bluuebunny/crossref_metadata_2025 huggingface dataset:
New Zealanders’ attitudes towards access to their electronic health records: Preliminary results from a national study using vignettes
Authors: Hunter Inga M. , Whiddett Richard J. , Norris Anthony C. , McDonald Barry W. , Waldon John A.
Published: August 2009

This project investigates public attitudes towards sharing confidential personal health information held in electronic health records (EHRs). The project uses computer assisted telephone interviewing (CATI) to conduct a quantitative national survey of the attitudes of New Zealanders towards access to their personal health information using vignettes. Respondents are presented with vignettes which describe ways in which their health information might be used, and asked about their attitude to and consent for each type of access. The project outcome will be a specification of requirements for an e-consent model meeting the needs of most New Zealanders, thus enabling the potential benefits of electronically sharing confidential health information from EHRs. This article presents preliminary results from the first 1828 respondents. Respondents were most willing to share their information for the purpose of providing care. However, removing their name and address greatly increased the acceptability of sharing information for other purposes.
The politics of names: rethinking the methodological and ethical significance of naming people, organizations, and places
Authors: Guenther Katja M.
Published: August 2009

This article examines how the decision to use real names or pseudonyms for people, organizations, and places involves consideration of the ethics of confidentiality, the power of naming, and strategies for fieldwork and presentation of findings. While these issues are infrequently discussed in published work, qualitative researchers need to attend to how we decide what names to use in presenting our findings. Rather than avoiding discussions of confidentiality, qualitative researchers should address the implications of their decisions regarding the use of pseudonyms or real names for the confidentiality of our respondents, for our relationships with respondents, for our commitments to transformative social science, and for our findings.
Stuck in the middle: research ethics caught between science and politics
Authors: Baarts Charlotte
Published: August 2009

The literature on research ethics tends to overlook the influence of the specific subject matter on the ethical dilemmas that emerge during the research process itself. In this article, the specific subject matter is complementary and alternative medicine (CAM). The article discusses the ethical dilemmas that derive from controversies about research within this highly politicized field, in which scientific knowledge is a potential object of misuse. The article shows that research ethics is no longer a matter of internalizing professional codes of conduct. Rather, it is embedded in the totality of scholarly practice. Ethically aware practice depends to a considerable extent on the qualities and skills of the researcher. The particular skills needed are discernment, imagination, partiality and personal authenticity.
The visual image as discussion point: increasing validity in boundary crossing research
Authors: Liebenberg Linda
Published: August 2009

This article is based on a larger study exploring the use of visual methods as a communication tool in research where the researcher is often a ‘border crosser’ (Giroux, 1992). To illustrate the value of this methodology, particularly in instances where power imbalances are heightened in the research context, a case study was conducted with five teenage mothers from a sub-economic community outside Cape Town, South Africa. This article will explore how use of visual methods contributes to increased validity of data. Specifically, this discussion will consider how the use of images as a communication tool, increase participant control over the research process, and incorporates participant self-representation via a period of self-exploration, improving contextual accuracy and relevance of data.
Explorations of Depression
Authors: Gallardo Heather L. , Furman Rich , Kulkarni Shanti
Published: August 2009

This article explores the uses of poetry in qualitative research. In this study of the first author’s lived experience with non-clinical depression and the second author’s experience of living with someone experiencing depression, poetry and responsive narrative are used as data, as means of data representation, and processes of inquiry. The authors explore the nature of poetry as a tool for investigating human phenomena and its congruence with post-modern methods of research. Autoethnographic poems are used as data and analyzed via narrative written by the original author of the poem on two separate occasions. A third researcher added an additional layer of narrative analysis for increased depth. This self-reflection provides reflexive analysis of our individual understanding of depression via narrative.
Understanding ‘Marginal’ Perspectives
Authors: Bottrell Dorothy
Published: August 2009

This article contributes to a social theory of resilience. It critiques aspects of developmental and individual-level analyses in the resilience literature, arguing for the significance of social identities and collective experience to resilience. Drawing on a study of the experiences of young people from an inner-city public housing estate in Sydney, key themes of the young people’s accounts engage with both classic and constructivist perspectives. Resistance based resilience is claimed to indicate the social constitution of individuals in local relations, suggesting that interventions for resilience building need to recognize the embeddedness of resilience in social inequities, social processes and the differentiated societal and ideological expectations of young people. How resilience is conceptualized is central to resilience building interventions. Here the case is put for the importance of resources to support and strengthen the resilience of marginalized youth.
Collecting Data from Mothers who have Experienced Childhood Family Violence with the use of a Feminist Methodology
Authors: Mendis Kathy
Published: August 2009

Family violence has been found to have a variety of negative impacts on children. Children exposed to violence often fail to develop positive social skills, which may impact on their ability to function as healthy, productive adults. The aim of my Masters research, titled: ‘The Impacts of Childhood Exposure to Family Violence on Subsequent Mothering’ was to investigate the long-term impacts of girls’ exposure to family violence. The interviews involved discussions of intimate and sensitive issues. In this article, I discuss the feminist methodology within which I conducted my research, highlighting the concepts that proved invaluable in collecting rich data of a sensitive nature. By sharing my field experience, I intend to make a small contribution to the research methodology literature as many others have done before me.
Pharmacodynamic Interactions with Exercise and Beta-Blocker Medications
Authors: Lenz Thomas L.
Published: August 2009

It is recommended that all individuals who have high blood pressure should also participate in a regular exercise program to help control their blood pressure and decrease their risk for cardiovascular disease. Most of these individuals will also be on medications, and many will be on a medication from the class of antihypertensives called beta-blockers. Research has shown that a pharmacodynamic drug-exercise interaction exists when beta-blockers and exercise are taken together. Hemodynamic changes occur with this interaction, causing a decrease in exercising heart rate and cardiac output. Clinically, this results in patients feeling fatigued and that their ability to exercise is more difficult, which can result in poor exercise adherence. Health care professionals should routinely talk with their patients who are taking beta-blocker therapy about what to expect when the 2 treatments are taken together. This article provides background information about this drug-exercise interaction and several points of information that health care professionals can discuss with their patients, including how to monitor their exercise intensity without using the exercise heart rate response method.
Efficiency of Hyaloglide® in the prevention of the recurrence of adhesions after tenolysis of flexor tendons in zone II: a randomized, controlled, multicentre clinical trial
Authors: Riccio M. , Battiston B. , Pajardi G. , Corradi M. , Passaretti U. , Atzei A. , Altissimi M. , Vaienti L. , Catalano F. , Del Bene M. , Fasolo P. , Ceruso M. , Luchetti R. , Landi A.
Published: August 2009

Hyaloglide® is a hyaluronan-based gel based on a novel auto-crosslinked technology designed to reduce postsurgical adhesions. Its efficacy was assessed in a multicentred randomized controlled trial comparing the results of flexor tenolysis in zone 2 following failed flexor tendon repairs. In the control group a standard release was performed. In the treated group, Hyaloglide® was applied into the flexor sheath and around the site of tenolysis. Forty-five patients, 19 controls and 26 treated with Hyaloglide®, were enrolled in 13 centres. All the patients were evaluated at 30, 60, 90 and 180 days after surgery by testing Total Active Motion, Quick-DASH questionnaire and number of working days lost after surgery. Patients in the Hyaloglide® group had a statistically better recovery of finger motion at all time intervals and returned earlier to work and daily activities. The use of Hyaloglide® did not appear to increase the complication rate.
Endotoxin tolerance does not limit mild ischemia-reperfusion injury in humans in vivo
Authors: Draisma Annelies , de Goeij Moniek , Wouters Constantijn W. , Riksen Niels P. , Oyen Wim J.G. , Rongen Gerard A. , Boerman Otto C. , van Deuren M. , van der Hoeven Johannes G. , Pickkers Peter
Published: August 2009

Animal studies have shown that previous exposure to lipopolysaccharide (LPS) can limit ischemia-reperfusion injury. We tested whether pretreatment with LPS also protects against ischemia-reperfusion injury in humans in vivo. Fourteen volunteers received bolus injections of incremental dosages of LPS on 5 consecutive days (LPS group). Before the first and 1 day after the last LPS administration, the forearm circulation of the non-dominant arm was occluded for 10 min, with concomitant intermittent handgripping to induce transient ischemia. After reperfusion, 0.1 mg of 99mTc-labeled annexin A5 (400 MBq) was injected intravenously to detect phosphatidylserine expression as an early marker of ischemia-reperfusion injury. Similarly, the control group (n = 10) underwent the ischemic exercise twice, but without pretreatment with LPS. Annexin A5 targeting was expressed as the percentage difference in radioactivity in the thenar muscle between both hands. Endotoxin tolerance developed during 5 consecutive days of LPS administration. Annexin A5 targeting was 12.1 ± 2.2% and 10.4 ± 2.1% before LPS treatment at 1 h and 4 h after reperfusion, compared to 12.2 ± 2.4% and 8.9 ± 2.1% at 1 h and 4 h after reperfusion on day 5 (P = 1.0 and 0.6, respectively). Also, no significant changes in annexin A5 targeting were found in the control group. So, in this model, LPS-tolerance does not protect against ischemia-reperfusion injury in humans in vivo.
Up-regulation of integrin expression in lung adenocarcinoma cells caused by bacterial infection: in vitro study
Authors: Gravelle Sean , Barnes Rebecca , Hawdon Nicole , Shewchuk Lee , Eibl Joseph , Lam Joseph S. , Ulanova Marina
Published: August 2009

Integrins are a large family of adhesion receptors that are known to be key signaling molecules in both physiological and pathological processes. Previous studies have demonstrated that the expression of integrin receptors in the pulmonary epithelium can change under various pathological conditions, such as injury, inflammation, or malignant transformation. We hypothesize that integrin expression can be altered by stimulation of lung epithelial cells with an opportunistic bacterial pathogen Pseudomonas aeruginosa. Using the A549 adenocarcinoma cell line that expressed a low level of several integrin subunits we have demonstrated that P. aeruginosa infection in vitro caused a rapid up-regulation of α5, αv, β1, and β4 integrins at both the mRNA and protein level. Neither heat-killed P. aeruginosa strain PAK nor its live isogenic mutants lacking pili or lipopolysaccharide (LPS) core oligosaccharide showed any effect on integrin expression in A549 cells as compared to the use of the wild-type PAK strain. These results establish that up-regulation of integrin expression is dependent on the internalization of live bacteria possessing intact pili and LPS. Gene silencing of integrin-linked kinase in A549 cells caused a significant decrease in the release of proinflammatory cytokines in response to P. aeruginosa stimulation. Although further studies are warranted towards understanding the precise role of integrin receptors in prominent inflammation caused by P. aeruginosa, our findings suggest a possibility of using specific integrin inhibitors for therapy of pulmonary inflammatory conditions caused by pathogenic micro-organisms.
Review: Lipopolysaccharide biosynthesis in Pseudomonas aeruginosa
Authors: King Jerry D. , Kocíncová Dana , Westman Erin L. , Lam Joseph S.
Published: August 2009

Pseudomonas aeruginosa causes serious nosocomial infections, and an important virulence factor produced by this organism is lipopolysaccharide (LPS). This review summarizes knowledge about biosynthesis of all three structural domains of LPS — lipid A, core oligosaccharide, and O polysaccharides. In addition, based on similarities with other bacterial species, this review proposes new hypothetical pathways for unstudied steps in the biosynthesis of P. aeruginosa LPS. Lipid A biosynthesis is discussed in relation to Escherichia coli and Salmonella, and the biosyntheses of core sugar precursors and core oligosaccharide are summarised. Pseudomonas aeruginosa attaches a Common Polysaccharide Antigen and O-Specific Antigen polysaccharides to lipid A-core. Both forms of O polysaccharide are discussed with respect to their independent synthesis mechanisms. Recent advances in understanding O-polysaccharide biosynthesis since the last major review on this subject, published nearly a decade ago, are highlighted. Since P. aeruginosa O polysaccharides contain unusual sugars, sugar-nucleotide biosynthesis pathways are reviewed in detail. Knowledge derived from detailed studies in the O5, O6 and O11 serotypes is applied to predict biosynthesis pathways of sugars in poorly-studied serotypes, especially O1, O4, and O13/O14. Although further work is required, a full understanding of LPS biosynthesis in P. aeruginosa is almost within reach.
Regulation of Toll-like receptor 4-associated MD-2 in intestinal epithelial cells: a comprehensive analysis
Authors: Vamadevan Arunan S. , Fukata Masayuki , Arnold Elizabeth T. , Thomas Lisa S. , Hsu David , Abreu Maria T.
Published: August 2009

The intestinal epithelium maintains a state of controlled inflammation despite continuous contact with Gram-negative commensal bacteria and lipopolysaccharide (LPS) on its luminal surface. Recognition of LPS by the Toll-like receptor (TLR) 4/MD-2 complex results in pro-inflammatory gene expression and cytokine secretion in intestinal epithelial cells (IECs). We have shown that IECs express low levels of MD-2 and TLR4 and are poorly responsive to LPS. In this study, we did a comprehensive analysis to understand the immune-mediated and epigenetic mechanisms by which IECs down-regulate MD-2 expression. Expression of MD-2 and TLR4 mRNA was examined in human inflammatory bowel disease and intestinal epithelial cell lines (T84, HT-29, Caco-2). Nuclear factor-κB transcriptional activation was used as a measure of LPS responsiveness. Intestinal epithelial cells in patients with inflammatory bowel disease exhibited increased expression of MD-2 and TLR4 mRNA. Lipopolysaccharide responsiveness in IECs was polarized to the basolateral membrane. Bisulfite sequencing of the MD-2 promoter demonstrated methylation of CpG dinucleotides. Inhibition of methylation by 5-azacytidine and histone de-actylation by trichostatin A, two forms of epigenetic silencing, resulted in increased mRNA expression of MD-2 in IECs. These results demonstrate various molecular mechanisms by which IECs down-regulate MD-2 and, thereby, protect against dysregulated inflammation to commensal bacteria in the intestinal lumen.
Anti-inflammatory effects of C1-Inhibitor in porcine and human whole blood are independent of its protease inhibition activity
Authors: Thorgersen Ebbe Billmann , Ludviksen Judith K. , Lambris John D. , Sfyroera Georgia , Nielsen Erik Waage , Mollnes Tom Eirik
Published: August 2009

C1-Inhibitor (C1-INH) is an important biological inhibitor, regulating several protein cascade systems. Recent research has shown that the molecule exhibits properties not dependent on its protease inhibition activity. Serum and whole blood from pigs and humans were pre-incubated with C1-INH, iC1-INH or the complement inhibitors SPICE or compstatin. Whole, live Escherichia coli were then added for further incubation. Complement activation, a range of cytokines, chemokines and growth factors, as well as the leukocyte activation markers wCD11R3 (pig) and CD11b (human) were measured. Both C1-INH and iC1-INH dose-dependently and significantly (P<0.05) reduced a range of E. coli-induced pro-inflammatory cytokines and chemokines in porcine and human whole blood, as well as growth factors in human whole blood. Differences between the two forms of C1-INH and between the two species were modest. Most of these anti-inflammatory effects could not be explained by complement inhibition, as specific complement inhibitors had minor effect on several of the mediators. C1-Inhibitor had no inhibitory effect on E. coli-induced complement activation, while iC1-INH enhanced complement activation. The presented data indicate that C1-INH has broad anti-inflammatory effects in E. coli-induced inflammation in pig and human whole blood. These effects are largely independent of the protease inhibition activity.
Hepatic gene expression changes in pigs experimentally infected with the lung pathogen Actinobacillus pleuropneumoniae as analysed with an innate immunity focused microarray
Authors: Skovgaard Kerstin , Mortensen Shila , Boye Mette , Hedegaard Jakob , Heegaard Peter M.H.
Published: August 2009

Knowledge on gene expression in the liver during respiratory infections is limited although it is well-established that this organ is an important site of synthesis of several systemic innate immune components as response to infections. In the present study, the early transcriptional hepatic response of genes associated with innate immune responses was studied in pigs 14—18 h after intranasal inoculation with Actinobacillus pleuropneumoniae, using innate immune focused microarrays and quantitative real-time PCR (qPCR). The microarray analysis of liver tissue established that 51 genes were differentially expressed. A large group of these genes encoded proteins involved in the acute phase response, including serum amyloid A, C-reactive protein, fibrinogen, haptoglobin and tumor necrosis factor-α the expression of which were all found to be up-regulated and glutathione S-transferase, transthyretin, transferrin and albumin which were down-regulated. Additional genes associated with innate immune responses were investigated using qPCR; genes encoding interleukin-(IL-)1, IL-6, IL-8, lipopolysaccharide binding protein, lactotransferrin, and PigMAP were up-regulated and interferon 1α, α1-acid glycoprotein, mannan-binding lectin A, surfactant protein D, and surfactant protein A1 were down-regulated in the liver of infected animals. Down-regulation of α1-acid glycoprotein during infection has not been described previously in any species. These results confirm that the liver plays an important role in initiating and orchestrating the innate immune response to A. pleuropneumoniae infection.
Choral Student Perceptions of Effective Motivation Strategies
Authors: Stamer Rick A.
Published: August 2009

The purpose of this study is to determine differences in choral students’ perceptions of motivation strategies. A survey provided the opportunity for students ( N = 515) to identify effective motivation techniques. Students identified director/ student attention and knowledge of results as being highly effective, interest as being effective, and task achievement and level of concern as being somewhat effective in enhancing student motivation. Significant differences, compared by gender and grade level, were identified for several motivation strategies. Implications for choral music educators who wish to enhance their ability to motivate students to learn are provided, as are recommendations for further research.
Nf1 deficiency cooperates with oncogenic K-RAS to induce acute myeloid leukemia in mice
Authors: Cutts Briony A. , Sjogren Anna-Karin M. , Andersson Karin M. E. , Wahlstrom Annika M. , Karlsson Christin , Swolin Birgitta , Bergo Martin O.
Published: August 2009

Hyperactive RAS signaling is caused by mutations in RAS genes or a deficiency of the neurofibromatosis gene (NF1) and is common in myeloid malignancies. In mice, expression of oncogenic K-RAS or inactivation of Nf1 in hematopoietic cells results in myeloproliferative disorders (MPDs) that do not progress to acute myeloid leukemia (AML). Because NF1 is a RAS-GTPase–activating protein it has been proposed that NF1 deficiency is functionally equivalent to an oncogenic RAS. It is not clear, however, whether Nf1 deficiency would be redundant in K-RAS–induced MPD development or whether the 2 mutations would cooperate in leukemogenesis. Here, we show that the simultaneous inactivation of Nf1 and expression of K-RASG12D in mouse hematopoietic cells results in AML that was fatal in primary mice within 4 weeks and transplantable to sublethally irradiated secondary recipients. The data point to a strong cooperation between Nf1 deficiency and oncogenic K-RAS.
Expanding multiviral reactive T cells from cord blood
Authors: Childs Richard W. , Zerbe Christa S.
Published: August 2009

In this article, Hanley and colleagues describe a novel method to rapidly expand polyclonal populations of viral reactive CTLs from naive cord blood T cells that target CMV, adenovirus, and EBV.1
Fatness QTL on chicken chromosome 5 and interaction with sex
Authors: Abasht Behnam , Pitel Frédérique , Lagarrigue Sandrine , Le Bihan-Duval Elisabeth , Le Roy Pascale , Demeure Olivier , Vignoles Florence , Simon Jean , Cogburn Larry , Aggrey Sammy , Vignal Alain , Douaire Madeleine
Published: August 2009

Quantitative trait loci (QTL) affecting fatness in male chickens were previously identified on chromosome 5 (GGA5) in a three-generation design derived from two experimental chicken lines divergently selected for abdominal fat weight. A new design, established from the same pure lines, produced 407 F2 progenies (males and females) from 4 F1-sire families. Body weight and abdominal fat were measured on the F2 at 9 wk of age. In each sire family, selective genotyping was carried out for 48 extreme individuals for abdominal fat using seven microsatellite markers from GGA5. QTL analyses confirmed the presence of QTL for fatness on GGA5 and identified a QTL by sex interaction. By crossing one F1 sire heterozygous at the QTL with lean line dams, three recombinant backcross 1 (BC1) males were produced and their QTL genotypes were assessed in backcross 2 (BC2) progenies. These results confirmed the QTL by sex interaction identified in the F2 generation and they allow mapping of the female QTL to less than 8 Mb at the distal part of the GGA5. They also indicate that fat QTL alleles were segregating in both fat and lean lines.
Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies
Authors: Teber Erdahl T , Liu Jason Y , Ballouz Sara , Fatkin Diane , Wouters Merridee A
Published: August 2009

Background

Automated candidate gene prediction systems allow geneticists to hone in on disease genes more rapidly by identifying the most probable candidate genes linked to the disease phenotypes under investigation. Here we assessed the ability of eight different candidate gene prediction systems to predict disease genes in intervals previously associated with type 2 diabetes by benchmarking their performance against genes implicated by recent genome-wide association studies.

Results

Using a search space of 9556 genes, all but one of the systems pruned the genome in favour of genes associated with moderate to highly significant SNPs. Of the 11 genes associated with highly significant SNPs identified by the genome-wide association studies, eight were flagged as likely candidates by at least one of the prediction systems. A list of candidates produced by a previous consensus approach did not match any of the genes implicated by 706 moderate to highly significant SNPs flagged by the genome-wide association studies. We prioritized genes associated with medium significance SNPs.

Conclusion

The study appraises the relative success of several candidate gene prediction systems against independent genetic data. Even when confronted with challengingly large intervals, the candidate gene prediction systems can successfully select likely disease genes. Furthermore, they can be used to filter statistically less-well-supported genetic data to select more likely candidates. We suggest consensus approaches fail because they penalize novel predictions made from independent underlying databases. To realize their full potential further work needs to be done on prioritization and annotation of genes.
CGTS: a site-clustering graph based tagSNP selection algorithm in genotype data
Authors: Wang Jun , Guo Mao-zu , Wang Chun-yu
Published: August 2009

Background

Recent studies have shown genetic variation is the basis of the genome-wide disease association research. However, due to the high cost on genotyping large number of single nucleotide polymorphisms (SNPs), it is essential to choose a small subset of informative SNPs (tagSNPs), which are able to capture most variation in a population, to represent the rest SNPs. Several methods have been proposed to find the minimum set of tagSNPs, but most of them still have some disadvantages such as information loss and block-partition limit.

Results

This paper proposes a new hybrid method named CGTS which combines the ideas of the clustering and the graph algorithms to select tagSNPs on genotype data. This method aims to maximize the number of the discarding nontagSNPs in the given set. CGTS integrates the information of the LD association and the genotype diversity using the site graphs, discards redundant SNPs using the algorithm based on these graph structures. The clustering algorithm is used to reduce the running time of CGTS. The efficiency of the algorithm and quality of solutions are evaluated on biological data and the comparisons with three popular selecting methods are shown in the paper.

Conclusion

Our theoretical analysis and experimental results show that our algorithm CGTS is not only more efficient than other methods but also can be get higher accuracy in tagSNP selection.
Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations
Authors: Reumers Joke , Schymkowitz Joost , Rousseau Fréderic
Published: August 2009

Background

Linking structural effects of mutations to functional outcomes is a major issue in structural bioinformatics, and many tools and studies have shown that specific structural properties such as stability and residue burial can be used to distinguish neutral variations and disease associated mutations.

Results

We have investigated 39 structural properties on a set of SNPs and disease mutations from the Uniprot Knowledge Base that could be mapped on high quality crystal structures and show that none of these properties can be used as a sole classification criterion to separate the two data sets. Furthermore, we have reviewed the annotation process from mutation to result and identified the liabilities in each step.

Conclusion

Although excellent annotation results of various research groups underline the great potential of using structural bioinformatics to investigate the mechanisms underlying disease, the interpretation of such annotations cannot always be extrapolated to proteome wide variation studies. Difficulties for large-scale studies can be found both on the technical level, i.e. the scarcity of data and the incompleteness of the structural tool suites, and on the conceptual level, i.e. the correct interpretation of the results in a cellular context.
Interleukin-21 induces the differentiation of human umbilical cord blood CD34-lineage- cells into pseudomature lytic NK cells
Authors: Bonanno Giuseppina , Mariotti Andrea , Procoli Annabella , Corallo Maria , Scambia Giovanni , Pierelli Luca , Rutella Sergio
Published: August 2009

Background

Umbilical cord blood (UCB) is enriched with transplantable CD34+ cells. In addition to CD34-expressing haematopoietic stem cells (HSC), human UCB contains a rare population of CD34-lineage- cells endowed with the ability to differentiate along the T/NK pathway in response to interleukin (IL)-15 and a stromal cell support. IL-21 is a crucial regulator of NK cell function, whose influence on IL-15-induced differentiation of CD34-lineage- cells has not been investigated previously. The present study was designed and conducted to address whether IL-21 might replace the stromal cell requirements and foster the IL-15-induced NK differentiation of human UCB CD34-lineage- cells.

Results

CD34-lineage- cells were maintained in liquid culture with Flt3-L and SCF, with the addition of IL-15 and IL-21, either alone or in combination. Cultures were established in the absence of feeder cells or serum supplementation. Cytokine-treated cells were used to evaluate cell surface phenotype, expression of molecular determinants of lymphoid/NK cell differentiation, secretion of IFN-γ, GM-CSF, TNF-α and CCL3/MIP-1α, and cytolytic activity against NK-sensitive tumour cell targets. CD34-lineage- cells proliferated vigorously in response to IL-15 and IL-21 but not to IL-21 alone, and up-regulated phosphorylated Stat1 and Stat3 proteins. CD34-lineage- cells expanded by IL-21 in combination with IL-15 acquired lymphoid morphology and killer-cell immunoglobulin-like receptor (KIR)-CD56+CD16-/+ phenotype, consistent with pseudo-mature NK cells. IL-21/IL-15-differentiated cells expressed high levels of mRNA for Bcl-2, GATA-3 and Id2, a master switch required for NK-cell development, and harboured un-rearranged TCRγ genes. From a functional standpoint, IL-21/IL-15-treated cells secreted copious amounts of IFN-γ, GM-CSF and CCL3/MIP-1α, and expressed cell surface CD107a upon contact with NK-sensitive tumour targets, a measure of exocytosis of NK secretory granules.

Conclusion

This study underpins a novel role for IL-21 in the differentiation of pseudo-mature lytic NK cells in a synergistic context with IL-15, and identifies a potential strategy to expand functional NK cells for immunotherapy.
Extracellular secretion of Carocin S1 in Pectobacterium carotovorum subsp. carotovorumoccurs via the type III secretion system integral to the bacterial flagellum
Authors: Chan Yung-chieh , Wu Huang-Pin , Chuang Duen-yau
Published: August 2009

Background

Pectobacterium carotovorum subsp. carotovorum is a phytopathogenic enterobacterium responsible for soft rot, a disease characterized by extensive maceration of the affected plant tissue. This species also produces two or more antibacterial substances called bacteriocins, which enhance its competitiveness against related rival species. However, the secretion mechanism for low-molecular-weight bacteriocin is still unknown.

Results

A mutant (flhC::Tn5) that did not secrete the low-molecular-weight bacteriocin (LMWB), Carocin S1, was generated by Tn5 insertional mutagenesis. Sequence analysis indicated that this insertion disrupted open reading frame 2 (ORF2) and ORF3 of this strain. Deletion and rescue experiments indicated that ORF2 and ORF3 were both required for extracellular LMWB secretion. The ORF2 and ORF3 sequences showed high homology with the flhD and flhC gene sequences of Pectobacterium carotovorum subsp. atroseptica, Serratia marcescens, Yersinia enterocolitica, and Escherichia coli, indicating that they likely encoded key regulatory components of the type III flagella secretion system.

Conclusion

Thus, the extracellular export of Carocin S1 by Pectobacterium carotovorum subsp. carotovorum appears to utilize the type III secretion system integral to bacterial flagella.
Perceiving pitch absolutely: Comparing absolute and relative pitch possessors in a pitch memory task
Authors: Schulze Katrin , Gaab Nadine , Schlaug Gottfried
Published: August 2009

Background

The perceptual-cognitive mechanisms and neural correlates of Absolute Pitch (AP) are not fully understood. The aim of this fMRI study was to examine the neural network underlying AP using a pitch memory experiment and contrasting two groups of musicians with each other, those that have AP and those that do not.

Results

We found a common activation pattern for both groups that included the superior temporal gyrus (STG) extending into the adjacent superior temporal sulcus (STS), the inferior parietal lobule (IPL) extending into the adjacent intraparietal sulcus (IPS), the posterior part of the inferior frontal gyrus (IFG), the pre-supplementary motor area (pre-SMA), and superior lateral cerebellar regions. Significant between-group differences were seen in the left STS during the early encoding phase of the pitch memory task (more activation in AP musicians) and in the right superior parietal lobule (SPL)/intraparietal sulcus (IPS) during the early perceptual phase (ITP 0–3) and later working memory/multimodal encoding phase of the pitch memory task (more activation in non-AP musicians). Non-significant between-group trends were seen in the posterior IFG (more in AP musicians) and the IPL (more anterior activations in the non-AP group and more posterior activations in the AP group).

Conclusion

Since the increased activation of the left STS in AP musicians was observed during the early perceptual encoding phase and since the STS has been shown to be involved in categorization tasks, its activation might suggest that AP musicians involve categorization regions in tonal tasks. The increased activation of the right SPL/IPS in non-AP musicians indicates either an increased use of regions that are part of a tonal working memory (WM) network, or the use of a multimodal encoding strategy such as the utilization of a visual-spatial mapping scheme (i.e., imagining notes on a staff or using a spatial coding for their relative pitch height) for pitch information.
A mammalianized synthetic nitroreductase gene for high-level expression
Authors: Grohmann Maik , Paulmann Nils , Fleischhauer Sebastian , Vowinckel Jakob , Priller Josef , Walther Diego J
Published: August 2009

Background

The nitroreductase/5-(azaridin-1-yl)-2,4-dinitrobenzamide (NTR/CB1954) enzyme/prodrug system is considered as a promising candidate for anti-cancer strategies by gene-directed enzyme prodrug therapy (GDEPT) and has recently entered clinical trials. It requires the genetic modification of tumor cells to express the E. coli enzyme nitroreductase that bioactivates the prodrug CB1954 to a powerful cytotoxin. This metabolite causes apoptotic cell death by DNA interstrand crosslinking. Enhancing the enzymatic NTR activity for CB1954 should improve the therapeutical potential of this enzyme-prodrug combination in cancer gene therapy.

Methods

We performed de novo synthesis of the bacterial nitroreductase gene adapting codon usage to mammalian preferences. The synthetic gene was investigated for its expression efficacy and ability to sensitize mammalian cells to CB1954 using western blotting analysis and cytotoxicity assays.

Results

In our study, we detected cytoplasmic protein aggregates by expressing GFP-tagged NTR in COS-7 cells, suggesting an impaired translation by divergent codon usage between prokaryotes and eukaryotes. Therefore, we generated a synthetic variant of the nitroreductase gene, called ntro, adapted for high-level expression in mammalian cells. A total of 144 silent base substitutions were made within the bacterial ntr gene to change its codon usage to mammalian preferences. The codon-optimized ntro either tagged to gfp or c-myc showed higher expression levels in mammalian cell lines. Furthermore, the ntro rendered several cell lines ten times more sensitive to the prodrug CB1954 and also resulted in an improved bystander effect.

Conclusion

Our results show that codon optimization overcomes expression limitations of the bacterial ntr gene in mammalian cells, thereby improving the NTR/CB1954 system at translational level for cancer gene therapy in humans.
Inhibitory effect of IL-8 on insulin action in human adipocytes via MAP kinase pathway
Authors: Kobashi Chikaaki , Asamizu Sachie , Ishiki Manabu , Iwata Minoru , Usui Isao , Yamazaki Katusuya , Tobe Kazuyuki , Kobayashi Masashi , Urakaze Masaharu
Published: August 2009

Background

Various cytokines and other compounds are produced in human adipose tissue and might have functions in the adipose tissue. They might be involved in complications associated with obesity and diabetes. Recently, interleukin-8 (IL-8) has been shown to be produced and released from human adipose tissue and/or adipocytes, suggesting IL-8 involvement in some obesity-related health complications. Therefore, we found it of interest to investigate whether IL-8 is involved in the insulin action in human adipocytes.

Methods

The IL-8 levels in the medium were measured using ELISA. The IL-8 mRNA expression was analyzed using Northern blot analysis. The phosphorylation of Akt was analyzed using Western blot analysis. Furthermore, we examined the effect of IL-8 on the phosphorylation of Akt induced by insulin.

Results

The level of IL-8 in the medium and the IL-8 mRNA expression after stimulation with either TNF-α, IL-1β, or CRP was significantly enhanced in human adipocytes. It is particularly interesting that IL-8 per se also enhanced IL-8 mRNA expression. The IL-8 induced-IL-8 mRNA expression was inhibited by PD98059 (a MEK inhibitor) or SB203580 (a p38 MAPK inhibitor). The IL-8 inhibited insulin-induced Akt phosphorylation. The inhibitory effect of IL-8 was eliminated by either PD 98059 or SB203580.

Conclusion

These data suggest that IL-8 is a main adipocytokine producing insulin resistance via the inhibition of insulin-induced Akt phosphorylation in adipocytes. The attenuation of IL-8 action might be a target for prevention of diabetes and its complications.
A riot of rhythms: neuronal and glial circadian oscillators in the mediobasal hypothalamus
Authors: Guilding Clare , Hughes Alun TL , Brown Timothy M , Namvar Sara , Piggins Hugh D
Published: August 2009

Background

In mammals, the synchronized activity of cell autonomous clocks in the suprachiasmatic nuclei (SCN) enables this structure to function as the master circadian clock, coordinating daily rhythms in physiology and behavior. However, the dominance of this clock has been challenged by the observations that metabolic duress can over-ride SCN controlled rhythms, and that clock genes are expressed in many brain areas, including those implicated in the regulation of appetite and feeding. The recent development of mice in which clock gene/protein activity is reported by bioluminescent constructs (luciferase or luc) now enables us to track molecular oscillations in numerous tissues ex vivo. Consequently we determined both clock activities and responsiveness to metabolic perturbations of cells and tissues within the mediobasal hypothalamus (MBH), a site pivotal for optimal internal homeostatic regulation.

Results

Here we demonstrate endogenous circadian rhythms of PER2::LUC expression in discrete subdivisions of the arcuate (Arc) and dorsomedial nuclei (DMH). Rhythms resolved to single cells did not maintain long-term synchrony with one-another, leading to a damping of oscillations at both cell and tissue levels. Complementary electrophysiology recordings revealed rhythms in neuronal activity in the Arc and DMH. Further, PER2::LUC rhythms were detected in the ependymal layer of the third ventricle and in the median eminence/pars tuberalis (ME/PT). A high-fat diet had no effect on the molecular oscillations in the MBH, whereas food deprivation resulted in an altered phase in the ME/PT.

Conclusion

Our results provide the first single cell resolution of endogenous circadian rhythms in clock gene expression in any intact tissue outside the SCN, reveal the cellular basis for tissue level damping in extra-SCN oscillators and demonstrate that an oscillator in the ME/PT is responsive to changes in metabolism.
Different altered stage correlative expression of high abundance acute-phase proteins in sera of patients with epithelial ovarian carcinoma
Authors: Chen Yeng , Lim Boon-Kiong , Hashim Onn H
Published: August 2009

Background

The general enhanced expression of α1-antichymotrypsin (ACT), clusterin (CLU), α1-antitrypsin (AAT), haptoglobin β-chain (HAP), and leucine rich glycoprotein (LRG) in the sera of patients with epithelial ovarian carcinoma (EOCa) was recently reported. In the present study, we compared the expression of the serum acute-phase proteins (APPs) in the patients according to their stages of cancer.

Results

Different altered stage correlative expression of the high abundance serum APPs was demonstrated in sera of the patients studied. While the expression of ACT, HAP and AAT appeared to demonstrate positive correlation with the three initial stages of the cancer, inverse correlation was apparently detected in the expression of LRG and CLU. For patients who were diagnosed with stage IV of the cancer, expression of the serum APPs did not conform to the altered progression changes.

Conclusion

Our results highlight the potential prognostic significance of selective high abundance serum APPs in patients with EOCa.
Improved geometric-spreading approximation in layered transversely isotropic media
Authors: Stovas Alexey , Ursin Bjorn
Published: August 2009

A new approximation (direct approximation) for the relative geometric spreading of qP-waves in a layered transversely isotropic medium uses three traveltime parameters: two-way vertical traveltime, normal-moveout velocity, and the heterogeneity coefficient. These traveltime parameters, which can be estimated in velocity analysis, enter the parameters of geometric-spreading approximation. The new approximation is based on the acoustic approximation for a single-layer vertical transversely isotropic (VTI) medium with coefficients defined from Taylor expansion and asymptotic behavior at infinite offset. The acoustic approximation is used to reduce the number of parameters and to make the expression for the direct geometric-spreading approximation similar to a well-known traveltime approximation. The same traveltime parameters also allow for an independent approximation of the radiation pattern. Two numerical tests (single-layer and multilayered VTI models) prove that the new approximation is more accurate than standard approximations based on shifted hyperbola or two rational approximations.
New metrics for comparing and assessing discrepancies between RNA 3D structures and models
Authors: Parisien Marc , Cruz José Almeida , Westhof Éric , Major François
Published: August 2009

To benchmark progress made in RNA three-dimensional modeling and assess newly developed techniques, reliable and meaningful comparison metrics and associated tools are necessary. Generally, the average root-mean-square deviations (RMSDs) are quoted. However, RMSD can be misleading since errors are spread over the whole molecule and do not account for the specificity of RNA base interactions. Here, we introduce two new metrics that are particularly suitable to RNAs: the deformation index and deformation profile. The deformation index is calibrated by the interaction network fidelity, which considers base–base-stacking and base–base-pairing interactions within the target structure. The deformation profile highlights dissimilarities between structures at the nucleotide scale for both intradomain and interdomain interactions. Our results show that there is little correlation between RMSD and interaction network fidelity. The deformation profile is a tool that allows for rapid assessment of the origins of discrepancies.
The Thermus thermophilus DEAD box helicase Hera contains a modified RNA recognition motif domain loosely connected to the helicase core
Authors: Rudolph Markus G. , Klostermeier Dagmar
Published: August 2009

DEAD box family helicases consist of a helicase core that is formed by two flexibly linked RecA-like domains. The helicase activity can be regulated by N- or C-terminal extensions flanking the core. Thermus thermophilus heat resistant RNA-dependent ATPase (Hera) is the first DEAD box helicase that forms a dimer using a unique dimerization domain. In addition to the dimerization domain, Hera contains a C-terminal RNA binding domain (RBD) that shares sequence homology only to uncharacterized proteins of the Deinococcus/Thermus group. The crystal structure of Hera_RBD reveals the fold of an altered RNA recognition motif (RRM) with limited structural homology to the RBD of the DEAD box helicase YxiN from Bacillus subtilis. Comparison with RRM/RNA complexes shows that a RNA binding mode different than that suggested for YxiN, but similar to U1A, can be inferred for Hera. The orientation of the RBD relative to the helicase core was defined in a second crystal structure of a Hera fragment including the C-terminal RecA domain, the dimerization domain, and the RBD. The structures allow construction of a model for the entire Hera helicase dimer. A likely binding surface for large RNA substrates that spans both RecA-like domains and the RBD is identified.
Business Models for Media Firms: Does Competition Matter for How They Raise Revenue?
Authors: Kind Hans Jarle , Nilssen Tore , Sørgard Lars
Published: August 2009

The purpose of this article is to analyze how competitive forces may influence the way media firms like TV channels raise revenue. A media firm can either be financed by advertising revenue, by direct payment from the viewers (or the readers, if we consider newspapers), or by both. We show that the scope for raising revenues from consumer payment is constrained by other media firms offering close substitutes. This implies that the less differentiated the media firms' content, the larger is the fraction of their revenue coming from advertising. A media firm's scope for raising revenues from ads, on the other hand, is constrained by how many competitors it faces. We should thus expect that direct payment from the media consumers becomes more important the larger the number of competing media products.