bluuebunny/crossref_metadata_2025 huggingface dataset:
Nutrition Assessment in Advanced Heart Failure Patients Evaluated for Ventricular Assist Devices or Cardiac Transplantation
Authors: Aggarwal Ashim , Kumar Anup , Gregory Mary P. , Blair Christopher , Pauwaa Sunil , Tatooles Antone J. , Pappas Pat S. , Bhat Geetha
Published: October 2012

Background: Malnutrition has been shown to affect clinical outcomes in patients with heart failure. The aim of this study was to analyze the incidence of malnutrition and to assess its prognostic significance in patients with advanced heart failure (AHF) (being evaluated for left ventricular assist device [LVAD] or cardiac transplant) based on nutrition status as assessed by the Mini Nutritional Assessment (MNA). Methods: A retrospective analysis was conducted on 154 patients. During evaluation, a complete nutrition assessment was performed, and diagnosis of malnutrition and risk of malnutrition was done with the MNA. Its possible independent association with mortality was assessed. Results: The mean (SD) age of the patients was 59.3 (14.1) years, with 76% men. Twenty‐two percent were classified as malnourished, 68% at risk of malnutrition, and 10% well nourished. The mortality in the 3 groups was 26.5%, 42.0%, and 6.7%, respectively (P = .02). In the multivariate logistic regression analysis, the undernutrition state (malnourished + at risk) was an independent predictor of mortality (odds ratio, 7.9; confidence interval, 1.01–62.30; P = .04). Conclusions: The state of undernutrition is an independent predictor of mortality in patients with AHF. Early recognition of undernutrition through use of the MNA may affect the long‐term prognosis of these patients by enabling early intervention.
Synthesis, properties, and endothelial progenitor cells labeling stability of dextranes as polymeric magnetic resonance imaging contrast agents
Authors: Agudelo Carlos A , Tachibana Yoichi , Yamaoka Tetsuji
Published: October 2012

Magnetic resonance imaging is one of the most important fields for cellular imaging due to its non-invasive capacity, spatial resolution, and sensibility to visualized transplanted cells. An enhanced magnetic resonance image can be achieved by using contrast agents containing paramagnetic gadolinium chelates, which have the widest clinical use. To obtain a better contrast-enhancement and reduce the concentration of Gd for payload, one strategy is to conjugate the gadolinium(III) chelate to polymeric materials that will lead into an increase in the rotational correlation time and therefore improve the relaxivity. Four series of dextran gadolinium chelates were synthesized which are of interest as potential MRI contrast agents to track bone marrow-derived endothelial progenitor cells in vivo. The dextranes with molecular weights were characterized, introduced into the endothelial progenitor cells by electroporation, and injected in aqueous solution into rats to acquire the MR images. We have shown that by selecting polymers of the appropriate molecular weight, stability into the cell after labeling, relaxivity, and retention into the body can be accomplished.
Characterization of membranes prepared from PVDF/PAN blends and their modification with hydrolysis
Authors: Zhang Xuliang , Xiao Changfa , Hu Xiaoyu , Zhang Zhiying
Published: October 2012

In this study, the melt-spinning and stretching processes were used to prepare polyvinylidene fluoride (PVDF)/polyacrylonitrile (PAN) blend hollow-fiber membranes. These blend membranes have a higher tensile strength than those prepared via the wet phase inversion method. The influence of stretching temperature and draw ratios on the membrane microstructure, pure water flux, and porosity of the membranes was studied. The draw ratio and the stretching temperature can greatly affect the morphology and the permeation performance of the membranes. The Fourier transform infrared spectra demonstrate the differences in the PVDF/PAN blend membranes before and after hydrolysis. The water flux of the hydrolyzed PVDF/PAN blend membranes is sensitive to pH value and salt ionic strength. The effects of different salt ions on the permeability of the hydrolyzed membranes were also investigated.
Dimensional metrology of micro parts by optical three-dimensional profilometry and areal surface topography analysis
Authors: Senin Nicola , Blunt Liam A , Tolley Martin
Published: October 2012

A novel approach is proposed for the characterization of critical dimensions and geometric errors, suitable for application to micro-fabricated parts and devices characterized as step-like structured surfaces. The approach is based on acquiring areal maps with a high-precision optical three-dimensional profilometer and on processing topography data with novel techniques obtained by merging knowledge and algorithms from surface metrology, dimensional metrology and computer vision/image processing. Thin-foil laser targets for ion acceleration experiments are selected as the test subject. The main issues related to general applicability and metrological performance of the methodology are identified and discussed.
Open science and community norms
Authors: Joly Yann , Dove Edward S. , Kennedy Karen L. , Bobrow Martin , Ouellette B.F. Francis , Dyke Stephanie O.M. , Kato Kazuto , Knoppers Bartha M.
Published: October 2012

While modern genomics research often adheres to community norms emphasizing open data sharing, many genomics institutes and projects have recently nuanced such norms with a corpus of data release policies. In particular, publication moratoria and data retention policies have been enacted to ‘reward’ data producers and ensure data quality control. Given the novelty of these policies, this article seeks to identify and analyse the main features of data retention and publication moratoria policies of major genomics institutes and projects around the world. We find that as more collaborative genomics projects are created, and further genomic research discoveries are announced, the need for more sophisticated yet practical and effective policies will increase. Reward systems should be implemented that recognize contributions from data producers and acknowledge the need to remain dedicated to the goals of open data sharing. To this end, in addition to the current choices of employing data retention or publication moratoria policies, alternative models that would be easier to implement or less demanding on open science should also be considered.
Global integration along historic pathways: Vienna and Munich in the changing financial geography of Europe
Authors: Zademach Hans-Martin , Musil Robert
Published: October 2012

Taking the two second-tier financial centres Munich and Vienna as illustrative cases, this paper empirically evaluates the extent to which the restructuring of the banking and insurance industry and the emergence of new financial agents calls for a reappraisal of the geography of European finance against longer-term developments. Conceptually, the paper adopts an evolutionary perspective that conceives inter- and intra-sectoral corporate takeovers and mergers and the rise of the private equity industry as driving forces for diversification/specification of financial centres. The paper traces the historic origins and long-term evolution of financial services in Munich and Vienna and then provides a twofold investigation of new empirical data: first a static investigation of the location networks of the 50 largest private equity firms and the 30 most important European banks; and second a network analysis of 493 merger and acquisition transactions in the European banking and insurance industries between 1997 and 2009. The study reveals the varying roles that Munich and Vienna play today in Europe’s financial geography and elucidates to what extent this variation results from both longer-term and more recent developments.
The Relationship among Emotional Intelligence and Outcome Variables: A Study of Indian Employees
Authors: Maini Jiwan Jyoti , Singh Bhawdeep , Kaur Parminder
Published: October 2012

This study examined the relationship among four dimensions of emotional intelligence (EI) as predictor variables vis-à-vis five dimensions of organizational citizenship behaviour (OCB) and in-role behaviour (IRB) as criterion variables. Sample constituted of 250 superior–subordinate dyads working on technical and non-technical jobs in power plants in India. Canonical correlation analysis and hierarchical multiple regression analysis have been applied to investigate the relationship between the two sets of variables. Demographic variables have been controlled, to find the unique variance in the prediction of criterion variables. Significant relationship was found between emotional intelligence dimensions and outcome variables with Rc = 0.569. Among the outcome variables, sportsmanship had the highest canonical loading and IRB had the lowest canonical loading. Canonical loadings for predictor canonical variate were highest for utilization of emotion and lowest for perception of emotion. Sensitivity analysis was carried out to validate the results obtained through canonical correlation analysis by removing individual independent variable at a time. The results showed little difference, indicating stability of the results. Overall the results established significant relationship among the predictor and criterion variables. However, the dimensions of EI were better in predicting OCB dimensions as compared to IRB of the respondents.
Electroaeroelastic analysis of airfoil-based wind energy harvesting using piezoelectric transduction and electromagnetic induction
Authors: De Marqui Carlos , Erturk Alper
Published: October 2012

The concept of transforming aeroelastic vibrations into electricity for low-power generation has received growing attention in the last few years. The goal is to convert airflow energy into electricity for powering small electronic components employed in wireless applications. The potential applications for aeroelastic energy harvesting range from aircraft structures to several engineering problems involving wireless electronic components located in high wind areas. The use of a typical airfoil section is a convenient approach to create instabilities and persistent oscillations in aeroelastic energy harvesting. This article analyzes two airfoil-based aeroelastic energy harvesters using (a) piezoelectric transduction and (b) electromagnetic induction. An airfoil with two degrees of freedom is investigated by adding piezoelectric and electromagnetic couplings to the plunge degree of freedom in two separate cases. The governing dimensionless electroaeroelastic equations are given in each case with a resistive load in the electrical domain for predicting the power output at the flutter boundary. The effects of several dimensionless system parameters on the dimensionless electrical power output as well as the dimensionless linear flutter speed are investigated for piezoelectric and electromagnetic energy harvesting from airflow-induced vibrations. The simulations presented in this study can be employed for designing and optimizing airfoil-based wind energy harvesters.
Geometrical optimization of a hingeless deployment system for an active rotor blade
Authors: Paternoster Alexandre , Loendersloot Richard , de Boer Andre , Akkerman Remko
Published: October 2012

Deployment systems for the Gurney flap need to sustain large centrifugal loads and vibrations while maintaining precisely the displacement under aerodynamic loading. Designing such a mechanism relies on both the actuation technology and the link that transmits motion to the control surface. Flexible beams and piezoelectric patch actuators have been chosen as components to design this mechanism. Flexible beams provide a hingeless robust structure onto which the piezoelectric actuators are bonded. A candidate topology is determined by investigating the compliance of a simple wire structure with beam elements. A parameterized finite element model is then built and optimized for displacement and force through surrogate optimization.
Interfacial effect on the electromechanical behaviors of piezoelectric/elastic composite smart beams
Authors: Wang Huiming , Zou Long
Published: October 2012

An efficient electromechanical coupling model is developed to analyze the effect of the interfacial properties on the mechanical behaviors of piezoelectric/elastic composite smart beams. The interface of the composite smart beams is assumed to be imperfectly bonded and is modeled by the shear-lag model. An asymptotic expansion approximation is employed to construct the electric potential distribution in the piezoelectric layer. The governing equation is derived for the piezoelectric/elastic composite smart beams taking into account the electromechanical coupling effect and the interfacial imperfection. In the numerical analysis, both the mechanical and the electrical loadings are considered. The mechanical behaviors of the composite smart beams are illustrated graphically for three types of boundary conditions: (a) clamped supported–freely supported (C-F), (b) clamped supported–hinged supported (C-H), and (c) hinged supported–hinged supported (H-H). The results show that the interfacial properties have significant effect on the mechanical behaviors of the piezoelectric/elastic composite smart beams. For mechanically actuated case, a larger interfacial imperfection causes a larger transverse deflection, while it is contrary for electrically actuated case.
Validation of the Health-Promoting Lifestyle Profile II for Hispanic Male Truck Drivers in the Southwest
Authors: Mullins Iris L. , O’Day Trish , Kan Tsz Yin
Published: October 2012

The aims of the study were to validate the English and Spanish Versions of the Health-Promoting Lifestyle Profile II (HPLP II) with Hispanic male truck drivers and to determine if there were any differences in drivers’ responses based on driving responsibility. The methods included a descriptive correlation design, the HPLP II (English and Spanish versions), and a demographic questionnaire. Fifty-two Hispanic drivers participated in the study. There were no significant differences in long haul and short haul drivers’ responses to the HPLP II. Cronbach’s alpha for the Spanish version was .97 and the subscales alphas ranged from .74 to .94. The English version alpha was .92 and the subscales ranged from .68 to .84. Findings suggest the subscales of Health Responsibility, Physical Activities, Nutrition, and Spirituality Growth on the HPLP II Spanish and English versions may not adequately assess health-promoting behaviors and cultural influences for the Hispanic male population in the southwestern border region.
Asthma Education and Health Outcomes of Children Aged 8 to 12 Years
Authors: Bowen Felesia
Published: October 2012

The purpose of this study was to evaluate the health outcomes of 8- to 12-year-old urban-dwelling children with moderate to severe persistent asthma who participated in a modified Open Airways for Schools (OAS) asthma education program. It was hypothesized that the intervention group would have improved health outcomes when compared to control. A 2-group, 3-points-in-time method was used to conduct the study. The intervention group demonstrated significant and sustained improvement in asthma knowledge. There was no significant difference between groups for quality of life or pulmonary function. While OAS is a good program for asthma education, the program alone may not be sufficient to improve risk factors associated with poor pulmonary function. Future studies should incorporate environmental interventions.
Beliefs Regarding Stimulant Medication Effects Among College Students With a History of Past or Current Usage
Authors: Pillow David R. , Naylor Lavelda J. , Malone Glenn P.
Published: October 2012

Objective: To examine the beliefs of ADHD college students concerning stimulant medications and to apply the theory of planned behavior toward better understanding the factors instrumental in decisions regarding stimulant use. Method: A cross-sectional, correlational design was used, and students completed a survey under controlled laboratory conditions. Participants were 193 students taking introductory psychology who self-reported receiving a diagnosis of attention deficit disorder or ADHD and a treatment history of using stimulant medications. Results: Beliefs regarding the effects of medication use are represented by four factors ((i.e., improved attention/academics, loss of authentic self, social self-enhancement, and common side effects), where the first three significantly and systematically differentiate between those currently using stimulants and those who are not. Conclusion: To understand decisions regarding stimulant use, it is important to consider how college students perceive the positive and negative effects of the medication with respect to sense of self and social relationships.
Implementation of a Culturally Appropriate Positive Behavior Support Plan With a Japanese Mother of a Child With Autism
Authors: Cheremshynski Christy , Lucyshyn Joseph M. , Olson Deborah L.
Published: October 2012

The purpose of this study was to empirically investigate a family-centered approach to positive behavior support (PBS) that was designed to be culturally responsive to families of diverse linguistic and cultural backgrounds. A Japanese mother and a child with autism were the primary participants. Multiple research methods were used. A single-subject withdrawal design evaluated the functional relation between parent implementation of a culturally informed PBS plan and improvements in child behavior and participation in a dinner routine. Qualitative case study methods guided an understanding of the family’s culture, the mother’s perspectives on the PBS plan and outcomes, and the interventionist’s perspectives on the provision of behavior support to the family. Quantitative results documented a functional relation between implementation of the PBS plan and improvements in child behavior and participation in the dinner routine. Qualitative results provided a rich description of the parent’s and interventionist’s experience and perspective. Three themes emerged: (a) developing a rapport informed by family culture; (b) working with a cultural guide to facilitate understanding the family’s cultural values, beliefs, and parenting practices; and (c) accommodating the mother’s cross-cultural values and beliefs. Contributions to the literature and implications for behavior interventionists working with families of diverse cultural backgrounds are discussed.
“Sort of in your blood”: Inherent musicality survives cultural judgement
Authors: Ruddock Eve
Published: October 2012

This article reports on lived experiences of a cohort of 20 self-perceived non-musicians. Their stories reveal culturally based perceptions that humans are inherently “musical” or they are not. While recent inquiries are beginning to investigate this phenomenon, instinctive musicality of self-perceived non-musical individuals remains an under-researched area. Presented in narrative form, participant experiences reveal impositions that thwart developing musicality of individuals growing up in a western cultural tradition. Although they have “learned” that they are not musical, these individuals reveal intrinsic musicality.
Electric lighting at the workplace in offices: Efficiency improvement margins of automation systems
Authors: Chiogna M , Albatici R , Frattari A
Published: October 2012

Electric lighting is one of the major energy loads in non-residential buildings. It is strategic to examine the real behaviour of available lighting control systems for practical applications so as to allow the development of strategies that can improve the reliability of measured data (in terms of illuminance at the desktop) and the consequent response of the control system. This paper presents a case study of an office where lighting data measured at the desktop and read by the automation system have been analysed. It also investigates the consequent response of the control system. In particular, we extrapolate data on the system's improvement margins and suggest suitable correction functions to be applied to the illumination data measured by ceiling-mounted sensors.
Promoting Healthy Choices in Non-Chain Restaurants
Authors: Nothwehr Faryle K. , Snetselaar Linda , Dawson Jeffrey , Schultz Ulrike
Published: October 2012

This study tested a novel intervention to influence restaurant customer ordering behavior, with measurements at baseline and 3, 6, and 12 months postintervention in four owner-operated restaurants in the Midwest. A sample of 141 to 370 customers was surveyed at each time point. The response rate was 70% to 84% with 59% women, 98% White, and a mean age of 53 years. Table signs listed changes customers might consider, for example, asking for meat broiled instead of fried or requesting smaller portions. Customer surveys measured program reach and effectiveness. Owner interviews measured perceptions of program burden and customer response. Order slips were analyzed for evidence of changes in ordering. Window signs were noticed by 40%, 48%, and 45% of customers at each follow-up, respectively. Table signs were noticed by 67%, 71%, and 69% of customers, respectively. Of those, 34% at each time point stated that the signs influenced their order. Examples of how orders were influenced were elicited. Order slip data not only did not show significant changes but was also found to be an inadequate measure for the intervention. Owners reported no concerns or complaints. This intervention resulted in small but positive behavior changes among a portion of customers. Because of its simplicity and acceptability, it has great potential for dissemination.
The three alternative journalisms of Africa
Authors: Skjerdal Terje S
Published: October 2012

Much African journalism scholarship has had a critical stand towards ‘Western’ journalism models. The criticism has resulted in the submission of alternative African journalism models such as ujamaa journalism, ubuntu journalism and oral discourse journalism. The present article reviews a number of significant contributions to normative African journalism models over the past 50 years and argues that they constitute three major streams: journalism for social change, communal journalism and journalism based on oral discourse. The vital differences between these three journalism models are explicated along the dimensions of interventionism and cultural essentialism. The article goes on to enquire why the three journalism models of Africa, different as they are, appear to be in collective conflict with Western journalism paradigms. It is suggested that the dimensions of socio-historicity and professionalism best explain the conflict.
If they really wanted to, they would
Authors: Schneeweis Adina
Published: October 2012

This study explores the solidification of the discourse of integration of the Gypsy/Roma in the European press following the fall of Communism. A discourse analysis focuses on the British and Romanian press between 1990 and 2006, and it suggests that, in the midst of opening of EU borders and talks of a European Constitution, the idea and necessity of integration grew in political popularity as a means to peaceably alleviate interethnic conflict. However, the discourse of integration has continuously shifted between assimilationist voices and projects that attempt to change the Gypsy other into a non-Gypsy, on the one hand, and human rights-inspired defense and advocacy for the Roma, on the other. This article further suggests that the press does more than confirm stereotypes; instead, uncertainties, contradictions, and changes mark press writing.
An Intersectional Analysis of Differential Opportunity Structures for Community-Based Anticrime Efforts
Authors: Becker Sarah
Published: October 2012

Numerous studies document the positive ramifications of locally based crime prevention efforts, but also reveal that neighborhoods are not equally positioned to engage in such efforts. The same social–structural correlates of high crime rates also make locally based initiatives less likely to emerge and more difficult to sustain. Opportunities for organized anticrime work are therefore unequally allocated across neighborhoods. In this article, I adapt the differential opportunity structures framework to explore an additional dimension of unequal opportunities for crime prevention: those that exist within organizations themselves. Using an intersectional lens to analyze 3 years of ethnographic data on civilian-run anticrime efforts in a small east coast community, my findings illustrate how processes groups use to train and teach their members, the day-to-day realities of their work, and the contours of social interaction within a group all impact participation. Social status factors like race, gender, and age impact access to learning and performance structures associated with anticrime work at the local level.
Addition of bevacizumab to chemotherapy in acute myeloid leukemia at older age: a randomized phase 2 trial of the Dutch-Belgian Cooperative Trial Group for Hemato-Oncology (HOVON) and the Swiss Group for Clinical Cancer Research (SAKK)
Authors: Ossenkoppele Gert J. , Stussi Georg , Maertens Johan , van Montfort Kees , Biemond Bart J. , Breems Dimitri , Ferrant August , Graux Carlos , de Greef Georgine E. , Halkes C. J. M. , Hoogendoorn Mels , Hollestein Rene M. , Jongen-Lavrencic Mojca , Levin Mark D. , van de Loosdrecht Arjan A. , van Marwijk Kooij Marinus , van Norden Yvette , Pabst Thomas , Schouten Harry C. , Vellenga Edo , Verhoef Gregor E. G. , de Weerdt Okke , Wijermans Pierre , Passweg Jakob R. , Löwenberg Bob
Published: October 2012

An urgent need for new treatment modalities is emerging in elderly patients with acute myeloid leukemia (AML). We hypothesized that targeting VEGF might furnish an effective treatment modality in this population. Elderly patients with AML were randomly assigned in this phase 2 study (n = 171) to receive standard chemotherapy (3 + 7) with or without bevacizumab at a dose of 10 mg/kg intravenously at days 1 and 15. In the second cycle, patients received cytarabine 1000 mg/m2 twice daily on days 1-6 with or without bevacizumab. The complete remission rates in the 2 arms were not different (65%). Event-free survival at 12 months was 33% for the standard arm versus 30% for the bevacizumab arm; at 24 months, it was 22% and 16%, respectively (P = .42). The frequencies of severe adverse events (SAEs) were higher in the bevacizumab arm (n = 63) compared with the control arm (n = 28; P = .043), but the percentages of death or life-threatening SAEs were lower in the bevacizumab arm (60% vs 75% of SAEs). The results of the present study show that the addition of bevacizumab to standard chemotherapy does not improve the therapeutic outcome of older AML patients. This trial is registered as number NTR904 in The Nederlands Trial Register (www.trialregister.nl).
Murine regulatory T cells differ from conventional T cells in resisting the CTLA-4 reversal of TCR stop-signal
Authors: Lu Yuning , Schneider Helga , Rudd Christopher E.
Published: October 2012

CTLA-4 inhibits T-cell activation and protects against the development of autoimmunity. We and others previously showed that the coreceptor can induce T-cell motility and shorten dwell times with dendritic cells (DCs). However, it has been unclear whether this property of CTLA-4 affects both conventional T cells (Tconvs) and regulatory T cells (Tregs). Here, we report that CTLA-4 had significantly more potent effects on the motility and contact times of Tconvs than Tregs. This was shown firstly by anti–CTLA-4 reversal of the anti-CD3 stop-signal on FoxP3-negative cells at concentrations that had no effect on FoxP3-positive Tregs. Secondly, the presence of CTLA-4 reduced the contact times of DO11.10 x CD4+CD25− Tconvs, but not DO11.10 x CD4+CD25+ Tregs, with OVA peptide presenting DCs in lymph nodes. Thirdly, blocking of CTLA-4 with anti–CTLA-4 Fab increased the contact times of Tconvs, but not Tregs with DCs. By contrast, the presence of CD28 in a comparison of Cd28−/− and Cd28+/+ DO11.10 T cells had no detectable effect on the contact times of either Tconvs or Tregs with DCs. Our findings identify for the first time a mechanistic explanation to account for CTLA-4–negative regulation of Tconv cells but not Tregs in immune responses.
High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations
Authors: Edelmann Jennifer , Holzmann Karlheinz , Miller Florian , Winkler Dirk , Bühler Andreas , Zenz Thorsten , Bullinger Lars , Kühn Michael W. M. , Gerhardinger Andreas , Bloehdorn Johannes , Radtke Ina , Su Xiaoping , Ma Jing , Pounds Stanley , Hallek Michael , Lichter Peter , Korbel Jan , Busch Raymonde , Mertens Daniel , Downing James R. , Stilgenbauer Stephan , Döhner Hartmut
Published: October 2012

To identify genomic alterations in chronic lymphocytic leukemia (CLL), we performed single-nucleotide polymorphism–array analysis using Affymetrix Version 6.0 on 353 samples from untreated patients entered in the CLL8 treatment trial. Based on paired-sample analysis (n = 144), a mean of 1.8 copy number alterations per patient were identified; approximately 60% of patients carried no copy number alterations other than those detected by fluorescence in situ hybridization analysis. Copy-neutral loss-of-heterozygosity was detected in 6% of CLL patients and was found most frequently on 13q, 17p, and 11q. Minimally deleted regions were refined on 13q14 (deleted in 61% of patients) to the DLEU1 and DLEU2 genes, on 11q22.3 (27% of patients) to ATM, on 2p16.1-2p15 (gained in 7% of patients) to a 1.9-Mb fragment containing 9 genes, and on 8q24.21 (5% of patients) to a segment 486 kb proximal to the MYC locus. 13q deletions exhibited proximal and distal breakpoint cluster regions. Among the most common novel lesions were deletions at 15q15.1 (4% of patients), with the smallest deletion (70.48 kb) found in the MGA locus. Sequence analysis of MGA in 59 samples revealed a truncating mutation in one CLL patient lacking a 15q deletion. MNT at 17p13.3, which in addition to MGA and MYC encodes for the network of MAX-interacting proteins, was also deleted recurrently.
The Caulobacter crescentus phage phiCbK: genomics of a canonical phage
Authors: Gill Jason J , Berry Joel D , Russell William K , Lessor Lauren , Escobar-Garcia Diego A , Hernandez Daniel , Kane Ashley , Keene Jennifer , Maddox Matthew , Martin Rebecca , Mohan Sheba , Thorn Ashlyn M , Russell David H , Young Ry
Published: October 2012

Background

The bacteriumCaulobacter crescentusis a popular model for the study of cell cycle regulation and senescence. The large prolate siphophage phiCbK has been an important tool inC. crescentusbiology, and has been studied in its own right as a model for viral morphogenesis. Although a system of some interest, to date little genomic information is available on phiCbK or its relatives.

Results

Five novel phiCbK-likeC. crescentusbacteriophages, CcrMagneto, CcrSwift, CcrKarma, CcrRogue and CcrColossus, were isolated from the environment. The genomes of phage phiCbK and these five environmental phage isolates were obtained by 454 pyrosequencing. The phiCbK-like phage genomes range in size from 205 kb encoding 318 proteins (phiCbK) to 280 kb encoding 448 proteins (CcrColossus), and were found to contain nonpermuted terminal redundancies of 10 to 17 kb. A novel method of terminal ligation was developed to map genomic termini, which confirmed termini predicted by coverage analysis. This suggests that sequence coverage discontinuities may be useable as predictors of genomic termini in phage genomes. Genomic modules encoding virion morphogenesis, lysis and DNA replication proteins were identified. The phiCbK-like phages were also found to encode a number of intriguing proteins; all contain a clearly T7-like DNA polymerase, and five of the six encode a possible homolog of theC. crescentuscell cycle regulator GcrA, which may allow the phage to alter the host cell’s replicative state. The structural proteome of phage phiCbK was determined, identifying the portal, major and minor capsid proteins, the tail tape measure and possible tail fiber proteins. All six phage genomes are clearly related; phiCbK, CcrMagneto, CcrSwift, CcrKarma and CcrRogue form a group related at the DNA level, while CcrColossus is more diverged but retains significant similarity at the protein level.

Conclusions

Due to their lack of any apparent relationship to other described phages, this group is proposed as the founding cohort of a new phage type, the phiCbK-like phages. This work will serve as a foundation for future studies on morphogenesis, infection and phage-host interactions inC. crescentus.
Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis
Authors: Katiyar Amit , Smita Shuchi , Lenka Sangram Keshari , Rajwanshi Ravi , Chinnusamy Viswanathan , Bansal Kailash Chander
Published: October 2012

Background

The MYB gene family comprises one of the richest groups of transcription factors in plants. Plant MYB proteins are characterized by a highly conserved MYB DNA-binding domain. MYB proteins are classified into four major groups namely, 1R-MYB, 2R-MYB, 3R-MYB and 4R-MYB based on the number and position of MYB repeats. MYB transcription factors are involved in plant development, secondary metabolism, hormone signal transduction, disease resistance and abiotic stress tolerance. A comparative analysis of MYB family genes in rice and Arabidopsis will help reveal the evolution and function of MYB genes in plants.

Results

A genome-wide analysis identified at least 155 and 197 MYB genes in rice and Arabidopsis, respectively. Gene structure analysis revealed that MYB family genes possess relatively more number of introns in the middle as compared with C- and N-terminal regions of the predicted genes. Intronless MYB-genes are highly conserved both in rice and Arabidopsis. MYB genes encoding R2R3 repeat MYB proteins retained conserved gene structure with three exons and two introns, whereas genes encoding R1R2R3 repeat containing proteins consist of six exons and five introns. The splicing pattern is similar among R1R2R3 MYB genes in Arabidopsis. In contrast, variation in splicing pattern was observed among R1R2R3 MYB members of rice. Consensus motif analysis of 1kb upstream region (5′ to translation initiation codon) of MYB gene ORFs led to the identification of conserved and over-represented cis-motifs in both rice and Arabidopsis. Real-time quantitative RT-PCR analysis showed that several members of MYBs are up-regulated by various abiotic stresses both in rice and Arabidopsis.

Conclusion

A comprehensive genome-wide analysis of chromosomal distribution, tandem repeats and phylogenetic relationship of MYB family genes in rice and Arabidopsis suggested their evolution via duplication. Genome-wide comparative analysis of MYB genes and their expression analysis identified several MYBs with potential role in development and stress response of plants.
An olfactory demography of a diverse metropolitan population
Authors: Keller Andreas , Hempstead Margaret , Gomez Iran A , Gilbert Avery N , Vosshall Leslie B
Published: October 2012

Background

Human perception of the odour environment is highly variable. People vary both in their general olfactory acuity as well as in if and how they perceive specific odours. In recent years, it has been shown that genetic differences contribute to variability in both general olfactory acuity and the perception of specific odours. Odour perception also depends on other factors such as age and gender. Here we investigate the influence of these factors on both general olfactory acuity and on the perception of 66 structurally and perceptually different odours in a diverse subject population.

Results

We carried out a large human olfactory psychophysics study of 391 adult subjects in metropolitan New York City, an ethnically and culturally diverse North American metropolis. 210 of the subjects were women and the median age was 34.6 years (range 19–75). We recorded ~2,300 data points per subject to obtain a comprehensive perceptual phenotype, comprising multiple perceptual measures of 66 diverse odours. We show that general olfactory acuity correlates with gender, age, race, smoking habits, and body type. Young, female, non-smoking subjects had the highest average olfactory acuity. Deviations from normal body type in either direction were associated with decreased olfactory acuity. Beyond these factors we also show that, surprisingly, there are many odour-specific influences of race, age, and gender on olfactory perception. We show over 100 instances in which the intensity or pleasantness perception of an odour is significantly different between two demographic groups.

Conclusions

These data provide a comprehensive snapshot of the olfactory sense of a diverse population. Olfactory acuity in the population is most strongly influenced by age, followed by gender. We also show a large number of diverse correlations between demographic factors and the perception of individual odours that may reflect genetic differences as well as different prior experiences with these odours between demographic groups.
Two putative-aquaporin genes are differentially expressed during arbuscular mycorrhizal symbiosis in Lotus japonicus
Authors: Giovannetti Marco , Balestrini Raffaella , Volpe Veronica , Guether Mike , Straub Daniel , Costa Alex , Ludewig Uwe , Bonfante Paola
Published: October 2012

Background

Arbuscular mycorrhizas (AM) are widespread symbioses that provide great advantages to the plant, improving its nutritional status and allowing the fungus to complete its life cycle. Nevertheless, molecular mechanisms that lead to the development of AM symbiosis are not yet fully deciphered. Here, we have focused on two putative aquaporin genes, LjNIP1 and LjXIP1, which resulted to be upregulated in a transcriptomic analysis performed on mycorrhizal roots of Lotus japonicus.

Results

A phylogenetic analysis has shown that the two putative aquaporins belong to different functional families: NIPs and XIPs. Transcriptomic experiments have shown the independence of their expression from their nutritional status but also a close correlation with mycorrhizal and rhizobial interaction. Further transcript quantification has revealed a good correlation between the expression of one of them, LjNIP1, and LjPT4, the phosphate transporter which is considered a marker gene for mycorrhizal functionality. By using laser microdissection, we have demonstrated that one of the two genes, LjNIP1, is expressed exclusively in arbuscule-containing cells. LjNIP1, in agreement with its putative role as an aquaporin, is capable of transferring water when expressed in yeast protoplasts. Confocal analysis have demonstrated that eGFP-LjNIP1, under its endogenous promoter, accumulates in the inner membrane system of arbusculated cells.

Conclusions

Overall, the results have shown different functionality and expression specificity of two mycorrhiza-inducible aquaporins in L. japonicus. One of them, LjNIP1 can be considered a novel molecular marker of mycorrhizal status at different developmental stages of the arbuscule. At the same time, LjXIP1 results to be the first XIP family aquaporin to be transcriptionally regulated during symbiosis.
The role of aspirin in post-polypectomy bleeding – a retrospective survey
Authors: Pan Antony , Schlup Martin , Lubcke Ralf , Chou Annie , Schultz Michael
Published: October 2012

Background

Bleeding following colonoscopic polypectomy is a common complication and has been reported to occur in up to 6.1% of patients. Several risk factors have been discussed but their overall contribution to post-polypectomy bleeding remains controversial. The aim of the study was to determine the rate of post polypectomy bleeding and to analyse the role of potential risk factors especially the role of aspirin.

Methods

We conducted a retrospective cohort study of all patients who underwent polypectomy at Dunedin Hospital, New Zealand between January 2007 and June 2009.

Results

During the study period, 514 patients underwent colonoscopy with polypectomy and a total of 1502 polyps were removed. From further analysis we excluded 21 patients; 15 patients had surgery immediately after colonoscopy for the diagnosis of colorectal carcinoma and 6 patients presented with symptoms of an acute lower gastrointestinal bleed prior to colonoscopy. Of the remaining 493 patients, 11 patients (2.2%) presented with post-polypectomy bleeding within 30 days of the investigation of which 8 were on aspirin. In total 145 patients were taking aspirin prior to colonoscopy and 348 patients were not taking aspirin. The use of aspirin was associated with an increased prevalence of post-polypectomy bleeding (OR=6.72, 95% C.I. 1.76 to 25.7). Interestingly, the use of non-steroidal anti-inflammatory drugs (NSAIDs) was not associated with risk of bleeding after polypectomy (OR=2.82, 95% C.I, 0.34 to 23.3).

Conclusion

Our study confirmed a significantly increased risk of lower gastrointestinal bleeding following polypectomy in patients taking aspirin. We would recommend approaching the patient on aspirin coming forward for a colonoscopy with potential polypectomy with caution.
Identification of a novel enhancer that binds Sp1 and contributes to induction of cold-inducible RNA-binding protein (cirp) expression in mammalian cells
Authors: Sumitomo Yasuhiko , Higashitsuji Hiroaki , Higashitsuji Hisako , Liu Yu , Fujita Takanori , Sakurai Toshiharu , Candeias Marco M , Itoh Katsuhiko , Chiba Tsutomu , Fujita Jun
Published: October 2012

Background

There are a growing number of reports on the sub-physiological temperature culturing of mammalian cells for increased recombinant protein yields. However, the effect varies and the reasons for the enhancement are not fully elucidated. Expression of cold-inducible RNA-binding protein (cirp, also called cirbp or hnRNP A18) is known to be induced in response to mild, but not severe, hypothermia in mammalian cells. To clarify the molecular mechanism underlying the induction and to exploit this to improve the productivity of recombinant proteins, we tried to identify the regulatory sequence(s) in the 5′ flanking region of the mouse cirp gene.

Results

By transiently transfecting HEK293 cells with plasmids expressing chloramphenicol acetyltransferase as a reporter, we found that the cirp 5′ flanking region octanucleotide 5′-TCCCCGCC-3′ is a mild-cold responsive element (MCRE). When 3 copies of MCRE were placed upstream of the CMV promoter and used in transient transfection, reporter gene expression was increased 3- to 7-fold at 32°C relative to 37°C in various cell lines including HEK293, U-2 OS, NIH/3T3, BALB/3T3 and CHO-K1 cells. In stable transfectants, MCRE also enhanced the reporter gene expression at 32°C, although more copy numbers of MCRE were necessary. Sp1 transcription factor bound to MCRE in vitro. Immunohistochemistry and chromatin immunoprecipitation assays demonstrated that more Sp1, but not Sp3, was localized in the nucleus to bind to the cirp regulatory region containing MCRE at 32°C than 37°C. Overexpression of Sp1 protein increased the expression of endogenous Cirp as well as a reporter gene driven by the 5′ flanking region of the cirp gene, and down-regulation of Sp1 had the opposite effect. Mutations within the MCRE sequence in the 5′ flanking region abolished the effects of Sp1 on the reporter gene expression both at 37°C and 32°C.

Conclusions

Cold-induced, as well as constitutive, expression of cirp is dependent, at least partly, on MCRE and Sp1. The present novel enhancer permits conditional high-level gene expression at moderately low culture temperatures and could be utilized to increase the yield of recombinant proteins in mammalian cells.
Aggravation of cold-induced injury in Vero-B4 cells by RPMI 1640 medium – Identification of the responsible medium components
Authors: Pless-Petig Gesine , Metzenmacher Martin , Türk Tobias R , Rauen Ursula
Published: October 2012

Background

In modern biotechnology, there is a need for pausing cell lines by cold storage to adapt large-scale cell cultures to the variable demand for their products. We compared various cell culture media/solutions for cold storage of Vero-B4 kidney cells, a cell line widely used in biotechnology.

Results

Cold storage in RPMI 1640 medium, a recommended cell culture medium for Vero-B4 cells, surprisingly, strongly enhanced cold-induced cell injury in these cells in comparison to cold storage in Krebs-Henseleit buffer or other cell culture media (DMEM, L-15 and M199). Manufacturer, batch, medium supplements and the most likely components with concentrations outside the range of the other media/solutions (vitamin B12, inositol, biotin, p-aminobenzoic acid) did not cause this aggravation of cold-induced injury in RPMI 1640. However, a modified Krebs-Henseleit buffer with a low calcium concentration (0.42 mM), a high concentration of inorganic phosphate (5.6 mM), and glucose (11.1 mM; i.e. concentrations as in RPMI 1640) evoked a cell injury and loss of metabolic function corresponding to that observed in RPMI 1640. Deferoxamine improved cell survival and preserved metabolic function in modified Krebs-Henseleit buffer as well as in RPMI 1640. Similar Ca2+ and phosphate concentrations did not increase cold-induced cell injury in the kidney cell line LLC-PK1, porcine aortic endothelial cells or rat hepatocytes. However, more extreme conditions (Ca2+ was nominally absent and phosphate concentration raised to 25 mM as in the organ preservation solution University of Wisconsin solution) also increased cold-induced injury in rat hepatocytes and porcine aortic endothelial cells.

Conclusion

These data suggest that the combination of low calcium and high phosphate concentrations in the presence of glucose enhances cold-induced, iron-dependent injury drastically in Vero-B4 cells, and that a tendency for this pathomechanism also exists in other cell types.