bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic Characterization of Mycobacteriophage Giles: Evidence for Phage Acquisition of Host DNA by Illegitimate Recombination
Authors: Morris Peter , Marinelli Laura J. , Jacobs-Sera Deborah , Hendrix Roger W. , Hatfull Graham F. 
Published: January 2008

ABSTRACTA characteristic feature of bacteriophage genomes is that they are architecturally mosaic, with each individual genome representing a unique assemblage of individual exchangeable modules. Plausible mechanisms for generating mosaicism include homologous recombination at shared boundary sequences of module junctions, illegitimate recombination in a non-sequence-directed process, and site-specific recombination. Analysis of the novel mycobacteriophage Giles genome not only extends our current perspective on bacteriophage genetic diversity, with more than 60% of the genes unrelated to other mycobacteriophages, but offers novel insights into how mosaic genomes are created. In one example, the integration/excision cassette is atypically situated within the structural gene operon and could have moved there either by illegitimate recombination or more plausibly via integrase-mediated site-specific recombination. In a second example, a DNA segment has been recently acquired from the host bacterial chromosome by illegitimate recombination, providing further evidence that phage genomic mosaicism is generated by nontargeted recombination processes.
Identification of Amino Acid Residues within the N-Terminal Domain of EspA That Play a Role in EspA Filament Biogenesis and Function
Authors: Singh Mona P. , Shaw Robert K. , Knutton Stuart , Pallen Mark J. , Crepin Valerie F. , Frankel Gad 
Published: January 2008

ABSTRACT

Enteropathogenic
Escherichia coli
employs a filamentous type III secretion system, made by homopolymerization of the translocator protein EspA. In this study, we have shown that the N-terminal region of EspA has a role in EspA's protein stability, interaction with the CesAB chaperone, and filament biogenesis and function.
CmeR Functions as a Pleiotropic Regulator and Is Required for Optimal Colonization of
Campylobacter jejuni
In Vivo
Authors: Guo Baoqing , Wang Ying , Shi Feng , Barton Yi-Wen , Plummer Paul , Reynolds Donald L. , Nettleton Dan , Grinnage-Pulley Tara , Lin Jun , Zhang Qijing 
Published: January 2008

ABSTRACT

CmeR functions as a transcriptional repressor modulating the expression of the multidrug efflux pump CmeABC in
Campylobacter jejuni
. To determine if CmeR also regulates other genes in
C. jejuni
, we compared the transcriptome of the
cmeR
mutant with that of the wild-type strain using a DNA microarray. This comparison identified 28 genes that showed a ≥2-fold change in expression in the
cmeR
mutant. Independent real-time quantitative reverse transcription-PCR experiments confirmed 27 of the 28 differentially expressed genes. The CmeR-regulated genes encode membrane transporters, proteins involved in C
4
-dicarboxylate transport and utilization, enzymes for biosynthesis of capsular polysaccharide, and hypothetical proteins with unknown functions. Among the genes whose expression was upregulated in the
cmeR
mutant, Cj0561c (encoding a putative periplasmic protein) showed the greatest increase in expression. Subsequent experiments demonstrated that this gene is strongly repressed by CmeR. The presence of the known CmeR-binding site, an inverted repeat of TGTAAT, in the promoter region of Cj0561c suggests that CmeR directly inhibits the transcription of Cj0561c. Similar to expression of
cmeABC
, transcription of Cj0561c is strongly induced by bile compounds, which are normally present in the intestinal tracts of animals. Inactivation of Cj0561c did not affect the susceptibility of
C. jejuni
to antimicrobial compounds in vitro but reduced the fitness of
C. jejuni
in chickens. Loss-of-function mutation of
cmeR
severely reduced the ability of
C. jejuni
to colonize chickens. Together, these findings indicate that CmeR governs the expression of multiple genes with diverse functions and is required for
Campylobacter
adaptation in the chicken host.
SarA ofStaphylococcus aureusBinds to thesarAPromoter To Regulate Gene Expression
Authors: Cheung Ambrose L. , Nishina Koren , Manna Adhar C. 
Published: January 2008

ABSTRACTThe 375-bpsarAopen reading frame is driven by three promoters, P1, P3, and P2. Using gel shift and DNase I footprinting assays, we found that SarA binds to two 26-bp sequences and one 31-bp sequence within the P1 and P3 promoters, respectively. Together with the results of transcription analyses, our data indicate that SarA binds to its own promoter to down-regulatesarAexpression.
C-reactive protein in schoolchildren and its relation to adiposity, physical activity, aerobic fitness and habitual diet
Authors: Thomas N-E , Baker J S , Graham M R , Cooper S-M , Davies B 
Published: January 2008

Objective:To investigate the relation between C-reactive protein (CRP), adiposity, physical activity, aerobic fitness and habitual diet in a cohort of schoolchildren.Methods:A cross-sectional study of 164 schoolchildren aged 12–13 years was conducted in two schools. Adiposity was estimated using body mass index and waist circumference. Blood samples were taken after an overnight fast and measured for CRP. Aerobic fitness and habitual physical activity were assessed using the 20 metres multistage fitness test, and a seven-day recall, respectively. A seven-day food diary provided measures of dietary intake.Results:To improve the distribution of this variable, CRP levels were logarithmically transformed in all analyses. There was no significant difference in mean CRP concentration between boys (1.07 (1.33) mg/l) and girls (1.24 (1.87) mg/l) (p⩾0.05). Compared to girls, boys reported significantly higher (i) aerobic fitness 59.2 (20.3) shuttles vs 42.9 (15.3) shuttles, (ii) vigorous activity levels per week 92 (123) minutes vs 11.2 (34.6) minutes and (iii) waist circumference 69.8 (1.1) cm vs 65.2 (0.9) cm (p⩽0.05). Among boys and girls, adiposity was significantly associated with log transformed CRP (p⩽0.05). CRP was not significantly related to any other variable.Conclusion:Elevated CRP was evident in this cohort; however, whether high CRP levels during childhood and adolescence leads to an increased risk of CVD in later life has not been determined. Adiposity was related to CRP concentration, suggesting that reducing adiposity may be effective in lowering CRP and preventing future cardiovascular events.
Sharing Meals with Non-Christians in Canon Law Commentaries, Circa 1160-1260: A Case Study in Legal Development
Authors: Freidenreich David 
Published: January 2008

AbstractCanon law scholarship flourished in the twelfth and thirteenth centuries, and its practitioners left a remarkable paper trail. Surviving documents capture the intellectual evolution that occurred during this formative period and offer historians a rare opportunity to trace legal development in premodern times. This article examines the evolution of laws regulating the sharing of meals with non-Christians, with particular attention to the ways in which medieval canonists conceptualized foreigners. These canonists struggle to fit Islam into traditional legal categories, concluding that Muslims are "judaizing pagans" on account of their dietary practices. This outcome, and its implications for the way canonists understood not only commensality with Muslims but also with Jews and pagans, reflects the degree to which medieval scholars of canon law were both unfamiliar with other religious traditions and uninterested in acquiring such knowledge. The ideas of these scholars about non-Christians reflect their detatchment from realia and their commitment, as participants in the canon law tradition, to the conservation of existing paradigms, laws, and interpretations. This case study thus sheds light both on medieval Christian conceptions of foreigners and on the ways in which great works of premodern law developed.
Qoheleth and the Syriac Apocalypse of Baruch
Authors: Henze Matthias 
Published: January 2008

AbstractThe roots of early Jewish apocalypticism are diverse. Within the realm of ancient Israel, one of the main contributory streams is the wisdom tradition. The present essay examines the impact of Israel's sapiential tradition, and specifically of that of the book of Qoheleth, on the Syriac Apocalypse of Baruch, a Jewish apocalypse of the late first century C.E. My thesis is that, while both authors agree in their assessment of the present human condition, they draw dramatically different conclusions. Qoheleth persistently points to the limits and fallibility of this world and advises his readers to enjoy life before they die, whereas the author of 2 Baruch looks to the world to come and, in the meantime, calls on his readers to live their lives in compliance with the Mosaic Torah.
Die Rede des Rabsake vor Jerusalem (2 Kön. xviii / Jes. xxxvi) im Kontext anderer Kapitulationsforderungen
Authors: Höffken Peter 
Published: January 2008

AbstractThe speech of the Rabshakeh in 2 Kings xviii has its counterparts in a number of texts from Egypt, Greece, Assyria, and in Josephus Flavius. These texts allow to interpret the speech of the Rabshakeh in some distance to the military needs and questions, which such speeches usually try to answer or to solve. The Josephan version of the speech of the Rabshakeh testifies to this military-oriented form of speech.
The Restrictive Syntax of Genesis i 1
Authors: Holmstedt Robert 
Published: January 2008

AbstractAlthough many Hebraists have departed from the traditional understanding of in Gen i 1 as an independent phrase with grammatical reference to "THE beginning," it is a view that continues to thrive, and is reflected by the majority of modern translations. Even advocates of the dependent phrase position (e.g., "when God began") struggle with a precise and compelling linguistic analysis. In this article I offer a linguistic argument that will both provide a simpler analysis of the grammar of Gen i 1 and make it clear that the traditional understanding of a reference to an 'absolute beginning' cannot be derived from the grammar of the verse. Instead, the syntax of the verse, based on well-attested features within biblical Hebrew grammar, dictates that there were potentially multiple periods or stages to God's creative work.
Aux commencements des livres grecs d'Esther: Le songe de Mardochée
Authors: Vialle Catherine 
Published: January 2008

AbstractThough mainly known in its Hebrew version, the book of Esther have also come to us in three Greek textual forms, the three of them significantly diverging from each other as well as from the MT. As biblical scholars know, they open with a chapter commonly referred to as "Addition A". I intend in this essay to compare this addition and especially the three following topics: the space and time structure, the narrative of the dream, and the characterization of Mordecai. In all three Greek versions, the very presence of the dream (its meaning however remains rather obscure) installs the reader in the same position as Mordecai: he has to wait to see what happens next in order to perceive some elements of interpretation and fulfilment.
Impact of Globalization on Core Engineering Education in India
Authors: Arun-Kumar Duru 
Published: January 2008

AbstractThe education system in India continued to be based on the colonial legacy of bureaucratic administration even after fifty years of independence. But, under globalization and liberalization policies of the government, engineering higher education has acquired a new interpretation of increasing credential value, where the degree per se is more important for securing a high-paying job, primarily in the software and information technology sector, than for acquiring specific knowledge and skills. This is reflected in the employment pattern of the graduates with a core engineering background.
University Policies for the Knowledge Society: Global Standardization, Local Reinvention
Authors: Beerkens Eric 
Published: January 2008

AbstractAlthough the ideas of the knowledge society and knowledge-based economy originate from the 1960s and 1970s, they became popular as a policy idea especially at the end of the twentieth century. Developed and less developed countries alike portray the path towards the knowledge society as the way forward, bringing economic prosperity and social advancement. In adapting to this move towards knowledge societies, universities apply specific organizational forms that have gradually evolved into global models. This spread of globalized models shows an inherent tendency towards processes of convergence, isomorphism, or homogenization. On the surface, a convergence of higher education and science policies seems to have occurred in the past decade or so. A closer look at organizational practices, however, might reveal more local variation in the adoption of these global university models for the knowledge society.
A Simple Predictive Tool for Lower Brahmaputra River Basin Monsoon Flooding
Authors: Kamal-Heikman Shithi , Derry Louis A. , Stedinger Jery R. , Duncan Christopher C. 
Published: January 2008

AbstractThe Brahmaputra River of South Asia is the fourth largest river in the world in terms of annual discharge. The lower Brahmaputra River basin is susceptible to catastrophic flooding with major social, economic, and public health impacts. There is relatively little rainfall and snowpack information for the watershed, and the system is poorly understood hydrologically. Using a combination of available remotely sensed and gauge data, this study analyzes snow cover, rainfall, and monsoon period discharge for a 14-yr time period (1986–99). It is found that interannual rainfall variability is low and is a weak predictor of monsoon discharge volumes. Strong evidence is found, however, that maximum spring snow cover in the upper Brahmaputra basin is a good predictor of the monsoon flood volume. Despite the temporal and spatial limitations of the data, this study’s analysis demonstrates the potential for developing an empirical tool for predicting large flood events that may allow an annual early window for mitigating flood damages in the lower Brahmaputra basin, home to 300 million people.
Distinct roles of sphingosine kinases 1 and 2 in human mast-cell functions
Authors: Oskeritzian Carole A. , Alvarez Sergio E. , Hait Nitai C. , Price Megan M. , Milstien Sheldon , Spiegel Sarah 
Published: January 2008

AbstractSphingosine-1-phosphate (S1P) is now emerging as a potent lipid mediator produced by mast cells that contributes to inflammatory and allergic responses. In contrast to its weak effect on degranulation of murine mast cells, S1P potently induced degranulation of the human LAD2 mast-cell line and cord blood–derived human mast cells (hMCs). S1P also stimulated production and secretion of cytokines, TNF-α and IL-6, and markedly enhanced secretion of a chemokine, CCL2/MCP-1, important modulators of inflammation. S1P is produced in mast cells by the 2 sphingosine kinases, SphK1 and SphK2. SphK1 but not SphK2 plays a critical role in IgE/Ag-induced degranulation, migration toward antigen, and CCL2 secretion from hMCs, as determined by specifically down-regulating their expression. However, both isoenzymes were required for efficient TNF-α secretion. Taken together, our data suggest that differential formation of S1P by SphK1 and SphK2 has distinct and important actions in hMCs.
Targeting dendritic cell signaling to regulate the response to immunization
Authors: Escors David , Lopes Luciene , Lin Rongtuan , Hiscott John , Akira Shizuo , Davis Roger J. , Collins Mary K. 
Published: January 2008

AbstractDendritic cells (DCs) are key regulators of the immune system; they capture antigens and then can either stimulate an immune response or induce tolerance. Our aim was to activate individual DC signaling pathways to regulate the immune response. We therefore expressed constitutive activators of mitogen-activated protein kinase (MAPK) pathways or the interferon pathway, together with tumor antigens, using lentivectors. Triggering of p38 activated DCs substantially enhanced the antitumor immune response and prolonged survival of tumor-bearing mice. Activation of extracellular signal–regulated kinase (ERK) increased TGF-β expression while expression of a constitutively activated interferon regulatory factor-3 (IRF3) stimulated IL-10 secretion by DCs. ERK and IRF3 suppressed the immune response and stimulated expansion of regulatory T cells. These results provide a toolkit to regulate immune responses to viral vector or DC immunization; vaccine responses to foreign or tumor antigens can be enhanced and harmful responses to self-antigens or introduced transgenes can be reduced.
EndoS from Streptococcus pyogenes is hydrolyzed by the cysteine proteinase SpeB and requires glutamic acid 235 and tryptophans for IgG glycan-hydrolyzing activity
Authors: Allhorn Maria , Olsén Arne , Collin Mattias 
Published: January 2008

AbstractBackgroundThe endoglycosidase EndoS and the cysteine proteinase SpeB from the human pathogenStreptococcus pyogenesare functionally related in that they both hydrolyze IgG leading to impairment of opsonizing antibodies and thus enhance bacterial survival in human blood. In this study, we further investigated the relationship between EndoS and SpeB by examining theirin vitrotemporal production and stability and activity of EndoS. Furthermore, theoretical structure modeling of EndoS combined with site-directed mutagenesis and chemical blocking of amino acids was used to identify amino acids required for the IgG glycan-hydrolyzing activity of EndoS.ResultsWe could show that during growthin vitro S. pyogenessecretes the IgG glycan-hydrolyzing endoglycosidase EndoS prior to the cysteine proteinase SpeB. Upon maturation SpeB hydrolyzes EndoS that then loses its IgG glycan-hydrolyzing activity. Sequence analysis and structural homology modeling of EndoS provided a basis for further analysis of the prerequisites for IgG glycan-hydrolysis. Site-directed mutagenesis and chemical modification of amino acids revealed that glutamic acid 235 is an essential catalytic residue, and that tryptophan residues, but not the abundant lysine or the single cysteine residues, are important for EndoS activity.ConclusionWe present novel information about the amino acid requirements for IgG glycan-hydrolyzing activity of the immunomodulating enzyme EndoS. Furthermore, we show that the cysteine proteinase SpeB processes/degrades EndoS and thus emphasize the importance of the SpeB as a degrading/processing enzyme of proteins from the bacterium itself.
PlantDB – a versatile database for managing plant research
Authors: Exner Vivien , Hirsch-Hoffmann Matthias , Gruissem Wilhelm , Hennig Lars 
Published: January 2008

Abstract

Background
Research in plant science laboratories often involves usage of many different species, cultivars, ecotypes, mutants, alleles or transgenic lines. This creates a great challenge to keep track of the identity of experimental plants and stored samples or seeds.

Results
Here, we describe PlantDB – a Microsoft® Office Access database – with a user-friendly front-end for managing information relevant for experimental plants. PlantDB can hold information about plants of different species, cultivars or genetic composition. Introduction of a concise identifier system allows easy generation of pedigree trees. In addition, all information about any experimental plant – from growth conditions and dates over extracted samples such as RNA to files containing images of the plants – can be linked unequivocally.

Conclusion
We have been using PlantDB for several years in our laboratory and found that it greatly facilitates access to relevant information.
Phase I-II Study of Oxaliplatin, Fludarabine, Cytarabine, and Rituximab Combination Therapy in Patients With Richter's Syndrome or Fludarabine-Refractory Chronic Lymphocytic Leukemia
Authors: Tsimberidou Apostolia M. , Wierda William G. , Plunkett William , Kurzrock Razelle , O'Brien Susan , Wen Sijin , Ferrajoli Alessandra , Ravandi-Kashani Farhad , Garcia-Manero Guillermo , Estrov Zeev , Kipps Thomas J. , Brown Jennifer R. , Fiorentino Albert , Lerner Susan , Kantarjian Hagop M. , Keating Michael J. 
Published: January 2008

Purpose Richter's syndrome (RS) and fludarabine-refractory chronic lymphocytic leukemia (CLL) are associated with poor clinical outcomes. We conducted a phase I-II trial of oxaliplatin, fludarabine, cytarabine, and rituximab (OFAR) in these diseases. Patients and Methods The OFAR regimen consisted of increasing doses of oxaliplatin (17.5, 20, or 25 mg/m2/d) on days 1 to 4 (phase I), fludarabine 30 mg/m2 on days 2 to 3, cytarabine 1 g/m2 on days 2 to 3, rituximab 375 mg/m2 on day 3 of cycle 1 and day 1 of subsequent cycles, and pegfilgrastim 6 mg on day 6, every 4 weeks for a maximum of six courses. Dose-limiting toxicity (DLT) was defined as any nonhematologic, treatment-related toxicity ≥ grade 3. Results Fifty patients were treated (20 patients had RS, and 30 had CLL). The highest tolerated oxaliplatin dose was 25 mg/m2, which was the highest dose tested. DLT was not observed. Pharmacodynamic analyses demonstrated enhanced leukemia cell killing by oxaliplatin in the presence of fludarabine and cytarabine. The overall response rates were 50% in RS and 33% in fludarabine-refractory CLL. The overall response rate in 14 patients with age ≥ 70 years was 50%. Responses were achieved in seven (35%) of 20 patients with 17p deletion, two (29%) of seven patients with 11q deletion, all four patients with trisomy 12, and two (40%) of five patients with 13q deletion. The median response duration was 10 months. Toxicities were mainly hematologic; prolonged myelosuppression was not observed. Conclusion The OFAR regimen is highly active in RS and has activity in fludarabine-refractory patients with CLL. This regimen warrants further investigation in the treatment of these disorders.
Receiving the Diagnosis of Lung Cancer: Patient Recall of Information and Satisfaction With Physician Communication
Authors: Gabrijel Sabine , Grize Leticia , Helfenstein Erich , Brutsche Martin , Grossman Paul , Tamm Michael , Kiss Alexander 
Published: January 2008

Purpose Little is known about the information newly diagnosed patients with lung cancer recall and how satisfied they are with physicians' communication. Patients and Methods Seventy-one consecutive patients with newly diagnosed lung cancer were surveyed 1 to 3 days after the disclosure of diagnosis. Patients' recall of the given information was assessed, as well as their satisfaction with physicians' communication of diagnosis, treatment procedure, and goal of treatment as curative or palliative. Physicians who provided diagnosis were asked to complete a questionnaire concerning what information they had given to the patient. Congruence between physician information and patient recall of that information was then evaluated. Results Ninety percent (62 of 69 patients) correctly recalled their physician's information about the diagnosis, 83% (55 of 66 patients) knew what treatment procedure their physicians proposed, and 49% (32 of 65 patients) accurately recalled information about the goal of treatment. Seventy-six and 73% of patients were highly satisfied with their physician's communication of diagnosis and treatment procedure, respectively. Only 39% were highly satisfied with communication of the treatment goal. Patients who correctly recalled information regarding the treatment procedure were significantly more satisfied with its communication. Conclusion Recall of information about the intent of treatment is poor, and satisfaction with communication of the intent of treatment is lacking among newly diagnosed patients with lung cancer. Future studies should address whether specific interventions can improve these deficiencies.