bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role ofCD14Promoter Polymorphisms inHelicobacter pyloriInfection–Related Gastric Carcinoma
Authors: Zhao Dan , Sun Tong , Zhang Xuemei , Guo Yongli , Yu Dianke , Yang Ming , Tan Wen , Wang Guiqi , Lin Dongxin 
Published: April 2007

AbstractPurpose: Genetic variation in CD14 may affect CD14 expression and susceptibility to Helicobacter pylori infection–related cancers. This study examined functional single nucleotide polymorphisms (SNP) in the CD14 promoter and their associations with risk of developing gastric carcinoma in relation to H. pylori infection.Experimental Design: Thirty individual DNAs were sequenced to identify variants, and the function of the variants was examined by reporter gene assays. Genotypes and haplotypes were analyzed in 470 patients and 470 controls, and odds ratios (OR) and 95% confidence intervals (95% CI) were estimated by logistic regression. Serologic H. pylori antibody and soluble CD14 (sCD14) levels were measured by ELISA.Results: Two SNPs (−651C&gt;T and −260C&gt;T) were identified, of which the −260CT and −260TT genotypes were associated with elevated risk of gastric carcinoma (OR, 1.77; 95% CI, 1.09-2.85 and OR, 1.95; 95% CI, 1.20-3.16, respectively). Haplotype analysis suggested a synergistic effect of the two SNPs (OR for the T−651-T−260 haplotype, 3.39 versus OR for the C−651-T−260 haplotype, 1.45; P = 0.02), which is consistent with reporter gene assays. A multiplicative joint effect between H. pylori infection and −260C&gt;T polymorphism was observed (OR for the presence of both −260TT genotype and H. pylori infection, 4.03; 95% CI, 1.80-9.04). Patients had significantly higher sCD14 than controls (1,866 ± 2,535 ng/mL versus 1,343 ± 2,119 ng/mL; P &lt; 0.001), and this difference was associated with the CD14 −260 polymorphism and H. pylori infection.Conclusions: Functional polymorphism in CD14 is associated with greater risk of H. pylori–related gastric carcinoma, which might be mediated by elevated sCD14.
Vorinostat for Treatment of Cutaneous Manifestations of Advanced Primary Cutaneous T-Cell Lymphoma
Authors: Mann Bhupinder S. , Johnson John R. , He Kun , Sridhara Rajeshwari , Abraham Sophia , Booth Brian P. , Verbois Leigh , Morse David E. , Jee Josephine M. , Pope Sarah , Harapanhalli Ravi S. , Dagher Ramzi , Farrell Ann , Justice Robert , Pazdur Richard 
Published: April 2007

Abstract
Purpose: To discuss vorinostat approval for treatment of cutaneous manifestations of advanced cutaneous T-cell lymphoma (CTCL).
Experimental Design: Data from 1 single-arm, open-label, multicenter pivotal trial and 11 other trials submitted to support the new drug application for vorinostat in the treatment of advanced primary CTCL were reviewed. The pivotal trial assessed responses by changes in overall skin disease score using a severity-weighted assessment tool (SWAT). Vorinostat could be considered active in CTCL if observed response rate was at least 20% and the lower bound of the corresponding 95% confidence interval (95% CI) excluded 5%. Patients reported pruritis relief using a questionnaire and a visual analogue scale.
Results: The pivotal trial enrolled 74 patients with stage IB or higher CTCL. Median number of prior treatments was 3, and 61 patients (82%) had stage IIB or higher disease. The objective response rate in the skin disease assessed by change in the overall SWAT score from the baseline was 30% (95% CI, 18.5 to 42.6) in patients with stage IIB or higher disease. Median response duration (end of response defined by 50% increase in SWAT score from the nadir) was 168 days. Median time to tumor progression was 148 days for overall population and 169 days for patients with stage IIB or higher disease. Assessment of pruritis relief was considered unreliable.
Conclusions: Vorinostat showed activity in CTCL, and skin responses were a clinical benefit. Vorinostat was approved for treatment of cutaneous manifestations of CTCL. A nonblinded, single-arm trial did not allow a reliable assessment of pruritis relief.
Proteomics of Canine Lymphoma Identifies Potential Cancer-Specific Protein Markers
Authors: McCaw Dudley L. , Chan Arvan S. , Stegner Andrew L. , Mooney Brian , Bryan Jeffrey N. , Turnquist Susan E. , Henry Carolyn J. , Alexander Hannah , Alexander Stephen 
Published: April 2007

Abstract
Purpose: Early diagnosis of cancer is crucial for the success of treatment of the disease, and there is a need for markers whose differential expression between disease and normal tissue could be used as a diagnostic tool. Spontaneously occurring malignancies in pets provide a logical tool for translational research for human oncology. Lymphoma, one of the most common neoplasms in dogs, is similar to human non–Hodgkin's lymphoma and could serve as an experimental model system.
Experimental Design: Thirteen lymph nodes from normal dogs and 11 lymph nodes from dogs with B-cell lymphoma were subjected to proteomic analysis using two-dimensional PAGE separation and matrix-assisted laser desorption/ionization time-of-flight analysis.
Results: A total of 93 differentially expressed spots was subjected to matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry analysis, and several proteins that showed differential expression were identified. Of these, prolidase (proline dipeptidase), triosephosphate isomerase, and glutathione S-transferase were down-regulated in lymphoma samples, whereas macrophage capping protein was up-regulated in the lymphoma samples.
Conclusions: These proteins represent potential markers for the diagnosis of lymphoma and should be further investigated in human samples for validation of their utility as diagnostic markers.
Targeting TRAIL Agonistic Receptors for Cancer Therapy
Authors: Carlo-Stella Carmelo , Lavazza Cristiana , Locatelli Alberta , Viganò Lucia , Gianni Alessandro M. , Gianni Luca 
Published: April 2007

Abstract
Based on preclinical studies demonstrating that tumor necrosis factor–related apoptosis-inducing ligand (TRAIL) exerts a potent and cancer cell–specific proapoptotic activity, recombinant TRAIL as well as agonistic anti–TRAIL-R1 and anti–TRAIL-R2 antibodies recently entered clinical trials. Additionally, gene therapy approaches using TRAIL-encoding adenovirus (Ad-TRAIL) are currently being developed to overcome the limitations inherent to TRAIL receptor targeting, i.e., pharmacokinetic of soluble TRAIL, pattern of receptor expression, and tumor cell resistance. To optimize gene therapy approaches, CD34+ cells transduced with Ad-TRAIL (CD34-TRAIL+) have been investigated as cellular vehicles for TRAIL delivery. Transduced cells exhibit a potent tumor killing activity on a variety of tumor cell types both in vitro and in vivo and are also cytotoxic against tumor cells resistant to soluble TRAIL. Studies in tumor-bearing nonobese diabetic/severe combined immunodeficient mice suggest that the antitumor effect of CD34-TRAIL+ cells is mediated by both direct tumor cell killing due to apoptosis and indirect tumor cell killing due to vascular-disrupting mechanisms. The clinical translation of cell and gene therapy approaches represent a challenging strategy that might achieve systemic tumor targeting and increased intratumor delivery of the therapeutic agent.
HLA-DQB1*02–Restricted HPV-16 E7 Peptide–Specific CD4+ T-Cell Immune Responses Correlate with Regression of HPV-16–Associated High-Grade Squamous Intraepithelial Lesions
Authors: Peng Shiwen , Trimble Cornelia , Wu Lee , Pardoll Drew , Roden Richard , Hung Chien-Fu , Wu T.-C. 
Published: April 2007

AbstractPurpose: The fact that up to 30% of established high-grade squamous intraepithelial lesions (HSIL) of the cervix regress spontaneously presents the opportunity to identify clinically relevant human papillomavirus (HPV) viral epitopes associated with disease outcome. Two human HPV antigens, E6 and E7, are functionally required for initiation and maintenance of cervical cancer precursor lesions and invasive cervical cancer. The identification and characterization of endogenously processed HPV antigenic epitopes in closely characterized patient cohorts will provide insight into the reasons for success or failure of therapeutic approaches.Experimental Design: We characterized the HPV-16 E6/E7–specific T-cell epitopes using E6/E7 overlapping peptide pools with peripheral blood lymphocytes obtained from normal healthy donors. We then analyzed the difference in the HPV-16 T-cell immune responses in HPV-16+ HSIL patients with or without spontaneous regression of lesions using the statistical methods.Results: We have identified an HPV-16 E7–specific CD4+ T-cell epitope [amino acids (aa) 71-85] that was restricted by HLA-DQB1*0201. Analysis of peripheral blood lymphocytes obtained from 14 HLA-DQB1*02 patients with HPV-16+ HSILs showed that the HPV-16+ E7 peptide (aa 71-85)–specific CD4+ T-cell immune response was significantly higher in the group of patients with regression compared with the patients without regression (P value &lt;0.05).Conclusions: The HPV-16 E7 peptide–specific CD4+ T-cell immune response correlates with spontaneous regression of established HPV16+ HSILs. Thus, this E7 epitope may be useful for the characterization of HPV-specific immune responses in patients infected with HPV-16 or immunized with HPV vaccines.
Modeling the Interactions between Aerosols and Liquid Water Clouds with a Self-Consistent Cloud Scheme in a General Circulation Model
Authors: Ming Yi , Ramaswamy V. , Donner Leo J. , Phillips Vaughan T. J. , Klein Stephen A. , Ginoux Paul A. , Horowitz Larry W. 
Published: April 2007

Abstract
To model aerosol–cloud interactions in general circulation models (GCMs), a prognostic cloud scheme of cloud liquid water and amount is expanded to include droplet number concentration (Nd) in a way that allows them to be calculated using the same large-scale and convective updraft velocity field. In the scheme, the evolution of droplets fully interacts with the model meteorology. An explicit treatment of cloud condensation nuclei (CCN) activation enables the scheme to take into account the contributions to Nd of multiple aerosol species (i.e., sulfate, organic, and sea-salt aerosols) and to consider kinetic limitations of the activation process. An implementation of the prognostic scheme in the Geophysical Fluid Dynamics Laboratory (GFDL) AM2 GCM yields a vertical distribution of Nd with a characteristic maximum in the lower troposphere; this feature differs from the profile that would be obtained if Nd is diagnosed from the sulfate mass concentration based on an often-used empirical relationship. Prognosticated Nd exhibits large variations with respect to the sulfate mass concentration. The mean values are generally consistent with the empirical relationship over ocean, but show negative biases over the Northern Hemisphere midlatitude land, perhaps owing to the neglect of subgrid variations of large-scale ascents and inadequate convective sources. The prognostic scheme leads to a substantial improvement in the agreement of model-predicted present-day liquid water path (LWP) and cloud forcing with satellite measurements compared to using the empirical relationship.
The simulations with preindustrial and present-day aerosols show that the combined first and second indirect effects of anthropogenic sulfate and organic aerosols give rise to a steady-state global annual mean flux change of −1.8 W m−2, consisting of −2.0 W m−2 in shortwave and 0.2 W m−2 in longwave. The ratios of the flux changes in the Northern Hemisphere (NH) to that in Southern Hemisphere (SH) and of the flux changes over ocean to that over land are 2.9 and 0.73, respectively. These estimates are consistent with the averages of values from previous studies stated in a recent review. The model response to higher Nd alters the cloud field; LWP and total cloud amount increase by 19% and 0.6%, respectively. Largely owing to high sulfate concentrations from fossil fuel burning, the NH midlatitude land and oceans experience strong radiative cooling. So does the tropical land, which is dominated by biomass burning–derived organic aerosol. The computed annual, zonal-mean flux changes are determined to be statistically significant, exceeding the model’s natural variations in the NH low and midlatitudes and in the SH low latitudes. This study reaffirms the major role of sulfate in providing CCN for cloud formation.
Vortex Street Dynamics: The Selection Mechanism for the Areas and Locations of Jupiter’s Vortices
Authors: Humphreys Tom , Marcus Philip S. 
Published: April 2007

Abstract
With the exception of the Great Red Spot, Jupiter’s long-lived vortices are not isolated, but occur in east–west rows. Each row is centered about a westward-going jet stream with anticyclones on the poleward side and cyclones on the equatorial. Vortices are staggered so that like-signed vortices are never longitudinally adjacent. These double rows of vortices, called here Jovian vortex streets (JVSs) are robust. Calculations with no forcing and no dissipation (i.e., Hamiltonian dynamics) allow a continuum of JVS solutions, so they cannot be used to determine the physics that selects the observed values of the areas, circulations, and locations of Jupiter’s vortices. Constraints imposed by stability put few bounds on these values. When small amounts of dissipation and forcing are added to the governing equations, there is no longer a continuum of solutions; an initial JVS that was a solution of the Hamiltonian equations is now out of equilibrium and evolves to an attractor. For fixed forcing, all initial JVS evolve to the same attractor, so that the area of the vortices in the late-time JVS is selected uniquely as is the separation width in latitude between the row of cyclones and row of anticyclones. The separation width of the attracting JVS is nearly independent of the forcing, but the areas of the vortices in the attracting JVS depend strongly on the strength of the forcing, which is a measure of the ambient Jovian turbulence. Results are compared with observations.
Vertical-Mode and Cloud Decomposition of Large-Scale Convectively Coupled Gravity Waves in a Two-Dimensional Cloud-Resolving Model
Authors: Tulich Stefan N. , Randall David A. , Mapes Brian E. 
Published: April 2007

Abstract
This paper describes an analysis of large-scale [O(1000 km)] convectively coupled gravity waves simulated using a two-dimensional cloud-resolving model. The waves develop spontaneously under uniform radiative cooling and approximately zero-mean-flow conditions, with wavenumber 2 of the domain appearing most prominently and right-moving components dominating over left-moving components for random reasons. The analysis discretizes the model output in two ways. First, a vertical-mode transform projects profiles of winds, temperature, and heating onto the vertical modes of the model’s base-state atmosphere. Second, a cloud-partitioning algorithm sorts sufficiently cloudy grid columns into three categories: shallow convective, deep convective, and stratiform anvil.
Results show that much of the tilted structures of the waves can be captured by just two main vertical spectral “bands,” each consisting of a pair of vertical modes. The “slow” modes have propagation speeds of 16 and 18 m s−1 (and roughly a full-wavelength vertical structure through the troposphere), while the “fast” modes have speeds of 35 and 45 m s−1 (and roughly a half-wavelength structure). Deep convection anomalies in the waves are more or less in phase with the low-level cold temperature anomalies of the slow modes and in quadrature with those of the fast modes. Owing to the characteristic life cycle of deep convective cloud systems, shallow convective heating peaks ∼2 h prior to maximum deep convective heating, while stratiform heating peaks ∼3 h after. The onset of deep convection in the waves is preceded by a gradual deepening of shallow convection lasting a period of many hours.
Results of this study are in broad agreement with simple two-mode models of unstable large-scale wave growth, under the name “stratiform instability.” Differences here are that 1) the key dynamical modes have speeds in the range 16–18 m s−1, rather than 23–25 m s−1 (owing to a shallower depth of imposed radiative cooling), and 2) deep convective heating, as well as stratiform heating, is essential for the generation and maintenance of the slow modes.
Assessing Predictability with a Local Ensemble Kalman Filter
Authors: Kuhl David , Szunyogh Istvan , Kostelich Eric J. , Gyarmati Gyorgyi , Patil D. J. , Oczkowski Michael , Hunt Brian R. , Kalnay Eugenia , Ott Edward , Yorke James A. 
Published: April 2007

Abstract
In this paper, the spatiotemporally changing nature of predictability is studied in a reduced-resolution version of the National Centers for Environmental Prediction (NCEP) Global Forecast System (GFS), a state-of-the-art numerical weather prediction model. Atmospheric predictability is assessed in the perfect model scenario for which forecast uncertainties are entirely due to uncertainties in the estimates of the initial states. Uncertain initial conditions (analyses) are obtained by assimilating simulated noisy vertical soundings of the “true” atmospheric states with the local ensemble Kalman filter (LEKF) data assimilation scheme. This data assimilation scheme provides an ensemble of initial conditions. The ensemble mean defines the initial condition of 5-day deterministic model forecasts, while the time-evolved members of the ensemble provide an estimate of the evolving forecast uncertainties. The observations are randomly distributed in space to ensure that the geographical distribution of the analysis and forecast errors reflect predictability limits due to the model dynamics and are not affected by inhomogeneities of the observational coverage.
Analysis and forecast error statistics are calculated for the deterministic forecasts. It is found that short-term forecast errors tend to grow exponentially in the extratropics and linearly in the Tropics. The behavior of the ensemble is explained by using the ensemble dimension (E dimension), a spatiotemporally evolving measure of the evenness of the distribution of the variance between the principal components of the ensemble-based forecast error covariance matrix.
It is shown that in the extratropics the largest forecast errors occur for the smallest E dimensions. Since a low value of the E dimension guarantees that the ensemble can capture a large portion of the forecast error, the larger the forecast error the more certain that the ensemble can fully capture the forecast error. In particular, in regions of low E dimension, ensemble averaging is an efficient error filter and the ensemble spread provides an accurate prediction of the upper bound of the error in the ensemble-mean forecast.
A Combined Eddy-Diffusivity Mass-Flux Approach for the Convective Boundary Layer
Authors: Siebesma A. Pier , Soares Pedro M. M. , Teixeira João 
Published: April 2007

Abstract
A better conceptual understanding and more realistic parameterizations of convective boundary layers in climate and weather prediction models have been major challenges in meteorological research. In particular, parameterizations of the dry convective boundary layer, in spite of the absence of water phase-changes and its consequent simplicity as compared to moist convection, typically suffer from problems in attempting to represent realistically the boundary layer growth and what is often referred to as countergradient fluxes. The eddy-diffusivity (ED) approach has been relatively successful in representing some characteristics of neutral boundary layers and surface layers in general. The mass-flux (MF) approach, on the other hand, has been used for the parameterization of shallow and deep moist convection. In this paper, a new approach that relies on a combination of the ED and MF parameterizations (EDMF) is proposed for the dry convective boundary layer. It is shown that the EDMF approach follows naturally from a decomposition of the turbulent fluxes into 1) a part that includes strong organized updrafts, and 2) a remaining turbulent field. At the basis of the EDMF approach is the concept that nonlocal subgrid transport due to the strong updrafts is taken into account by the MF approach, while the remaining transport is taken into account by an ED closure. Large-eddy simulation (LES) results of the dry convective boundary layer are used to support the theoretical framework of this new approach and to determine the parameters of the EDMF model. The performance of the new formulation is evaluated against LES results, and it is shown that the EDMF closure is able to reproduce the main properties of dry convective boundary layers in a realistic manner. Furthermore, it will be shown that this approach has strong advantages over the more traditional countergradient approach, especially in the entrainment layer. As a result, this EDMF approach opens the way to parameterize the clear and cumulus-topped boundary layer in a simple and unified way.
Choosing the Smoothing Parameters within a Multiple-Pass Barnes Objective Analysis Scheme: A Cautionary Note
Authors: Spencer Phillip L. , Askelson Mark A. , Doswell Charles A. 
Published: April 2007

Abstract
Various combinations of smoothing parameters within a two-pass Barnes objective analysis scheme are applied to analytic observations obtained by regular and irregular sampling of a one-dimensional sinusoidal analytic wave to obtain gridded fields. Each of these various combinations of smoothing parameters would produce equivalent analyses if the observations were continuous and infinite (unbounded). The authors demonstrate that owing to the discreteness of the analytic observations, the actual analyses resulting from these various combinations of smoothing parameters are different. When derivatives are computed and as stations become more irregularly distributed, these differences increase. An awareness of these potentially significant analysis differences should prompt the analyst to consider carefully the choice of smoothing parameters when applying an objective analysis scheme to real observations.