bluuebunny/crossref_metadata_2025 huggingface dataset:
Educational level and changes in health across Europe: longitudinal results from SHARE
Authors: Avendano Mauricio , Jürges Hendrik , Mackenbach Johan P.
Published: October 2009

We use cross-national, longitudinal data to explore the impact of educational level on changes in health outcomes among Europeans aged over 50. Our analyses are performed separately for Northern, Western and Southern Europe, as these regions broadly represent different welfare state regimes. We find that low education is associated with higher incident events — over a two-year period — of poor health, chronic diseases and disability, but it is less consistently associated with new events of long-standing illness. Net of behavioural risk factors, educational effects are more consistent in Western and Southern Europe than in the Nordic welfare states. In Northern Europe, lower education is associated with less financial and employment disadvantage than in Southern or Western Europe. After controlling for educational differences in these factors, effects of educational level on health deterioration remain significant for most outcomes in Western and Southern Europe, whereas they are weaker and non-significant after adjustment in Northern Europe.
The social connectedness of older Europeans: patterns, dynamics and contexts
Authors: Kohli Martin , Hank Karsten , Künemund Harald
Published: October 2009

Using longitudinal data from the Survey of Health, Ageing and Retirement in Europe (SHARE), our article shows that the population aged 50 or older is socially connected in several ways. The various dimensions of social connectedness turn out to be complementary rather than substitutive, except for the relationship between informal social relations and family relations, which tends to be characterized by substitution. Our longitudinal analysis reveals that the dynamics of formal and informal social relations as well as family relations tend to be driven by individuals’ resources and needs. While the associations between elders’ social connectedness and individual characteristics are very similar across countries, we find significant regional variation regarding the levels and the dynamics of social connectedness.
“What Should We Tell the Children About Relationships and Sex?”©: Development of a Program for Parents Using Intervention Mapping
Authors: Newby Katie , Bayley Julie , Wallace L. M.
Published: October 2009

This article describes the development of an intervention that aims to increase the quantity and quality of parent—child communication about sex and relationships. The intervention has been designed as part of a local strategic approach to teenage pregnancy and sexual health. The process and findings of Intervention Mapping (IM), a tool for the development of theory-and evidence-based interventions, are presented. The process involves a detailed assessment of the difficulties parents experience in communicating with their children about sex and relationships. The findings are translated into program and change objectives that specify what parents need to do to improve their communication. Theory-based practical strategies most likely to bring about the desired behavioral change are then identified and pretested. The intervention developed consists of a six-session facilitator-led program that targets parents’ attitudes, knowledge, communication skills, and self-efficacy. Following on from Bartholomew’s seminal work on IM, this article develops and extends the application of this process by presenting explicit detail on the behavioral change techniques used and their theoretical underpinnings. The strengths and weaknesses of IM as a process for the development of health behavior interventions are discussed.
Seated Bilateral Leg Exercise Effects on Hemiparetic Lower Extremity Function in Chronic Stroke
Authors: Johannsen Leif , Wing Alan Miles , Pelton Trudy , Kitaka Kizito , Zietz Doerte , Brittle Nicola , van Vliet Paulette , Riddoch Jane , Sackley Cath , McManus Richard
Published: October 2009

Background. Bilateral arm training with rhythmic auditory cueing (BATRAC) improves hemiparetic upper extremity (UE) function in stroke. It is unknown whether a similar exercise for the hemiparetic lower extremity (LE) is effective. Objective. The authors sought to test whether the BATRAC strategy would transfer to the legs by improving LE motor function following ten 30-minute sessions of bilateral leg training with rhythmic auditory cueing (BLETRAC). Methods. Twenty-four chronic stroke participants, recruited from the community, were randomized to either the BLETRAC or the BATRAC intervention. Assessments were performed before (week 0) and after (week 6) training as well as 3 months later (week 18). Change in the Fugl-Meyer LE and UE subscales served as primary outcomes. Timed 10-m walk, movement parameters during treadmill walking, and a repetitive aiming task for both feet and hands were the secondary outcomes. Results . Following an intention-to-treat approach, data from 21 subjects were analyzed. After training, improvements in the Fugl-Meyer LE and UE subscales tended to be better for the corresponding intervention group. The BLETRAC group also showed increases in step length during treadmill walking and performance in the repetitive foot and hand aiming tasks. No differences between the intervention groups were found at follow-up. Conclusions. This exploratory trial demonstrates that transfer of the BATRAC approach to the legs is feasible. Transient improvements of limb motor function in chronic stroke participants were induced by targeted exercise (BATRAC for the UE and BLETRAC for the LE). It may be that further periods of training would increase and maintain effects.
Review: Toward a Better Understanding of Coordination in Healthy and Poststroke Gait
Authors: Krasovsky Tal , Levin Mindy F.
Published: October 2009

Locomotor coordination characterizes healthy gait and rehabilitation effectiveness in poststroke individuals. However, despite a large number of clinic-based and laboratory-based measurement options, to date there is no gold standard for measurement of locomotor coordination. A lack of a common definition for locomotor coordination may be a cause of this confusion. Coordination during gait includes both spatial and temporal components that may be measured in extrinsic or intrinsic reference frames. Measurement tools have been used to evaluate one or both aspects of coordination. The authors suggest an operational definition of locomotor coordination and describe how current measures in healthy and poststroke individuals fit with this definition. They define locomotor coordination as an ability to maintain a context-dependent and phase-dependent cyclical relationship between different body segments or joints in both spatial and temporal domains. Advantages and disadvantages of laboratory-based measures, such as cyclograms, discrete and continuous relative phase, power spectral density, and others are summarized and discussed. In addition to the definition, the authors propose a clinically feasible measurement paradigm that accentuates the adaptive component of coordination and that may be useful in merging the clinical and laboratory-based approaches to locomotor coordination.
News Framing During a Time of Impending War
Authors: Melkote Srinivas R.
Published: October 2009

This article is an empirical analysis that falls under the category of media criticism and accountability. Specifically, the study investigated the manner in which The New York Times framed the events, issues and actors during the month prior to the start of the 2003 war with Iraq. The study focused on: Saddam Hussein, George Bush Jr, the United Nations, weapons of mass destruction, the US Armed Forces (in Iraq) and France, Germany and Russia. The study discovered negative bias in the coverage, especially toward Saddam Hussein, WMDs, the UN and France, Germany and Russia.
Television Drama, Narrative Engagement and Audience Buying Behavior
Authors: Do Kyun Kim  , Singhal Arvind , Hanaki Toru , Dunn Jennifer , Chitnis Ketan , Min Wha Han
Published: October 2009

In the past few years, the popularity of Korean television dramas, songs and movies has skyrocketed in countries of North and Southeast Asia. This huge wave of Korean pop culture is referred to as the Hanryu (the Korean wave). One of the most significant trendsetters of the Hanryu was the Korean television drama Winter Sonata, which was remarkably popular in every Asian country where it was broadcast. The present article investigates the perception of Japanese audience members toward Winter Sonata’s narrative and how this perception influenced their buying behavior of Winter Sonata memorabilia, such as clothing, cosmetics, DVDs/CDs of the program, trips to Korea and the like. Employing both qualitative and quantitative methods, this study finds that the popularity of the drama was generated by Japanese audiences’ engagement with its narrative. Further, the audience perception of the narrative’s quality was found to predict whether or not they purchased a Winter Sonata product.
A Product of Their Culture
Authors: Hanusch Folker
Published: October 2009

Past approaches adopted by scholars in comparing international news have tended to concentrate on political and economic perspectives, while the role that culture plays in determining news has been somewhat neglected until recently. This article examines the role of culture in the development of journalistic practices and how a value systems approach can be applied to understanding journalism practices across cultures. Specifically, the article compares German and Anglo-American journalism practices with a view to locating differences between these traditions. The study demonstrates that using value systems as developed by Dutch anthropologist Geert Hofstede can be immensely useful in comparing the differences between the two traditions, as well as in understanding how journalists in these traditions report about the world.
An anatomic study of flexor tendon sheaths: a cadaveric study
Authors: FUSSEY J. M. , CHIN K. F. , GOGI N. , GELLA S. , DESHMUKH S. C.
Published: October 2009

Previous descriptions of the pattern of communication between the digital flexor tendon sheaths have been largely based on imaging studies. An anatomic study on 12 cadaveric hands was conducted using water soluble dye and directly observed patterns of communication between the digital flexor tendon sheaths and the radial and ulnar bursae. Four out of twelve specimens (33%) demonstrated a communication between the radial and ulnar bursae. The ulnar bursa communicated with the ring finger flexor sheath in two specimens, and the index finger flexor sheath in two specimens. One hand (8.3%) showed communication between the middle finger tendon sheath and radial bursa and between the index finger flexor tendon sheath and radial bursa. These findings show a considerable level of variation in communicating patterns between the synovial sheaths of the hand and wrist. Clinicians should be aware of the possibility of variations to the classical presentation of spread of infection through the digital flexor sheaths.
Leukotriene modifiers in the treatment of asthma in children
Authors: del Giudice Michele Miraglia , Pezzulo Assunta , Capristo Carlo , Alterio Emilia , Caggiano Serena , de Benedictis Diletta , Capristo Angelo F.
Published: October 2009

Asthma is one of the most common respiratory disorders in clinical practice, affecting up to 13% of people worldwide. Inflammation is the most important component of asthma and inhaled corticosteroids (ICS) are recommended as the first line controller treatment for patients of all ages. Treatment with corticosteroids is often unable to fully control asthma symptoms and progression. Recently, leukotrienes have come to the forefront of research as they have been found play a pivotal role in the airway inflammatory process, and specific drugs have been developed to target them. Cysteiny leukotriene antagonists (LTRAs) have recently emerged as important therapeutic options that show a large potential clinical utility. Three specific LTRAs are licensed for clinical use: montelukast, zafirlukast and pranlukast, although montelukast is the only drug approved in the paediatric age range. It is well tolerated (although adverse effects such as headaches, abdominal pain, rashes, angioedema, pulmonary eosinophilia and arthralgia have been reported) and shows many positive effects in asthmatic patients. Current Global Initiative for Asthma guidelines recommend LTRAs as: (1) a second choice treatment to ICS for patients with mild persistent asthma, (2) an add-on therapy to reduce the dose of ICS in patients with moderate or severe asthma, due to the different and complementary mechanisms of action of these agents. LTRAs may be particularly appropriate choices in a number of clinical situations, including the following: patients with concomitant rhinitis; patients with viral-induced wheeze; patients with exercise-induced bronchoconstriction (EIB) and, in children aged 2-5 years, to reduce the frequency of asthma exacerbations.
ATG-induced expression of FOXP3 in human CD4+ T cells in vitro is associated with T-cell activation and not the induction of FOXP3+ T regulatory cells
Authors: Broady Raewyn , Yu Jie , Levings Megan K.
Published: October 2009

Several recent reports have suggested that in vitro exposure of CD4+ T cells to rabbit antithymocyte globulin (rATG), which is commonly used to prevent and treat graft-versus-host disease and allograft rejection, is an effective method to induce CD4+CD25+FOXP3+ T regulatory cells (Tregs). We and others, however, have shown that FOXP3 is also expressed in activated T cells. We therefore investigated whether the induction of FOXP3 expression by rATG resulted in a stable population of suppressive Tregs. We found that exposure of peripheral blood mononuclear cells (PBMCs) or conventional T cells to rATG resulted in induction of transient rather than stable expression of CD25 and FOXP3. Furthermore, rATG-treated T effector cells acquired neither an immunosuppressive profile of cytokine production nor suppressive capacity, even at the time of maximal FOXP3 expression. These findings indicate that the notion that rATG can be used to induce Tregs in vitro for cellular therapy in vivo should be re-evaluated.
Differential roles for ETS, CREB, and EGR binding sites in mediating VEGF receptor 1 expression in vivo
Authors: Jin Enjing , Liu Ju , Suehiro Jun-ichi , Yuan Lei , Okada Yoshiaki , Nikolova-Krstevski Vesna , Yano Kiichiro , Janes Lauren , Beeler David , Spokes Katherine C. , Li Dan , Regan Erzsébet , Shih Shou-Ching , Oettgen Peter , Minami Takashi , Aird William C.
Published: October 2009

Vascular endothelial growth factor receptor 1 (VEGFR1) is a marker for endothelial-specific gene expression. We previously reported that the human VEGFR1 promoter (between −748 and +284) contains information for expression in the intact endothelium of transgenic mice. The objective of this study was to dissect the cis-regulatory elements underlying VEGFR1 promoter activity in vitro and in vivo. In primary endothelial cells, binding sites for E74-like factor 1 (ELF-1; between −49 and −52), cyclic adenosine monophosphate response element binding (CREB; between −74 and −81), and early growth response factor 1/3 (EGR-1/3; between −16 to −25) were shown to play a positive role in gene transcription, whereas a putative E26 transformation-specificsequence (ETS) motif between −36 and −39 had a net negative effect on promoter activity. When targeted to the Hprt locus of mice, mutations of the ELF-1 binding site and the CRE element reduced promoter activity in the embryonic vasculature and resulted in a virtual loss of expression in adult endothelium. Postnatally, the EGR binding site mutant displayed significantly reduced promoter activity in a subset of vascular beds. In contrast, mutation of the −39 ETS site resulted in increased LacZ staining in multiple vascular beds. Together, these results provide new insights into the transcriptional regulatory mechanisms of VEGFR1.
Pericyte recruitment during vasculogenic tube assembly stimulates endothelial basement membrane matrix formation
Authors: Stratman Amber N. , Malotte Kristine M. , Mahan Rachel D. , Davis Michael J. , Davis George E.
Published: October 2009

We show that endothelial cell (EC)–generated vascular guidance tunnels (ie, matrix spaces created during tube formation) serve as conduits for the recruitment and motility of pericytes along EC ablumenal surfaces to facilitate vessel maturation events, including vascular basement membrane matrix assembly and restriction of EC tube diameter. During quail development, pericyte recruitment along microvascular tubes directly correlates with vascular basement membrane matrix deposition. Pericyte recruitment to EC tubes leads to specific induction of fibronectin and nidogen-1 (ie, matrix-bridging proteins that link together basement membrane components) as well as perlecan and laminin isoforms. Coincident with these events, up-regulation of integrins, α5β1, α3β1, α6β1, and α1β1, which bind fibronectin, nidogens, laminin isoforms, and collagen type IV, occurs in EC-pericyte cocultures, but not EC-only cultures. Integrin-blocking antibodies to these receptors, disruption of fibronectin matrix assembly, and small interfering RNA suppression of pericyte tissue inhibitor of metalloproteinase (TIMP)-3 (a known regulator of vascular tube stabilization) all lead to decreased EC basement membrane, resulting in increased vessel lumen diameter, a key indicator of dysfunctional EC-pericyte interactions. Thus, pericyte recruitment to EC-lined tubes during vasculogenesis is a stimulatory event controlling vascular basement membrane matrix assembly, a fundamental maturation step regulating the transition from vascular morphogenesis to stabilization.
The impact of prophylactic fresh-frozen plasma and cryoprecipitate on the incidence of central nervous system thrombosis and hemorrhage in children with acute lymphoblastic leukemia receiving asparaginase
Authors: Abbott Lesleigh S. , Deevska Mariana , Fernandez Conrad V. , Dix David , Price Victoria E. , Wang Hao , Parker Louise , Yhap Margaret , Fitzgerald Colleen , Barnard Dorothy R. , Berman Jason N.
Published: October 2009

Asparaginase (ASP) therapy is associated with depletion of antithrombin (AT) and fibrinogen (FG). Potential toxicities include central nervous system thrombosis (CNST) and hemorrhage. Historical practice at the Izaak Walton Killam Health Centre (IWK) involves measuring AT and FG levels after ASP administration and transfusing fresh-frozen plasma (FFP) or cryoprecipitate (CRY) to prevent thrombotic and hemorrhagic complications. To determine whether this reduced these complications in children with acute lymphoblastic leukemia (ALL), incidence, outcome, and clinical characteristics of ASP-related CNST in ALL patients at IWK were compared with a similar cohort from BC Children's Hospital (BCCH), where prophylaxis was not performed. Costs associated with preventative versus expectant management were estimated. From 1990 to 2005, 240 patients were treated at IWK and 479 at BCCH. Seven BCCH patients developed venous CNST (1.5%), compared with none at IWK. CNST occurred exclusively during induction. Six patients received anticoagulation and continued ASP. All 7 patients remain in remission. National Cancer Institute high-risk ALL predicted CNST risk (P = .02), whereas sex, age, race, and body mass index did not. Neither FFP nor CRY protected against CNST, suggesting prophylaxis is unwarranted for unselected ALL patients. However, prophylactic replacement for HR patients in induction may be cost-effective.
Immunoglobulin aggregation leading to Russell body formation is prevented by the antibody light chain
Authors: Corcos Daniel , Osborn Michael J. , Matheson Louise S. , Santos Fatima , Zou Xiangang , Smith Jennifer A. , Morgan Geoff , Hutchings Amanda , Hamon Maureen , Oxley David , Brüggemann Marianne
Published: October 2009

Russell bodies (RBs) are intracellular inclusions filled with protein aggregates. In diverse lymphoid disorders these occur as immunoglobulin (Ig) deposits, accumulating in abnormal plasma or Mott cells. In heavy-chain deposition disease truncated antibody heavy-chains (HCs) are found, which bear a resemblance to diverse polypeptides produced in Ig light-chain (LC)–deficient (L−/−) mice. In L−/− animals, the known functions of LC, providing part of the antigen-binding site of an antibody and securing progression of B-cell development, may not be required. Here, we show a novel function of LC in preventing antibody aggregation. L−/− mice produce truncated HC naturally, constant region (C)γ and Cα lack CH1, and Cμ is without CH1 or CH1 and CH2. Most plasma cells found in these mice are CD138+ Mott cells, filled with RBs, formed by aggregation of HCs of different isotypes. The importance of LC in preventing HC aggregation is evident in knock-in mice, expressing Cμ without CH1 and CH2, which only develop an abundance of RBs when LC is absent. These results reveal that preventing antibody aggregation is a major function of LC, important for understanding the physiology of heavy-chain deposition disease, and in general recognizing the mechanisms, which initiate protein conformational diseases.
VANLO - Interactive visual exploration of aligned biological networks
Authors: Brasch Steffen , Linsen Lars , Fuellen Georg
Published: October 2009

Background

Protein-protein interaction (PPI) is fundamental to many biological processes. In the course of evolution, biological networks such as protein-protein interaction networks have developed. Biological networks of different species can be aligned by finding instances (e.g. proteins) with the same common ancestor in the evolutionary process, so-called orthologs. For a better understanding of the evolution of biological networks, such aligned networks have to be explored. Visualization can play a key role in making the various relationships transparent.

Results

We present a novel visualization system for aligned biological networks in 3D space that naturally embeds existing 2D layouts. In addition to displaying the intra-network connectivities, we also provide insight into how the individual networks relate to each other by placing aligned entities on top of each other in separate layers. We optimize the layout of the entire alignment graph in a global fashion that takes into account inter- as well as intra-network relationships. The layout algorithm includes a step of merging aligned networks into one graph, laying out the graph with respect to application-specific requirements, splitting the merged graph again into individual networks, and displaying the network alignment in layers. In addition to representing the data in a static way, we also provide different interaction techniques to explore the data with respect to application-specific tasks.

Conclusion

Our system provides an intuitive global understanding of aligned PPI networks and it allows the investigation of key biological questions. We evaluate our system by applying it to real-world examples documenting how our system can be used to investigate the data with respect to these key questions. Our tool VANLO (Visualization of Aligned Networks with Layout Optimization) can be accessed at http://www.math-inf.uni-greifswald.de/VANLO.
miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression
Authors: Wang Wei-Chi , Lin Feng-Mao , Chang Wen-Chi , Lin Kuan-Yu , Huang Hsien-Da , Lin Na-Sheng
Published: October 2009

Background

MicroRNAs (miRNAs), small non-coding RNAs of 19 to 25 nt, play important roles in gene regulation in both animals and plants. In the last few years, the oligonucleotide microarray is one high-throughput and robust method for detecting miRNA expression. However, the approach is restricted to detecting the expression of known miRNAs. Second-generation sequencing is an inexpensive and high-throughput sequencing method. This new method is a promising tool with high sensitivity and specificity and can be used to measure the abundance of small-RNA sequences in a sample. Hence, the expression profiling of miRNAs can involve use of sequencing rather than an oligonucleotide array. Additionally, this method can be adopted to discover novel miRNAs.

Results

This work presents a systematic approach, miRExpress, for extracting miRNA expression profiles from sequencing reads obtained by second-generation sequencing technology. A stand-alone software package is implemented for generating miRNA expression profiles from high-throughput sequencing of RNA without the need for sequenced genomes. The software is also a database-supported, efficient and flexible tool for investigating miRNA regulation. Moreover, we demonstrate the utility of miRExpress in extracting miRNA expression profiles from two Illumina data sets constructed for the human and a plant species.

Conclusion

We develop miRExpress, which is a database-supported, efficient and flexible tool for detecting miRNA expression profile. The analysis of two Illumina data sets constructed from human and plant demonstrate the effectiveness of miRExpress to obtain miRNA expression profiles and show the usability in finding novel miRNAs.
BASE - 2nd generation software for microarray data management and analysis
Authors: Vallon-Christersson Johan , Nordborg Nicklas , Svensson Martin , Häkkinen Jari
Published: October 2009

Background

Microarray experiments are increasing in size and samples are collected asynchronously over long time. Available data are re-analysed as more samples are hybridized. Systematic use of collected data requires tracking of biomaterials, array information, raw data, and assembly of annotations. To meet the information tracking and data analysis challenges in microarray experiments we reimplemented and improved BASE version 1.2.

Results

The new BASE presented in this report is a comprehensive annotable local microarray data repository and analysis application providing researchers with an efficient information management and analysis tool. The information management system tracks all material from biosource, via sample and through extraction and labelling to raw data and analysis. All items in BASE can be annotated and the annotations can be used as experimental factors in downstream analysis. BASE stores all microarray experiment related data regardless if analysis tools for specific techniques or data formats are readily available. The BASE team is committed to continue improving and extending BASE to make it usable for even more experimental setups and techniques, and we encourage other groups to target their specific needs leveraging on the infrastructure provided by BASE.

Conclusion

BASE is a comprehensive management application for information, data, and analysis of microarray experiments, available as free open source software at http://base.thep.lu.se under the terms of the GPLv3 license.
A tamoxifen inducible knock-in allele for investigation of E2A function
Authors: Jones Mary E , Kondo Motonari , Zhuang Yuan
Published: October 2009

Background

E-proteins are transcription factors important for the development of a variety of cell types, including neural, muscle and lymphocytes of the immune system. E2A, the best characterized E-protein family member in mammals, has been shown to have stage specific roles in cell differentiation, lineage commitment, proliferation, and survival. However, due to the complexity of E2A function, it is often difficult to separate these roles using conventional genetic approaches. Here, we have developed a new genetic model for reversible control of E2A protein activity at physiological levels. This system was created by inserting a tamoxifen-responsive region of the estrogen receptor (ER) at the carboxyl end of the tcfe2a gene to generate E2AER fusion proteins. We have characterized and analyzed the efficiency and kinetics of this inducible E2AER system in the context of B cell development.

Results

B cell development has been shown previously to be blocked at an early stage in E2A deficient animals. Our E2AER/ER mice demonstrated this predicted block in B cell development, and E2AER DNA binding activity was not detected in the absence of ligand. In vitro studies verified rapid induction of E2AER DNA binding activity upon tamoxifen treatment. While tamoxifen treatment of E2AER/ER mice showed inefficient rescue of B cell development in live animals, direct exposure of bone marrow cells to tamoxifen in an ex vivo culture was sufficient to rescue and support early B cell development from the pre-proB cell stage.

Conclusion

The E2AER system provides inducible and reversible regulation of E2A function at the protein level. Many previous studies have utilized over-expression systems to induce E2A function, which are complicated by the toxicity often resulting from high levels of E2A. The E2AER model instead restores E2A activity at an endogenous level and in addition, allows for tight regulation of the timing of induction. These features make our E2AER
ex vivo culture system attractive to study both immediate and gradual downstream E2A-mediated events.
Cyto-nuclear discordance in the phylogeny of Ficus section Galoglychia and host shifts in plant-pollinator associations
Authors: Renoult Julien P , Kjellberg Finn , Grout Cinderella , Santoni Sylvain , Khadari Bouchaïb
Published: October 2009

Background

Hybridization events are relatively common in vascular plants. However, the frequency of these events is unevenly distributed across the plant phylogeny. Plant families in which individual species are pollinated by specific pollinator species are predicted to be less prone to hybridization than other families. However, exceptions may occur within these families, when pollinators shift host-plant species. Indeed, host shifts are expected to increase the rate of hybridization events. Pollinators of Ficus section Galoglychia are suspected to have changed host repeatedly, based on several cases of incongruence between plant phylogeny and taxonomy, and insect phylogeny and taxonomy. We tracked cyto-nuclear discordance across section Galoglychia as evidence for hybridization. To achieve a proper global view, we first clarified the monophyly of section Galoglychia as it had been questioned by recent phylogenetic studies. Moreover, we investigated if fig size could be a factor facilitating host shifts.

Results

Phylogenetic chloroplast and nuclear results demonstrated the monophyly of section Galoglychia. Within section Galoglychia, we detected several cases of statistically significant cyto-nuclear discordance. Discordances concern both terminal nodes of the phylogenetic trees and one deep node defining relationships between subsections. Because nuclear phylogeny is congruent with morphological taxonomy, discordances were caused by the chloroplast phylogeny. Introgressive hybridization was the most likely explanation for these discordances. We also detected that subsections pollinated by several wasp genera had smaller figs and were pollinated by smaller wasps than subsections pollinated by a single wasp genus.

Conclusion

As hypothesized, we discovered evidences of past hybridization in Ficus section Galoglychia. Further, introgression was only detected in subsections presenting incongruence between plant and pollinator phylogenies and taxonomy. This supports the hypothesis that host shift is the cause for plant-pollinator incongruence. Moreover, small fig size could facilitate host shifts. Eventually, this study demonstrates that non-coding chloroplast markers are valuable to resolve deep nodes in Ficus phylogeny.
An oligo-based microarray offers novel transcriptomic approaches for the analysis of pathogen resistance and fruit quality traits in melon (Cucumis melo L.)
Authors: Mascarell-Creus Albert , Cañizares Joaquin , Vilarrasa-Blasi Josep , Mora-García Santiago , Blanca José , Gonzalez-Ibeas Daniel , Saladié Montserrat , Roig Cristina , Deleu Wim , Picó-Silvent Belén , López-Bigas Nuria , Aranda Miguel A , Garcia-Mas Jordi , Nuez Fernando , Puigdomènech Pere , Caño-Delgado Ana I
Published: October 2009

Background

Melon (Cucumis melo) is a horticultural specie of significant nutritional value, which belongs to the Cucurbitaceae family, whose economic importance is second only to the Solanaceae. Its small genome of approx. 450 Mb coupled to the high genetic diversity has prompted the development of genetic tools in the last decade. However, the unprecedented existence of a transcriptomic approaches in melon, highlight the importance of designing new tools for high-throughput analysis of gene expression.

Results

We report the construction of an oligo-based microarray using a total of 17,510 unigenes derived from 33,418 high-quality melon ESTs. This chip is particularly enriched with genes that are expressed in fruit and during interaction with pathogens. Hybridizations for three independent experiments allowed the characterization of global gene expression profiles during fruit ripening, as well as in response to viral and fungal infections in plant cotyledons and roots, respectively. Microarray construction, statistical analyses and validation together with functional-enrichment analysis are presented in this study.

Conclusion

The platform validation and enrichment analyses shown in our study indicate that this oligo-based microarray is amenable for future genetic and functional genomic studies of a wide range of experimental conditions in melon.
Insertion sequence content reflects genome plasticity in strains of the root nodule actinobacterium Frankia
Authors: Bickhart Derek M , Gogarten Johann P , Lapierre Pascal , Tisa Louis S , Normand Philippe , Benson David R
Published: October 2009

Background

Genome analysis of three Frankia sp. strains has revealed a high number of transposable elements in two of the strains. Twelve out of the 20 major families of bacterial Insertion Sequence (IS) elements are represented in the 148 annotated transposases of Frankia strain HFPCcI3 (CcI3) comprising 3% of its total coding sequences (CDS). EAN1pec (EAN) has 183 transposase ORFs from 13 IS families comprising 2.2% of its CDS. Strain ACN14a (ACN) differs significantly from the other strains with only 33 transposase ORFs (0.5% of the total CDS) from 9 IS families.

Results

Insertion sequences in the Frankia genomes were analyzed using BLAST searches, PHYML phylogenies and the IRF (Inverted Repeat Finder) algorithms. To identify putative or decaying IS elements, a PSI-TBLASTN search was performed on all three genomes, identifying 36%, 39% and 12% additional putative transposase ORFs than originally annotated in strains CcI3, EAN and ACN, respectively. The distribution of transposase ORFs in each strain was then analysed using a sliding window, revealing significant clustering of elements in regions of the EAN and CcI3 genomes. Lastly the three genomes were aligned with the MAUVE multiple genome alignment tool, revealing several Large Chromosome Rearrangement (LCR) events; many of which correlate to transposase clusters.

Conclusion

Analysis of transposase ORFs in Frankia sp. revealed low inter-strain diversity of transposases, suggesting that the majority of transposase proliferation occurred without recent horizontal transfer of novel mobile elements from outside the genus. Exceptions to this include representatives from the IS3 family in strain EAN and seven IS4 transposases in all three strains that have a lower G+C content, suggesting recent horizontal transfer. The clustering of transposase ORFs near LCRs revealed a tendency for IS elements to be associated with regions of chromosome instability in the three strains. The results of this study suggest that IS elements may help drive chromosome differences in different Frankia sp. strains as they have adapted to a variety of hosts and environments.
Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades
Authors: Förster Frank , Liang Chunguang , Shkumatov Alexander , Beisser Daniela , Engelmann Julia C , Schnölzer Martina , Frohme Marcus , Müller Tobias , Schill Ralph O , Dandekar Thomas
Published: October 2009

Background

Tardigrades represent an animal phylum with extraordinary resistance to environmental stress.

Results

To gain insights into their stress-specific adaptation potential, major clusters of related and similar proteins are identified, as well as specific functional clusters delineated comparing all tardigrades and individual species (Milnesium tardigradum, Hypsibius dujardini, Echiniscus testudo, Tulinus stephaniae, Richtersius coronifer) and functional elements in tardigrade mRNAs are analysed. We find that 39.3% of the total sequences clustered in 58 clusters of more than 20 proteins. Among these are ten tardigrade specific as well as a number of stress-specific protein clusters. Tardigrade-specific functional adaptations include strong protein, DNA- and redox protection, maintenance and protein recycling. Specific regulatory elements regulate tardigrade mRNA stability such as lox P DICE elements whereas 14 other RNA elements of higher eukaryotes are not found. Further features of tardigrade specific adaption are rapidly identified by sequence and/or pattern search on the web-tool tardigrade analyzer http://waterbear.bioapps.biozentrum.uni-wuerzburg.de. The work-bench offers nucleotide pattern analysis for promotor and regulatory element detection (tardigrade specific; nrdb) as well as rapid COG search for function assignments including species-specific repositories of all analysed data.

Conclusion

Different protein clusters and regulatory elements implicated in tardigrade stress adaptations are analysed including unpublished tardigrade sequences.
Environmental and intracellular regulation of Francisella tularensis ripA
Authors: Fuller James R , Kijek Todd M , Taft-Benz Sharon , Kawula Thomas H
Published: October 2009

Background

Francisella tularensisis a highly virulent, facultative intracellular pathogen and the etiologic agent of the zoonotic disease Tularemia. RipA is a cytoplasmic membrane protein that is conserved amongFrancisellaspecies and is required for intracellular growth.F. tularensis ripAdeletion mutants escape the phagosome of infected cells, but unlike wild type organisms fail to replicate in the host cell cytoplasm.

Results

Further analysis ofripAwith respect to environmental effects on the growth of mutant strains and expression levels revealed that RipA is required for optimal growth at pH 7.5 but not pH 6.5. Using a combination of RT-PCR,ripA-lacZtranscriptional and translational fusions, and a RipA-tetracysteine tag fusion protein we found that bothripAtranscription and RipA protein levels were elevated in organisms grown at pH 7.5 as compared to organisms grown at pH 5.5. A number of genes, includingiglA, that are required for intracellular growth are regulated by the transcriptional regulators MglA and SspA, and are induced upon infection of host cells. We quantifiedripAandiglAexpression at different stages of intracellular growth and found that the expression of each increased between 1 and 6 hours post infection. Given the similar intracellular expression patterns ofripAandiglAand that MglA and SspA are positive regulators ofiglAwe tested the impact ofmglAandsspAdeletions onripAandiglAexpression. In the deletion mutant strainsiglAexpression was reduced dramatically as expected, howeverripAexpression was increased over 2-fold.

Conclusion

Expression ofripAis required for growth at neutral pH, is pH sensitive, and is responsive to the intracellular environment. The intracellular expression pattern ofripAcoincided withiglA, which is positively regulated by MglA and SspA. However, in contrast to their positive impact oniglAexpression, MglA and SspA negatively impactedripAexpressionin vitro.
Noninvasive cardiac output and blood pressure monitoring cannot replace an invasive monitoring system in critically ill patients
Authors: Stover John F , Stocker Reto , Lenherr Renato , Neff Thomas A , Cottini Silvia R , Zoller Bernhard , Béchir Markus
Published: October 2009

Background

Monitoring of cardiac output and blood pressure are standard procedures in critical care medicine. Traditionally, invasive techniques like pulmonary artery catheter (PAC) and arterial catheters are widely used. Invasiveness bears many risks of deleterious complications. Therefore, a noninvasive reliable cardiac output (CO) and blood pressure monitoring system could improve the safety of cardiac monitoring. The aim of the present study was to compare a noninvasive versus a standard invasive cardiovascular monitoring system.

Methods

Nexfin HD is a continuous noninvasive blood pressure and cardiac output monitor system and is based on the development of the pulsatile unloading of the finger arterial walls using an inflatable finger cuff. During continuous BP measurement CO is calculated. We included 10 patients with standard invasive cardiac monitoring system (pulmonary artery catheter and arterial catheter) comparing invasively obtained data to the data collected noninvasively using the Nexfin HD.

Results

Correlation between mean arterial pressure measured with the standard arterial monitoring system and the Nexfin HD was r2 = 0.67 with a bias of -2 mmHg and two standard deviations of ± 16 mmHg. Correlation between CO derived from PAC and the Nexfin HD was r2 = 0.83 with a bias of 0.23 l/min and two standard deviations of ± 2.1 l/min; the percentage error was 29%.

Conclusion

Although the noninvasive CO measurement appears promising, the noninvasive blood pressure assessment is clearly less reliable than the invasively measured blood pressure. Therefore, according to the present data application of the Nexfin HD monitoring system in the ICU cannot be recommended generally. Whether such a tool might be reliable in certain critically ill patients remains to be determined.
Genetic factors associated with intestinal metaplasia in a high risk Singapore-Chinese population: a cohort study
Authors: Zhu Feng , Loh Marie , Hill Jeffrey , Lee Sumarlin , Koh King Xin , Lai Kin Wai , Salto-Tellez Manuel , Iacopetta Barry , Yeoh Khay Guan , Soong Richie ,   the Singapore Gastric Cancer Consortium
Published: October 2009

Background

Intestinal metaplasia (IM) is an important precursor lesion in the development of gastric cancer (GC). The aim of this study was to investigate genetic factors previously linked to GC risk for their possible association with IM. A total of 18 polymorphisms in 14 candidate genes were evaluated in a Singapore-Chinese population at high risk of developing GC.

Methods

Genotype frequencies were compared between individuals presenting with (n = 128) or without (n = 246) IM by both univariate and multivariate analysis.

Results

Carriers of the NQO1 609 T allele showed an association with IM in individuals who were seropositive for Helicobacter pylori (HP+; OR = 2.61, 95%CI: 1.18-5.80, P = .018). The IL-10 819 C allele was also associated with IM in HP+ individuals (OR = 2.32, 95%CI: 1.21-4.43, P = 0.011), while the PTPN11 A allele was associated with IM in HP- individuals (OR = 2.51, 95%CI: 1.16-5.40, P = 0.019), but showed an inverse association in HP+ subjects (OR = 0.46, 95%CI: 0.21-0.99, P = 0.048).

Conclusion

Polymorphisms in NQO1, IL-10 and PTPN11, in combination with HP status, could be used to identify individuals who are more likely to develop IM and therefore GC.
Adiponectin is associated with cardiovascular disease in male renal transplant recipients: baseline results from the LANDMARK 2 study
Authors: Kaisar Mohd O , Armstrong Kirsty , Hawley Carmel , Campbell Scott , Mudge David , Johnson David W , Prins John B , Isbel Nicole M
Published: October 2009

Background

Adiponectin is a major adipocyte-derived protein with insulin-sensitizing, anti-inflammatory and anti-atherogenic properties. Adiponectin levels correlate inversely with renal function and higher levels are predictive of lower cardiovascular disease (CVD) in patients with normal renal function and chronic kidney disease. No data exists on the association between adiponectin and CVD in renal transplant recipients (RTR).

Methods

Standard biochemistry, clinical data and adiponectin were collected from 137 RTR recruited to the LANDMARK 2 study at baseline. The LANDMARK 2 study is an ongoing randomized controlled study that compares the outcome of aggressive risk factor modification for cardiovascular disease versus standard post-transplant care in renal transplant recipients with impaired glucose tolerance or diabetes mellitus.

Results

Mean patient age was 53.4 ± 12 years and the median post-transplantation period was 5 (0.5-31.9) years. Mean serum adiponectin level was 12.3 ± 7.1 μg/mL. On univariate analysis, adiponectin was positively associated with female gender (P = 0.01) and serum high-density lipoprotein (HDL) concentration (P < 0.001), and inversely with body mass index (P = 0.009), metabolic syndrome (P = 0.047), abnormal glucose tolerance (P = 0.01), C-reactive protein (P = 0.001) and serum triglyceride (P < 0.001). On stepwise multivariate analysis, adiponectin in males was negatively correlated with combined baseline CVD (P = 0.03), waist-hip ratio (P = 0.003) and glomerular filtration rate (P = 0.046), and positively with HDL (P < 0.001). In contrast, in females adiponectin was inversely associated with C-reactive protein (P = 0.001) and serum triglyceride.

Conclusion

In conclusion, adiponectin is positively correlated with inflammation, dyslipidemia and abnormal glucose tolerance in RTR. Furthermore, hypoadiponectinemia correlated with increased baseline CVD in male RTR.