bluuebunny/crossref_metadata_2025_split huggingface dataset:
Between Myth and Reality: Approaches to Ibn Khaldun in the Arab World
Authors: Tomar Cengiz 
Published: September 2008

AbstractIbn Khaldun is one of most discussed social philosophers in the modern Arab World. The most important reasons for this are that he lived in a time of crisis that resembles the one that Muslims find themselves in at the present time, that his thoughts have found approval from Western scientists, and that they possess modern characteristics. It is for these reasons that the thought of Ibn Khaldun, from the 19th century onwards, have given rise to a wide variety of interpretations, including pan-Islamism, nationalism, socialism and other ideologies that have found interest in the Arab world. In this article, after examining the heritage of thought bequeathed by Ibn Khaldun to Arab culture, starting from the time in which he lived, we will try to evaluate interpretations of the Muqaddimah in the modern Arab world.
Escaping the Reformation in the Republic of Letters: Confessional Silence in Latin Emblem Books
Authors: Visser Arnoud 
Published: September 2008

AbstractRecent scholarship has advanced paradoxical conclusions about the relationship between Renaissance humanism and the Reformation. While humanist techniques are considered to have played an instrumental role in the development, spread, and implementation of the Reformation, the humanist community is generally regarded as a supra-confessional “Republic of Letters.” This article addresses this paradox by looking at the religious language in Latin emblem books. These highly popular works emphasized a personal, intellectual spirituality, and expressed reservations against institutionalised religion. They have often been interpreted ideologically, as a humanistic, irenical response to the religious turmoil. When read in the context of the authors' and readers' practical interests, however, they reveal a more pragmatic strategy. Rather than promoting religious ideals, they used an a-confessional language to accommodate religious pluriformity. Examples of the reception by individual readers, e.g., in alba amicorum, further exemplify how confessional silence served as a communicative strategy in the Republic of Letters.
Johann Heinrich Hottinger (1620–1667) and the “Historia Orientalis”
Authors: Loop Jan 
Published: September 2008

AbstractGenerally neglected by scholars of the history of oriental studies, Johann Heinrich Hottinger's Historia Orientalis (1651, 2nd ed. 1660) is one of the most significant contributions to the history of Islam to have been published in the seventeenth century. This article analyses Hottinger's interest in Islam and in Arabic sources across the range of his writings and his correspondence, with a special focus on the Historia Orientalis. It discusses the philological and antiquarian standards by which he assessed Arab history and it describes the numerous Islamic manuscripts he exploited. It also examines the manifold ways in which Hottinger used the Koran and other Islamic sources to corroborate his apologetic Protestant interpretation of Church history. It thus sheds a light on the impact that a combination of confessional commitment, antiquarianism, and philology had on the rise of oriental studies in seventeenth-century Europe.
Johann Nikolaus von Hontheim's Febronius: A Censored Bishop and His Ecclesiology
Authors: Lehner Ulrich 
Published: September 2008

AbstractIn the second half of the eighteenth century, the greatest enemy of the Roman Curia was no longer French Gallicanism but German Febronianism, since it challenged papal primacy. It gained its name from the pseudonymous author of the book, De statu Ecclesiae (1763). The author, auxiliary Bishop Johann Nikolaus von Hontheim, was immediately censored and later forced to sign a retraction. This essay will provide the first English synthesis and overview of the publishing history of this important work and its ecclesiology, as well as show how the Curia dealt with this dissident theologian.
Neo-Calvinist Culture Protestantism: Abraham Kuyper's Stone Lectures
Authors: Molendijk Arie 
Published: September 2008

AbstractThe article addresses Kuyper's re-interpretation of Calvinism, which allegedly combined the richness of its tradition with an endorsement of modern principles and ways of life (except for gambling, theater going, and some other minor activities). Yet the acceptance of the modern way of life did not mean secularism; on the contrary, according to Kuyper Calvinism in itself was a modern principle, which could – against the prevailing powers of a secularizing modernity – penetrate society as a whole.
State Leadership for School Improvement: An Analysis of Three States
Authors: Seashore Louis Karen , Thomas Emanda , Gordon Molly F. , Febey Karen S. 
Published: September 2008

Purpose: Extant reports on states'policy differences are mostly descriptive and largely ignore the pervasive role of political culture on their educational policy-making processes. This article examines the effect of policy culture on states' policy-making mechanisms. There is evidence that a state's political culture is a significant mediating influence on its educational policy making and leadership practices at the state, district, and local level.Data Collection and Analysis: We conducted an empirical, comparative case study of educational leadership and policy-making mechanisms in three states—Indiana, Nebraska, and Oregon. Those three states, chosen because of their similarities in size but differences in educational policy histories, were part of a larger leadership study of nine states. Within each state, researchers interviewed between 8 and 11 educational policymakers who represented a diverse array of positions and organizations. The interviews were 1 hr in length, conducted in a semistructured format, and revolved around their states' accountability and school leadership policies, key educational stakeholders, and levels of collaboration among those stakeholders.Findings: Each state in the study had very different means through which they pursued educational policies. Indiana had centralized decision-making structures that sought to promote leadership and accountability through policies that revolved around equity and efficiency. Oregon had a high level of participation and collaboration at all levels in the state's mostly decentralized but very open educational policy-making process that emphasized quality. Nebraska's policy culture, which was more independent and decentralized than Oregon's, was highly collaborative but had comparatively low levels of support for state-supported leadership and accountability initiatives. Conclusions: Our findings suggest that political culture is a mediating factor for states' responses to increasing demands for leadership and accountability initiatives; it is therefore necessary to account for the impact of each state's unique political culture when planning for and explaining results of these initiatives.
Characterization and quantification of clonal heterogeneity among hematopoietic stem cells: a model-based approach
Authors: Roeder Ingo , Horn Katrin , Sieburg Hans-Bernd , Cho Rebecca , Muller-Sieburg Christa , Loeffler Markus 
Published: September 2008

AbstractHematopoietic stem cells (HSCs) show pronounced heterogeneity in self-renewal and differentiation behavior, which is reflected in their repopulation kinetics. Here, a single-cell–based mathematical model of HSC organization is used to examine the basis of HSC heterogeneity. Our modeling results, which are based on the analysis of limiting dilution competitive repopulation experiments in mice, demonstrate that small quantitative but clonally fixed differences of cellular properties are necessary and sufficient to account for the observed functional heterogeneity. The model predicts, and experimental data validate, that competitive pressures will amplify small clonal differences into large changes in the number of differentiated progeny. We further predict that the repertoire of HSC clones will evolve over time. Last, our results suggest that larger differences in cellular properties have to be assumed to account for genetically determined differences in HSC behavior as observed in different inbred mice strains. The model provides comprehensive systemic and quantitative insights into the clonal heterogeneity among HSCs with potential applications in predicting the behavior of malignant and/or genetically modified cells.
Vaccination with autologous tumor-loaded dendritic cells induces clinical and immunologic responses in indolent B-cell lymphoma patients with relapsed and measurable disease: a pilot study
Authors: Di Nicola Massimo , Zappasodi Roberta , Carlo-Stella Carmelo , Mortarini Roberta , Pupa Serenella M. , Magni Michele , Devizzi Liliana , Matteucci Paola , Baldassari Paola , Ravagnani Fernando , Cabras Antonello , Anichini Andrea , Gianni Alessandro M. 
Published: September 2008

AbstractEighteen relapsed patients with measurable indolent non-Hodgkin lymphoma (NHL) were vaccinated with dendritic cells (DCs) loaded with killed autologous tumor cells. Six patients had objective clinical responses including 3 continuous complete responses (CRs) and 3 partial responses (PRs), with a median follow up of 50.5 months. Eight patients had stable disease, whereas 4 had progressive disease. Clinical responses were significantly associated with a reduction in CD4+CD25+FOXP3+ regulatory T cells, an increase in CD3−CD56dimCD16+ natural killer (NK) cells, and maturation of lymphocytes to the effector memory stage in either postvaccination peripheral blood or tumor specimen samples. In partial responding patients, vaccination significantly boosted the IFN-γ–producing T-cell response to autologous tumor challenge. In one HLA-A*0201+ patient who achieved CR, IL-4 release by circulating T cells in response to tumor-specific IgH-encoded peptides was also documented. Immunohistochemical analysis of tumor biopsies using biotin-conjugated autologous serum samples revealed a tumor-restricted humoral response only in the postvaccination serum from responding patients. Collectively these results demonstrate that vaccination with tumor-loaded DCs may induce both T- and B-cell responses and produces clinical benefits in indolent NHL patients with measurable disease. This study is registered with the Istituto Superiore di Sanità: http://www.iss.it with protocol number 7578-PRE 21-801.
Localization of the Carnation Italian ringspot virus replication protein p36 to the mitochondrial outer membrane is mediated by an internal targeting signal and the TOM complex
Authors: Hwang Yeen Ting , McCartney Andrew W , Gidda Satinder K , Mullen Robert T 
Published: September 2008

Abstract

Background

Carnation Italian ringspot virus (CIRV) is a positive-strand RNA virus that causes massive structural alterations of mitochondria in infected host cells, the most conspicuous being the formation of numerous internal vesicles/spherules that are derived from the mitochondrial outer membrane and serve as the sites for viral RNA replication. While the membrane-bound components of the CIRV replication complex, including a 36-kD RNA-binding protein (p36), are known to be essential for these changes in mitochondrial morphology and are relatively well characterized in terms of their roles in nascent viral RNA synthesis, how these proteins are specifically targeted and inserted into mitochondria is poorly defined.

Results
Here we report on the molecular signal responsible for sorting p36 to the mitochondrial outer membrane. Using a combination of gain-of-function assays with portions of p36 fused to reporter proteins and domain-swapping assays with p36 and another closely-related viral RNA-binding protein, p33, that sorts specifically to the peroxisomal boundary membrane, we show that the mitochondrial targeting information in p36 resides within its two transmembrane domains (TMDs) and intervening hydrophilic loop sequence. Comprehensive mutational analysis of these regions in p36 revealed that the primary targeting determinants are the moderate hydrophobicity of both TMDs and the positively-charged face of an amphipathic helix within the intervening loop sequence. We show also using bimolecular fluorescence complementation (BiFC) that p36 interacts with certain components of the translocase complex in the mitochondrial outer membrane (TOM), but not with the sorting and assembly machinery (SAM).

Conclusion
Our results provide insight to how viruses, such as CIRV, exploit specific host-cell protein sorting pathways to facilitate their replication. The characterization of the targeting and insertion of p36 into the mitochondrial outer membrane also sheds light on the mechanisms involved in sorting of host-cell membrane proteins to mitochondria, a process that has been largely unexplored in plants.
The rules of gene expression in plants: Organ identity and gene body methylation are key factors for regulation of gene expression in Arabidopsis thaliana
Authors: Aceituno Felipe F , Moseyko Nick , Rhee Seung Y , Gutiérrez Rodrigo A 
Published: September 2008

AbstractBackgroundMicroarray technology is a widely used approach for monitoring genome-wide gene expression. For Arabidopsis, there are over 1,800 microarray hybridizations representing many different experimental conditions on Affymetrix™ ATH1 gene chips alone. This huge amount of data offers a unique opportunity to infer the principles that govern the regulation of gene expression in plants.ResultsWe used bioinformatics methods to analyze publicly available data obtained using the ATH1 chip from Affymetrix. A total of 1887 ATH1 hybridizations were normalized and filtered to eliminate low-quality hybridizations. We classified and compared control and treatment hybridizations and determined differential gene expression. The largest differences in gene expression were observed when comparing samples obtained from different organs. On average, ten-fold more genes were differentially expressed between organs as compared to any other experimental variable. We defined "gene responsiveness" as the number of comparisons in which a gene changed its expression significantly. We defined genes with the highest and lowest responsiveness levels as hypervariable and housekeeping genes, respectively. Remarkably, housekeeping genes were best distinguished from hypervariable genes by differences in methylation status in their transcribed regions. Moreover, methylation in the transcribed region was inversely correlated (R2= 0.8) with gene responsiveness on a genome-wide scale. We provide an example of this negative relationship using genes encoding TCA cycle enzymes, by contrasting their regulatory responsiveness to nitrate and methylation status in their transcribed regions.ConclusionOur results indicate that the Arabidopsis transcriptome is largely established during development and is comparatively stable when faced with external perturbations. We suggest a novel functional role for DNA methylation in the transcribed region as a key determinant capable of restraining the capacity of a gene to respond to internal/external cues. Our findings suggest a prominent role for epigenetic mechanisms in the regulation of gene expression in plants.
Passive administration of monoclonal antibodies to Anthrolysin O prolong survival in mice lethally infected with Bacillus anthracis
Authors: Nakouzi Antonio , Rivera Johanna , Rest Richard F , Casadevall Arturo 
Published: September 2008

AbstractBackgroundBacillus anthracishas two major virulence factors: a tripartite toxin that produces lethal and edema toxins and a polyglutamic acid capsule. A recent report suggested that a toxin belonging to the cholesterol dependant cytolysin (CDC) family, anthrolysin O (ALO) was a new virulence factor forB. anthracisbut subsequent studies have questioned its relevance in pathogenesis. In this study, we examined the immunogenicity of recombinant anthrolysin O (rALO) in mice.ResultsBALB/c mice immunized with rALO and boosted after two weeks, produce sera with strong Ab responses with a predominance of IgG1 and IgG2a. Five hybridomas to rALO were recovered representing the IgM, IgG1, and IgG2b isotypes. Passive administration of 3 of the five monoclonal antibodies (mAbs) to rALO prior to infection with lethal intravenous (i.v.)B. anthracisSterne strain infection in mice was associated with enhanced average survival and a greater likelihood of surviving infection. A combination of two mAbs to ALO was more effective than either mAb separately. One mAb (64F8) slowed the toxicity of rALO for J774.16 macrophage-like cells.ConclusionOur results suggest that ALO contributes to the virulence ofB. anthracisSterne strain in this infection model and that Ab response to ALO may contribute to protection in certain circumstances.
MalVac: Database of malarial vaccine candidates
Authors: Chaudhuri Rupanjali , Ahmed Shakil , Ansari Faraz Alam , Singh Harinder Vir , Ramachandran Srinivasan 
Published: September 2008

AbstractBackgroundThe sequencing of genomes of the Plasmodium species causing malaria, offers immense opportunities to aid in the development of new therapeutics and vaccine candidates through Bioinformatics tools and resources.MethodsThe starting point of MalVac database is the collection of known vaccine candidates and a set of predicted vaccine candidates identified from the whole proteome sequences of Plasmodium species provided by PlasmoDb 5.4 release (31st October 2007). These predicted vaccine candidates are the adhesins and adhesin-like proteins from Plasmodium species,Plasmodium falciparum,Plasmodium vivaxandPlasmodium yoelii. Subsequently, these protein sequences were analysed through 20 publicly available algorithms to obtain Orthologs, Paralogs, BetaWraps, TargetP, TMHMM, SignalP, CDDSearch, BLAST with Human Ref. Proteins, T-cell epitopes, B-cell epitopes, Discotopes, and allergen predictions. All of this information was collected and organized with the ORFids of the protein sequences as primary keys. This information is relevant from the view point of Reverse Vaccinology in facilitating decision making on the most probable choice for vaccine strategy.ResultsDetailed information on the patterning of the epitopes and other motifs of importance from the viewpoint of reverse vaccinology has been obtained on the most probable protein candidates for vaccine investigation from three major malarial species. Analysis data are available on 161 adhesin proteins fromP. falciparum, 137 adhesin proteins fromP. vivaxand 34 adhesin proteins fromP. yoelii. The results are displayed in convenient tabular format and a facility to export the entire data has been provided. The MalVac database is a "community resource". Users are encouraged to export data and further contribute by value addition. Value added data may be sent back to the community either through MalVac or PlasmoDB.ConclusionA web server MalVac for facilitation of the identification of probable vaccine candidates has been developed and can be freely accessed.
Distinction of Plasmodium falciparum recrudescence and re-infection by MSP2 genotyping: A caution about unstandardized classification criteria
Authors: Rouse Petrica , Mkulama Mtawa AP , Thuma Philip E , Mharakurwa Sungano 
Published: September 2008

Abstract

Background

Plasmodium falciparum genotyping with molecular polymorphic markers is widely employed to distinguish recrudescence from re-infection in antimalarial drug efficacy monitoring programmes. However, limitations occur on agarose gel DNA measurements used to resolve the polymorphisms. Without empirical data, the current distinction of pre- and post-treatment bands, as persistent or new infection, is subjective and often varying by author. This study measures empirical tolerance limits for classifying different-sized bands as same or different alleles during MSP2 genotyping.

Methods

P. falciparum field samples from 161 volunteers were genotyped by nested PCR using polymorphic MSP2 family-specific primers. Data were analysed to determine variability of band size measurements between identical MSP2 alleles randomized into different agarose lanes.

Results
The mean (95% CI) paired difference in band size between identical alleles was 9.8 bp (1.48 – 18.16 bp, p = 0.022) for 3D7/IC and 2.54 (-3.04 – 8.05 bp, p = 0.362) for FC27. Based on these findings, pre- and post-treatment samples with 3D7/IC alleles showing less than 18 bp difference corresponded to recrudescence, with 95% confidence, while greater difference indicated new infection. FC27 allele differences were much narrower. For both 3D7/IC and FC27 amplicon, allele detection sensitivity was significantly higher with 13 μl compared to 20 μl or 30 μl lane loading volumes.

Conclusion
During MSP genotyping, it is useful to standardize classifications against measurement of background variability on identical alleles, in order to obtain reliable findings. It is critical to use a fixed optimal lane loading volume for constant allele patency, to avoid the disappearance or false appearance of new infection.
Tissue specific promoters improve specificity of AAV9 mediated transgene expression following intra-vascular gene delivery in neonatal mice
Authors: Pacak Christina A , Sakai Yoshihisa , Thattaliyath Bijoy D , Mah Cathryn S , Byrne Barry J 
Published: September 2008

Abstract
The AAV9 capsid displays a high natural affinity for the heart following a single intravenous (IV) administration in both newborn and adult mice. It also results in substantial albeit relatively lower expression levels in many other tissues. To increase the overall safety of this gene delivery method we sought to identify which one of a group of promoters is able to confer the highest level of cardiac specific expression and concurrently, which is able to provide a broad biodistribution of expression across both cardiac and skeletal muscle. The in vivo behavior of five different promoters was compared: CMV, desmin (Des), alpha-myosin heavy chain (α-MHC), myosin light chain 2 (MLC-2) and cardiac troponin C (cTnC). Following IV administration to newborn mice, LacZ expression was measured by enzyme activity assays. Results showed that rAAV2/9-mediated gene delivery using the α-MHC promoter is effective for focal transgene expression in the heart and the Des promoter is highly suitable for achieving gene expression in cardiac and skeletal muscle following systemic vector administration. Importantly, these promoters provide an added layer of control over transgene activity following systemic gene delivery.
Microbial Diagnostic Array Workstation (MDAW): a web server for diagnostic array data storage, sharing and analysis
Authors: Scaria Joy , Sreedharan Aswathy , Chang Yung-Fu 
Published: September 2008

Abstract

Background
Microarrays are becoming a very popular tool for microbial detection and diagnostics. Although these diagnostic arrays are much simpler when compared to the traditional transcriptome arrays, due to the high throughput nature of the arrays, the data analysis requirements still form a bottle neck for the widespread use of these diagnostic arrays. Hence we developed a new online data sharing and analysis environment customised for diagnostic arrays.

Methods
Microbial Diagnostic Array Workstation (MDAW) is a database driven application designed in MS Access and front end designed in ASP.NET.

Conclusion
MDAW is a new resource that is customised for the data analysis requirements for microbial diagnostic arrays.