bluuebunny/crossref_metadata_2025_split huggingface dataset:
Duration of Naturally Acquired Antibody Responses to Blood-StagePlasmodium falciparumIs Age Dependent and Antigen Specific
Authors: Akpogheneta Onome J. , Duah Nancy O. , Tetteh Kevin K. A. , Dunyo Samuel , Lanar David E. , Pinder Margaret , Conway David J. 
Published: January 2008

ABSTRACTNaturally acquired antibody responses provide partial protection from clinical malaria, and blood-stage parasite vaccines under development aim to prime such responses. To investigate the determinants of antibody response longevity, immunoglobulin G (IgG) antibodies to several blood-stage vaccine candidate antigens in the sera of two cohorts of children of up to 6 years of age during the dry seasons of 2003 and 2004 in The Gambia were examined. The first cohort showed that most antibodies were lost within less than 4 months of the first sampling if a persistent infection was not present, so the study of the second-year cohort involved collecting samples from individuals every 2 weeks over a 3-month period. Antibody responses in the second cohort were also influenced by persistent malaria infection, so analysis focused particularly on children in whom parasites were not detected after the first time point. Antibodies to most antigens declined more slowly in children in the oldest age group (>5 years old) and more rapidly in children in the youngest group (<3 years old). However, antibodies to merozoite surface protein 2 were shorter lived than antibodies to other antigens and were not more persistent in older children. The age-specific and antigen-specific differences were not explained by different IgG subclass response profiles, indicating the probable importance of differential longevities of plasma cell populations rather than antibody molecules. It is likely that young children mostly have short-lived plasma cells and thus experience rapid declines in antibody levels but that older children have longer-lasting antibody responses that depend on long-lived plasma cells.
Identification of an HLA-A*0201-Restricted T-Cell Epitope on the MPT51 Protein, a Major Secreted Protein Derived fromMycobacterium tuberculosis, by MPT51 Overlapping Peptide Screening
Authors: Aoshi Taiki , Nagata Toshi , Suzuki Mina , Uchijima Masato , Hashimoto Dai , Rafiei Alireza , Suda Takafumi , Chida Kingo , Koide Yukio 
Published: January 2008

ABSTRACTCD8+T cells play a pivotal role in protection againstMycobacterium tuberculosisinfection. We identified a novel HLA-A*0201-restricted CD8+T-cell epitope on a dominant secreted antigen ofM. tuberculosis, MPT51, in HLA-A*0201 transgenic HHD mice. HHD mice were immunized with plasmid DNA encoding MPT51 with gene gun bombardment, and gamma interferon (IFN-γ) production by the immune splenocytes was analyzed. In response to overlapping synthetic peptides covering the mature MPT51 sequence, the splenocytes were stimulated to produce IFN-γ by only one peptide, p51-70. Three-color flow cytometric analysis of intracellular IFN-γ and cell surface CD4 and CD8 staining revealed that the MPT51 p51-70 peptide contains an immunodominant CD8+T-cell epitope. Further analysis using computer algorithms permitted identification of a bona fide T-cell epitope, p53-62. A major histocompatibility complex class I stabilization assay using T2 cells confirmed that this epitope binds to HLA-A*0201. The T cells were capable of lysing MPT51 p53-62 peptide-pulsed T2 cells. In addition, MPT51 p53-62-specific memory CD8+T cells were found in tuberculin skin test-positive HLA-A*0201+healthy individuals. Use of this HLA-A*0201-restricted CD8+T-cell epitope for analysis of the role of MPT51-specific T cells inM. tuberculosisinfection and for design of vaccines against tuberculosis is feasible.
A Variable-Length PCR Target Protein of
Ehrlichia chaffeensis
Contains Major Species-Specific Antibody Epitopes in Acidic Serine-Rich Tandem Repeats
Authors: Luo Tian , Zhang Xiaofeng , Wakeel Abdul , Popov Vsevolod L. , McBride Jere W. 
Published: January 2008

ABSTRACT

Ehrlichia chaffeensis
and
E. canis
have a small subset of tandem repeat (TR)-containing proteins that elicit strong host immune responses and are associated with host-pathogen interactions. In a previous study, we molecularly characterized a highly conserved 19-kDa major immunoreactive protein (gp19) of
E. canis
and identified the corresponding TR-containing ortholog variable-length PCR target (VLPT) protein in
E. chaffeensis
. In this study, the native 32-kDa VLPT protein was identified and the immunodeterminants defined in order to further understand the molecular basis of the host immune response to
E. chaffeensis
. Synthetic and/or recombinant polypeptides corresponding to various regions of VLPT were used to localize major antibody epitopes to the TR-containing region. Major antibody epitopes were identified in three nonidentical repeats (R2, R3, and R4), which reacted strongly with antibodies in sera from an
E. chaffeensis
-infected dog and human monocytotropic ehrlichiosis patients. VLPT-R3 and VLPT-R2 reacted most strongly with antibody, and the epitope was further localized to a nearly identical proximal 17-amino-acid region common between these repeats that was species specific. The epitope in R4 was distinct from that of R2 and R3 and was found to have conformational dependence. VLPT was detected in supernatants from infected cells, indicating that the protein was secreted. VLPT was localized on both reticulate and dense-core cells, and it was found extracellularly in the morula fibrillar matrix and associated with the morula membrane.
Externally assessed psychosocial work characteristics and diagnoses of anxiety and depression
Authors: Waldenström K , Ahlberg G , Bergman P , Forsell Y , Stoetzer U , Waldenström M , Lundberg I 
Published: January 2008

Background:Interpretations of relationships between work characteristics and psychiatric disorders may be biased by over-reporting of unfavourable work characteristics among those with psychiatric disorders. This study attempts to account for this bias by using external assessments of work characteristics.Methods:Psychiatric symptoms were assessed in an interview and psychiatric diagnoses were established according to DSM-IV. Current work characteristics and work characteristics three years ago were assessed in an interview with predetermined criteria and included cognitive requirements, possibility of influence, and required conformance to schedule, time pressure, and hindrances concerning goals, resources and instrumental support. Deterioration in work characteristics during the study period was also assessed. The sample consisted of 672 employed men and women in different occupations.Results:Lack of instrumental support from colleagues and supervisors (OR 6.4, 95% CI 2.6 to 15.8) assessed as a hindrance to work performance, and deterioration in work characteristics during the study period (OR 2.8, 95% CI 1.3 to 6.1) were associated with increased odds ratios for depression after adjustment for confounding factors, including symptoms of mental illness at baseline. Findings for anxiety were similar but not statistically significant.Conclusion:Externally assessed lack of instrumental social support at work and deteriorating work characteristics were associated with an increased risk for depression.
ROBUSTNESS OF THE REGRESSION MODELS FOR UNCERTAIN CATEGORIES
Authors: BOLOTIN ARKADY 
Published: January 2008

Dichotomization of the outcome by a single cut-off point is an important part of medical studies. Usually the relationship between the resulted dichotomized dependent variable and explanatory variables is analyzed with linear regression, probit or logistic regression. However, in many real-life situations, a certain cut-off point is unknown and can be specified only approximately, i.e. surrounded by some (small) uncertainty. It means that in order to have any practical meaning the regression model must be robust to this uncertainty. In this paper, we test the robustness of the linear regression model and get that neither the beta in the model, nor its significance level is robust to the small variations in the dichotomization cut-off point. As an alternative robust approach to the problem of uncertain categories, we propose to make use of the linear regression model with the fuzzy membership function as a dependent variable. In the paper, we test the robustness of the linear regression model of such fuzzy dependent variable and get that this model can be insensitive against the uncertainty in the cut-off point location. To demonstrate theoretical conclusions, in the paper we present the modelling results from the real study of low haemoglobin levels in infants.
Function of Heparanase in Prostate Tumorigenesis: Potential for Therapy
Authors: Lerner Immanuel , Baraz Leah , Pikarsky Eli , Meirovitz Amichay , Edovitsky Evgeny , Peretz Tamar , Vlodavsky Israel , Elkin Michael 
Published: January 2008

AbstractPurpose: Heparanase is the predominant enzyme that cleaves heparan sulfate, the main polysaccharide in the extracellular matrix. Whereas the role of heparanase in sustaining the pathology of human cancer is well documented, its association with prostate carcinoma remains uncertain. Our research was undertaken to elucidate the significance of heparanase in prostate tumorigenesis and bone metastasis.Experimental Design: We applied immunohistochemical analysis of tissue microarray, in vitro adhesion and invasion assays, as well as mouse models of intraosseous growth and spontaneous metastasis of prostate cancer, monitored by whole-body bioluminescent imaging. Electroporation-assisted administration of anti-heparanase small interfering RNA in vivo was applied as a therapeutic approach.Results: We report a highly statistically significant (P &lt; 0.0001) prevalence of heparanase overexpression in prostate carcinomas versus noncancerous tissue, as well as strong correlation between tumor grade and the extent of heparanase expression. We observed &gt;5-fold increase in the metastatic potential of PC-3 prostate carcinoma cells engineered to overexpress heparanase. Notably, overexpression of a secreted form of the enzyme also led to a dramatic increase in intraosseous prostate tumor growth. Local in vivo silencing of heparanase resulted in a 4-fold inhibition of prostate tumor growth, representing the first successful application of anticancer therapy based on heparanase small interfering RNA and validating the potential of heparanase as a target for prostate cancer treatment.Conclusions: Heparanase directly contributes to prostate tumor growth in bone and its ability to metastasize to distant organs. Thus, anti-heparanase strategy may become an important modality in the treatment of prostate cancer patients, particularly those with bone metastases.
Dynamic Instabilities of Simulated Hurricane-like Vortices and Their Impacts on the Core Structure of Hurricanes. Part II: Moist Experiments
Authors: Kwon Young C. , Frank William M. 
Published: January 2008

Abstract
The energy flows of a simulated moist hurricane-like vortex are analyzed to examine the processes that change the intensity and structure of tropical cyclones. The moist vortex used in this study is initially axisymmetric on an f plane and is placed on a uniform surface—an ocean with constant sea surface temperature of 29°C. Two simulations are performed using the following different environmental flows: one in a calm environment and the other in weak environmental vertical shear. The differences between the intensities and structures of the two simulated vortices are discussed in terms of energy flows.
While the structure and intensity of the vortex without shear are relatively steady, those of the vortex with shear experience dramatic changes. The sheared vortex shows delayed weakening, persistent wavenumber 1 asymmetry with maximum rainfall on the downshear left side, and top-down breakdown. In both vortices barotropic energy conversion is stronger than baroclinic energy conversion. However, baroclinic processes in the upper levels of the sheared vortex play an important role in weakening the vortex. The energy flow diagram and the cross section of energy conversion terms show the existence of multiple baroclinic eddy life cycles at the upper levels of the sheared vortex. The activity of the baroclinic eddies continues until ventilation of the upper-level warm-core structure is sufficient to weaken the sheared vortex.
Size Spectra of Snow Particles Measured in Wintertime Precipitation in the Pacific Northwest
Authors: Woods Christopher P. , Stoelinga Mark T. , Locatelli John D. 
Published: January 2008

Abstract
Particle size spectra collected by the University of Washington’s Convair-580 research aircraft at a variety of altitudes and temperatures in winter frontal and orographic precipitation systems during the Improvement of Microphysical Parameterization through Observational Verification Experiment (IMPROVE) are analyzed in this study. The particle size spectra generally appeared to conform to an exponential size distribution, with well-correlated linear fits between the log of the number concentration and particle diameter. When the particle size spectra were grouped according to the habit composition as determined from airborne imagery, significantly improved correlations between the size spectrum parameters and temperature were obtained. This result could potentially be exploited for specifying the size distribution in a single-moment bulk microphysical scheme, if particle habit is predicted by the scheme. Analyses of “spectral trajectories” suggest that the rime-splintering process was likely responsible for the presence of needle and column habit types and the positive shift in both N0s and λs at temperatures warmer than −10°C.
A Stochastic Parameterization for Deep Convection Based on Equilibrium Statistics
Authors: Plant R. S. , Craig G. C. 
Published: January 2008

AbstractA stochastic parameterization scheme for deep convection is described, suitable for use in both climate and NWP models. Theoretical arguments and the results of cloud-resolving models are discussed in order to motivate the form of the scheme. In the deterministic limit, it tends to a spectrum of entraining/detraining plumes and is similar to other current parameterizations. The stochastic variability describes the local fluctuations about a large-scale equilibrium state. Plumes are drawn at random from a probability distribution function (PDF) that defines the chance of finding a plume of given cloud-base mass flux within each model grid box. The normalization of the PDF is given by the ensemble-mean mass flux, and this is computed with a CAPE closure method. The characteristics of each plume produced are determined using an adaptation of the plume model from the Kain–Fritsch parameterization. Initial tests in the single-column version of the Unified Model verify that the scheme is effective in producing the desired distributions of convective variability without adversely affecting the mean state.
Potential Vorticity Diagnosis in the Quasigeostrophic and Nonlinear Balance Systems
Authors: Nielsen-Gammon John W. , Gold David A. 
Published: January 2008

Abstract
Quantitative diagnosis of low-Rossby-number flows using potential vorticity (PV) includes using elements of PV advection to deduce instantaneous tendencies of the balanced atmospheric state, most commonly the geopotential field. This technique, piecewise tendency diagnosis (PTD), is here applied with the prognostic balance equations (Bal-PTD) to obtain a quantitative dynamical diagnosis that in principle may be much more accurate than similar diagnoses using the quasigeostrophic (QG) equations.
When both are applied systematically to a case of rapid oceanic cyclogenesis, differences are found to arise owing to a variety of factors. The dominant factor is differences in the vertical influence of PV anomalies, which affects the partitioning between local and remote processes. QG overestimates the effect of lower-level PV, including surface potential temperature, in amplifying and controlling the motion of the upper-level system. Other differences are found, but overall the QG diagnosis gives results that are qualitatively similar to the nonlinear balance diagnosis. Quantitative accuracy requires the use of Bal-PTD.
The Capacitance of Pristine Ice Crystals and Aggregate Snowflakes
Authors: Westbrook Christopher David , Hogan Robin J. , Illingworth Anthony J. 
Published: January 2008

Abstract
A new method of accurately calculating the capacitance of realistic ice particles is described: such values are key to accurate estimates of deposition and evaporation (sublimation) rates in numerical weather models. The trajectories of diffusing water molecules are directly sampled, using random “walkers.” By counting how many of these trajectories intersect the surface of the ice particle (which may be any shape) and how many escape outside a spherical boundary far from the particle, the capacitances of a number of model ice particle habits have been estimated, including hexagonal columns and plates, “scalene” columns and plates, bullets, bullet rosettes, dendrites, and realistic aggregate snowflakes. For ice particles with sharp edges and corners this method is an efficient and straightforward way of solving Laplace’s equation for the capacitance. Provided that a large enough number of random walkers are used to sample the particle geometry (∼104) the authors expect the calculated capacitances to be accurate to within ∼1%. The capacitance for the modeled aggregate snowflakes (C/Dmax = 0.25, normalized by the maximum dimension Dmax) is shown to be in close agreement with recent aircraft measurements of snowflake sublimation rates. This result shows that the capacitance of a sphere (C/Dmax = 0.5), which is commonly used in numerical models, overestimates the evaporation rate of snowflakes by a factor of 2.
The effect of vapor “screening” by crystals growing in the vicinity of one another has also been investigated. The results clearly show that neighboring crystals growing on a filament in cloud chamber experiments can strongly constrict the vapor supply to one another, and the resulting growth rate measurements may severely underestimate the rate for a single crystal in isolation (by a factor of 3 in this model setup).
Retrieval of Urban Boundary Layer Structures from Doppler Lidar Data. Part I: Accuracy Assessment
Authors: Xia Quanxin , Lin Ching-Long , Calhoun Ronald , Newsom Rob K. 
Published: January 2008

Abstract
Two coherent Doppler lidars from the U.S. Army Research Laboratory (ARL) and Arizona State University (ASU) were deployed in the Joint Urban 2003 atmospheric dispersion field experiment (JU2003) held in Oklahoma City, Oklahoma. The dual-lidar data were used to evaluate the accuracy of a four-dimensional variational data assimilation (4DVAR) method and to identify the coherent flow structures in the urban boundary layer. The objectives of the study are threefold. The first objective is to examine the effect of eddy viscosity models on the quality of retrieved velocity data. The second objective is to determine the fidelity of single-lidar 4DVAR and evaluate the difference between single- and dual-lidar retrievals. The third objective is to inspect flow structures above some geospatial features on the land surface. It is found that the approach of treating eddy viscosity as part of the control variables yields better results than the approach of prescribing viscosity. The ARL single-lidar 4DVAR is able to retrieve radial velocity fields with an accuracy of 98% in the along-beam direction and 80%–90% in the cross-beam direction. For the dual-lidar 4DVAR, the accuracy of retrieved radial velocity in the ARL cross-beam direction improves to 90%–94% of the ASU radial velocity data. By using the dual-lidar-retrieved data as a reference, the single-lidar 4DVAR is able to recover fluctuating velocity fields with 70%–80% accuracy in the along-beam direction and 60%–70% accuracy in the cross-beam direction. Large-scale convective roll structures are found in the vicinity of the downtown airport and parks. Vortical structures are identified near the business district. Strong up- and downdrafts are also found above a cluster of restaurants.
Retrieval of Urban Boundary Layer Structures from Doppler Lidar Data. Part II: Proper Orthogonal Decomposition
Authors: Lin Ching-Long , Xia Quanxin , Calhoun Ronald 
Published: January 2008

Abstract
The proper orthogonal decomposition technique is applied to 74 snapshots of 3D wind and temperature fields to study turbulent coherent structures and their interplay in the urban boundary layer over Oklahoma City, Oklahoma. These snapshots of data are extracted from single-lidar data via a four-dimensional variational data assimilation technique. The total velocities and fluctuating temperature are used to construct the data matrix for the decomposition; thus the first eigenmode represents the temporal mean of these data. Roll vortices with a wavelength–height ratio of 3.2 are identified in the first, most energetic eigenmode and are attributed to the inflection-point instability. The second and third spatial eigenmodes also exhibit roll characteristics with different time and length scales, resulting in clockwise- and counterclockwise-rotating roll vortices above the airport and the central business districts. Their positive correlation with temperature fluctuation suggests that those roll structures are driven by thermal as well as wind shear. Their limited horizontal extent seems to coincide with the path of the Oklahoma River. With decreasing rank, coherent structures undergo a transition from roll to polygon patterns. A localized downdraft or updraft located above a cluster of restaurants is captured by the fourth eigenmode. In the capping inversion layer, gravity wave eigenmodes are observed and may be attributed to convection waves. The representation of instantaneous snapshots by high-ranking eigenmodes is then examined by reconstruction of reduced-order fields. It is found that the first four eigenmodes are sufficient to capture the overall characteristics of the 74 snapshots of data.