bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enforcing a Turning Point and Imposing a Deal: An Analysis of the Darfur Abuja Negotiations of 2006
Authors: Brooks Sean 
Published: November 2008

AbstractLow expectations and international impatience forced the African Union to shift from a classical integrative approach to negotiations to “deadline diplomacy” during the final months of the Abuja talks between the Sudanese government and the Darfur rebel movements. As a result, the AU mediators – who had served as communicators and formulators – assumed the responsibility of manipulators. This transition scuttled plans for gradually arriving at the implementing details for a formula. Instead, acquiescence to power served as the chief reason for the signature of one of the movements, while the mediators showed disinterest and inflexibility in reigning in the other two movements that required a package of additional threats and inducements. Important lessons regarding the credibility of deadlines, the appropriateness of the formula, the necessity of ownership, inclusivity/exclusivity of the talks, and sufficient support for the movements in the prenegotiation and diagnosis phases can be drawn from the Abuja process.
Association les Témoins de Jéhovah versus France The Jurisprudence of the European Court of Human Rights on Religious Activities and Taxation Issues
Authors: Garay Alain 
Published: November 2008

AbstractAccording to the jurisprudence of the judicial bodies of the Council of Europe, association and financial laws has considerable influence on the fiscal status of religious activities. To a certain extent, it conditions the choice of statutes and juridical structures by religious institutions. At the national level, the tax system in consequence submits the activities in question to particular regulations which have led many religious institutions to opt for elaborate fiscal and legal arrangements, compartmentalized into distinct sectors or into separate structures. Such is the case with the activities of the religious economy sector: publishing, agricultural and vinicultural production, tourism services which require recourse to complex legal and fiscal organizational schemas. A series of examples related to the taxation of religious bodies can demonstrate the extent of some contradictions: – differences of treatment by the national Administrations in refusing tax exemptions or denying religious status to certain movements; – recourse to fiscal controls or audits as a “tactical weapon”. In many countries the debate continues today due to changes in the financial regulations affecting religious activities and discriminatory applications of the principle of equality of religions before the law. This debate is based on the never-ending questions about criteria relying on the historical presence, representative nature and social utility of religions, issues that have been the object of legal distinctions.
Average Predictability Time. Part I: Theory
Authors: DelSole Timothy , Tippett Michael K. 
Published: November 2008

AbstractThis paper introduces the average predictability time (APT) for characterizing the overall predictability of a system. APT is the integral of a predictability measure over all lead times. The underlying predictability measure is based on the Mahalanobis metric, which is invariant to linear transformation of the prediction variables and hence gives results that are independent of the (arbitrary) basis set used to represent the state. The APT is superior to some integral time scales used to characterize the time scale of a random process because the latter vanishes in situations when it should not, whereas the APT converges to reasonable values. The APT also can be written in terms of the power spectrum, thereby clarifying the connection between predictability and the power spectrum. In essence, predictability is related to the width of spectral peaks, with strong, narrow peaks associated with high predictability and nearly flat spectra associated with low predictability. Closed form expressions for the APT for linear stochastic models are derived. For a given dynamical operator, the stochastic forcing that minimizes APT is one that allows transformation of the original stochastic model into a set of uncoupled, independent stochastic models. Loosely speaking, coupling enhances predictability. A rigorous upper bound on the predictability of linear stochastic models is derived, which clarifies the connection between predictability at short and long lead times, as well as the choice of norm for measuring error growth. Surprisingly, APT can itself be interpreted as the “total variance” of an alternative stochastic model, which means that generalized stability theory and dynamical systems theory can be used to understand APT. The APT can be decomposed into an uncorrelated set of components that maximize predictability time, analogous to the way principle component analysis decomposes variance. Part II of this paper develops a practical method for performing this decomposition and applies it to meteorological data.
Tropical Intraseasonal Variability in the MRI-20km60L AGCM*
Authors: Liu Ping , Kajikawa Yoshiyuki , Wang Bin , Kitoh Akio , Yasunari Tetsuzo , Li Tim , Annamalai H. , Fu Xiouhua , Kikuchi Kazuyoshi , Mizuta Ryo , Rajendran Kavirajan , Waliser Duane E. , Kim Daehyun 
Published: November 2008

Abstract
This study documents the detailed characteristics of the tropical intraseasonal variability (TISV) in the MRI-20km60L AGCM that uses a variant of the Arakawa–Schubert cumulus parameterization. Mean states, power spectra, propagation features, leading EOF modes, horizontal and vertical structures, and seasonality associated with the TISV are analyzed. Results show that the model reproduces the mean states in winds realistically and in convection comparable to that of the observations. However, the simulated TISV is less realistic. It shows low amplitudes in convection and low-level winds in the 30–60-day band. Filtered anomalies have standing structures. Power spectra and lag correlation of the signals do not propagate dominantly either in the eastward direction during boreal winter or in the northward direction during boreal summer. A combined EOF (CEOF) analysis shows that winds and convection have a loose coupling that cannot sustain the simulated TISV as realistically as that observed. In the composited mature phase of the simulated MJO, the low-level convergence does not lead convection clearly so that the moisture anomalies do not tilt westward in the vertical, indicating that the low-level convergence does not favor the eastward propagation. The less realistic TISV suggests that the representation of cumulus convection needs to be improved in this model.
Evaluating the “Rich-Get-Richer” Mechanism in Tropical Precipitation Change under Global Warming
Authors: Chou Chia , Neelin J. David , Chen Chao-An , Tu Jien-Yi 
Published: November 2008

Abstract
Examining tropical regional precipitation anomalies under global warming in 10 coupled global climate models, several mechanisms are consistently found. The tendency of rainfall to increase in convergence zones with large climatological precipitation and to decrease in subsidence regions—the rich-get-richer mechanism—has previously been examined in different approximations by Chou and Neelin, and Held and Soden. The effect of increased moisture transported by the mean circulation (the “direct moisture effect” or “thermodynamic component” in respective terminology) is relatively robust, while dynamic feedback is poorly understood and differs among models. The argument outlined states that the thermodynamic component should be a good approximation for large-scale averages; this is confirmed for averages across convection zones and descent regions, respectively. Within the convergence zones, however, dynamic feedback can substantially increase or decrease precipitation anomalies. Regions of negative precipitation anomalies within the convergence zones are associated with local weakening of ascent, and some of these exhibit horizontal dry advection associated with the “upped-ante” mechanism. Regions of increased ascent have strong positive precipitation anomalies enhanced by moisture convergence. This dynamic feedback is consistent with reduced gross moist stability due to increased moisture not being entirely compensated by effects of tropospheric warming and a vertical extent of convection. Regions of reduced ascent with positive precipitation anomalies are on average associated with changes in the vertical structure of vertical velocity, which extends to higher levels. This yields an increase in the gross moist stability that opposes ascent. The reductions in ascent associated with gross moist stability and upped-ante effects, respectively, combine to yield reduced ascent averaged across the convergence zones. Over climatological subsidence regions, positive precipitation anomalies can be associated with a convergence zone shift induced locally by anomalous heat flux from the ocean. Negative precipitation anomalies have a contribution from the thermodynamic component but can be enhanced or reduced by changes in the vertical velocity. Regions of enhanced subsidence are associated with an increased outgoing longwave radiation or horizontal cold convection. Reductions of subsidence are associated with changes of the vertical profile of vertical velocity, increasing gross moist stability.
An Analysis of Moisture Fluxes into the Gulf of California
Authors: Wu Man-Li C. , Schubert Siegfried D. , Suarez Max J. , Huang Norden E. 
Published: November 2008

Abstract
This study examines the nature of episodes of enhanced warm-season moisture flux into the Gulf of California. Both spatial structure and primary time scales of the fluxes are examined using the 40-yr ECMWF Re-Analysis data for the period 1980–2001. The analysis approach consists of a compositing technique that is keyed on the low-level moisture fluxes into the Gulf of California. The results show that the fluxes have a rich spectrum of temporal variability, with periods of enhanced transport over the gulf linked to African easterly waves on subweekly (3–8 day) time scales, the Madden–Julian oscillation (MJO) at intraseasonal time scales (20–90 day), and intermediate (10–15 day) time-scale disturbances that appear to originate primarily in the Caribbean Sea–western Atlantic Ocean.
In the case of the MJO, enhanced low-level westerlies and large-scale rising motion provide an environment that favors large-scale cyclonic development near the west coast of Central America that, over the course of about 2 weeks, expands northward along the coast eventually reaching the mouth of the Gulf of California where it acts to enhance the southerly moisture flux in that region. On a larger scale, the development includes a northward shift in the eastern Pacific ITCZ, enhanced precipitation over much of Mexico and the southwestern United States, and enhanced southerly/southeasterly fluxes from the Gulf of Mexico into Mexico and the southwestern and central United States. In the case of the easterly waves, the systems that reach Mexico appear to redevelop/reorganize on the Pacific coast and then move rapidly to the northwest to contribute to the moisture flux into the Gulf of California. The most intense fluxes into the gulf on these time scales appear to be synchronized with a midlatitude short-wave trough over the U.S. West Coast and enhanced low-level southerly fluxes over the U.S. Great Plains. The intermediate (10–15 day) time-scale systems have zonal wavelengths roughly twice that of the easterly waves, and their initiation appears to be linked to an extratropical U.S. East Coast ridge and associated northeasterly winds that extend well into the Caribbean Sea during their development phase. The short (3–8 day) and, to a lesser extent, the intermediate (10–15 day) time-scale fluxes tend to be enhanced when the convectively active phase of the MJO is situated over the Americas.
Why the Western Pacific Subtropical High Has Extended Westward since the Late 1970s
Authors: Zhou Tianjun , Yu Rucong , Zhang Jie , Drange Helge , Cassou Christophe , Deser Clara , Hodson Daniel L. R. , Sanchez-Gomez Emilia , Li Jian , Keenlyside Noel , Xin Xiaoge , Okumura Yuko 
Published: November 2008

Abstract
The western Pacific subtropical high (WPSH) is closely related to Asian climate. Previous examination of changes in the WPSH found a westward extension since the late 1970s, which has contributed to the interdecadal transition of East Asian climate. The reason for the westward extension is unknown, however. The present study suggests that this significant change of WPSH is partly due to the atmosphere’s response to the observed Indian Ocean–western Pacific (IWP) warming. Coordinated by a European Union’s Sixth Framework Programme, Understanding the Dynamics of the Coupled Climate System (DYNAMITE), five AGCMs were forced by identical idealized sea surface temperature patterns representative of the IWP warming and cooling. The results of these numerical experiments suggest that the negative heating in the central and eastern tropical Pacific and increased convective heating in the equatorial Indian Ocean/Maritime Continent associated with IWP warming are in favor of the westward extension of WPSH. The SST changes in IWP influences the Walker circulation, with a subsequent reduction of convections in the tropical central and eastern Pacific, which then forces an ENSO/Gill-type response that modulates the WPSH. The monsoon diabatic heating mechanism proposed by Rodwell and Hoskins plays a secondary reinforcing role in the westward extension of WPSH. The low-level equatorial flank of WPSH is interpreted as a Kelvin response to monsoon condensational heating, while the intensified poleward flow along the western flank of WPSH is in accord with Sverdrup vorticity balance. The IWP warming has led to an expansion of the South Asian high in the upper troposphere, as seen in the reanalysis.
Contributions of Indian Ocean and Monsoon Biases to the Excessive Biennial ENSO in CCSM3
Authors: Yu Jin-Yi , Sun Fengpeng , Kao Hsun-Ying 
Published: November 2008

Abstract
The Community Climate System Model, version 3 (CCSM3), is known to produce many aspects of El Niño–Southern Oscillation (ENSO) realistically, but the simulated ENSO exhibits an overly strong biennial periodicity. Hypotheses on the cause of this excessive biennial tendency have thus far focused primarily on the model’s biases within the tropical Pacific. This study conducts CCSM3 experiments to show that the model’s biases in simulating the Indian Ocean mean sea surface temperatures (SSTs) and the Indian and Australian monsoon variability also contribute to the biennial ENSO tendency. Two CCSM3 simulations are contrasted: a control run that includes global ocean–atmosphere coupling and an experiment in which the air–sea coupling in the tropical Indian Ocean is turned off by replacing simulated SSTs with an observed monthly climatology. The decoupling experiment removes CCSM3’s warm bias in the tropical Indian Ocean and reduces the biennial variability in Indian and Australian monsoons by about 40% and 60%, respectively. The excessive biennial ENSO is found to reduce dramatically by about 75% in the decoupled experiment. It is shown that the biennial monsoon variability in CCSM3 excites an anomalous surface wind pattern in the western Pacific that projects well into the wind pattern associated with the onset phase of the simulated biennial ENSO. Therefore, the biennial monsoon variability is very effective in exciting biennial ENSO variability in CCSM3. The warm SST bias in the tropical Indian Ocean also increases ENSO variability by inducing stronger mean surface easterlies along the equatorial Pacific, which strengthen the Pacific ocean–atmosphere coupling and enhance the ENSO intensity.
Influence of Moist Physics and Norms on Singular Vectors for a Tropical Cyclone
Authors: Kim Hyun Mee , Jung Byoung-Joo 
Published: November 2008

Abstract
In this study, the structures and growth rates of singular vectors (SVs) for Typhoon Usagi were investigated using different moist physics and norms. The fifth-generation Pennsylvania State University–National Center for Atmospheric Research Mesoscale Model (MM5) and its tangent linear and adjoint models with a Lanczos algorithm were used to calculate SVs over a 36-h period. The moist physics used for linear (i.e., tangent linear and adjoint model) integrations is large-scale precipitation, and the norms used are dry and moist total energy (TE) norms. Overall, moist physics in linear integrations and a moist TE norm increase the growth rates of SVs and cause smaller horizontal structures and vertical distributions closer to the lower boundary. With a dry TE norm, the SV energy distributions show similar (dissimilar) large- (small-) scale horizontal SV structures for experiments, regardless of physics. The SVs with moist linear physics and a moist TE norm have maximum horizontal energy structures near the typhoon center. With a small weighting on the moisture term in the moist TE norm, both the remote and nearby influences on the TC are indicated by the horizontal SV energy distributions. The kinetic energy shows the largest contributions to the vertical SV TE distributions in most of the experiments, except for the largest moisture (potential energy) contributions to the SV TE at the final (initial) time in the moist TE norm (dry and weighted moist TE norms at uppermost levels). In contrast, the SV vorticity distributions show more consistent structures among experiments with different linear physics and norms, implying that, in terms of the rotational component of the wind field, the SVs are not sensitive to the choice of moist physics and norms. Given large-scale precipitation as the linear moist physics, the SV energy structures and growth rate with a moist TE norm show the largest difference when compared with those with other norms.
NemaPath: online exploration of KEGG-based metabolic pathways for nematodes
Authors: Wylie Todd , Martin John , Abubucker Sahar , Yin Yong , Messina David , Wang Zhengyuan , McCarter James P , Mitreva Makedonka 
Published: November 2008

Abstract

Background
Nematode.net http://www.nematode.net is a web-accessible resource for investigating gene sequences from parasitic and free-living nematode genomes. Beyond the well-characterized model nematode C. elegans, over 500,000 expressed sequence tags (ESTs) and nearly 600,000 genome survey sequences (GSSs) have been generated from 36 nematode species as part of the Parasitic Nematode Genomics Program undertaken by the Genome Center at Washington University School of Medicine. However, these sequencing data are not present in most publicly available protein databases, which only include sequences in Swiss-Prot. Swiss-Prot, in turn, relies on GenBank/Embl/DDJP for predicted proteins from complete genomes or full-length proteins.

Description
Here we present the NemaPath pathway server, a web-based pathway-level visualization tool for navigating putative metabolic pathways for over 30 nematode species, including 27 parasites. The NemaPath approach consists of two parts: 1) a backend tool to align and evaluate nematode genomic sequences (curated EST contigs) against the annotated Kyoto Encyclopedia of Genes and Genomes (KEGG) protein database; 2) a web viewing application that displays annotated KEGG pathway maps based on desired confidence levels of primary sequence similarity as defined by a user. NemaPath also provides cross-referenced access to nematode genome information provided by other tools available on Nematode.net, including: detailed NemaGene EST cluster information; putative translations; GBrowse EST cluster views; links from nematode data to external databases for corresponding synonymous C. elegans counterparts, subject matches in KEGG's gene database, and also KEGG Ontology (KO) identification.

Conclusion
The NemaPath server hosts metabolic pathway mappings for 30 nematode species and is available on the World Wide Web at http://nematode.net/cgi-bin/keggview.cgi. The nematode source sequences used for the metabolic pathway mappings are available via FTP http://www.nematode.net/FTP/index.php, as provided by the Genome Center at Washington University School of Medicine.
Identification of human thioredoxin as a novel IFN-gamma-induced factor: Mechanism of induction and its role in cytokine production
Authors: Kim Seol-Hee , Oh Jiyoung , Choi Ja-Young , Jang Ji-Young , Kang Myoung-Wha , Lee Choong-Eun 
Published: November 2008

AbstractBackgroundIFN-γ is a multifunctional peptide with a potent immune defense function which is also known as a prototypic Th1 cytokine. While screening for genes differentially expressed by Th1 and Th2 cytokines, human thioredoxin was identified as a novel target gene induced by IFN-γ. The mechanism by which thioredoxin is induced by IFN-γ and the signaling pathways involved in its induction were analyzed. In addition, the effects of thioredoxin on immune cell survival and cytokine production were examined by thioredoxin over-expression and recombinant thioredoxin treatment.ResultsHuman thioredoxin was selectively induced by IFN-γ in monocytic and T cell lines. In monocytic cells, the induction of thioredoxin gene expression by IFN-γ was dose-dependent, and both the mRNA and protein levels were increased by 2~3 fold within 4 to 24 h hours of IFN-γ treatment. The thioredoxin induction by IFN-γ was insensitive to cycloheximide treatment, suggesting that it is a primary response gene induced by IFN-γ. Subsequent analysis of the signaling pathways indicated that the Jak/Stat, Akt, and Erk pathways play a role in IFN-γ signaling that leads to thioredoxin gene expression. Thioredoxin was induced by oxidative or radiation stresses, and it protected the immune cells from apoptosis by reducing the levels of reactive oxygen species. Furthermore, thioredoxin modulated the oxidant-induced cytokine balance toward Th1 by counter-regulating the production of IL-4 and IFN-γ in T cells.ConclusionThese data suggest that thioredoxin is an IFN-γ-induced factor that may play a role in developing Th1 immunity and in the maintenance of immune homeostasis upon infection, radiation, and oxidative stress.
LRRML: a conformational database and an XML description of leucine-rich repeats (LRRs)
Authors: Wei Tiandi , Gong Jing , Jamitzky Ferdinand , Heckl Wolfgang M , Stark Robert W , Rössle Shaila C 
Published: November 2008

Abstract

Background
Leucine-rich repeats (LRRs) are present in more than 6000 proteins. They are found in organisms ranging from viruses to eukaryotes and play an important role in protein-ligand interactions. To date, more than one hundred crystal structures of LRR containing proteins have been determined. This knowledge has increased our ability to use the crystal structures as templates to model LRR proteins with unknown structures. Since the individual three-dimensional LRR structures are not directly available from the established databases and since there are only a few detailed annotations for them, a conformational LRR database useful for homology modeling of LRR proteins is desirable.

Description
We developed LRRML, a conformational database and an extensible markup language (XML) description of LRRs. The release 0.2 contains 1261 individual LRR structures, which were identified from 112 PDB structures and annotated manually. An XML structure was defined to exchange and store the LRRs. LRRML provides a source for homology modeling and structural analysis of LRR proteins. In order to demonstrate the capabilities of the database we modeled the mouse Toll-like receptor 3 (TLR3) by multiple templates homology modeling and compared the result with the crystal structure.

Conclusion
LRRML is an information source for investigators involved in both theoretical and applied research on LRR proteins. It is available at http://zeus.krist.geo.uni-muenchen.de/~lrrml.