bluuebunny/crossref_metadata_2025_split huggingface dataset:
Turkish Views on Christians: Implications for Armenian-Turkish Relations
Authors: Kluge Pascal 
Published: February 2009

AbstractSamuel Huntington argues in The Clash of Civilizations that a principal cultural fault line is to be found between the Muslim world and the Western non-Muslim world. In this context it is not surprising that the Christian West often assumes Muslims to be suspicious or even hostile towards Christians. Periodic cases of anti-Christian public statements and actions support this impression and are indicative of profound inter-religious tensions. This notion also influences the relations between peoples and nations. In the South-Caucasian case, the Armenian-Turkish relations are affected most by this phenomenon. When conflicts arise, religion plays a role in the perception of the Other. What is needed, therefore, is more inter-religious understanding on all societal levels. Although politics play a key role in establishing friendly ties between nations, it is the grassroots of the population upon which fruitful relations stand and which secure a more consistent quality to the results of political efforts. When considering Turkish views on Christians, field research indicates that the average Turk harbours an overall benevolent view of Christians and, therefore, that there exists considerable potential for successful inter-religious dialogue. Christians are generally regarded with respect, and most Turkish participants showed little to no negative attitudes towards them. The Christians of Turkey, notably Armenians and Greeks, were, furthermore, perceived as part of Turkey's society. The reason for these predominantly positive attitudes may be sought in the institutional incorporation of Christians and Jews into the broader context of Islamic society or, more inherent to Turkish history, in the positive remembrance of the multi-religious and multi-ethnic face of the Ottoman Empire—and thus in the appreciation of religious diversity as an asset and historical obligation.
Eprem Khan and the Constitutional Failure in Iran: (Some Random Notes)
Authors: Jalali Seyyed Sa'id 
Published: February 2009

AbstractThis article includes some thoughts on reappraising the role of Eprem Khan in the constitutional failure in Iran during the early 20th century. Eprem Khan's crucial role in this event has always been the centre of scholarly discussions. While often criticised for having capitulated to the Russian threat and for not standing steadfast with the parliamentarians, an unbiased look at some primary accounts helps create a more adequate picture of the Armenian-Iranian military man. It is through an objective, though very brief, review of the historical facts that scholars are suggested to re-evaluate the role of Eprem Khan and form an opinion based on the options he faced, rather than judge him by the outcome of the momentous events of 1911.
Encyclopaedia Iranica — 35: A New Agenda for Persian Studies?
Authors: Trompf Garry 
Published: February 2009

AbstractThis paper is a revised version of a Lecture delivered at the Celebrations of 35 Years of the "Encyclopaedia Iranica" project, delivered on 3 May 2008, at the University of Sydney, and on 7 June 2008, at the Arya International University, Yerevan, during the International Conference "Iran and the Caucasus: Unity and Diversity".
Fighting exclusion with culture and art Examples from Brazil
Authors: Reiter Bernd 
Published: February 2009

English This article demonstrates that artistic activity is an important tool for deepening democracy, because it provides a vehicle for the excluded to reach the public sphere, thus making it more heterogeneous. As artists, they become active citizens and step out of the invisibility into which racism and exclusion has forced them. French Cet article montre que l’activité artistique est un important outil d’enracinement de la démocratie, parce qu’elle offre aux exclus un moyen de joindre la sphère publique, la rendant ainsi plus hétérogène. En qualité d’artistes, les exclus deviennent des citoyens actifs et ils émergent de l’invisibilité où le racisme et l’exclusion les avaient confinés. Spanish Este artículo demuestra que la actividad artística es una herramienta importante para la profundización de la democracia porque la expresión artística constituye un vehículo para que los excluidos lleguen a la esfera pública, con lo que ésta se enriquece y se hace más heterogénea. Como artistas, se convierten en ciudadanos activos y salen de la invisibilidad a la que el racismo y la exclusión los ha empujado.
Victim—offender mediation as a social work practice
Authors: Bradt Lieve , Bouverne-De Bie Maria 
Published: February 2009

English Based on the Flemish practice of victim–offender mediation for adult offenders, this article shows how mediation can be a social work practice that goes beyond being an instrument for the responsibilization of offenders, but instead recognizes social workers as policymakers. French Basé sur la pratique flamande de la médiation entre les victimes et les auteurs adultes de délits, cet article montre comment la médiation peut être une pratique de travail social allant au delà du simple instrument de responsabilisation les auteurs de délits, en reconnaissant plutôt les travailleurs sociaux comme décideurs politiques. Spanish Basándose en la práctica flamenca de mediar entre víctima y ofensor adulto, este artículo muestra cómo la mediación puede ser una práctica de trabajo social que a más de ser un instrumento para responsabilizar a los ofensores, reconoce a los trabajadores sociales como diseñadores de política social.
E-learning
Authors: Bozalek Vivienne , Matthews Lear 
Published: February 2009

English Exploration of the impact of cultural and economic factors on the personal and professional identities of adult learners as critical friends across geographical locations becomes possible through e-learning. Correspondence between adult learners can create a space for intellectual and emotional sharing, thus enhancing the learners’ abilities to function reflexively as professional practitioners. French L’apprentissage électronique permet d’explorer l’impact des dimensions culturelles et économiques sur l’identité personnelle et professionnelle des apprenants adultes répartis géographiquement. En correspondant entre eux, les apprenants adultes peuvent mettre en place un espace de partage intellectuel et émotionnel, ce qui leur permettrait d’accroître leurs capacités à fonctionner de façon réflexive comme praticiens professionnels. Spanish La exploración del impacto de factores culturales y económicos en las identidades personales y profesionales de los aprendices adultos como amigos críticos, a través de localidades geográficas, se hace posible a través del aprendizaje a distancia. La correspondencia entre aprendices adultos creó un espacio para compartir intelectual y emocionalmente, aumentando así las habilidades de los aprendices para funcionar reflexivamente como practicantes profesionales.
Battening down the hatches
Authors: Foster Allan 
Published: February 2009

Survey of corporate business information services based on in-depth interviews with leading information and knowledge managers. Key findings are: 1. Greater coordination and management of global corporate information management networks 2. Although information budget reductions in the light of the recession have been relatively modest so far — 50 per cent of respondents have experienced cuts of 10 per cent and upwards — most predict more substantial reductions in their 2009 budgets 3. The business climate is still rather uneven — banking and financial services are struggling whilst some other sectors, most notably corporate law, are generally busy 4. Great efforts to establish very tight cost control 5. Constant search for ways for Information Department to add more value to the business 6. Rolling back of desk-top deployment of data sources in some companies due to financial pressures and non-use; other companies continue to expand desk-top access to information products 7. Financial restrictions have affected service development capability and speed of response 8. Use of sophisticated metrics to track and assess costs and use for client feedback 9. Seventy-five per cent of respondents have already lost staff or expect to do so in 2009 10. Information discovery skills, that most traditional part of the Library and Information Service (LIS) professional's armoury, are increasingly being recognized as a key priority by senior information managers looking at their skill mix 11. Twenty per cent of companies committed to offshore operations are consolidating; 80 per cent have no immediate plans to follow this strategy but don't necessarily rule it out further into the future 12. Some sustained Knowledge Management (KM) initiatives ongoing in 50 per cent of respondent companies, albeit if sometimes of a `Guerrilla KM' flavour 13. Social technologies for corporate deployment — a third of respondents are believers, a third agnostics and a third atheists 14. Vendor management and relationships: respondents demand more creativity and understanding on charging levels and flexibility 15. Brokers' reports becoming unaffordable and therefore unavailable 16. Information risks such as password misuse, Intellectual Property (IP) and copyright breaches and licensing violations should be better understood and managed 17. BvD ousts Factiva in ranking of top three vendors 18. There's a continued commitment to user training albeit in terms of coaching and support rather than formal programmes 19. Strategic concerns focus on organizational management and financial issues above all else.
RankAggreg, an R package for weighted rank aggregation
Authors: Pihur Vasyl , Datta Susmita , Datta Somnath 
Published: February 2009

Abstract

Background
Researchers in the field of bioinformatics often face a challenge of combining several ordered lists in a proper and efficient manner. Rank aggregation techniques offer a general and flexible framework that allows one to objectively perform the necessary aggregation. With the rapid growth of high-throughput genomic and proteomic studies, the potential utility of rank aggregation in the context of meta-analysis becomes even more apparent. One of the major strengths of rank-based aggregation is the ability to combine lists coming from different sources and platforms, for example different microarray chips, which may or may not be directly comparable otherwise.

Results
The RankAggreg package provides two methods for combining the ordered lists: the Cross-Entropy method and the Genetic Algorithm. Two examples of rank aggregation using the package are given in the manuscript: one in the context of clustering based on gene expression, and the other one in the context of meta-analysis of prostate cancer microarray experiments.

Conclusion
The two examples described in the manuscript clearly show the utility of the RankAggreg package in the current bioinformatics context where ordered lists are routinely produced as a result of modern high-throughput technologies.
"Tandem duplication-random loss" is not a real feature of oyster mitochondrial genomes
Authors: Ren Jianfeng , Liu Xiao , Zhang Guofan , Liu Bin , Guo Ximing 
Published: February 2009

Abstract
Duplications and rearrangements of coding genes are major themes in the evolution of mitochondrial genomes, bearing important consequences in the function of mitochondria and the fitness of organisms. Yu et al. (BMC Genomics 2008, 9:477) reported the complete mt genome sequence of the oyster Crassostrea hongkongensis (16,475 bp) and found that a DNA segment containing four tRNA genes (trnK

1
, trnC, trnQ

1
and trnN), a duplicated (rrnS) and a split rRNA gene (rrnL5') was absent compared with that of two other Crassostrea species. It was suggested that the absence was a novel case of "tandem duplication-random loss" with evolutionary significance. We independently sequenced the complete mt genome of three C. hongkongensis individuals, all of which were 18,622 bp and contained the segment that was missing in Yu et al.'s sequence. Further, we designed primers, verified sequences and demonstrated that the sequence loss in Yu et al.'s study was an artifact caused by placing primers in a duplicated region. The duplication and split of ribosomal RNA genes are unique for Crassostrea oysters and not lost in C. hongkongensis. Our study highlights the need for caution when amplifying and sequencing through duplicated regions of the genome.
Gene Ontology annotation highlights shared and divergent pathogenic strategies of type III effector proteins deployed by the plant pathogen Pseudomonas syringae pv tomato DC3000 and animal pathogenic Escherichia coli strains
Authors: Lindeberg Magdalen , Biehl Bryan S , Glasner Jeremy D , Perna Nicole T , Collmer Alan , Collmer Candace W 
Published: February 2009

Abstract
Genome-informed identification and characterization of Type III effector repertoires in various bacterial strains and species is revealing important insights into the critical roles that these proteins play in the pathogenic strategies of diverse bacteria. However, non-systematic discipline-specific approaches to their annotation impede analysis of the accumulating wealth of data and inhibit easy communication of findings among researchers working on different experimental systems. The development of Gene Ontology (GO) terms to capture biological processes occurring during the interaction between organisms creates a common language that facilitates cross-genome analyses. The application of these terms to annotate type III effector genes in different bacterial species – the plant pathogen Pseudomonas syringae pv tomato DC3000 and animal pathogenic strains of Escherichia coli – illustrates how GO can effectively describe fundamental similarities and differences among different gene products deployed as part of diverse pathogenic strategies. In depth descriptions of the GO annotations for P. syringae pv tomato DC3000 effector AvrPtoB and the E. coli effector Tir are described, with special emphasis given to GO capability for capturing information about interacting proteins and taxa. GO-highlighted similarities in biological process and molecular function for effectors from additional pathosystems are also discussed.
Programmed cell death in host-symbiont associations, viewed through the Gene Ontology
Authors: Chibucos Marcus C , Collmer Candace W , Torto-Alalibo Trudy , Gwinn-Giglio Michelle , Lindeberg Magdalen , Li Donghui , Tyler Brett M 
Published: February 2009

AbstractManipulation of programmed cell death (PCD) is central to many host microbe interactions. Both plant and animal cells use PCD as a powerful weapon against biotrophic pathogens, including viruses, which draw their nutrition from living tissue. Thus, diverse biotrophic pathogens have evolved many mechanisms to suppress programmed cell death, and mutualistic and commensal microbes may employ similar mechanisms. Necrotrophic pathogens derive their nutrition from dead tissue, and many produce toxins specifically to trigger programmed cell death in their hosts. Hemibiotrophic pathogens manipulate PCD in a most exquisite way, suppressing PCD during the biotrophic phase and stimulating it during the necrotrophic phase. This mini-review will summarize the mechanisms that have evolved in diverse microbes and hosts for controlling PCD and the Gene Ontology terms developed by the Plant-Associated Microbe Gene Ontology (PAMGO) Consortium for describing those mechanisms.
Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae
Authors: Meng Shaowu , Brown Douglas E , Ebbole Daniel J , Torto-Alalibo Trudy , Oh Yeon Yee , Deng Jixin , Mitchell Thomas K , Dean Ralph A 
Published: February 2009

Abstract

Background

Magnaporthe oryzae, the causal agent of blast disease of rice, is the most destructive disease of rice worldwide. The genome of this fungal pathogen has been sequenced and an automated annotation has recently been updated to Version 6 http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/MultiDownloads.html. However, a comprehensive manual curation remains to be performed. Gene Ontology (GO) annotation is a valuable means of assigning functional information using standardized vocabulary. We report an overview of the GO annotation for Version 5 of M. oryzae genome assembly.

Methods
A similarity-based (i.e., computational) GO annotation with manual review was conducted, which was then integrated with a literature-based GO annotation with computational assistance. For similarity-based GO annotation a stringent reciprocal best hits method was used to identify similarity between predicted proteins of M. oryzae and GO proteins from multiple organisms with published associations to GO terms. Significant alignment pairs were manually reviewed. Functional assignments were further cross-validated with manually reviewed data, conserved domains, or data determined by wet lab experiments. Additionally, biological appropriateness of the functional assignments was manually checked.

Results
In total, 6,286 proteins received GO term assignment via the homology-based annotation, including 2,870 hypothetical proteins. Literature-based experimental evidence, such as microarray, MPSS, T-DNA insertion mutation, or gene knockout mutation, resulted in 2,810 proteins being annotated with GO terms. Of these, 1,673 proteins were annotated with new terms developed for Plant-Associated Microbe Gene Ontology (PAMGO). In addition, 67 experiment-determined secreted proteins were annotated with PAMGO terms. Integration of the two data sets resulted in 7,412 proteins (57%) being annotated with 1,957 distinct and specific GO terms. Unannotated proteins were assigned to the 3 root terms. The Version 5 GO annotation is publically queryable via the GO site http://amigo.geneontology.org/cgi-bin/amigo/go.cgi. Additionally, the genome of M. oryzae is constantly being refined and updated as new information is incorporated. For the latest GO annotation of Version 6 genome, please visit our website http://scotland.fgl.ncsu.edu/smeng/GoAnnotationMagnaporthegrisea.html. The preliminary GO annotation of Version 6 genome is placed at a local MySql database that is publically queryable via a user-friendly interface Adhoc Query System.

Conclusion
Our analysis provides comprehensive and robust GO annotations of the M. oryzae genome assemblies that will be solid foundations for further functional interrogation of M. oryzae.
Expression of Bmi-1 is a prognostic marker in bladder cancer
Authors: Qin Zi-Ke , Yang Jian-An , Ye Yun-lin , Zhang Xing , Xu Li-Hua , Zhou Fang-Jian , Han Hui , Liu Zuo-Wei , Song Li-Bing , Zeng Mu-Sheng 
Published: February 2009

Abstract

Background
The molecular mechanisms of the development and progression of bladder cancer are poorly understood. The objective of this study was to analyze the expression of Bmi-1 protein and its clinical significance in human bladder cancer.

Methods
We examined the expression of Bmi-1 mRNA and Bmi-1 protein by RT-PCR and Western blot, respectively in 14 paired bladder cancers and the adjacent normal tissues. The expression of Bmi-1 protein in 137 specimens of bladder cancer and 30 specimens of adjacent normal bladder tissue was determined by immunohistochemistry. Statistical analyses were applied to test the relationship between expression of Bmi-1, and clinicopathologic features and prognosis.

Results
Expression of Bmi-1 mRNA and protein was higher in bladder cancers than in the adjacent normal tissues in 14 paired samples (P < 0.01). By immunohistochemical examination, five of 30 adjacent normal bladder specimens (16.7%) versus 75 of 137 bladder cancers (54.3%) showed Bmi-1 protein expression (P < 0.05). Bmi-1 protein expression was intense in 20.6%, 54.3%, and 78.8% of tumors of histopathological stages G1, G2, and G3, respectively (P < 0.05). Expression of Bmi-1 protein was greater in invasive bladder cancers than in superficial bladder cancers (81.5% versus 32.5%, P < 0.05). In invasive bladder cancers, the expression of Bmi-1 protein in progression-free cancers was similar to that of cancers that have progressed (80.0% versus 82.4%, P > 0.5). In superficial bladder cancers, the expression of Bmi-1 protein in recurrent cases was higher than in recurrence-free cases (62.5% versus 13.7%, P < 0.05). Bmi-1 expression was positively correlated with tumor classification and TNM stage (P < 0.05), but not with tumor number (P > 0.05). Five-year survival in the group with higher Bmi-1 expression was 50.8%, while it was 78.5% in the group with lower Bmi-1 expression (P < 0.05). Patients with higher Bmi-1 expression had shorter survival time, whereas patients with lower Bmi-1 expression had longer survival time (P < 0.05).

Conclusion
Expression of Bmi-1 was greater in bladder cancers than in the adjacent normal tissues. The examination of Bmi-1 protein expression is potentially valuable in prognostic evaluation of bladder cancer.
Influence of HFE variants and cellular iron on monocyte chemoattractant protein-1
Authors: Mitchell Ryan M , Lee Sang Y , Randazzo William T , Simmons Zachary , Connor James R 
Published: February 2009

AbstractBackgroundPolymorphisms in theMHC class 1-likegene known asHFEhave been proposed as genetic modifiers of neurodegenerative diseases that include neuroinflammation as part of the disease process. Variants ofHFEare relatively common in the general population and are most commonly associated with iron overload, but can promote subclinical cellular iron loading even in the absence of clinically identified disease. The effects of the variants as well as the resulting cellular iron dyshomeostasis potentially impact a number of disease-associated pathways. We tested the hypothesis that the two most common HFE variants, H63D and C282Y, would affect cellular secretion of cytokines and trophic factors.MethodsWe screened a panel of cytokines and trophic factors using a multiplexed immunoassay in human neuroblastoma SH-SY5Y cells expressing different variants of HFE. The influence of cellular iron secretion on the potent chemokine monocyte chemoattractant protein-1 (MCP-1) was assessed using ferric ammonium citrate and the iron chelator, desferroxamine. Additionally, an antioxidant, Trolox, and an anti-inflammatory, minocycline, were tested for their effects on MCP-1 secretion in the presence of HFE variants.ResultsExpression of the HFE variants altered the labile iron pool in SH-SY5Y cells. Of the panel of cytokines and trophic factors analyzed, only the release of MCP-1 was affected by the HFE variants. We further examined the relationship between iron and MCP-1 and found MCP-1 secretion tightly associated with intracellular iron status. A potential direct effect of HFE is considered because, despite having similar levels of intracellular iron, the association between HFE genotype and MCP-1 expression was different for the H63D and C282Y HFE variants. Moreover, HFE genotype was a factor in the effect of minocycline, a multifaceted antibiotic used in treating a number of neurologic conditions associated with inflammation, on MCP-1 secretion.ConclusionOur results demonstrate that HFE polymorphisms influence the synthesis and release of MCP-1. The mechanism of action involves cellular iron status but it appears there could be additional influences such as ER stress. Finally, these data demonstrate a pharmacogenetic effect of HFE polymorphisms on the ability of minocycline to inhibit MCP-1 secretion.