bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wesley's Sanctification Narrative: A Tool for Understanding the Holy Spirit's Work in a More Physical Soul
Authors: Shrier Paul , Shrier Cahleen 
Published: December 2009

AbstractRapid advances in neuroscience during the past fifteen years require Christians to rethink traditional understandings of the human soul, sin, salvation, and sanctification. John Wesley's understanding of means of grace and his theology of the Holy Spirit provide tools to integrate our understanding of the soul and sanctification with current neuroscience. First, a new, more physical, Christian understanding of the soul is suggested. Then Wesley's theology of sanctification through acts of mercy is explained and related to current concepts of empathy. The relationship between empathy and sanctification, as understood by Wesley, is then compared with new neurological findings about human mirror neuron systems that are prerequisite for empathizing with others. The final section suggests a new sanctification narrative based on the interactions of the Holy Spirit, mirror neuron systems, and empathy, and then makes recommendations for Christian actions based on the correlation of brain function and operations of the Holy Spirit.
Hymnody and Liturgy in the Azusa Street Revival, 1906-1908
Authors: Dove Stephen 
Published: December 2009

AbstractParticipants in the Azusa Street Revival regularly emphasized the nonliturgical nature of their Spirit-led worship. This article argues, however, that while worshippers eschewed traditional devices such as lectionaries and set schedules, they did create their own, unique form of liturgy through hymnody. The liturgical functions served by music at Azusa Street included selecting Scripture readings, ordering services, and providing theological balance. To make this case, the author surveys references to music, singing, and hymn writing in the official publications of the revival and in later accounts of the revival recorded by participants. From these sources, the author identifies three types of music used at Azusa Street: singing in the Spirit, new compositions written in a conventional style, and traditional hymns. The article further demonstrates how these genres served specific functions in the community, one of the most important of which was to emphasize the christological, as opposed to pneumatological, aspects of Pentecostal theology.
Response to Reviews of, In Jesus' Name
Authors: Reed David 
Published: December 2009

AbstractThis article is a response by Reed to two reviews of his book. Both reviewers write as Oneness or "Apostolic" Pentecostals, Millner from an African-American tradition and French from a predominantly white organization. Reed briefly examines three issues raised in the reviews based on their implications for race within OP identity: the historical roots of OP theology in early evangelicalism, OP's heterodox beliefs and tenuous relationship with other Christian bodies, and Reed's historical-theological methodology.
A Stochastic Analysis of the Impact of Small-Scale Fluctuations on the Tropospheric Temperature Response to CO2 Doubling
Authors: Seiffert Rita , von Storch Jin-Song 
Published: December 2009

Abstract
The climate response to increased CO2 concentration is generally studied using climate models that have finite spatial and temporal resolutions. Different parameterizations of the effect of unresolved processes can result in different representations of small-scale fluctuations in the climate model. The representation of small-scale fluctuations can, on the other hand, affect the modeled climate response. In this study the mechanisms by which enhanced small-scale fluctuations alter the climate response to CO2 doubling are investigated. Climate experiments with preindustrial and doubled CO2 concentrations obtained from a comprehensive climate model [ECHAM5/Max Planck Institute Ocean Model (MPI-OM)] are analyzed both with and without enhanced small-scale fluctuations. By applying a stochastic model to the experimental results, two different mechanisms are found. First, the small-scale fluctuations can change the statistical behavior of the global mean temperature as measured by its statistical damping. The statistical damping acts as a restoring force that determines, according to the fluctuation–dissipation theory, the amplitude of the climate response to a change in external forcing (here, CO2 doubling). Second, the small-scale fluctuations can affect processes that occur only in response to the CO2 increase, thereby altering the change of the effective forcing on the global mean temperature.
Why Is ENSO Influencing Northwest India Winter Precipitation in Recent Decades?
Authors: Yadav R. K. , Yoo J. H. , Kucharski F. , Abid M. A. 
Published: December 2009

AbstractThis study examines decadal changes of the El Niño–Southern Oscillation (ENSO) influence on the interannual variability of northwest India winter precipitation (NWIWP). The analysis is based on correlations and regressions performed using India Meteorological Department (IMD) records based on station data and reanalysis fields from 1950 to 2008. The authors find that the interannual variability of NWIWP is influenced by the ENSO phenomenon in the recent decades. This conclusion is supported by a consistency across the different observational datasets employed in this study and confirmed by numerical modeling. A physical mechanism for such an influence is proposed, by which western disturbances (WDs) are intensified over northwest India because of a baroclinic response due to Sverdrup balance related to large-scale sinking motion over the western Pacific during the warm phase of ENSO. This response causes an upper-level cyclonic circulation anomaly north of India and a low-level anticyclonic anomaly over southern and central India. The cyclonic circulation anomaly intensifies the WDs passing over northwest India.
Social consequences of multiple sclerosis (1): early pension and temporary unemployment—a historical prospective cohort study
Authors: Hilt Pfleger Claudia Christina , Meulengracht Flachs Esben , Koch-Henriksen Nils 
Published: December 2009

Multiple sclerosis affects young and middle-aged people and often leads to physical and cognitive handicaps. There is a need for detailed knowledge of the social consequences of the disease. We aim here to describe the course of the working life and career of multiple sclerosis patients at the time of onset and thereafter, in terms of probability of early pension and income development. All 2538 patients with multiple sclerosis in Denmark with disease onset between 1980 and 1989, identified through the Danish MS-Registry, were included in this study. Twenty matched control persons per patient were randomly drawn from the civil registration system. Information on economic status was retrieved from Statistics Denmark. A survival analysis technique was used with onset as the starting point. We found that the probability of remaining without early pension was at 5 years 70% for patients and 97% for controls, and at 20 years 22% for patients and 86% for controls. Due to lower rates for early pension, gross income with time was lower in patients than controls. We conclude that multiple sclerosis seriously affects the economic life of multiple sclerosis patients, even within a few years of onset.
Cbfb/Runx1 repression–independent blockage of differentiation and accumulation of Csf2rb-expressing cells by Cbfb-MYH11
Authors: Hyde R. Katherine , Kamikubo Yasuhiko , Anderson Stacie , Kirby Martha , Alemu Lemlem , Zhao Ling , Liu P. Paul 
Published: December 2009

AbstractIt is known that CBFB-MYH11, the fusion gene generated by inversion of chromosome 16 in human acute myeloid leukemia, is causative for oncogenic transformation. However, the mechanism by which CBFB-MYH11 initiates leukemogenesis is not clear. Previously published reports showed that CBFB-MYH11 dominantly inhibits RUNX1 and CBFB, and such inhibition has been suggested as the mechanism for leukemogenesis. Here we show that Cbfb-MYH11 caused Cbfb/Runx1 repression–independent defects in both primitive and definitive hematopoiesis. During primitive hematopoiesis, Cbfb-MYH11 delayed differentiation characterized by sustained expression of Gata2, Il1rl1, and Csf2rb, a phenotype not found in Cbfb and Runx1 knockout mice. Expression of Cbfb-MYH11 in the bone marrow induced the accumulation of abnormal progenitor-like cells expressing Csf2rb in preleukemic mice. The expression of all 3 genes was detected in most human and murine CBFB-MYH11+ leukemia samples. Interestingly, Cbfb-MYH11+ preleukemic progenitors and leukemia-initiating cells did not express Csf2rb, although the majority of leukemia cells in our Cbfb-MYH11 knockin mice were Csf2rb+. Therefore Csf2rb can be used as a negative selection marker to enrich preleukemic progenitor cells and leukemia-initiating cells from Cbfb-MYH11 mice. These results suggest that Cbfb/Runx1 repression–independent activities contribute to leukemogenesis by Cbfb-MYH11.
Persons with Quebec platelet disorder have a tandem duplication of PLAU, the urokinase plasminogen activator gene
Authors: Paterson Andrew D. , Rommens Johanna M. , Bharaj Bhupinder , Blavignac Jessica , Wong Isidro , Diamandis Maria , Waye John S. , Rivard Georges E. , Hayward Catherine P. M. 
Published: December 2009

Abstract
Quebec platelet disorder (QPD) is an autosomal dominant bleeding disorder linked to a region on chromosome 10 that includes PLAU, the urokinase plasminogen activator gene. QPD increases urokinase plasminogen activator mRNA levels, particularly during megakaryocyte differentiation, without altering expression of flanking genes. Because PLAU sequence changes were excluded as the cause of this bleeding disorder, we investigated whether the QPD mutation involved PLAU copy number variation. All 38 subjects with QPD had a direct tandem duplication of a 78-kb genomic segment that includes PLAU. This mutation was specific to QPD as it was not present in any unaffected family members (n = 114), unrelated French Canadians (n = 221), or other persons tested (n = 90). This new information on the genetic mutation will facilitate diagnostic testing for QPD and studies of its pathogenesis and prevalence. QPD is the first bleeding disorder to be associated with a gene duplication event and a PLAU mutation.
Eradication of intracellular Francisella tularensis in THP-1 human macrophages with a novel autophagy inducing agent
Authors: Chiu Hao-Chieh , Soni Shilpa , Kulp Samuel K , Curry Heather , Wang Dasheng , Gunn John S , Schlesinger Larry S , Chen Ching-Shih 
Published: December 2009

Abstract

Background
Autophagy has been shown recently to play an important role in the intracellular survival of several pathogenic bacteria. In this study, we investigated the effect of a novel small-molecule autophagy-inducing agent, AR-12, on the survival of Francisella tularensis, the causative bacterium of tularemia in humans and a potential bioterrorism agent, in macrophages.

Methods and results
Our results show that AR-12 induces autophagy in THP-1 macrophages, as indicated by increased autophagosome formation, and potently inhibits the intracellular survival of F. tularensis (type A strain, Schu S4) and F. novicida in macrophages in association with increased bacterial co-localization with autophagosomes. The effect of AR-12 on intracellular F. novicida was fully reversed in the presence of the autophagy inhibitor, 3-methyl adenine or the lysosome inhibitor, chloroquine. Intracellular F. novicida were not susceptible to the inhibitory activity of AR-12 added at 12 h post-infection in THP-1 macrophages, and this lack of susceptibility was independent of the intracellular location of bacteria.

Conclusion
Together, AR-12 represents a proof-of-principle that intracellular F. tularensis can be eradicated by small-molecule agents that target innate immunity.
Protein-protein docking using region-based 3D Zernike descriptors
Authors: Venkatraman Vishwesh , Yang Yifeng D , Sael Lee , Kihara Daisuke 
Published: December 2009

Abstract

Background
Protein-protein interactions are a pivotal component of many biological processes and mediate a variety of functions. Knowing the tertiary structure of a protein complex is therefore essential for understanding the interaction mechanism. However, experimental techniques to solve the structure of the complex are often found to be difficult. To this end, computational protein-protein docking approaches can provide a useful alternative to address this issue. Prediction of docking conformations relies on methods that effectively capture shape features of the participating proteins while giving due consideration to conformational changes that may occur.

Results
We present a novel protein docking algorithm based on the use of 3D Zernike descriptors as regional features of molecular shape. The key motivation of using these descriptors is their invariance to transformation, in addition to a compact representation of local surface shape characteristics. Docking decoys are generated using geometric hashing, which are then ranked by a scoring function that incorporates a buried surface area and a novel geometric complementarity term based on normals associated with the 3D Zernike shape description. Our docking algorithm was tested on both bound and unbound cases in the ZDOCK benchmark 2.0 dataset. In 74% of the bound docking predictions, our method was able to find a near-native solution (interface C-α RMSD ≤ 2.5 Å) within the top 1000 ranks. For unbound docking, among the 60 complexes for which our algorithm returned at least one hit, 60% of the cases were ranked within the top 2000. Comparison with existing shape-based docking algorithms shows that our method has a better performance than the others in unbound docking while remaining competitive for bound docking cases.

Conclusion
We show for the first time that the 3D Zernike descriptors are adept in capturing shape complementarity at the protein-protein interface and useful for protein docking prediction. Rigorous benchmark studies show that our docking approach has a superior performance compared to existing methods.
RFX2 is a candidate downstream amplifier of A-MYB regulation in mouse spermatogenesis
Authors: Horvath Gary C , Kistler Malathi K , Kistler W Stephen 
Published: December 2009

AbstractBackgroundMammalian spermatogenesis involves formation of haploid cells from the male germline and then a complex morphological transformation to generate motile sperm. Focusing on meiotic prophase, some tissue-specific transcription factors are known (A-MYB) or suspected (RFX2) to play important roles in modulating gene expression in pachytene spermatocytes. The current work was initiated to identify both downstream and upstream regulatory connections forRfx2.ResultsSearches of pachytene up-regulated genes identified high affinity RFX binding sites (X boxes) in promoter regions of several new genes:Adam5,Pdcl2, andSpag6. We confirmed a strong promoter-region X-box forAlf, a germ cell-specific variant of general transcription factor TFIIA. UsingAlfas an example of a target gene, we showed that its promoter is stimulated by RFX2 in transfected cells and used ChIP analysis to show that the promoter is occupied by RFX2 in vivo. Turning to upstream regulation of theRfx2promoter, we identified a cluster of three binding sites (MBS) for the MYB family of transcription factors. Because testis is one of the few sites ofA-mybexpression, and because spermatogenesis arrests in pachytene inA-mybknockout mice, the MBS cluster implicatesRfx2as anA-mybtarget. Electrophoretic gel-shift, ChIP, and co-transfection assays all support a role for these MYB sites inRfx2expression. Further,Rfx2expression was virtually eliminated inA-mybknockout testes. Immunohistology on testis sections showed that A-MYB expression is up-regulated only after pachytene spermatocytes have clearly moved away from the tubule wall, which correlates with onset of RFX2 expression, whereas B-MYB expression, by contrast, is prevalent only in earlier spermatocytes and spermatogonia.ConclusionWith an expanding list of likely target genes, RFX2 is potentially an important transcriptional regulator in pachytene spermatocytes.Rfx2itself is a good candidate to be regulated by A-MYB, which is essential for meiotic progression. IfAlfis a genuine RFX2 target, thenA-myb,Rfx2, andAlfmay form part of a transcriptional network that is vital for completion of meiosis and preparation for post-meiotic differentiation.
Expansion of tandem repeats in sea anemone Nematostella vectensis proteome: A source for gene novelty?
Authors: Naamati Guy , Fromer Menachem , Linial Michal 
Published: December 2009

Abstract

Background
The complete proteome of the starlet sea anemone, Nematostella vectensis, provides insights into gene invention dating back to the Cnidarian-Bilaterian ancestor. With the addition of the complete proteomes of Hydra magnipapillata and Monosiga brevicollis, the investigation of proteins having unique features in early metazoan life has become practical. We focused on the properties and the evolutionary trends of tandem repeat (TR) sequences in Cnidaria proteomes.

Results
We found that 11-16% of N. vectensis proteins contain tandem repeats. Most TRs cover 150 amino acid segments that are comprised of basic units of 5-20 amino acids. In total, the N. Vectensis proteome has about 3300 unique TR-units, but only a small fraction of them are shared with H. magnipapillata, M. brevicollis, or mammalian proteomes. The overall abundance of these TRs stands out relative to that of 14 proteomes representing the diversity among eukaryotes and within the metazoan world. TR-units are characterized by a unique composition of amino acids, with cysteine and histidine being over-represented. Structurally, most TR-segments are associated with coiled and disordered regions. Interestingly, 80% of the TR-segments can be read in more than one open reading frame. For over 100 of them, translation of the alternative frames would result in long proteins. Most domain families that are characterized as repeats in eukaryotes are found in the TR-proteomes from Nematostella and Hydra.

Conclusions
While most TR-proteins have originated from prediction tools and are still awaiting experimental validations, supportive evidence exists for hundreds of TR-units in Nematostella. The existence of TR-proteins in early metazoan life may have served as a robust mode for novel genes with previously overlooked structural and functional characteristics.
Deciphering the transcriptional circuitry of microRNA genes expressed during human monocytic differentiation
Authors: Schmeier Sebastian , MacPherson Cameron R , Essack Magbubah , Kaur Mandeep , Schaefer Ulf , Suzuki Harukazu , Hayashizaki Yoshihide , Bajic Vladimir B 
Published: December 2009

Abstract

Background
Macrophages are immune cells involved in various biological processes including host defence, homeostasis, differentiation, and organogenesis. Disruption of macrophage biology has been linked to increased pathogen infection, inflammation and malignant diseases. Differential gene expression observed in monocytic differentiation is primarily regulated by interacting transcription factors (TFs). Current research suggests that microRNAs (miRNAs) degrade and repress translation of mRNA, but also may target genes involved in differentiation. We focus on getting insights into the transcriptional circuitry regulating miRNA genes expressed during monocytic differentiation.

Results
We computationally analysed the transcriptional circuitry of miRNA genes during monocytic differentiation using in vitro time-course expression data for TFs and miRNAs. A set of TF→miRNA associations was derived from predicted TF binding sites in promoter regions of miRNA genes. Time-lagged expression correlation analysis was utilised to evaluate the TF→miRNA associations. Our analysis identified 12 TFs that potentially play a central role in regulating miRNAs throughout the differentiation process. Six of these 12 TFs (ATF2, E2F3, HOXA4, NFE2L1, SP3, and YY1) have not previously been described to be important for monocytic differentiation. The remaining six TFs are CEBPB, CREB1, ELK1, NFE2L2, RUNX1, and USF2. For several miRNAs (miR-21, miR-155, miR-424, and miR-17-92), we show how their inferred transcriptional regulation impacts monocytic differentiation.

Conclusions
The study demonstrates that miRNAs and their transcriptional regulatory control are integral molecular mechanisms during differentiation. Furthermore, it is the first study to decipher on a large-scale, how miRNAs are controlled by TFs during human monocytic differentiation. Subsequently, we have identified 12 candidate key controllers of miRNAs during this differentiation process.
Inactivation of the fliY gene encoding a flagellar motor switch protein attenuates mobility and virulence of Leptospira interrogansstrain Lai
Authors: Liao Sumei , Sun Aihua , Ojcius David M , Wu Senlin , Zhao Jinfang , Yan Jie 
Published: December 2009

Abstract

Background
Pathogenic Leptospira species cause leptospirosis, a zoonotic disease of global importance. The spirochete displays active rotative mobility which may contribute to invasion and diffusion of the pathogen in hosts. FliY is a flagellar motor switch protein that controls flagellar motor direction in other microbes, but its role in Leptospira, and paricularly in pathogenicity remains unknown.

Results
A suicide plasmid for the fliY gene of Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai strain Lai that was disrupted by inserting the ampicillin resistance gene (bla) was constructed, and the inactivation of fliY gene in a mutant (fliY
-) was confirmed by PCR and Western Blot analysis. The inactivation resulted in the mRNA absence of fliP and fliQ genes which are located downstream of the fliY gene in the same operon. The mutant displayed visibly weakened rotative motion in liquid medium and its migration on semisolid medium was also markedly attenuated compared to the wild-type strain. Compared to the wild-type strain, the mutant showed much lower levels of adhesion to murine macrophages and apoptosis-inducing ability, and its lethality to guinea pigs was also significantly decreased.

Conclusion
Inactivation of fliY, by the method used in this paper, clearly had polar effects on downstream genes. The phentotypes observed, including lower pathogenicity, could be a consequence of fliY inactivation, but also a consequence of the polar effects.