bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of Clouds and Rain Using a z-Coordinate Nonhydrostatic Model
Authors: Steppeler J. , Bitzer H. W. , Janjic Z. , Schättler U. , Prohl P. , Gjertsen U. , Torrisi L. , Parfinievicz J. , Avgoustoglou E. , Damrath U. 
Published: December 2006

Abstract
The most common option for numerical models of the atmosphere is to use model layers following the surface of the earth, using a terrain-following vertical coordinate. The present paper investigates the forecast of clouds and precipitation using the z-coordinate nonhydrostatic version of the Lokalmodell (LM-z). This model uses model layers that are parallel to the surface of the sphere and consequently intersect the orography. Physical processes are computed on a special grid, allowing adequate grid spacing even over high mountains. In other respects the model is identical to the nonhydrostatic terrain-following version of the LM, which in a number of European countries is used for operational mesoscale forecasting. The terrain-following version of the LM (LM-tf) is used for comparison with the forecasts of the LM-z. Terrain-following coordinates are accurate when the orography is shallow and smooth, while z-coordinate models need not satisfy this condition. Because the condition of smooth orography is rarely satisfied in reality, z-coordinate models should lead to a better representation of the atmospheric flow near mountains and consequently to a better representation of fog, low stratus, and precipitation. A number of real-data cases, computed with a grid spacing of 7 and 14 km, are investigated. A total of 39 real-data cases have been used to evaluate forecast scores. A rather systematic improvement of precipitation forecasts resulted in a substantial increase of threat scores. Furthermore, RMS verification against radiosondes showed an improvement of the 24-h forecast, both for wind and temperature. To investigate the possibility of flow separation at mountain tops, the flow in the lee of southern Italy was investigated.
Climate Modeling with Spectral Elements
Authors: Baer Ferdinand , Wang Houjun , Tribbia Joseph J. , Fournier Aimé 
Published: December 2006

Abstract
As an effort toward improving climate model–component performance and accuracy, an atmospheric-component climate model has been developed, entitled the Spectral Element Atmospheric Climate Model and denoted as CAM_SEM. CAM_SEM includes a unique dynamical core coupled at this time to the physics component of the Community Atmosphere Model (CAM) as well as the Community Land Model. This model allows the inclusion of local mesh refinement to seamlessly study imbedded higher-resolution regional climate concurrently with the global climate. Additionally, the numerical structure of the model based on spectral elements allows for application of state-of-the-art computing hardware most effectively and economically to produce the best prediction/simulation results with minimal expenditure of computing resources. The model has been tested under various conditions beginning with the shallow water equations and ending with an Atmospheric Model Intercomparison Project (AMIP)-style run that uses initial conditions and physics comparable to the CAM2 (version 2 of the NCAR CAM climate model) experiments. For uniform resolution, the output of the model compares favorably with the published output from the CAM2 experiments. Further integrations with local mesh refinement included indicate that while greater detail in the prediction of mesh-refined regions—that is, regional climate—is observed, the remaining coarse-grid results are similar to results obtained from a uniform-grid integration of the model with identical conditions. It should be noted that in addition to spectral elements, other efficient schemes have lately been considered, in particular the finite-volume scheme. This scheme has not yet been incorporated into CAM_SEM. The two schemes—finite volume and spectral element—are quasi-independent and generally compatible, dealing with different aspects of the integration process. Their impact can be assessed separately and the omission of the finite-volume process herein will not detract from the evaluation of the results using the spectral-element method alone.
Objective Estimation of Tropical Cyclone Wind Structure from Infrared Satellite Data
Authors: Mueller Kimberly J. , DeMaria Mark , Knaff John , Kossin James P. , Vonder Haar Thomas H. 
Published: December 2006

Abstract
Geostationary infrared (IR) satellite data are used to provide estimates of the symmetric and total low-level wind fields in tropical cyclones, constructed from estimations of an azimuthally averaged radius of maximum wind (RMAX), a symmetric tangential wind speed at a radius of 182 km (V182), a storm motion vector, and the maximum intensity (VMAX). The algorithm is derived using geostationary IR data from 405 cases from 87 tropical systems in the Atlantic and east Pacific Ocean basins during the 1995–2003 hurricane seasons that had corresponding aircraft data available. The algorithm is tested on 50 cases from seven tropical storms and hurricanes during the 2004 season. Aircraft-reconnaissance-measured RMAX and V182 are used as dependent variables in a multiple linear regression technique, and VMAX and the storm motion vector are estimated using conventional methods. Estimates of RMAX and V182 exhibit mean absolute errors (MAEs) of 27.3 km and 6.5 kt, respectively, for the dependent samples. A modified combined Rankine vortex model is used to estimate the one-dimensional symmetric tangential wind field from VMAX, RMAX, and V182. Next, the storm motion vector is added to the symmetric wind to produce estimates of the total wind field. The MAE of the IR total wind retrievals is 10.4 kt, and the variance explained is 53%, when compared with the two-dimensional wind fields from the aircraft data for the independent cases.
MM5 Ensemble Mean Forecasts in the Taiwan Area for the 2003 Mei-Yu Season
Authors: Chien Fang-Ching , Liu Yi-Chin , Jou Ben Jong-Dao 
Published: December 2006

Abstract
This paper presents an evaluation study of a real-time fifth-generation Pennsylvania State University–NCAR Mesoscale Model (MM5) mesoscale ensemble prediction system in the Taiwan area during the 2003 mei-yu season. The ensemble system consists of 16 members that used the same nested domains of 45- and 15-km resolutions, but different model settings of the initial conditions (ICs), the cumulus parameterization scheme (CPS), and the microphysics scheme (MS). Verification of geopotential height, temperature, relative humidity, and winds in the 15-km grid shows that the members using the Kain–Fritsch CPS performed better than those using the Grell CPS, and those using the Central Weather Bureau (CWB) Nonhydrostatic Forecast System (NFS) ICs fared better than those using the CWB Global Forecast System (GFS) ICs. The members applying the mixed-phase MS generally exhibited the smallest errors among the four MSs. Precipitation verification shows that the members using the Grell CPS, in general, had higher equitable threat scores (ETSs) than those using the Kain–Fritsch CPS, that the members with the GFS ICs performed better than with the NFS ICs, and that the mixed-phase and Goddard MSs gave relatively high ETSs in the rainfall simulation. The bias scores show that, overall, all 16 members underforecasted rainfall. Comparisons of the ensemble means show that, on average, an ensemble mean, no matter how many members it contains, can produce better forecasts than an individual member. Among the three possible elements (IC, CPS, and MS) that can be varied to compose an ensemble, the ensemble that contains members with all three elements varying performed the best, while that with two elements varying was second best, and that with only one varying was the worst. Furthermore, the first choice for composing an ensemble is to use perturbed ICs, followed by the perturbed CPS, and then the perturbed MS.
NK4, an antagonist of hepatocyte growth factor (HGF), inhibits growth of multiple myeloma cells: molecular targeting of angiogenic growth factor
Authors: Du Wenlin , Hattori Yutaka , Yamada Taketo , Matsumoto Kunio , Nakamura Toshikazu , Sagawa Morihiko , Otsuki Takemi , Niikura Takako , Nukiwa Toshihiro , Ikeda Yasuo 
Published: December 2006

Abstract
Hepatocyte growth factor (HGF) promotes cell growth and motility and also increases neovascularization. Multiple myeloma (MM) cells produce HGF, and the plasma concentration of HGF is significantly elevated in patients with clinically active MM, suggesting that HGF might play a role in the pathogenesis of MM. NK4, an antagonist of HGF, is structurally homologous to angiostatin, and our previous report showed that NK4 inhibited the proliferation of vascular endothelial cells induced by HGF stimulation. The purposes of this study were to elucidate the contribution of HGF to the growth of MM cells as well as to investigate the possibility of the therapeutic use of NK4. In vitro study showed that NK4 protein stabilized the growth of MM cell lines and regulated the activation of c-MET, ERK1/2, STAT3, and AKT-1. Recombinant adenovirus containing NK4 cDNA (AdCMV.NK4) was injected intramuscularly into lcr/scid mice bearing tumors derived from HGF-producing MM cells. AdCMV.NK4 significantly inhibited the growth of these tumors in vivo. Histologic examination revealed that AdCMV.NK4 induced apoptosis of MM cells, accompanied by a reduction in neovascularization in the tumors. Thus, NK4 inhibited the growth of MM cells via antiangiogenic as well as direct antitumor mechanisms. The molecular targeting of HGF by NK4 could be applied as a novel therapeutic approach to MM.
A minimally invasive multiple marker approach allows highly efficient detection of meningioma tumors
Authors: Keller Andreas , Ludwig Nicole , Comtesse Nicole , Hildebrandt Andreas , Meese Eckart , Lenhof Hans-Peter 
Published: December 2006

AbstractBackgroundThe development of effective frameworks that permit an accurate diagnosis of tumors, especially in their early stages, remains a grand challenge in the field of bioinformatics. Our approach uses statistical learning techniques applied to multiple antigen tumor antigen markers utilizing the immune system as a very sensitive marker of molecular pathological processes. For validation purposes we choose the intracranial meningioma tumors as model system since they occur very frequently, are mostly benign, and are genetically stable.ResultsA total of 183 blood samples from 93 meningioma patients (WHO stages I-III) and 90 healthy controls were screened for seroreactivity with a set of 57 meningioma-associated antigens. We tested several established statistical learning methods on the resulting reactivity patterns using 10-fold cross validation. The best performance was achieved by Naïve Bayes Classifiers. With this classification method, our framework, called Minimally Invasive Multiple Marker (MIMM) approach, yielded a specificity of 96.2%, a sensitivity of 84.5%, and an accuracy of 90.3%, the respective area under the ROC curve was 0.957. Detailed analysis revealed that prediction performs particularly well on low-grade (WHO I) tumors, consistent with our goal of early stage tumor detection. For these tumors the best classification result with a specificity of 97.5%, a sensitivity of 91.3%, an accuracy of 95.6%, and an area under the ROC curve of 0.971 was achieved using a set of 12 antigen markers only. This antigen set was detected by a subset selection method based on Mutual Information. Remarkably, our study proves that the inclusion of non-specific antigens, detected not only in tumor but also in normal sera, increases the performance significantly, since non-specific antigens contribute additional diagnostic information.ConclusionOur approach offers the possibility to screen members of risk groups as a matter of routine such that tumors hopefully can be diagnosed immediately after their genesis. The early detection will finally result in a higher cure- and lower morbidity-rate.
Chemoresistance induces enhanced adhesion and transendothelial penetration of neuroblastoma cells by down-regulating NCAM surface expression
Authors: Blaheta Roman A , Daher Frederick H , Michaelis Martin , Hasenberg Christoph , Weich Eva M , Jonas Dietger , Kotchetkov Rouslan , Doerr Hans Willhelm , Cinatl Jindrich 
Published: December 2006

Abstract

Background
Drug resistance to chemotherapy is often associated with increased malignancy in neuroblastoma (NB). One explanation for the link between resistance and malignancy might be that resistance facilitates cancer progression and invasion. To investigate this hypothesis, adhesion, transendothelial penetration and NCAM (CD56) adhesion receptor expression of drug-resistant versus drug-sensitive NB tumor cells were evaluated.

Methods
Acquired drug resistance was mimicked by exposing parental UKF-NB-2, UKF-NB-3 or IMR-32 tumor cells to increasing concentrations of vincristine- (VCR) or doxorubicin (DOX) to establish the resistant tumor cell sublines UKF-NB-2VCR, UKF-NB-2DOX, UKF-NB-3VCR, UKF-NB-3DOX, IMR-32VCR and IMR-32DOX. Additionally, the malignant behaviour of UKF-NB-4, which already possessed the intrinsic multidrug resistance (MDR) phenotype, was analyzed. UKF-NB-4 exposed to VCR or DOX were designated UKF-NB-4VCR or UKF-NB-4DOX. Combined phase contrast – reflection interference contrast microscopy was used to separately evaluate NB cell adhesion and penetration. NCAM was analyzed by flow cytometry, western blot and RT-PCR.

Results
VCR and DOX resistant tumor sublines showed enhanced adhesion and penetration capacity, compared to their drug naïve controls. Strongest effects were seen with UKF-NB-2VCR, UKF-NB-3VCR and IMR-32DOX. DOX or VCR treatment also evoked increased invasive behaviour of UKF-NB-4. The process of accelerated tumor invasion was accompanied by decreased NCAM surface and protein expression, and down-regulation of NCAM coding mRNA. Transfection of UKF-NB-4VCR cells with NCAM cDNA led to a significant receptor up-regulation, paralleled by diminished adhesion to an endothelial cell monolayer.

Conclusion
It is concluded that NB cells resistant to anticancer drugs acquire increased invasive capacity relative to non-resistant parental cells, and that enhanced invasion is caused by strong down-regulation of NCAM adhesion receptors.
An ecometric analysis of neighbourhood cohesion
Authors: Fone David L , Farewell Daniel M , Dunstan Frank D 
Published: December 2006

AbstractBackgroundIt is widely believed that the social environment has an important influence on health, but there is less certainty about how to measure specific factors within the social environment that could link the neighbourhood of residence to a health outcome. The objectives of the study were to examine the underlying constructs captured by an adapted version of Buckner's neighbourhood cohesion scale, and to assess the reliability of the scale at the small-area-level by combining ecometric methodology with ordinal modelling of a five-point scale.MethodsData were analysed from 11,078 participants in the Caerphilly Health and Social Needs Study, who were sampled from within 325 UK census enumeration districts in Caerphilly county borough, Wales, UK. The responses of interest came from 15 question items designed to capture different facets of neighbourhood cohesion. Factor analysis was used to identify constructs underlying the neighbourhood cohesion item responses. Using a multilevel ecometric model, the variability present in these ordinal responses was decomposed into contextual, compositional, item-level and residual components.ResultsTwo constructs labelled neighbourhood belonging and social cohesion were identified, and variability in both constructs was modelled at each level of the multilevel structure. The intra-neighbourhood correlations were 6.4% and 1.0% for the neighbourhood belonging and social cohesion subscales, respectively. Given the large sample size, contextual neighbourhood cohesion scores can be estimated reliably. The wide variation in the observed frequency of occurence of the scale item activities suggests that the two subscales have desirable ecometric properties. Further, the majority of between-neighbourhood variation is not explained by the socio-demographic characteristics of the individual respondents.ConclusionAssessment of the properties of the adapted neighbourhood cohesion scale using factor analysis and ecometric analysis extended to an ordinal scale has shown that the items allow fine discrimination between individuals. However, large sample sizes are needed in order to accurately estimate contextual neighbourhood cohesion. The scale is therefore appropriate for use in the measurement of neighbourhood cohesion at small-area-level in future studies of neighbourhoods and health.
17β-estradiol effects on human coronaries and grafts employed in myocardial revascularization: a preliminary study
Authors: Polvani Gianluca , Barili Fabio , Rossoni Giuseppe , Dainese Luca , Ossola Manuela Wally , Topkara Veli K , Grillo Francesco , Penza Eleonora , Tremoli Elena , Biglioli Paolo 
Published: December 2006

Abstract

Background
This study was undertaken to compare the in vitro effects of 17β-estradiol on human epicardial coronary arteries, resistance coronary arteries and on arterial vessels usually employed as grafts in surgical myocardial revascularization.

Methods
Coronary artery rings (descending coronary artery, right coronary artery, circumflex coronary artery, first septal branch) and arterial graft rings (internal thoracic artery, gastro-epiploic artery) obtained from human heart donors with heart not suitable to cardiac transplantation were connected to force transducer for isometric force recording. Precontracted specimens with and without endothelium were exposed to increasing concentration of 17β-estradiol (3–30–300–3000 nmol/l) and to vehicle (0.1% v/v ethanol). We also evaluated the effects of 17β-estradiol on vessels before and 20 minutes after exposure to L-monomethyl-arginine and indomethacin.

Results
17β-estradiol induced a significant relaxation in all precontracted vessels (mean maximum effect: 78,6% ± 8,5). This effect was not different among the different rings and was not related to the presence of endothelium. N-monomethyl-L-arginine and indomethacin did not modify 17β-estradiol relaxant effect.

Conclusion
The vasodilator action of the 17β-estradiol is similar on coronary arteries, resistance coronary arteries and arterial vessels usually employed as grafts in myocardial revascularization.
Genetic polymorphisms in the cyclooxygenase-2 gene, use of nonsteroidal anti-inflammatory drugs, and breast cancer risk
Authors: Shen Jing , Gammon Marilie D , Terry Mary Beth , Teitelbaum Susan L , Neugut Alfred I , Santella Regina M 
Published: December 2006

Abstract
Introduction
The association between use of nonsteroidal anti-inflammatory drugs (NSAIDs) and breast cancer risk remains unclear. Inconsistencies in previously reported findings may be partly due to differences in expression of cyclooxygenase (COX)-2. We hypothesized that genetic polymorphisms (COX-2 .926, COX-2 .5209, and COX-2 .8473) may reduce overall breast cancer risk or risk for subtypes of breast cancer by modulating the inflammatory response and may interact with aspirin or any NSAID use.

Methods
We conducted a population-based, case-control study in which we genotyped 1,067 breast cancer cases and 1,110 control individuals included in the Long Island Breast Cancer Study Project.

Results
No major effects of the three COX-2 variant alleles on breast cancer risk were found. A total of eight distinct haplotypes and 18 diplotypes were observed in the population. Overall, no significant associations between COX-2 haplotypes/diplotypes and breast cancer risk were observed. Among women who used aspirin or any NSAID there was little evidence for an interaction with the at-risk COX-2 genotypes, with one exception. Among women with hormone receptor positive breast cancer, the reduced risk for any NSAID use was only evident among those who had at least one variant C allele of COX-2 .8473 (odds ratio = 0.7, 95% confidence interval = 0.5 to 1.0; P for the interaction = 0.02). There was no corresponding interaction for aspirin use, possibly because of limited power.

Conclusion
These data provide modest evidence that the C allele of COX-2 .8473 may interact with NSAIDs to reduce risk for hormone receptor positive breast cancer.
Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian introns
Authors: Sironi Manuela , Menozzi Giorgia , Comi Giacomo P , Cereda Matteo , Cagliani Rachele , Bresolin Nereo , Pozzoli Uberto 
Published: December 2006

Abstract
Background
Transposable elements (TEs) represent more than 45% of the human and mouse genomes. Both parasitic and mutualistic features have been shown to apply to the host-TE relationship but a comprehensive scenario of the forces driving TE fixation within mammalian genes is still missing.

Results
We show that intronic multispecies conserved sequences (MCSs) have been affecting TE integration frequency over time. We verify that a selective economizing pressure has been acting on TEs to decrease their frequency in highly expressed genes. After correcting for GC content, MCS density and intron size, we identified TE-enriched and TE-depleted gene categories. In addition to developmental regulators and transcription factors, TE-depleted regions encompass loci that might require subtle regulation of transcript levels or precise activation timing, such as growth factors, cytokines, hormones, and genes involved in the immune response. The latter, despite having reduced frequencies of most TE types, are significantly enriched in mammalian-wide interspersed repeats (MIRs). Analysis of orthologous genes indicated that MIR over-representation also occurs in dog and opossum immune response genes, suggesting, given the partially independent origin of MIR sequences in eutheria and metatheria, the evolutionary conservation of a specific function for MIRs located in these loci. Consistently, the core MIR sequence is over-represented in defense response genes compared to the background intronic frequency.

Conclusion
Our data indicate that gene function, expression level, and sequence conservation influence TE insertion/fixation in mammalian introns. Moreover, we provide the first report showing that a specific TE family is evolutionarily associated with a gene function category.