bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-Resolution Simulation of Mean Convection and Its Intraseasonal Variability over the Tropics in the MRI/JMA 20-km Mesh AGCM
Authors: Rajendran K. , Kitoh A. , Mizuta R. , Sajani S. , Nakazawa T. 
Published: February 2008

Abstract
Tropical mean convection and its organization on different spatiotemporal scales in a simulation using the Meteorological Research Institute/Japan Meteorological Agency (MRI/JMA) global atmospheric general circulation model (AGCM) at 20-km resolution (TL959L60) has been investigated. Comparison with two lower resolution simulations of 120 km (TL159L40) and 180 km (TL95L40) shows that convection, climatological fields, and moist stability over the Indian Ocean and South Pacific convergence zone are better represented in TL959L60 than in lower resolution simulations. However, the simulated three-dimensional structure of the Walker and Hadley cells, and the vertical structure of convective heating, do not show marked improvement relative to lower resolution simulations. The amplitude and phase speed of convectively coupled equatorial waves show that, although the Kelvin waves, the observed hierarchical structure of cloud clusters associated with the Madden–Julian oscillation (MJO) convection, and the wave interrelationship among MJO, Kelvin, and equatorial Rossby waves are marginally improved in TL959L60, increased resolution does not impact the simulation of the MJO itself. In the model, the MJO appears as a standing oscillation with much weaker variance compared to observations. Power spectra and a composite MJO life cycle constructed based on extended empirical orthogonal functions reveal that the amplitude, structure, and propagation characteristics of the MJO remain deficient at all resolutions. Thus, while the very high resolution yields improvements in some aspects of tropical mean convection, these appear to be less important compared to the basic deficiency of the parameterized convection in capturing tropical convection and its spatiotemporal variability.
Summer Precipitation Frequency, Intensity, and Diurnal Cycle over China: A Comparison of Satellite Data with Rain Gauge Observations
Authors: Zhou Tianjun , Yu Rucong , Chen Haoming , Dai Aiguo , Pan Yang 
Published: February 2008

Abstract
Hourly or 3-hourly precipitation data from Precipitation Estimation from Remotely Sensed Information using Artificial Neural Networks (PERSIANN) and Tropical Rainfall Measuring Mission (TRMM) 3B42 satellite products and rain gauge records are used to characterize East Asian summer monsoon rainfall, including spatial patterns in June–August (JJA) mean precipitation amount, frequency, and intensity, as well as the diurnal and semidiurnal cycles. The results show that the satellite products are comparable to rain gauge data in revealing the spatial patterns of JJA precipitation amount, frequency, and intensity, with pattern correlation coefficients for five subregions ranging from 0.66 to 0.94. The pattern correlation of rainfall amount is higher than that of frequency and intensity. Relative to PERSIANN, the TRMM product has a better resemblance with rain gauge observations in terms of both the pattern correlation and root-mean-square error. The satellite products overestimate rainfall frequency but underestimate its intensity. The diurnal (24 h) harmonic dominates subdaily variations of precipitation over most of eastern China. A late-afternoon maximum over southeastern and northeastern China and a near-midnight maximum over the eastern periphery of the Tibetan Plateau are seen in the rain gauge data. The diurnal phases of precipitation frequency and intensity are similar to those of rainfall amount in most regions, except for the middle Yangtze River valley. Both frequency and intensity contribute to the diurnal variation of rainfall amount over most of eastern China. The contribution of frequency to the diurnal cycle of rainfall amount is generally overestimated in both satellite products. Both satellite products capture well the nocturnal peak over the eastern periphery of the Tibetan Plateau and the late-afternoon peak in southern and northeastern China. Rain gauge data over the region between the Yangtze and Yellow Rivers show two peaks, with one in the early morning and the other later in the afternoon. The satellite products only capture the major late-afternoon peak.
A New Two-Moment Bulk Stratiform Cloud Microphysics Scheme in the Community Atmosphere Model, Version 3 (CAM3). Part II: Single-Column and Global Results
Authors: Gettelman A. , Morrison H. , Ghan S. J. 
Published: February 2008

Abstract
The global performance of a new two-moment cloud microphysics scheme for a general circulation model (GCM) is presented and evaluated relative to observations. The scheme produces reasonable representations of cloud particle size and number concentration when compared to observations, and it represents expected and observed spatial variations in cloud microphysical quantities. The scheme has smaller particles and higher number concentrations over land than the standard bulk microphysics in the GCM and is able to balance the top-of-atmosphere radiation budget with 60% the liquid water of the standard scheme, in better agreement with retrieved values. The new scheme diagnostically treats both the mixing ratio and number concentration of rain and snow, and it is therefore able to differentiate the two key regimes, consisting of drizzle in shallow, warm clouds and larger rain drops in deeper cloud systems. The modeled rain and snow size distributions are consistent with observations.
Influence of Modes of Climate Variability on Global Temperature Extremes
Authors: Kenyon Jesse , Hegerl Gabriele C. 
Published: February 2008

Abstract
The influence of large-scale modes of climate variability on worldwide summer and winter temperature extremes has been analyzed, namely, that of the El Niño–Southern Oscillation, the North Atlantic Oscillation, and Pacific interdecadal climate variability. Monthly indexes for temperature extremes from worldwide land areas are used describe moderate extremes, such as the number of exceedences of the 90th and 10th climatological percentiles, and more extreme events such as the annual, most extreme temperature. This study examines which extremes show a statistically significant (5%) difference between the positive and negative phases of a circulation regime. Results show that temperature extremes are substantially affected by large-scale circulation patterns, and they show distinct regional patterns of response to modes of climate variability. The effects of the El Niño–Southern Oscillation are seen throughout the world but most clearly around the Pacific Rim and throughout all of North America. Likewise, the influence of Pacific interdecadal variability is strongest in the Northern Hemisphere, especially around the Pacific region and North America, but it extends to the Southern Hemisphere. The North Atlantic Oscillation has a strong continent-wide effect for Eurasia, with a clear but weaker effect over North America. Modes of variability influence the shape of the daily temperature distribution beyond a simple shift, often affecting cold and warm extremes and sometimes daytime and nighttime temperatures differently. Therefore, for reliable attribution of changes in extremes as well as prediction of future changes, changes in modes of variability need to be accounted for.
The Kuroshio Extension Northern Recirculation Gyre: Profiling Float Measurements and Forcing Mechanism
Authors: Qiu Bo , Chen Shuiming , Hacker Peter , Hogg Nelson G. , Jayne Steven R. , Sasaki Hideharu 
Published: February 2008

Abstract
Middepth, time-mean circulation in the western North Pacific Ocean (28°–45°N, 140°–165°E) is investigated using drift information from the profiling floats deployed in the Kuroshio Extension System Study (KESS) and the International Argo programs. A well-defined, cyclonic recirculation gyre (RG) is found to exist north of the Kuroshio Extension jet, confined zonally between the Japan Trench (∼145°E) and the Shatsky Rise (∼156°E), and bordered to the north by the subarctic boundary along ∼40°N. This northern RG, which is simulated favorably in the eddy-resolving OGCM for the Earth Simulator (OFES) hindcast run model, has a maximum volume transport at 26.4 Sv across 159°E and its presence persists on the interannual and longer time scales. An examination of the time-mean x-momentum balance from the OFES hindcast run output reveals that horizontal convergence of Reynolds stresses works to accelerate both the eastward-flowing Kuroshio Extension jet and a westward mean flow north of the meandering jet. The fact that the northern RG is eddy driven is further confirmed by examining the turbulent Sverdrup balance, in which convergent eddy potential vorticity fluxes are found to induce the cyclonic RG across the background potential vorticity gradient field. For the strength of the simulated northern RG, the authors find the eddy dissipation effect to be important as well.
A Simple Seasonal Forecast Update of Tropical Cyclone Activity
Authors: Chan Johnny C. L. 
Published: February 2008

Abstract
A simple method based on the cumulative number of tropical cyclones (TCs) up to a given month in the early season is proposed to update the seasonal prediction of the annual number of TCs in a given ocean basin. For the western North Pacific, if this number is below normal by July or August, it is very likely that the annual activity will also be below normal. The reverse (for relating above-normal number with above-normal annual activity) is also true although the probability is smaller than for the below-normal category. Similar results are found for TCs in the eastern North Pacific and the North Atlantic, with the latter having the smallest likelihood. These results change only slightly when the samples are separated into dependent and independent subsets.
Hydrometeorological Short-Range Ensemble Forecasts in Complex Terrain. Part I: Meteorological Evaluation
Authors: McCollor Doug , Stull Roland 
Published: February 2008

Abstract
This paper addresses the question of whether it is better to include lower-resolution members of a nested suite of numerical precipitation forecasts to increase ensemble size, or to utilize high-resolution members only to maximize forecast details in regions of complex terrain. A short-range ensemble forecast (SREF) system is formed from three models running in nested configurations at 108-, 36-, 12-, and 4-km horizontal grid spacings. The forecasts are sampled at 27 precipitation-gauge locations, representing 15 pluvial watersheds in southwestern British Columbia, Canada. This is a region of complex topography characterized by high mountains, glaciers, fjords, and land–ocean boundaries. Matching forecast–observation pairs are analyzed for two consecutive wet seasons: October 2003–March 2004 and October 2004–March 2005. The northwest coast of North America is typically subject to intense landfalling Pacific cyclones and frontal systems during these months.
Using forecast analysis tools that are well designed for SREF systems, it is found that utilizing the full suite of ensemble members, including the lowest-resolution members, produced the highest quality probabilistic forecasts of precipitation. A companion paper assesses the economic value of SREF probabilistic forecasts for hydroelectric operations.
Psychological Processes Underlying Persuasion
Authors: Petty Richard E. , Briñol Pablo 
Published: February 2008

AbstractIn this article, the authors review a contemporary social psychological perspective on persuasion with an emphasis on explicating the psychological processes that underlie successful attitude change. Those mechanisms by which variables in the persuasion setting can influence attitude change are: (a) affect the amount of information processing; (b) bias the thoughts that are generated or (c) one's confidence in those thoughts (or other structural features); (d) serve as persuasive arguments or evidence or (e) affect attitudes by serving as simple cues and heuristics. By grouping the persuasion processes into meaningful categories, the authors aim to provide a useful guide to organize and facilitate access to key findings in this literature. They also describe a theoretical framework to understand the circumstances for which the different processes are more likely to influence our judgments, such as when variables precede or follow thought-generation, and when the extent of thinking is relatively low, medium, or high.
Science and Society: To Indicate, to Motivate or to Persuade?
Authors: Nascimento-Schulze Clélia Maria 
Published: February 2008

AbstractThis paper deals with the recent policies introduced in Brazil in order to foster a public interest towards science. Persuasive messages and strategies aiming at increasing a public awareness of the importance of scientific literacy for the development of the country are introduced at different levels and targeting different kinds of publics. These policies are analysed in view of classical models of social influence and persuasion.
Myeloma in patients younger than age 50 years presents with more favorable features and shows better survival: an analysis of 10 549 patients from the International Myeloma Working Group
Authors: Ludwig Heinz , Durie Brian G. M. , Bolejack Vanessa , Turesson Ingemar , Kyle Robert A. , Blade Joan , Fonseca Rafael , Dimopoulos Meletios , Shimizu Kazuyuki , San Miguel Jesus , Westin Jan , Harousseau Jean-Luc , Beksac Meral , Boccadoro Mario , Palumbo Antonio , Barlogie Bart , Shustik Chaim , Cavo Michele , Greipp Philip R. , Joshua Douglas , Attal Michel , Sonneveld Pieter , Crowley John 
Published: February 2008

AbstractWe analyzed the presenting features and survival in 1689 patients with multiple myeloma aged younger than 50 years compared with 8860 patients 50 years of age and older. Of the total 10 549 patients, 7765 received conventional therapy and 2784 received high-dose therapy. Young patients were more frequently male, had more favorable features such as low International Staging System (ISS) and Durie-Salmon stage as well as less frequently adverse prognostic factors including high C-reactive protein (CRP), low hemoglobin, increased serum creatinine, and poor performance status. Survival was significantly longer in young patients (median, 5.2 years vs 3.7 years; P < .001) both after conventional (median, 4.5 years vs 3.3 years; P < .001) or high-dose therapy (median, 7.5 years vs 5.7 years; P = .04). The 10-year survival rate was 19% after conventional therapy and 43% after high-dose therapy in young patients, and 8% and 29%, respectively, in older patients. Multivariate analysis revealed age as an independent risk factor during conventional therapy, but not after autologous transplantation. A total of 5 of the 10 independent risk factors identified for conventional therapy were also relevant for autologous transplantation. After adjusting for normal mortality, lower ISS stage and other favorable prognostic features seem to account for the significantly longer survival of young patients with multiple myeloma with age remaining a risk factor during conventional therapy.
Activation of the aryl hydrocarbon receptor is essential for mediating the anti-inflammatory effects of a novel low-molecular-weight compound
Authors: Lawrence B. Paige , Denison Michael S. , Novak Hermann , Vorderstrasse Beth A. , Harrer Nathalie , Neruda Wolfgang , Reichel Claudia , Woisetschläger Maximilian 
Published: February 2008

AbstractVAF347 is a low-molecular-weight compound that inhibits allergic lung inflammation in vivo. This effect is likely the result of a block of dendritic cell (DC) function to generate proinflammatory T-helper (Th) cells because VAF347 inhibits interleukin (IL)–6, CD86, and human leukocyte antigen (HLA)–DR expression by human monocyte-derived DC, 3 relevant molecules for Th-cell generation. Here we demonstrate that VAF347 interacts with the aryl hydrocarbon receptor (AhR) protein, resulting in activation of the AhR signaling pathway. Functional AhR is responsible for the biologic activity of VAF347 because (1) other AhR agonists display an identical activity profile in vitro, (2) gene silencing of wild-type AhR expression or forced overexpression of a trans-dominant negative AhR ablates VAF347 activity to inhibit cytokine induced IL-6 expression in a human monocytic cell line, and (3) AhR-deficient mice are resistant to the compound's ability to block allergic lung inflammation in vivo. These data identify the AhR protein as key molecular target of VAF347 and its essential role for mediating the anti-inflammatory effects of the compound in vitro and in vivo.
In silico analysis of expressed sequence tags from Trichostrongylus vitrinus (Nematoda): comparison of the automated ESTExplorer workflow platform with conventional database searches
Authors: Nagaraj Shivashankar H , Gasser Robin B , Nisbet Alasdair J , Ranganathan Shoba 
Published: February 2008

Abstract

Background
The analysis of expressed sequence tags (EST) offers a rapid and cost effective approach to elucidate the transcriptome of an organism, but requires several computational methods for assembly and annotation. Researchers frequently analyse each step manually, which is laborious and time consuming. We have recently developed ESTExplorer, a semi-automated computational workflow system, in order to achieve the rapid analysis of EST datasets. In this study, we evaluated EST data analysis for the parasitic nematode Trichostrongylus vitrinus (order Strongylida) using ESTExplorer, compared with database matching alone.

Results
We functionally annotated 1776 ESTs obtained via suppressive-subtractive hybridisation from T. vitrinus, an important parasitic trichostrongylid of small ruminants. Cluster and comparative genomic analyses of the transcripts using ESTExplorer indicated that 290 (41%) sequences had homologues in Caenorhabditis elegans, 329 (42%) in parasitic nematodes, 202 (28%) in organisms other than nematodes, and 218 (31%) had no significant match to any sequence in the current databases. Of the C. elegans homologues, 90 were associated with 'non-wildtype' double-stranded RNA interference (RNAi) phenotypes, including embryonic lethality, maternal sterility, sterile progeny, larval arrest and slow growth. We could functionally classify 267 (38%) sequences using the Gene Ontologies (GO) and establish pathway associations for 230 (33%) sequences using the Kyoto Encyclopedia of Genes and Genomes (KEGG). Further examination of this EST dataset revealed a number of signalling molecules, proteases, protease inhibitors, enzymes, ion channels and immune-related genes. In addition, we identified 40 putative secreted proteins that could represent potential candidates for developing novel anthelmintics or vaccines. We further compared the automated EST sequence annotations, using ESTExplorer, with database search results for individual T. vitrinus ESTs. ESTExplorer reliably and rapidly annotated 301 ESTs, with pathway and GO information, eliminating 60 low quality hits from database searches.

Conclusion
We evaluated the efficacy of ESTExplorer in analysing EST data, and demonstrate that computational tools can be used to accelerate the process of gene discovery in EST sequencing projects. The present study has elucidated sets of relatively conserved and potentially novel genes for biological investigation, and the annotated EST set provides further insight into the molecular biology of T. vitrinus, towards the identification of novel drug targets.
Preferential binding of allosteric modulators to active and inactive conformational states of metabotropic glutamate receptors
Authors: Yanamala Naveena , Tirupula Kalyan C , Klein-Seetharaman Judith 
Published: February 2008

Abstract
Metabotropic glutamate receptors (mGluRs) are G protein coupled receptors that play important roles in synaptic plasticity and other neuro-physiological and pathological processes. Allosteric mGluR ligands are particularly promising drug targets because of their modulatory effects – enhancing or suppressing the response of mGluRs to glutamate. The mechanism by which this modulation occurs is not known. Here, we propose the hypothesis that positive and negative modulators will differentially stabilize the active and inactive conformations of the receptors, respectively. To test this hypothesis, we have generated computational models of the transmembrane regions of different mGluR subtypes in two different conformations. The inactive conformation was modeled using the crystal structure of the inactive, dark state of rhodopsin as template and the active conformation was created based on a recent model of the light-activated state of rhodopsin. Ligands for which the nature of their allosteric effects on mGluRs is experimentally known were docked to the modeled mGluR structures using ArgusLab and Autodock softwares. We find that the allosteric ligand binding pockets of mGluRs are overlapping with the retinal binding pocket of rhodopsin, and that ligands have strong preferences for the active and inactive states depending on their modulatory nature. In 8 out of 14 cases (57%), the negative modulators bound the inactive conformations with significant preference using both docking programs, and 6 out of 9 cases (67%), the positive modulators bound the active conformations. Considering results by the individual programs only, even higher correlations were observed: 12/14 (86%) and 8/9 (89%) for ArgusLab and 10/14 (71%) and 7/9 (78%) for AutoDock. These findings strongly support the hypothesis that mGluR allosteric modulation occurs via stabilization of different conformations analogous to those identified in rhodopsin where they are induced by photochemical isomerization of the retinal ligand – despite the extensive differences in sequences between mGluRs and rhodopsin.
Motif-directed network component analysis for regulatory network inference
Authors: Wang Chen , Xuan Jianhua , Chen Li , Zhao Po , Wang Yue , Clarke Robert , Hoffman Eric 
Published: February 2008

Abstract

Background
Network Component Analysis (NCA) has shown its effectiveness in discovering regulators and inferring transcription factor activities (TFAs) when both microarray data and ChIP-on-chip data are available. However, a NCA scheme is not applicable to many biological studies due to limited topology information available, such as lack of ChIP-on-chip data. We propose a new approach, motif-directed NCA (mNCA), to integrate motif information and gene expression data to infer regulatory networks.

Results
We develop motif-directed NCA (mNCA) to incorporate motif information into NCA for regulatory network inference. While motif information is readily available from knowledge databases, it is a "noisy" source of network topology information consisting of many false positives. To overcome this problem, we develop a stability analysis procedure embedded in mNCA to resolve the inconsistency between motif information and gene expression data, and to enable the identification of stable TFAs. The mNCA approach has been applied to a time course microarray data set of muscle regeneration. The experimental results show that the inferred TFAs are not only numerically stable but also biologically relevant to muscle differentiation process. In particular, several inferred TFAs like those of MyoD, myogenin and YY1 are well supported by biological experiments.

Conclusion
A novel computational approach, mNCA, has been developed to integrate motif information and gene expression data for regulatory network reconstruction. Specifically, motif analysis is used to obtain initial network topology, and stability analysis is developed and applied with mNCA to extract stable TFAs. Experimental results on muscle regeneration microarray data have demonstrated that mNCA is a practical and reliable computational method for regulatory network inference and pathway discovery.