogue of cyclopropanes containing two endocyclic silicon and one tin atom was prepared from 1 and Me2SnCl2. All new compounds were characterised by multinuclear NMR spectroscopy and the thus deduced structural assignments corroborated by single‐crystal X‐ray diffraction.
A Spectroscopic and Structural Study of M(3d)2+‐Doped β‐Tricalcium Phosphate – the Binding Properties of Ni2+ and Cu2+ in the Pseudo‐Octahedral Ca(5)O6 Host‐Sites
Authors: Mayer Isaac , Gdalya Sarit , Burghaus Olaf , Reinen Dirk 
Published: August 2009

AbstractThe pseudo‐octahedral Ca(5)2+ position in β‐Ca3(PO4)2 is a highly interesting host site with unexpectedly short Ca–O bond lengths, which can be easily substituted by small 3d‐cations, such as Ni2+. Also Cu2+ may fully replace Ca(5)2+, leading to remarkably large energetic and steric distortion effects due to Eg⊗ϵg Jahn–Teller coupling – with a ground‐state splitting of about 1.25 eV. The Cu(Ni)–O bond is strongly ionic according to a 3d‐mixing coefficient of the eg‐electrons above 0.90, as revealed by EPR‐ and d–d spectroscopy. It is suggested that the flexibility of the Ca(5)O6 host polyhedra, which lie isolated in the lattice, in respect to deformations and to substitutions by smaller cations is one reason that β‐TCP is a useful biomaterial.