bluuebunny/crossref_metadata_2025 huggingface dataset:
Sleep Faster! (Somebody else needs your blanket...)
Authors: Anstey Matthew H. R. , Gildfind Stephen P. , Litvak Eugene
Published: July 2012

One of the elements of the health reform plan, as agreed to by Australian state and federal governments, is to introduce a 4-h National Access Target, to reduce emergency department (ED) waiting times. This article highlights the flawed rationale behind the 4-h rule, the UK experience of this rule and discusses the potential dangers it poses to Australian patients. An alternative solution proposed is the separation of elective and emergency surgical streams to reduce the variability in demand for inpatient services.
Unplanned return visits to emergency in a regional hospital
Authors: Kirby Sue E. , Dennis Sarah M. , Jayasinghe Upali W. , Harris Mark F.
Published: July 2012

Objective. The aim of this study was to determine the patient characteristics associated with unplanned return visits, using routinely collected hospital data, to assist in developing strategies to reduce their occurrence. Methods. Emergency department data from a regional hospital were analysed using univariate and multivariate methods to determine the influence of clinical, service usage and demographic patient characteristics on unplanned return visits. Results. Around 80% of the 16 000 patients attending emergency presented on only one occasion in a year. Five per cent of patients presented with an unplanned return visit. Older patients, those with minor and low urgency conditions and with non-psychotic mental health conditions, those presenting during winter and after hours were significantly more likely to present as unplanned return visits. Conclusion. Although patient characteristics associated with unplanned return visits have been identified, the reasons underpinning the unplanned return visit rate, such as patient service preference and attitudes, need to be more fully investigated. What is known about the topic? Patients who present as unplanned return visits are older and have a range of chronic and acute conditions. Some unplanned return visits occur because of limited access to other non-hospital service. What does this paper add? This paper adds to the field by providing information from a regional hospital in NSW Australia on the patient characteristics associated with unplanned return visits. It provides a basis for differentiating between other groups of frequent emergency department patients. However, the reasons behind the unplanned return visit rate need to be more fully investigated. What are the implications for practitioners? The implications of the findings of this study for policy makers, administrators and clinicians are that access to alternative services for the conditions associated with unplanned return visits need to be further investigated in the context of the role for emergency department services.
Access to same day, next day and after-hours appointments: the views of Australian general practitioners
Authors: Harris Mark F. , Davies Patrick G. Powell , Fanaian Mahnaz , Zwar Nicholas A. , Liaw Siaw-Teng
Published: July 2012

Objective. To evaluate factors associated with the availability of same or next day appointments and after-hours access reported by Australian general practitioners (GPs). Methods. Secondary analysis of a survey of primary care practitioners conducted by the Commonwealth Fund in 2009 in 11 countries. Analysis of factors likely to be associated with reported availability of same or next day appointments and after-hours access. Findings. Of 1016 Australian GPs, 78.8% reported that most patients in their practice had access to an appointment on the same or next day and 50% that their practice had arrangements for after-hours access. Access to same or next day care was better in practices where practitioners reported larger numbers of patients seen per GP per week and reviewed their performance against annual targets, but worse in rural areas and practices routinely reviewing outcomes data. Arrangements for after-hours care were more common among GPs who were planning to retire in the next 5 years; worked in practices with high electronic functioning information systems; and received and reviewed clinical outcome data and incentives for performance. Conclusions. Improving after-hours access requires a comprehensive approach which includes incentives, improvements to information management and organised systems of care with review of data on clinical outcomes. What is known about the topic? Access to general practice is an important priority for the health system and the subject of several reforms and initiatives over the past decade in Australia. Access to same or next day appointments and after-hours has been an increasing concern related to workforce availability, and limited access to general practice is one factor influencing the demand on hospitals, especially their emergency departments. What does this paper add? This paper reports on secondary analysis of a survey of over 1000 general practitioners in Australia. Responses to questions about access to same or next day appointments or after-hours arrangements were analysed for associations with practitioner and practice characteristics and their processes and systems of care. Access to same day appointments is particularly challenging in rural general practice but is more likely to be reported by GPs working in larger practices. Incentives, quality improvement and better information management may be important strategies to improve after-hours access. What are the implications for practitioners? Strategies to improve access to appointments and to after-hours care need to be considered as part of a comprehensive approach which includes financial incentives, strengthening information systems and quality improvement activities.
International medical graduates' reflections on facilitators and barriers to undertaking the Australian Medical Council examination
Authors: McGrath Pam , Henderson Saras , Holewa Hamish A. , Henderson David , Tamargo John
Published: July 2012

Objective. In Australia, 25% of international medical graduates (IMGs) make up the medical workforce. Concern is expressed in the literature about the lack of awareness and knowledge of issues that impinge on IMGs’ education. Although there is literature alluding to difficulties IMGs face with undertaking the Australian Medical Council (AMC) examination, there is little research detailing this experience. We therefore explored IMGs’ reflections on facilitators and barriers in undertaking the AMC examination. Methods. After ethics approval, in-depth telephone interviews were conducted with 30 IMGs selected from a hospital in Queensland. Data were coded and analysed using thematic analysis principles. Results. Two facilitating themes were identified: ability to sit for the first part of the examination in country of origin; and having access to resources such as bridging courses and study groups. Three themes represented barriers: not understanding procedural steps; financial issues; and lack of information on examination content and standards. Conclusion. The themes provide new insights and add depth to existing literature that can be used to improve procedural processes and education for IMGs towards successful outcomes in the AMC examination. What is known about the topic? There is concern expressed in the literature about the lack of awareness and knowledge of issues that impinge on IMGs education. The Australian work that is available only depicts educational experience of fellowships or education and training strategies after IMGs have passed their AMC examination. What does this paper add? The findings indicate that the process of sitting for the AMC examination is perceived as one of the major difficulties associated with entering and integrating into the Australian health system. The findings indicate a range of practical, financial and resource problems faced by IMGs attempting to sit for the AMC examination. What are the implications for practitioners? The detailed accounts from IMGs about their experience with undertaking the AMC examination will provide up-skilling program coordinators with the information they need to better assist IMGs to prepare for the examination. The provision of appropriate medical training and educational support will contribute to more effective integration of IMGs into the healthcare system.
A model-based evaluation of collaborative care in management of patients with type 2 diabetes in Australia: an initial report
Authors: Afzali Hossein Haji Ali , Karnon Jonathan , Gray Jodi , Beilby Justin
Published: July 2012

Objectives.
To analyse the short- and long-term costs and benefits of alternative models of primary care for the management of patients with type 2 diabetes in Australia. The models of care reflect differential uptake of primary care-based incentive programs, including reminder systems and involvement of practice nurses in management. This paper describes our study protocol and its progress.

Methods.
We are undertaking an observational study using a cluster sample design that links retrospective patient data from a range of sources to estimate costs and intermediate outcomes (such as the level of glycosylated haemoglobin (HbA1c)) over a 3-year time horizon. We use the short-term data as a basis to estimate lifetime costs and benefits of alternative models of care using a decision analytic model.

Initial report.
We recruited 15 practices from a metropolitan area (Adelaide) and allocated them to three models of care. Three hundred and ninety-nine patients agreed to participate. We use multilevel analysis to evaluate the association between different models of care and patient-level outcomes, while controlling for several covariates.

Discussion/conclusions.
Given the large amount of funding currently used to maintain primary care-based incentives in general practices in Australia, the results of this study generate the knowledge required to promote investment in the most cost-effective incentives.

What is known about the topic?
Collaborative models of care can improve the outcomes in patients with chronic diseases such as type 2 diabetes (T2D), and the large amount of funding is currently used to maintain primary care-based initiatives to provide incentives for general practices to take a more multidisciplinary approach in management of chronic diseases.

What does this paper add?
There are few model-based studies of the cost-effectiveness of alternative models of care defined on the basis of the uptake of financial incentives within Australian primary care settings for diabetes management. Using routinely collected data, this project evaluates the effectiveness of alternative models of care and estimates long-term costs and benefits of various models of care.

What are the implications for practitioners?
This study explores opportunities for the use of linked, routinely collected data to evaluate clinical practice, and identifies the optimal model of care in management of patients with T2D, with respect to differences in long-term costs and outcomes.
How best to measure health workforce turnover and retention: five key metrics
Authors: Russell Deborah J , Humphreys John S , Wakerman John
Published: July 2012

Objective. This article identifies, critically appraises and illustrates the use of five key workforce turnover and retention metrics that are well suited for use by Australian rural health workforce planners. These are crude turnover (separation) rates, stability rates, survival probabilities, median survival and Cox proportional hazard ratios. Examples of their calculation are presented using actual data obtained from payroll records in Australian rural and remote health services. Conclusion. The use of this small number of metrics as a ‘workforce measurement package’ can help overcome many of the limitations evident when a single measure is reported in isolation, by providing a more comprehensive picture of turnover and retention patterns. We suggest that health services themselves can calculate the simplest measures, whereas regional and centralised health authorities with higher levels of expertise undertake survival analysis and comparisons of compiled data. Implications. These key metrics can be used routinely to measure baseline levels of health worker turnover and retention, to quantify important determinants of turnover and retention, and importantly, to make valid comparisons. This enables areas for improvement to be better targeted using appropriate retention strategies, and changes resulting from retention interventions to be evaluated effectively. What is known about the topic? A vast array of turnover and retention metrics has been described in the literature. However, which of these are likely to be most useful for measuring Australian rural and remote health workforce turnover and retention is not well understood. What does this paper add? In recognition of the shortcomings of using single measures in isolation, this article identifies, critically appraises and illustrates the use of five key workforce turnover and retention metrics, recommending their use as a ‘package’. What are the implications for practitioners? Regular use of the identified metrics can enable health workforce planners to recognise which areas to target for improvement, devise appropriate retention strategies and evaluate changes occurring as a result of retention incentives or interventions.
On the need for a theory of wildland fire spread
Authors: Finney Mark A. , Cohen Jack D. , McAllister Sara S. , Jolly W. Matt
Published: July 2012

We explore the basis of understanding wildland fire behaviour with the intention of stimulating curiosity and promoting fundamental investigations of fire spread problems that persist even in the presence of tremendous modelling advances. Internationally, many fire models have been developed based on a variety of assumptions and expressions for the fundamental heat transfer and combustion processes. The diversity of these assumptions raises the question as to whether the absence of a sound and coherent fire spread theory is partly responsible. We explore the thesis that, without a common understanding of what processes occur and how they occur, model reliability cannot be confirmed. A theory is defined as a collection of logically connected hypotheses that provide a coherent explanation of some aspect of reality. Models implement theory for a particular purpose, including hypotheses of phenomena and practical uses, such as prediction. We emphasise the need for theory and demonstrate the difference between theory and modelling. Increasingly sophisticated fire management requires modelling capabilities well beyond the fundamental basis of current models. These capabilities can only be met with fundamental fire behaviour research. Furthermore, possibilities as well as limitations for modelling may not be known or knowable without first having the theory.
Firebrand generation data obtained from a full-scale structure burn
Authors: Suzuki Sayaka , Manzello Samuel L. , Lage Matthew , Laing George
Published: July 2012

A full-scale, proof-of-concept experiment was conducted to investigate firebrand production from a burning structure. In this experiment, researchers from National Institute of Standards and Technology (NIST) were invited to set up instrumentation and collect firebrands using an array of water pans during a structure burn-down. The size and mass distribution of firebrands collected from the burning structure was compared with those measured from vegetation as well as historical firebrand investigations and found to be larger and broader than those of prior studies from historical firebrand investigations.
Origin of metazoan cadherin diversity and the antiquity of the classical cadherin/β-catenin complex
Authors: Nichols Scott Anthony , Roberts Brock William , Richter Daniel Joseph , Fairclough Stephen Robert , King Nicole
Published: July 2012

The evolution of cadherins, which are essential for metazoan multicellularity and restricted to metazoans and their closest relatives, has special relevance for understanding metazoan origins. To reconstruct the ancestry and evolution of cadherin gene families, we analyzed the genomes of the choanoflagellate
Salpingoeca rosetta
, the unicellular outgroup of choanoflagellates and metazoans
Capsaspora owczarzaki
, and a draft genome assembly from the homoscleromorph sponge
Oscarella carmela
. Our finding of a cadherin gene in
C. owczarzaki
reveals that cadherins predate the divergence of the
C. owczarzaki
, choanoflagellate, and metazoan lineages. Data from these analyses also suggest that the last common ancestor of metazoans and choanoflagellates contained representatives of at least three cadherin families, lefftyrin, coherin, and hedgling. Additionally, we find that an
O. carmela
classical cadherin has predicted structural features that, in bilaterian classical cadherins, facilitate binding to the cytoplasmic protein β-catenin and, thereby, promote cadherin-mediated cell adhesion. In contrast with premetazoan cadherin families (i.e., those conserved between choanoflagellates and metazoans), the later appearance of classical cadherins coincides with metazoan origins.
Functional genetic screen of human diversity reveals that a methionine salvage enzyme regulates inflammatory cell death
Authors: Ko Dennis C. , Gamazon Eric R. , Shukla Kajal P. , Pfuetzner Richard A. , Whittington Dale , Holden Tarah D. , Brittnacher Mitchell J. , Fong Christine , Radey Matthew , Ogohara Cassandra , Stark Amy L. , Akey Joshua M. , Dolan M. Eileen , Wurfel Mark M. , Miller Samuel I.
Published: July 2012

Genome-wide association studies can identify common differences that contribute to human phenotypic diversity and disease. When genome-wide association studies are combined with approaches that test how variants alter physiology, biological insights can emerge. Here, we used such an approach to reveal regulation of cell death by the methionine salvage pathway. A common SNP associated with reduced expression of a putative methionine salvage pathway dehydratase, apoptotic protease activating factor 1 (APAF1)-interacting protein (
APIP
), was associated with increased caspase-1–mediated cell death in response to
Salmonella
. The role of APIP in methionine salvage was confirmed by growth assays with methionine-deficient media and quantitation of the methionine salvage substrate, 5′-methylthioadenosine. Reducing expression of
APIP
or exogenous addition of 5′-methylthioadenosine increased Salmonellae-induced cell death. Consistent with APIP originally being identified as an inhibitor of caspase-9–dependent apoptosis, the same allele was also associated with increased sensitivity to the chemotherapeutic agent carboplatin. Our results show that common human variation affecting expression of a single gene can alter susceptibility to two distinct cell death programs. Furthermore, the same allele that promotes cell death is associated with improved survival of individuals with systemic inflammatory response syndrome, suggesting a possible evolutionary pressure that may explain the geographic pattern observed for the frequency of this SNP. Our study shows that in vitro association screens of disease-related traits can not only reveal human genetic differences that contribute to disease but also provide unexpected insights into cell biology.
Neurons expressing trace amine-associated receptors project to discrete glomeruli and constitute an olfactory subsystem
Authors: Johnson Mark A. , Tsai Lulu , Roy Dheeraj S. , Valenzuela David H. , Mosley Colleen , Magklara Angeliki , Lomvardas Stavros , Liberles Stephen D. , Barnea Gilad
Published: July 2012

Some chemoreceptors of the trace amine-associated receptor (TAAR) family detect innately aversive odors and are proposed to activate hardwired olfactory circuits. However, the wiring of TAAR neurons, the regulatory mechanisms of
Taar
gene choice, and the subcellular localization of TAAR proteins remain unknown. Here, we reveal similarities between neurons expressing TAARs and odorant receptors (ORs), but also unexpected differences. Like ORs, TAARs seem to be monoallelically expressed and localized both in cilia, the site of odor detection, and in axons, where they may participate in guidance. TAAR neurons project to discrete glomeruli predominantly localized to a confined bulb region.
Taar
expression involves different regulatory logic than
OR
expression, as neurons choosing a
Taar5
knockout allele frequently express a second
Taar
without silencing the deleted allele. Moreover, the epigenetic signature of
OR
gene choice is absent from
Taar
genes. The unique molecular and anatomical features of the TAAR neurons suggest that they constitute a distinct olfactory subsystem.
Micromagnetic simulations using Graphics Processing Units
Authors: Lopez-Diaz L , Aurelio D , Torres L , Martinez E , Hernandez-Lopez M A , Gomez J , Alejos O , Carpentieri M , Finocchio G , Consolo G
Published: July 2012

The methodology for adapting a standard micromagnetic code to run on graphics processing units (GPUs) and exploit the potential for parallel calculations of this platform is discussed. GPMagnet, a general purpose finite-difference GPU-based micromagnetic tool, is used as an example. Speed-up factors of two orders of magnitude can be achieved with GPMagnet with respect to a serial code. This allows for running extensive simulations, nearly inaccessible with a standard micromagnetic solver, at reasonable computational times.
Transparent indium oxide films doped with high Lewis acid strength Ge dopant for phosphorescent organic light-emitting diodes
Authors: Kang Sin-Bi , Lim Jong-Wook , Lee Sunghun , Kim Jang-Joo , Kim Han-Ki
Published: July 2012

We report on Ge-doped In2O3(IGO) films prepared by co-sputtering GeO2 and In2O3 targets for anode of phosphorescent organic light-emitting diodes (POLEDs). Under optimized annealing conditions, the IGO film exhibited a low sheet resistance of 14.0 Ω/square, a high optical transmittance of 86.9% and a work function of 5.2 eV, comparable to conventional Sn-doped In2O3 (ITO) films. Due to the higher Lewis acid strength of the Ge4+ ion (3.06) than that of Sn3+(1.62), the IGO film showed higher transparency in the near infrared and higher carrier mobility of 39.16 cm2 V−1 s−1 than the ITO films. In addition, the strongly preferred (2 2 2) orientation of the IGO grains, caused by Zone II grain growth during rapid thermal annealing, increased the carrier mobility and improved the surface morphology of the IGO film. POLEDs fabricated on IGO anodes showed identical current density–voltage–luminance curves and efficiencies to POLEDs with ITO electrodes due to the low sheet resistance and high transmittance of the IGO anode.
Facet temperature distribution of a room temperature continuous-wave operating quantum cascade laser
Authors: Hu Yongzheng , Wang Lijun , Zhang Jinchuan , Li Lu , Liu Junqi , Liu Fengqi , Wang Zhanguo
Published: July 2012

The facet temperature distribution of a room temperature continuous-wave (CW) operating quantum cascade laser was experimentally measured based on the micro-Raman intensity ratio analysis of the Stokes and anti-Stokes phonon lines. A ‘W’-shaped temperature distribution was observed in the active region. We found that the traditional thermal simulation using the Fourier law is not sufficient in explaining our experimental results and other simulation models need to be explored. The active region temperatures at different CW operating currents were also measured. Our work is useful for device failure analysis and optimization of thermal management.
Oxygen vacancy induced phase formation and room temperature ferromagnetism in undoped and Co-doped TiO2 thin films
Authors: Mohanty P , Mishra N C , Choudhary R J , Banerjee A , Shripathi T , Lalla N P , Annapoorni S , Rath Chandana
Published: July 2012

TiO2 and Co-doped TiO2 (CTO) thin films deposited at various oxygen partial pressures by pulsed laser deposition exhibit room temperature ferromagnetism (RTFM) independent of their phase. Films deposited at 0.1 mTorr oxygen partial pressure show a complete rutile phase confirmed from glancing angle x-ray diffraction and Raman spectroscopy. At the highest oxygen partial pressure, i.e. 300 mTorr, although the TiO2 film shows a complete anatase phase, a small peak corresponding to the rutile phase along with the anatase phase is identified in the case of CTO film. An increase in O to Ti/(Ti+Co) ratio with increase in oxygen partial pressure is observed from Rutherford backscattering spectroscopy. It is revealed from x-ray photoelectron spectroscopy (XPS) that oxygen vacancies are found to be higher in the CTO film than TiO2, while the valency of cobalt remains in the +2 state. Therefore, the CTO film deposited at 300 mTorr does not show a complete anatase phase unlike the TiO2 film deposited at the same partial pressure. We conclude that RTFM in both films is not due to impurities/contaminants, as confirmed from XPS depth profiling and cross-sectional transmission electron microscopy (TEM), but due to oxygen vacancies. The magnitude of moment, however, depends not only on the phase of TiO2 but also on the crystallinity of the films.
Circulating growth differentiation factor‐15 correlates with myocardial fibrosis in patients with non‐ischaemic dilated cardiomyopathy and decreases rapidly after left ventricular assist device support
Authors: Lok Sjoukje I. , Winkens Bjorn , Goldschmeding Roel , van Geffen Ankie J.P. , Nous Fay M.A. , van Kuik Joyce , van der Weide Petra , Klöpping Corinne , Kirkels J. Hans , Lahpor Jaap R. , Doevendans Pieter A. , de Jonge Nicolaas , de Weger Roel A.
Published: July 2012

Aims

Growth differentiation factor‐15 (GDF‐15) is a stress‐responsive cytokine and is emerging as a biomarker of cardiac remodelling. Left ventricular assist devices (LVADs) provide unloading of the left ventricle, resulting in partial reverse remodelling. Our aim was to study GDF‐15 in patients with a non‐ischaemic dilated cardiomyopathy (DCM) during LVAD support.

Methods and results

We analysed circulating GDF‐15 in 30 patients before and 1, 3, and 6 months after LVAD implantation and before heart transplantation or explantation. In addition, mRNA and protein expression of GDF‐15 were evaluated in myocardial tissue obtained prior to and after LVAD support. Circulating GDF‐15 was significantly higher before LVAD implantation as compared with healthy controls (P < 0.001). After 1 month of mechanical support, GDF‐15 levels were significantly decreased compared with pre‐implantation levels (P < 0.001) and remained stable thereafter. Circulating GDF‐15 was significantly correlated with kidney function and the severity of myocardial fibrosis. Interestingly, GDF‐15 mRNA and protein expression in the myocardium were hardly detectable.

Conclusions

High circulating levels of GDF‐15 in patients with end‐stage non‐ischaemic DCM correlate with myocardial fibrosis and kidney function and decline strongly after 1 month of mechanical unloading, remaining stable thereafter. However, cardiac mRNA and protein expression of GDF‐15 are very low, suggesting that the heart is not an important source of GDF‐15 production in these patients.
Analysis of stem-cell-like properties of human CD161++IL-18Rα+ memory CD8+ T cells
Authors: Havenith Simone H. C. , Yong Si La , Henson Sian M. , Piet Berber , Idu Mirza M. , Koch  Sven D. , Jonkers René E. , Kragten Natasja A. M. , Akbar Arne N. , van Lier René A. W. , ten Berge Ineke J. M.
Published: July 2012

CD161++IL-18Rα+CD8+ human T cells have recently been identified as a new subset of memory cells but their exact role remains unclear. CD161++IL-18Rα+CD8+, mucosal-associated invariant T cells express a semi-invariant TCR Vα7.2-Jα33, which recognizes the MHC-related protein 1. On the basis of properties including the expression of the ABC-B1 transporter, cKit expression and survival after chemotherapy, CD161++IL-18Rα+CD8+ T cells have been designated as ‘stem’ cells. Here we analyse location and functional properties of CD161++IL-18Rα+ CD8+ T cells and question whether they have other traits that would mark them as genuine ‘stem’ cells. CD161++IL-18Rα+CD8+ T cells were found in peripheral blood, spleen and bone marrow but interestingly hardly at all in lymph nodes (LNs), which may possibly be explained by the finding that these cells express a specific set of chemokine receptors that allows migration to inflamed tissue rather than to LNs. In addition to TCR ligation and co-stimulation, CD161++IL-18Rα+ CD8+ T cells require cytokines for proliferation. The CD161++IL-18Rα+ CD8+ pool contains cells reactive towards peptides, derived from both persisting and cleared viruses. Although CD161++IL-18Rα+ CD8+ T cells express the ABC-B1 transporter, they have shorter telomeres and less telomerase activity and do not express aldehyde dehydrogenase. Finally, CD161++IL-18Rα+ CD8+ T cells show similarities to terminally differentiated T cells, expressing IFNγ, KLRG1 and the transcription factor Blimp-1. In conclusion, CD161++IL-18Rα+ CD8+ T cells lack many features of typical ‘stem’ cells, but appear rather to be a subset of effector-type cells.
In planta localization and interactions of impatiens necrotic spot tospovirus proteins
Authors: Dietzgen Ralf G. , Martin Kathleen M. , Anderson Gavin , Goodin Michael M.
Published: July 2012

Impatiens necrotic spot tospovirus (INSV) is a significant pathogen of ornamentals. The tripartite negative- and ambi-sense RNA genome encodes six proteins that are involved in cytoplasmic replication, movement, assembly, insect transmission and defence. To gain insight into the associations of these viral proteins, we determined their intracellular localization and interactions in living plant cells. Nucleotide sequences encoding the nucleoprotein N, non-structural proteins NSs and NSm, and glycoproteins Gn and Gc of a Kentucky isolate of INSV were amplified by RT-PCR, cloned, sequenced and transiently expressed as fusions with autofluorescent proteins in leaf epidermal cells of Nicotiana benthamiana. All proteins accumulated at the cell periphery and co-localized with an endoplasmic reticulum marker. The Gc protein fusion also localized to the nucleus. N and NSm protein self-interactions and an NSm–N interaction were observed by using bimolecular fluorescence complementation. A tospovirus NSm homotypic interaction had not been reported previously.
Molecular evolution and phylogeography of potato virus Y based on the CP gene
Authors: Cuevas José M. , Delaunay Agnès , Rupar Matevz , Jacquot Emmanuel , Elena Santiago F.
Published: July 2012

Potato virus Y (PVY) is an important plant pathogen with a wide host range that includes, among others, potato, tobacco, tomato and pepper. The coat protein (CP) of PVY has been commonly used in phylogenetic studies for strain classification. In this study, we used a pool of 292 CP sequences from isolates collected worldwide. After detecting and removing recombinant sequences, we applied Bayesian techniques to study the influence of geography and host species in CP population structure and dynamics. Finally, we performed selection and covariation analyses to identify specific amino acids involved in adaptation. Our results show that PVY CP diversification is significantly accounted for by both geographical and host-driven adaptations. Amino acid positions detected as positively selected concentrate in the N-terminal region of the protein. Some of these selected positions may discriminate among strains, and to a much lesser extent, between potato and non-potato isolates.
Evolution of the hepatitis E virus hypervariable region
Authors: Smith Donald B. , Vanek Jeff , Ramalingam Sandeep , Johannessen Ingolfur , Templeton Kate , Simmonds Peter
Published: July 2012

The presence of a hypervariable (HVR) region within the genome of hepatitis E virus (HEV) remains unexplained. Previous studies have described the HVR as a proline-rich spacer between flanking functional domains of the ORF1 polyprotein. Others have proposed that the region has no function, that it reflects a hypermutable region of the virus genome, that it is derived from the insertion and evolution of host sequences or that it is subject to positive selection. This study attempts to differentiate between these explanations by documenting the evolutionary processes occurring within the HVR. We have measured the diversity of HVR sequences within acutely infected individuals or amongst sequences derived from epidemiologically linked samples and, surprisingly, find relative homogeneity amongst these datasets. We found no evidence of positive selection for amino acid substitution in the HVR. Through an analysis of published sequences, we conclude that the range of HVR diversity observed within virus genotypes can be explained by the accumulation of substitutions and, to a much lesser extent, through deletions or duplications of this region. All published HVR amino acid sequences display a relative overabundance of proline and serine residues that cannot be explained by a local bias towards cytosine in this part of the genome. Although all published HVRs contain one or more SH3-binding PxxP motifs, this motif does not occur more frequently than would be expected from the proportion of proline residues in these sequences. Taken together, these observations are consistent with the hypothesis that the HVR has a structural role that is dependent upon length and amino acid composition, rather than a specific sequence.
Positionally biased gene loss after whole genome duplication: Evidence from human, yeast, and plant
Authors: Makino Takashi , McLysaght Aoife
Published: July 2012

Whole genome duplication (WGD) has made a significant contribution to many eukaryotic genomes including yeast, plants, and vertebrates. Following WGD, some ohnologs (WGD paralogs) remain in the genome arranged in blocks of conserved gene order and content (paralogons). However, the most common outcome is loss of one of the ohnolog pair. It is unclear what factors, if any, govern gene loss from paralogons. Recent studies have reported physical clustering (genetic linkage) of functionally linked (interacting) genes in the human genome and propose a biological significance for the clustering of interacting genes such as coexpression or preservation of epistatic interactions. Here we conduct a novel test of a hypothesis that functionally linked genes in the same paralogon are preferentially retained in cis after WGD. We compare the number of protein–protein interactions (PPIs) between linked singletons within a paralogon (defined as cis-PPIs) with that of PPIs between singletons across paralogon pairs (defined as trans-PPIs). We find that paralogons in which the number of cis-PPIs is greater than that of trans-PPIs are significantly enriched in human and yeast. The trend is similar in plants, but it is difficult to assess statistical significance due to multiple, overlapping WGD events. Interestingly, human singletons participating in cis-PPIs tend to be classified into “response to stimulus.” We uncover strong evidence of biased gene loss after WGD, which further supports the hypothesis of biologically significant gene clusters in eukaryotic genomes. These observations give us new insight for understanding the evolution of genome structure and of protein interaction networks.
Novel roles for KLF1 in erythropoiesis revealed by mRNA-seq
Authors: Tallack Michael R. , Magor Graham W. , Dartigues Benjamin , Sun Lei , Huang Stephen , Fittock Jessica M. , Fry Sally V. , Glazov Evgeny A. , Bailey Timothy L. , Perkins Andrew C.
Published: July 2012

KLF1 (formerly known as EKLF) regulates the development of erythroid cells from bi-potent progenitor cells via the transcriptional activation of a diverse set of genes. Mice lacking Klf1 die in utero prior to E15 from severe anemia due to the inadequate expression of genes controlling hemoglobin production, cell membrane and cytoskeletal integrity, and the cell cycle. We have recently described the full repertoire of KLF1 binding sites in vivo by performing KLF1 ChIP-seq in primary erythroid tissue (E14.5 fetal liver). Here we describe the KLF1-dependent erythroid transcriptome by comparing mRNA-seq from Klf1+/+ and Klf1−/− erythroid tissue. This has revealed novel target genes not previously obtainable by traditional microarray technology, and provided novel insights into the function of KLF1 as a transcriptional activator. We define a cis-regulatory module bound by KLF1, GATA1, TAL1, and EP300 that coordinates a core set of erythroid genes. We also describe a novel set of erythroid-specific promoters that drive high-level expression of otherwise ubiquitously expressed genes in erythroid cells. Our study has identified two novel lncRNAs that are dynamically expressed during erythroid differentiation, and discovered a role for KLF1 in directing apoptotic gene expression to drive the terminal stages of erythroid maturation.
Microstructural organization of corpus callosum projections to prefrontal cortex predicts bimanual motor learning
Authors: Sisti Helene M. , Geurts Monique , Gooijers Jolien , Heitger Marcus H. , Caeyenberghs Karen , Beets Iseult A.M. , Serbruyns Leen , Leemans Alexander , Swinnen Stephan P.
Published: July 2012

The corpus callosum (CC) is the largest white matter tract in the brain. It enables interhemispheric communication, particularly with respect to bimanual coordination. Here, we use diffusion tensor imaging (DTI) in healthy humans to determine the extent to which structural organization of subregions within the CC would predict how well subjects learn a novel bimanual task. A single DTI scan was taken prior to training. Participants then practiced a bimanual visuomotor task over the course of 2 wk, consisting of multiple coordination patterns. Findings revealed that the predictive power of fractional anisotropy (FA) was a function of CC subregion and practice. That is, FA of the anterior CC, which projects to the prefrontal cortex, predicted bimanual learning rather than the middle CC regions, which connect primary motor cortex. This correlation was specific in that FA correlated significantly with performance of the most difficult frequency ratios tested and not the innately preferred, isochronous frequency ratio. Moreover, the effect was only evident after training and not at initiation of practice. This is the first DTI study in healthy adults which demonstrates that white matter organization of the interhemispheric connections between the prefrontal structures is strongly correlated with motor learning capability.
Auxin and Epigenetic Regulation of SKP2B, an F-Box That Represses Lateral Root Formation
Authors: Manzano Concepción , Ramirez-Parra Elena , Casimiro Ilda , Otero Sofía , Desvoyes Bénédicte , De Rybel Bert , Beeckman Tom , Casero Pedro , Gutierrez Crisanto , C. del Pozo Juan
Published: July 2012

In plants, lateral roots originate from pericycle founder cells that are specified at regular intervals along the main root. Here, we show that Arabidopsis (Arabidopsis thaliana) SKP2B (for S-Phase Kinase-Associated Protein2B), an F-box protein, negatively regulates cell cycle and lateral root formation as it represses meristematic and founder cell divisions. According to its function, SKP2B is expressed in founder cells, lateral root primordia and the root apical meristem. We identified a novel motif in the SKP2B promoter that is required for its specific root expression and auxin-dependent induction in the pericycle cells. Next to a transcriptional control by auxin, SKP2B expression is regulated by histone H3.1/H3.3 deposition in a CAF-dependent manner. The SKP2B promoter and the 5′ end of the transcribed region are enriched in H3.3, which is associated with active chromatin states, over H3.1. Furthermore, the SKP2B promoter is also regulated by H3 acetylation in an auxin- and IAA14-dependent manner, reinforcing the idea that epigenetics represents an important regulatory mechanism during lateral root formation.
Effects of Drought on Gene Expression in Maize Reproductive and Leaf Meristem Tissue Revealed by RNA-Seq
Authors: Kakumanu Akshay , Ambavaram Madana M.R. , Klumas Curtis , Krishnan Arjun , Batlang Utlwang , Myers Elijah , Grene Ruth , Pereira Andy
Published: July 2012

Drought stress affects cereals especially during the reproductive stage. The maize (Zea mays) drought transcriptome was studied using RNA-Seq analysis to compare drought-treated and well-watered fertilized ovary and basal leaf meristem tissue. More drought-responsive genes responded in the ovary compared with the leaf meristem. Gene Ontology enrichment analysis revealed a massive decrease in transcript abundance of cell division and cell cycle genes in the drought-stressed ovary only. Among Gene Ontology categories related to carbohydrate metabolism, changes in starch and Suc metabolism-related genes occurred in the ovary, consistent with a decrease in starch levels, and in Suc transporter function, with no comparable changes occurring in the leaf meristem. Abscisic acid (ABA)-related processes responded positively, but only in the ovaries. Related responses suggested the operation of low glucose sensing in drought-stressed ovaries. The data are discussed in the context of the susceptibility of maize kernel to drought stress leading to embryo abortion and the relative robustness of dividing vegetative tissue taken at the same time from the same plant subjected to the same conditions. Our working hypothesis involves signaling events associated with increased ABA levels, decreased glucose levels, disruption of ABA/sugar signaling, activation of programmed cell death/senescence through repression of a phospholipase C-mediated signaling pathway, and arrest of the cell cycle in the stressed ovary at 1 d after pollination. Increased invertase levels in the stressed leaf meristem, on the other hand, resulted in that tissue maintaining hexose levels at an “unstressed” level, and at lower ABA levels, which was correlated with successful resistance to drought stress.
Analysis of Xylem Sap from Functional (Nonembolized) and Nonfunctional (Embolized) Vessels of Populus nigra: Chemistry of Refilling
Authors: Secchi Francesca , Zwieniecki Maciej A.
Published: July 2012

It is assumed that the refilling of drought-induced embolism requires the creation of an osmotic gradient between xylem parenchyma cells and vessel lumens to generate the water efflux needed to fill the void. To assess the mechanism of embolism repair, it is crucial to determine if plants can up-regulate the efflux of osmotically active substances into embolized vessels and identify the major components of the released osmoticum. Here, we introduce a new approach of sap collection designed to separate water from nonembolized (functional) and embolized (nonfunctional) vessels. This new approach made possible the chemical analysis of liquid collected from both types of vessels in plants subjected to different levels of water stress. The technique also allowed us to determine the water volumes in nonfunctional vessels as a function of stress level. Overall, with the increase of water stress in plants, the osmotic potential of liquid collected from nonfunctional vessels increased while its volume decreased. These results revealed the presence of both sugars and ions in nonfunctional vessels at elevated levels in comparison with liquid collected from functional vessels, in which only traces of sugars were found. The increased sugar concentration was accompanied by decreased xylem sap pH. These results provide new insight into the biology of refilling, underlining the role of sugar and sugar transporters, and imply that a large degree of hydraulic compartmentalization must exist in the xylem during the refilling process.
Potential of Anti‐Cancer Therapy Based on Anti‐miR‐155 Oligonucleotides in Glioma and Brain Tumours
Authors: Poltronieri Palmiro , D’Urso Pietro I. , Mezzolla Valeria , D’Urso Oscar F.
Published: July 2012

MicroRNAs are aberrantly expressed in many cancers and can exert tumour‐suppressive or oncogenic functions. As oncomirs promote growth of cancer cells and support survival during chemotherapy, thus microRNA‐silencing therapies could be a valuable approach to be associated with anticancer drugs and chemotherapy treatments. miR‐155 microRNA was found overexpressed in different types of cancer, such as leukaemias (PML, B‐cell lymphomas), lung cancer and glioblastoma. GABA‐A receptor downregulation was found correlated with glioma grading, with decreasing levels associated with higher grade of malignancies. A relationship between knock‐down of miR‐155 and re‐expression of GABRA 1 protein in vivo was recently individuated. This finding has implication on the effectiveness of RNA‐silencing approaches against miR‐155 with the scope to control proliferation and signalling pathways regulated by GABA‐A receptor. Applying microRNAs for treatment of brain tumours poses several problems, and fields to be solved are mainly the passage of the brain–blood barrier and the targeted delivery to specific cell types. Glioblastoma multiforme cells bud off microvesicles that deliver cytoplasmic contents to nearby cells. Thus, the exploitation of these mechanisms to deliver antagomir therapeutics targeting microvescicles in the brain could take the lead in the near future in the treatment for brain cancers in substitution of invasive surgical intervention.
Superior Analgesic Effect of H‐Dmt‐D‐Arg‐Phe‐Lys‐NH2 ([Dmt1]DALDA), a Multifunctional Opioid Peptide, Compared to Morphine in a Rat Model of Neuropathic Pain
Authors: Shimoyama Megumi , Schiller Peter W. , Shimoyama Naohito , Toyama Satoshi , Szeto Hazel H.
Published: July 2012

H‐Dmt‐D‐Arg‐Phe‐Lys‐NH2 ([Dmt1]DALDA) is a synthetic tetrapeptide with extraordinary selectivity for the mu‐opioid receptor and is an extremely potent analgesic. [Dmt1]DALDA is unusual in the way that the greater part of its analgesic potency appears to be produced by its actions in the spinal cord. Furthermore, [Dmt1]DALDA inhibits norepinephrine re‐uptake and is a mitochondria‐targeted antioxidant. Such characteristics may make [Dmt1]DALDA particularly effective against neuropathic pain. The present study was designed to compare the effects of [Dmt1]DALDA and morphine on thermal hyperalgesia in an experimental neuropathic pain model. Neuropathic pain was induced in rats by surgical ligation of the L5 spinal nerve, and thermal pain thresholds were assessed by latencies of paw withdrawal to radiant heat. The increase in paw withdrawal latency was greater after the administration of [Dmt1]DALDA than that of morphine in neuropathic rats at doses that were equianalgesic in naïve animals. We conclude that [Dmt1]DALDA is more effective than morphine against thermal hyperalgesia in this experimental model of neuropathic pain.
Evaluation of Perylenediimide Derivatives for Potential Therapeutic Benefits on Cancer Chemotherapy
Authors: Keskin Taner , Isgor Belgin S. , Isgor Yasemin G. , Yukruk Funda
Published: July 2012

Perylene derivatives, known to have potential therapeutic benefits on particular cancer types as photosensitizers, may also function as small‐molecule inhibitors with promising therapeutic value for diverse diseases. This recently recognized biological activity was attributed to their capacity to modulate the function of various enzymes as biological targets in vitro. Although the inhibitory activity on glutathione transferase and Src tyrosine kinase is important in determining the anticancer potential of compounds for target‐specific drug design and development, to date, there are no successful inhibitors of this kind. Moreover, there are only a few studies about the effects of perylene derivatives on glutathione transferase and various kinases. In this study, four novel perylene compounds, N,N′‐disubstituted perylenediimides and their 1,7‐dibromo derivatives, were synthesized and evaluated for their biological activities. Here, among the compounds analyzed, one of them was identified with strong glutathione transferase inhibition and two with dual activity for both glutathione transferase and c‐src inhibition. These results revealed that perylene derivatives may be employed as potential chemosensitizers to prevent chemotherapy‐dependent drug resistance and identified as prospective anticancer agents with dual activity on both glutathione transferase and c‐src enzymes.