bluuebunny/crossref_metadata_2025_split huggingface dataset:
Healing as a Missiological Challenge
Authors: Grundmann Christoffer 
Published: June 2008

AbstractThe formal approbation of the study project "The Church as a Healing Community" by I.A.M.S. Executive Committee (see: Mission Studies No. 5, Vol. III-1, 1986, p. 77) sets the scene for missiologists to embark upon the whole issue of healing on a large scale. It is hoped that by tapping the resources of the international, ecumenical and cross-cultural membership of the association the long felt need can be met to adequately respond to the challenge healing puts before us not only by the new religious movements all over the world and by the traditional societies, but also by the African Independent Churches and the charismatic movement within the established churches. There do exist monographs on several aspects of healing from nearly all over the world of course. But mostly they are concerned with a particular technique or with the health system and healing methods of a certain ethnic group. When it comes to missiology the phenomenon of healing outside the Christian fold often is looked at as something demoniac which as such has to be refused for the sake of the gospel. The only more recent missiological thesis I came across so far addressing the issue in a broader sense is Harold E. Dollar's "A Cross-Cultural Theology of Healing" (1980, Fuller) which actually tries to develop a cross-cultural liturgy or model of healing instead of a theology. This article tries to identify some of the most relevant issues any qualified study of the matter in question has to pay attention to.
Believers' Struggle and Triumph in Christ
Authors: Karotemprel Sebastian 
Published: June 2008

AbstractWhat, then, shall we say in response to this? If God is for us, who can be against us? He who did not spare his own Son, but gave him up for us all - how will he not also, along with him, graciously give us all things? Who will bring any charge against those whom God has chosen? It is God who justifies. Who is he that condemns? Christ Jesus, who died - more than that, who was raised to life - is at the right hand of God and is also interceding for us. Who shall separate us from the love of Christ? Shall trouble or hardship or persecution or famine or nakedness or danger or sword? As it is written: 'For your sake we face death all day long we are considered as sheep to be slaughtered.' No, in all these things we are more than conquerors through him who loved us. For I am convinced that neither death nor life, neither angels nor demons, neither the present nor the future, nor any powers, neither height nor debth, nor anything else in all creation, will be able to separate us from the love of God that is in Christ Jesus our Lord. (Rom. 8: 31-39)
Nonlinear Generalization of Singular Vectors: Behavior in a Baroclinic Unstable Flow
Authors: Rivière Olivier , Lapeyre Guillaume , Talagrand Olivier 
Published: June 2008

Abstract
Singular vector (SV) analysis has proved to be helpful in understanding the linear instability properties of various types of flows. SVs are the perturbations with the largest amplification rate over a given time interval when linearizing the equations of a model along a particular solution. However, the linear approximation necessary to derive SVs has strong limitations and does not take into account several mechanisms present during the nonlinear development (such as wave–mean flow interactions). A new technique has been recently proposed that allows the generalization of SVs in terms of optimal perturbations with the largest amplification rate in the fully nonlinear regime. In the context of a two-layer quasigeostrophic model of baroclinic instability, the effect of nonlinearities on these nonlinear optimal perturbations [herein, nonlinear singular vectors (NLSVs)] is examined in terms of structure and dynamics. NLSVs essentially differ from SVs in the presence of a positive zonal-mean shear at initial time and in a broader meridional extension. As a result, NLSVs sustain a significant amplification in the nonlinear model while SVs exhibit a reduction of amplification in the nonlinear model. The presence of an initial zonal-mean shear in the NLSV increases the initial extraction of energy from the total shear (basic plus zonal-mean flows) and opposes wave–mean flow interactions that decrease the shear through the nonlinear evolution. The spatial shape of the NLSVs (and especially their meridional elongation) allows them to limit wave–wave interactions. These wave–wave interactions are responsible for the formation of vortices and for a smaller extraction of energy from the basic flow. Therefore, NLSVs are able to modify their shape in order to evolve quasi linearly to preserve a large nonlinear growth. Results are generalized for different norms and optimization times. When the streamfunction variance norm is used, the NLSV technique fails to converge because this norm selects very small scales at initial time. This indicates that this technique may be inadequate for problems for which the length scale of instability is not properly defined. For other norms (such as the potential enstrophy norm) and for different optimization times, the mechanisms of the NLSV amplification can still be viewed through wave–wave and wave–mean flow interactions.
Dynamical Relationship between the Phase of North Atlantic Oscillations and the Meridional Excursion of a Preexisting Jet: An Analytical Study
Authors: Luo Dehai , Gong Tingting , Zhong Linhao 
Published: June 2008

Abstract
In this paper, it is shown from an analytical solution that in the presence of a preexisting jet the interaction between the zonal jet and the topography of the land–sea contrast (LSC) in the Northern Hemisphere (NH) tends to induce a dipole component that depends crucially upon whether this zonal jet exhibits a north–south excursion. This phenomenon cannot be observed if the zonal jet has no north–south shift. When the preexisting jet is located more northward (southward), the induced dipole can have a low-over-high (high-over-low) structure and thus can make the center of the stationary wave anomaly shift southward (northward), which can be regarded as an initial state or embryo of a positive (negative) phase North Atlantic Oscillation (NAO). This dipole component can be amplified into a typical NAO event under the forcing of synoptic-scale eddies. To some extent, this result provides an explanation for why the positive (negative) phase of the NAO can be controlled by the northward (southward) shift of the zonal jet prior to the NAO.
In addition, the impact of the jet shift on the occurrence of NAO is examined in a weakly nonlinear NAO model if the initial state of an NAO is prespecified. It is found that the northward (southward) shift of a zonal jet favors the occurrence of the subsequent positive (negative) phase NAO event and then results in a northward (southward)-intensified jet relative to the preexisting jet. In addition, during the decaying of the positive phase NAO, a strong blocking activity is easily observed over Europe as the jet is moved to the north.
A Greenland Sea Perspective on the Dynamics of Postconvective Eddies*
Authors: Oliver K. I. C. , Eldevik T. , Stevens D. P. , Watson A. J. 
Published: June 2008

Abstract
Open ocean deep postconvection contributes to the formation of the dense waters that fill the global deep ocean. The dynamics of postconvective vortices are key to understanding the role of convection in ocean circulation. Submesoscale coherent vortices (SCVs) observed in convective regions are likely to be the anticyclonic components of hetons. Hetons are dipoles, consisting of a surface cyclone and a weakly stratified subsurface anticyclone, that can be formed by convection. Here, key postconvective processes are investigated using numerical experiments of increasing sophistication with two primary goals: 1) to understand how the ambient hydrography and topography influence the propagation of hetons and 2) to provide a theoretical context for recent observations of SCVs in the Greenland Sea.
It is found that the alignment of hetons is controlled by ambient horizontal density gradients and that hetons self-propagate into lighter waters as a result. This provides a mechanism for transporting convected water out of a cyclonic gyre, but the propagation is arrested if the heton meets large-amplitude topography. Upon interaction with topography, hetons usually separate, and the surface cyclone returns toward denser water. The anticyclone usually remains close to topography and may become trapped for several hundred days. These findings may explain the observed accumulation and longevity of SCVs at the Greenland Fracture Zone, on the rim of the Greenland Sea gyre. The separation and sorting of cyclones from anticyclones have likely implications for the density and vorticity budgets of convective regions.
The Regime Dependence of Optimally Weighted Ensemble Model Consensus Forecasts of Surface Temperature
Authors: Greybush Steven J. , Haupt Sue Ellen , Young George S. 
Published: June 2008

Abstract
Previous methods for creating consensus forecasts weight individual ensemble members based upon their relative performance over the previous N days, implicitly making a short-term persistence assumption about the underlying flow regime. A postprocessing scheme in which model performance is linked to underlying weather regimes could improve the skill of deterministic ensemble model consensus forecasts. Here, principal component analysis of several synoptic- and mesoscale fields from the North American Regional Reanalysis dataset provides an objective means for characterizing atmospheric regimes. Clustering techniques, including K-means and a genetic algorithm, are developed that use the resulting principal components to distinguish among the weather regimes. This pilot study creates a weighted consensus from 48-h surface temperature predictions produced by the University of Washington Mesoscale Ensemble, a varied-model (differing physics and parameterization schemes) multianalysis ensemble with eight members. Different optimal weights are generated for each weather regime. A second regime-dependent consensus technique uses linear regression to predict the relative performance of the ensemble members based upon the principal components. Consensus forecasts obtained by the regime-dependent schemes are compared using cross validation with traditional N-day ensemble consensus forecasts for four locations in the Pacific Northwest, and show improvement over methods that rely on the short-term persistence assumption.
Lessons from congenital neutropenia: 50 years of progress in understanding myelopoiesis
Authors: Berliner Nancy 
Published: June 2008

AbstractSevere congenital neutropenia (SCN) was first described just over 50 years ago. The progress in elucidating the clinical features and molecular pathophysiology of SCN closely parallels the progressive growth in our understanding of myelopoiesis. In this historical review, I have delineated this parallel progression in our understanding of the processes of granulocyte differentiation and the pathogenesis of congenital neutropenia. SCN is a heterogeneous disease that can serve as a model for the failure of myelopoiesis, and dissection of its pathogenesis has yielded important insights into the normal process of myeloid development.
Overlap between in vitro donor antihost and in vivo posttransplantation TCR Vβ use: a new paradigm for designer allogeneic blood and marrow transplantation
Authors: Friedman Thea M. , Goldgirsh Kira , Berger Stephanie A. , Zilberberg Jenny , Filicko-O'Hara Joanne , Flomenberg Neal , Donato Michele , Rowley Scott D. , Korngold Robert 
Published: June 2008

AbstractFollowing allogeneic blood and marrow transplantation (BMT), mature donor T cells can enhance engraftment, counteract opportunistic infections, and mount graft-versus-tumor (GVT) responses, but at the risk of developing graft-versus-host disease (GVHD). With the aim of separating the beneficial effects of donor T cells from GVHD, one approach would be to selectively deplete subsets of alloreactive T cells in the hematopoietic cell inoculum. In this regard, TCR Vβ repertoire analysis by CDR3-size spectratyping can be a powerful tool for the characterization of alloreactive T-cell responses. We investigated the potential of this spectratype approach by comparing the donor T-cell alloresponses generated in vitro against patient peripheral blood lymphocytes (PBLs) with those detected in vivo posttransplantation. The results indicated that for most Vβ families that exhibited alloreactive CDR3-size skewing, there was a robust overlap between the in vitro antipatient and in vivo spectratype histograms. Thus, in vitro spectratype analysis may be useful for determining the alloreactive T-cell response involved in GVHD development and, thereby, could serve to guide select Vβ family depletion for designer transplants to improve outcomes.
TiGER: A database for tissue-specific gene expression and regulation
Authors: Liu Xiong , Yu Xueping , Zack Donald J , Zhu Heng , Qian Jiang 
Published: June 2008

Abstract

Background
Understanding how genes are expressed and regulated in different tissues is a fundamental and challenging question. However, most of currently available biological databases do not focus on tissue-specific gene regulation.

Results
The recent development of computational methods for tissue-specific combinational gene regulation, based on transcription factor binding sites, enables us to perform a large-scale analysis of tissue-specific gene regulation in human tissues. The results are stored in a web database called TiGER (Tissue-specific Gene Expression and Regulation). The database contains three types of data including tissue-specific gene expression profiles, combinatorial gene regulations, and cis-regulatory module (CRM) detections. At present the database contains expression profiles for 19,526 UniGene genes, combinatorial regulations for 7,341 transcription factor pairs and 6,232 putative CRMs for 2,130 RefSeq genes.

Conclusion
We have developed and made publicly available a database, TiGER, which summarizes and provides large scale data sets for tissue-specific gene expression and regulation in a variety of human tissues. This resource is available at [1].
AMYPdb: A database dedicated to amyloid precursor proteins
Authors: Pawlicki Sandrine , Le Béchec Antony , Delamarche Christian 
Published: June 2008

Abstract

Background
Misfolding and aggregation of proteins into ordered fibrillar structures is associated with a number of severe pathologies, including Alzheimer's disease, prion diseases, and type II diabetes. The rapid accumulation of knowledge about the sequences and structures of these proteins allows using of in silico methods to investigate the molecular mechanisms of their abnormal conformational changes and assembly. However, such an approach requires the collection of accurate data, which are inconveniently dispersed among several generalist databases.

Results
We therefore created a free online knowledge database (AMYPdb) dedicated to amyloid precursor proteins and we have performed large scale sequence analysis of the included data. Currently, AMYPdb integrates data on 31 families, including 1,705 proteins from nearly 600 organisms. It displays links to more than 2,300 bibliographic references and 1,200 3D-structures. A Wiki system is available to insert data into the database, providing a sharing and collaboration environment. We generated and analyzed 3,621 amino acid sequence patterns, reporting highly specific patterns for each amyloid family, along with patterns likely to be involved in protein misfolding and aggregation.

Conclusion
AMYPdb is a comprehensive online database aiming at the centralization of bioinformatic data regarding all amyloid proteins and their precursors. Our sequence pattern discovery and analysis approach unveiled protein regions of significant interest. AMYPdb is freely accessible [1].
Comparative genomics of Lbx loci reveals conservation of identical Lbx ohnologs in bony vertebrates
Authors: Wotton Karl R , Weierud Frida K , Dietrich Susanne , Lewis Katharine E 
Published: June 2008

Abstract

Background

Lbx/ladybird genes originated as part of the metazoan cluster of Nk homeobox genes. In all animals investigated so far, both the protostome genes and the vertebrate Lbx1 genes were found to play crucial roles in neural and muscle development. Recently however, additional Lbx genes with divergent expression patterns were discovered in amniotes. Early in the evolution of vertebrates, two rounds of whole genome duplication are thought to have occurred, during which 4 Lbx genes were generated. Which of these genes were maintained in extant vertebrates, and how these genes and their functions evolved, is not known.

Results
Here we searched vertebrate genomes for Lbx genes and discovered novel members of this gene family. We also identified signature genes linked to particular Lbx loci and traced the remnants of 4 Lbx paralogons (two of which retain Lbx genes) in amniotes. In teleosts, that have undergone an additional genome duplication, 8 Lbx paralogons (three of which retain Lbx genes) were found. Phylogenetic analyses of Lbx and Lbx-associated genes show that in extant, bony vertebrates only Lbx1- and Lbx2-type genes are maintained. Of these, some Lbx2 sequences evolved faster and were probably subject to neofunctionalisation, while Lbx1 genes may have retained more features of the ancestral Lbx gene. Genes at Lbx1 and former Lbx4 loci are more closely related, as are genes at Lbx2 and former Lbx3 loci. This suggests that during the second vertebrate genome duplication, Lbx1/4 and Lbx2/3 paralogons were generated from the duplicated Lbx loci created during the first duplication event.

Conclusion
Our study establishes for the first time the evolutionary history of Lbx genes in bony vertebrates, including the order of gene duplication events, gene loss and phylogenetic relationships. Moreover, we identified genetic hallmarks for each of the Lbx paralogons that can be used to trace Lbx genes as other vertebrate genomes become available. Significantly, we show that bony vertebrates only retained copies of Lbx1 and Lbx2 genes, with some Lbx2 genes being highly divergent. Thus, we have established a base on which the evolution of Lbx gene function in vertebrate development can be evaluated.
Dating the time of viral subtype divergence
Authors: O'Brien John D , She Zhen-Su , Suchard Marc A 
Published: June 2008

AbstractPrecise dating of viral subtype divergence enables researchers to correlate divergence with geographic and demographic occurrences. When historical data are absent (that is, the overwhelming majority), viral sequence sampling on a time scale commensurate with the rate of substitution permits the inference of the times of subtype divergence. Currently, researchers use two strategies to approach this task, both requiring strong conditions on the molecular clock assumption of substitution rate. As the underlying structure of the substitution rate process at the time of subtype divergence is not understood and likely highly variable, we present a simple method that estimates rates of substitution, and from there, times of divergence, without use of an assumed molecular clock. We accomplish this by blending estimates of the substitution rate for triplets of dated sequences where each sequence draws from a distinct viral subtype, providing a zeroth-order approximation for the rate between subtypes. As an example, we calculate the time of divergence for three genes among influenza subtypes A-H3N2 and B using subtype C as an outgroup. We show a time of divergence approximately 100 years ago, substantially more recent than previous estimates which range from 250 to 3800 years ago.
Variation in expression of HMW1 and HMW2 adhesins in invasive nontypeable Haemophilus influenzae isolates
Authors: Giufrè Maria , Carattoli Alessandra , Cardines Rita , Mastrantonio Paola , Cerquetti Marina 
Published: June 2008

Abstract

Background
Among surface antigens of nontypeable Haemophilus influenzae (NTHi), the HMW1 and HMW2 proteins are the major adhesins promoting colonization of the upper respiratory tract. Since they are potential vaccine candidates, knowledge concerning variation in HMW proteins expression among clinical isolates is of great interest. In this study, expression of hmw1A and hmw2A genes was evaluated by quantitative real-time reverse transcription-PCR in 3 NTHi invasive isolates (strains 56, 72, 91) and in the prototype strain 12. Number of 7-bp repeats within the hmwA promoters and presence of HMW proteins by Western blotting were also determined.

Results
Results showed that gene transcription varied not only among different isolates but also between the hmw1A and hmw2A genes from the same isolate. Compared to that found in prototype strain 12, up-regulation of the hmw1A gene expression was found in strain 56, down-regulation of both hmw1A and hmw2A genes transcripts was observed in strain 72 whereas the two hmwA genes appeared differentially expressed in strain 91 with the hmw1A transcript enhanced but the hmw2A transcript reduced.

Conclusion
Increasing numbers of 7-bp repeats within the hmwA promoters generally correlated with decreased amounts of mRNA transcript, however additional control mechanisms contributing to modulation of hmw1A gene seem to be present.
Antibodies from women urogenitally infected with C. trachomatis predominantly recognized the plasmid protein pgp3 in a conformation-dependent manner
Authors: Li Zhongyu , Zhong Youmin , Lei Lei , Wu Yimou , Wang Shiping , Zhong Guangming 
Published: June 2008

AbstractBackgroundC. trachomatisorganisms carry a cryptic plasmid that encodes 8 open reading frames designated as pORF1 to 8. It is not clear whether all 8 pORFs are expressed duringC. trachomatisinfection in humans and information on the functionality of the plasmid proteins is also very limited.ResultsWhen antibodies from women urogenitally infected withC. trachomatiswere reacted with the plasmid proteins, all 8 pORFs were positively recognized by one or more human antibody samples with the recognition of pORF5 protein (known as pgp3) by most antibodies and with the highest titers. The antibody recognition of the pORFs was blocked byC. trachomatis-infected HeLa but not normal HeLa cell lysates. The pgp3 fusion protein-purified human IgG detected the endogenous pgp3 in the cytosol ofC. trachomatis-infected cells with an intracellular distribution pattern similar to that of CPAF, a chlamydial genome-encoded protease factor. However, the human antibodies no longer recognized pgp3 but maintained recognition of CPAF when both antigens were linearized or heat-denatured. The pgp3 conformation is likely maintained by the C-terminal 75% amino acid sequence since further deletion blocked the binding by the human antibodies and two conformation-dependent mouse monoclonal antibodies.ConclusionThe plasmid-encoded 8 proteins are both expressed and immunogenic with pgp3 as the most immunodominant antigen during chlamydial infection in humans. More importantly, the human anti-pgp3 antibodies are highly conformation-dependent. These observations have provided important information for further understanding the function of the plasmid-encoded proteins and exploring the utility of pgp3 in chlamydial diagnosis and vaccination.