bluuebunny/crossref_metadata_2025_split huggingface dataset:
The gravitational field of a light wave
Authors: van Holten J.W. 
Published: November 2010

AbstractAccording to the classical Einstein‐Maxwell theory of gravity and electromagnetism, a light‐wave traveling in empty space‐time is accompanied by a gravitational field of the pp‐type. Therefore point masses are scattered by a light wave, even if they carry no electric or magnetic charge, or dipole moment. In this paper I present the explicit form of the metric and curvature for both circularly and linearly polarized light, and discuss the geodesic motion of test masses. This is followed by a discussion of classical scattering of point particles by the gravitational field associated with a circularly polarized electromagnetic block wave. A generalization to a quantum theory of particles in the background of these classical wave fields is presented in terms of the covariant Klein‐Gordon equation. I derive the energy spectrum of quantum particles in the specific case of the circularly polarized block wave. Finally, a few general remarks on the extension to a quantum light wave are presented.
Prediction of protein binding regions
Authors: Chennamsetty Naresh , Voynov Vladimir , Kayser Veysel , Helk Bernhard , Trout Bernhardt L. 
Published: November 2010

AbstractIdentifying protein binding sites provides important clues to the function of a protein. Experimental methods to identify the binding sites such as determining the crystal structures of protein complexes are extremely laborious and expensive. Here, we present a computational technique called spatial aggregation propensity (SAP) based on molecular simulations to predict protein binding sites. We apply this technique to two model proteins, an IgG1 antibody and epidermal growth factor receptor (EGFR) and demonstrate that SAP predicts protein binding regions with very good accuracy. In the case of the IgG1 antibody, SAP accurately predicts binding regions with the Fc‐receptor, protein‐A, and protein‐G. For EGFR, SAP accurately predicts binding regions with EGF, TGFα, and with another EGFR. The resolution of SAP is varied to obtain a detailed picture of these binding sites. We also show that some of these binding sites overlap with protein self‐aggregation prone regions. We demonstrate how SAP analysis can be used to engineer the protein to remove unfavorable aggregation prone regions without disturbing protein binding regions. The SAP technique could be also used to predict the yet unknown binding sites of numerous proteins, thereby providing clues to their function. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Multi‐level composite nanostructures based on the arrays of vertically aligned carbon nanotubes and planar graphite layers
Authors: Labunov Vladimir , Shulitski Boris , Prudnikava Alena , Basaev Alexander 
Published: November 2010

AbstractNew composite nanostructures based on two allotropic forms of carbon, the arrays of vertically aligned carbon nanotubes (CNTs) and planar graphite layers (PGL) located at the top of the arrays, so‐called “CNT–PGL nanostacks”, have been synthesized by the injection CVD method using xylene/ferrocene solution. Two‐ and three‐level nanostacks were demonstrated. The possible scenario of the growth mechanism of these nanostructures is proposed, that is, each level of the nanostack grows by the simultaneous PGL and CNT array formation on the surface of the catalyst particles previously covered by a graphene layer. At the upper surface of the catalyst particles, which is in direct contact with the reactive species, the graphene layer becomes an origin of PGL, and at the interface between catalyst and substrate it transforms into CNTs. magnified image
Crystalline thin films of stoichiometric Cu3N and intercalated Cu3NMx (M = metals): Growth and physical properties
Authors: Ji Ailing , Yun Du , Gao Lei , Cao Zexian 
Published: November 2010

AbstractThe growth of stoichiometric samples of thermally unstable noble‐metal nitrides remains a challenge. Thin films of nearly stoichiometric Cu3N have been successfully grown on Si (100) wafers by reactive magnetron sputtering of Cu target with mixed nitrogen and argon. The controversies regarding bandgap, lattice constant, decomposition temperature, room‐temperature electrical resistivity, etc., can be resolved. Nitrogen re‐emission leads to the formation of Cu3N nanocrystallites, generally 40–60 nm in size, enclosed by Cu‐terminated {111} facets. Samples with a slight Cu excess may turn into a metallic conductor with excellent electrical conductivity via a percolation mechanism. Unfavorable growth conditions may give rise to blistering or even mesocaled fivefold symmetrical relief structures in the deposit. These structures result from the rearrangement of nanocrystals via gliding along the {111} facets. Ternary Cu3NMx (M = Pd, Cu, In, Zn, etc.) compounds, with the excessive metal atoms occupying the cell centers of the Cu3N lattice, can be obtained by cosputtering under similar conditions. Such ternary compounds can easily be made metallic. In Cu3NPd0.238 a constant electrical resistivity was measured in a temperature range ∼200 K. Incorporation of In or O atoms may raise the decomposition temperature but not to more than 400 °C if the decomposition products are required to be as good a conductor as Cu. The present results might be relevant for growing films of thermally unstable materials. The peculiar electrical conduction behavior in the Cu3NMx structures is expected to inspire the search for nearly zero‐band materials similar to Cu3NPd0.238 as well as to promote an indepth exploration of potential applications of these materials.
Simulated effects of host fish distribution on juvenile unionid mussel dispersal in a large river
Authors: Daraio J. A. , Weber L. J. , Zigler S. J. , Newton T. J. , Nestler J. M. 
Published: November 2010

ABSTRACTLarval mussels (Family Unionidae) are obligate parasites on fish, and after excystment from their host, as juveniles, they are transported with flow. We know relatively little about the mechanisms that affect dispersal and subsequent settlement of juvenile mussels in large rivers. We used a three‐dimensional hydrodynamic model of a reach of the Upper Mississippi River with stochastic Lagrangian particle tracking to simulate juvenile dispersal. Sensitivity analyses were used to determine the importance of excystment location in two‐dimensional space (lateral and longitudinal) and to assess the effects of vertical location (depth in the water column) on dispersal distances and juvenile settling distributions. In our simulations, greater than 50% of juveniles mussels settled on the river bottom within 500 m of their point of excystment, regardless of the vertical location of the fish in the water column. Dispersal distances were most variable in environments with higher velocity and high gradients in velocity, such as along channel margins, near the channel bed, or where effects of river bed morphology caused large changes in hydraulics. Dispersal distance was greater and variance was greater when juvenile excystment occurred in areas where vertical velocity (w) was positive (indicating an upward velocity) than when w was negative. Juvenile dispersal distance is likely to be more variable for mussels species whose hosts inhabit areas with steeper velocity gradients (e.g. channel margins) than a host that generally inhabits low‐flow environments (e.g. impounded areas). Copyright © 2010 John Wiley & Sons, Ltd.
Double‐robust estimation of an exposure‐outcome odds ratio adjusting for confounding in cohort and case‐control studies
Authors: Tchetgen Tchetgen Eric J. , Rotnitzky Andrea 
Published: November 2010

AbstractModern epidemiologic studies often aim to evaluate the causal effect of a point exposure on the risk of a disease from cohort or case‐control observational data. Because confounding bias is of serious concern in such non‐experimental studies, investigators routinely adjust for a large number of potential confounders in a logistic regression analysis of the effect of exposure on disease outcome. Unfortunately, when confounders are not correctly modeled, standard logistic regression is likely biased in its estimate of the effect of exposure, potentially leading to erroneous conclusions. We partially resolve this serious limitation of standard logistic regression analysis with a new iterative approach that we call ProRetroSpective estimation, which carefully combines standard logistic regression with a logistic regression analysis in which exposure is the dependent variable and the outcome and confounders are the independent variables. As a result, we obtain a correct estimate of the exposure‐outcome odds ratio, if either thestandard logistic regression of the outcome given exposure and confounding factors is correct, or the regression model of exposure given the outcome and confounding factors is correct but not necessarily both, that is, it is double‐robust. In fact, it also has certain advantadgeous efficiency properties. The approach is general in that it applies to both cohort and case‐control studies whether the design of the study is matched or unmatched on a subset of covariates. Finally, an application illustrates the methods using data from the National Cancer Institute's Black/White Cancer Survival Study. Copyright © 2010 John Wiley & Sons, Ltd.
Modelling bounded health scores with censored skew‐normal distributions
Authors: Hutton J. L. , Stanghellini E. 
Published: November 2010

AbstractHealth care interventions that use quality of life or health scores often provide data which are skewed and bounded. The scores are typically formed by adding up numerical responses to a number of questions. Different questions might have different weights, but the scores will be bounded, and are often scaled to the range 0–100. If improvement in health over time is measured, scores will tend to cluster near the ‘healthy’ or ‘good’ boundary as time progresses, leading to a skew distribution. Further, some patients will drop‐out as time progresses, hence the scores reflect a selected population.We fit models based on the skew‐normal distribution to data from a randomized controlled trial of treatments for sprained ankles, in which scores were recorded at baseline and at 1, 3 and 9 months after injury. We consider the extent to which skewness in the data can be explained by clustering at the boundary via a comparison between a censored normal and a censored skew‐normal model.As this analysis is based on the complete data only, a formula for the bias of the treatment effects due to informative drop‐out is given. This allows us to assess under what conditions the conclusions drawn from the complete data might be either reinforced or reversed, when the informative drop‐out process is taken into account. Copyright © 2010 John Wiley & Sons, Ltd.
A symmetrized Theil index measure of health disparities: An example using dental caries in U.S. children and adolescents
Authors: Borrell Luisa N. , Talih Makram 
Published: November 2010

AbstractWhile the health status of Americans has generally improved over time, health disparities among groups of the population have been pervasive. Designing a measure that tracks the resulting disparities remains a challenge. In this paper, we propose a new measure of health disparities the Symmetrized Theil Index (STI), and derive its design‐based sampling variance in grouped survey data. Because STI is symmetric, it circumvents the drawback of the Theil Index in how groups are weighted: indeed, the latter is mostly influenced by groups with high disease frequencies. Moreover, STI is related to Pearson's chi‐square test of independence for binary data, and to the F‐test in one‐way analysis‐of‐variance for continuous data. We illustrate our approach using data on dental caries for children and adolescents from the third National Health and Nutrition Examination Surveys (NHANES III; 1988–1994) and NHANES 1999–2004. Tooth decay remains the most common chronic disease in U.S. children and adolescents. Although their oral health has generally improved, we find no change in the prevalence or severity of untreated tooth decay in U.S. children and adolescents between surveys. These findings are consistently observed for both the overall STI and its between‐group component across gender, race/ethnicity, country of birth, survey respondent's education, income and poverty–income ratio. Copyright © 2010 John Wiley & Sons, Ltd.
Accounting for bias due to a non‐ignorable tracing mechanism in a retrospective breast cancer cohort study
Authors: Titman Andrew C. , Lancaster Gillian A. , Carmichael Katie , Scutt Diane 
Published: November 2010

AbstractWe consider the analysis of competing risks in a retrospective breast cancer cohort study where tracing of patients is dependent on survival to a pre‐specified truncation time. We demonstrate that if ignored, the observed cause‐specific hazards will become distorted before the truncation time. Two approaches to account for the tracing bias are considered. First, a likelihood‐based method using piecewise constant transition intensities under a Markov assumption. Second, a pseudo‐likelihood method using inverse probability of tracing weights. For the breast cancer example, both methods improve the precision of estimates compared with a conventional approach based on excluding patients. Copyright © 2010 John Wiley & Sons, Ltd.
Functional difference between Thy‐1‐positive and Thy‐1‐negative γδ T cells induced by Escherichia coli infection in mice
Authors: TAKADA H. , MATSUZAKI G. , YOSHIDA H. , SUMICHIKA H. , NOMOTO K. 
Published: November 2010

SummaryThere is an increase in number of γδ T cells in the peritoneal cavity after intraperitoneal (i.p.) inoculation with Escherichia coli. The E. coli‐induced γδ T cells in C3H/He mice contain a large amount of Thy‐1‐negative population in addition to the Thy‐1‐positive population. We investigated the difference between the Thy‐1‐positive and the Thy‐1‐negative γδ T cells. Although it was found that only up to 4% of the γδ T cells on day 5 after infection were in cycling phase, and that the γδ T cells did not proliferate by immobilized anti‐T‐cell receptor (TCR) γδ monoclonal antibody stimulation, the γδ T cells proliferated in the presence of interleukin‐2 (IL‐2) and IL‐7. The Thy‐1‐negative γδ T cells showed higher proliferative response compared with the Thy‐1‐positive γδ T cells. Furthermore, the Thy‐1‐negative γδ T cells showed lower IFN‐γ mRNA expression than the Thy‐1‐positive γδ T cells. On the other hand, both the Thy‐1‐positive and Thy‐1‐negative γδ T cells predominantly expressed Vγ1, Vγ4, Vγ5, Vγ6 and Vγ1, and no difference of V region usage was detected between them. These results suggest that functions of Thy‐1‐positive γδ T cells differ from Thy‐1‐negative γδ T cells although Thy‐1‐positive and Thy‐1‐negative γδ T cells may have similar V region repertoire and, possibly, similar antigen specificity.
Stem cell factor‐dependent human cord blood derived mast cells express α‐ and β‐tryptase, heparin and chondroitin sulphate
Authors: NILSSON G. , BLOM T. , HARVIMA I. , KUSCHE‐GULLBERG M. , NILSSON K. , HELLMAN L. 
Published: November 2010

SummaryThe present study sought to determine the expression of α‐ and β‐tryptase in in vitro differentiated human cord blood derived mast cells. We also analysed the glycosaminoglycan composition and the phenotype of the cells. The major protease in human mast cells is tryptase, and cDNAs for two different human tryptases have been characterized, the so‐called α‐ and β‐tryptase. By reverse transcriptase‐polymerase chain reaction (RT‐PCR) we could show that stem cell factor (SCF)‐dependent cord blood derived mast cells express both α‐ and β‐tryptase. Furthermore, the cells were stained with a monoclonal antibody (mAb) against tryptase, and the tryptase was enzymatically active cleaving the substrate Z‐Gly‐Pro‐Arg‐ methoxy‐2‐naphthylamide (MNA). The majority of the cord blood derived mast cells could also be stained with mAbs against chymase, cathepsin G and CD68. They also expressed Kit/SCFR (CD117), CD13, CD29 and CD45 on the cell surface. The proteoglycan‐derived polysaccharide composition of the cells was estimated to be 25–35% of heparin origin and 65–75% of chondroitin sulphate origin. Hence, the cord blood derived mast cells exhibit a phenotype in common with the so‐called MCTC type of human mast cells.
Differential recognition patterns of Schistosoma haematobium adult worm antigens by the human antibodies IgA, IgE, IgG1 and IgG4
Authors: MUTAPI F. , BOURKE C. , HARCUS Y. , MIDZI N. , MDULUZA T. , TURNER C. M. , BURCHMORE R. , MAIZELS R. M. 
Published: November 2010

Summary Schistosoma haematobium antigen recognition profiles of the human isotypes IgA, IgE, IgG1 and IgG4 were compared by image analysis of western blots. Adult worm antigens separated by two‐dimensional gel electrophoresis were probed with pooled sera from Zimbabweans resident in a S. haematobium endemic area, followed by the identification of individual antigenic parasite proteins using mass spectrometry. Overall, IgG1 reacted with the largest number of antigens, followed by IgE and IgA which detected the same number, while IgG4 detected the fewest antigens. IgE recognized all antigens reactive with IgG4 as well as an additional four antigens, an isoform of 28‐kDa GST, phosphoglycerate kinase, actin 1 and calreticulin. IgG1 additionally recognized fatty acid–binding protein, triose‐phosphate isomerase and heat shock protein 70, which were not recognized by IgA. Recognition patterns varied between some isoforms, e.g. the two fructose 1‐6‐bis‐phosphate aldolase isoforms were differentially recognized by IgA and IgG1. Although the majority of S. haematobium adult worm antigens are recognized by all of the four isotypes, there are clear restrictions in antibody recognition for some antigens. This may partly explain differences observed in isotype dynamics at a population level. Differential recognition patterns for some isoforms indicated in the study have potential importance for vaccine development.
Gene expression changes during short day induced terminal bud formation in Norway spruce
Authors: ASANTE DANIEL K. A. , YAKOVLEV IGOR A. , FOSSDAL CARL GUNNAR , HOLEFORS ANNA , OPSETH LARS , OLSEN JORUNN E. , JUNTTILA OLAVI , JOHNSEN ØYSTEIN 
Published: November 2010

ABSTRACTThe molecular basis for terminal bud formation in autumn is not well understood in conifers. By combining suppression subtractive hybridization and monitoring of gene expression by qRT‐PCR analysis, we aimed to identify genes involved in photoperiodic control of growth cessation and bud set in Norway spruce. Close to 1400 ESTs were generated and their functional distribution differed between short day (SD‐12 h photoperiod) and long day (LD‐24 h photoperiod) libraries. Many genes with putative roles in protection against stress appeared differentially regulated under SD and LD, and also differed in transcript levels between 6 and 20 SDs. Of these,PaTFL1(TERMINAL FLOWER LIKE 1) showed strongly increased transcript levels at 6 SDs.PaCCCH(CCCH‐TYPE ZINC FINGER) andPaCBF2&3(C‐REPEAT BINDING FACTOR 2&3) showed a later response at 20 SDs, with increased and decreased transcript levels, respectively. For rhythmically expressed genes such asCBFs, such differences might represent a phase shift in peak expression, but might also suggest a putative role in response to SD. Multivariate analyses revealed strong differences in gene expression between LD, 6 SD and 20 SD. The robustness of the gene expression patterns was verified in 6 families differing in bud‐set timing under natural light with gradually decreasing photoperiod.
Sodium cromoglycate and eformoterol attenuate sensitivity and reactivity to inhaled mannitol in subjects with bronchiectasis
Authors: BRIFFA Peter J. , ANDERSON Sandra D. , BURTON Deborah L. , YOUNG Iven H. 
Published: November 2010

ABSTRACTBackground and objective:  Dry powder mannitol has the potential to be used to enhance clearance of mucus in subjects with bronchiectasis. A reduction in FEV1 has been recorded in some subjects with bronchiectasis after inhaling mannitol. The aim of this study was to investigate if pre‐medicating with either sodium cromoglycate (SCG) or eformoterol could inhibit this reduction in FEV1.Methods:  A double‐blind, placebo‐controlled, randomized cross‐over study was conducted. Lung function and airway response to mannitol was assessed on a control day and then re‐assessed after pre‐medication with placebo, SCG and eformoterol in nine subjects. Sensitivity to mannitol, expressed as the dose required to induce a 15% fall in FEV1 (PD15), and reactivity to mannitol, expressed as the % fall in FEV1 per mg of mannitol (response–dose ratio, RDR), are reported.Results:  Subjects had an FEV1 of 68 ± 14% predicted, FVC of 97 ± 15% predicted and FEV1/FVC of 71 ± 8%. They were mildly hypoxemic and the SpO2 was 95 ± 2%.They had a PD15 to mannitol of 235 mg (95% CI: 150–368 mg) and a RDR of 0.057% fall in FEV1 per mg (95% CI: 0.038–0.085). After pre‐medication with SCG, PD15 increased (773 mg, P < 0.05) and RDR was reduced (0.013, P < 0.05). Pre‐medication with eformoterol also resulted in an increased PD15 (1141 mg, P < 0.01) and a reduced RDR (0.009, P < 0.01). A small but significant decrease in SpO2 from baseline was noted after mannitol in the presence of SCG (P < 0.05).Conclusions:  Pre‐medication with either SCG or eformoterol protects patients with bronchiectasis from developing a significant reduction in FEV1 after inhaling mannitol.
Minimally invasive imaging method based on second harmonic generation and multiphoton excitation fluorescence in translational respiratory research
Authors: ABRAHAM Thomas , WADSWORTH Samuel , CARTHY Jon M. , PECHKOVSKY Dmitri V. , McMANUS Bruce 
Published: November 2010

ABSTRACTFor translational respiratory research including in the development of clinical diagnostic tools, a minimally invasive imaging method, which can provide both cellular and extracellular structural details with sufficient specificity, sensitivity and spatial resolution, is particularly useful. Multiphoton microscopy causes excitation of endogenously fluorescent macromolecular systems and induces highly specific second harmonic generation signals from non‐centrosymmetric macromolecules such as fibrillar collagens. Both these signals can be captured simultaneously to provide spatially resolved 3D structural organization of extracellular matrix as well as the cellular morphologies in their native states. Besides briefly discussing the fundamentals of multiphoton excitation fluorescence and harmonic generation signals and the instrumentation details, this review focuses on the specific applications of these imaging modalities in lung structural imaging, particularly morphological features of alveolar structures, visualizing and quantifying extracellular matrix remodelling accompanying emphysematous destructions as well as the IPF, detecting lung cancers and the potential use in the tissue engineering applications.