bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogeography of Asian wild rice, Oryza rufipogon: a genome‐wide view
Authors: HUANG PU , MOLINA JEANMAIRE , FLOWERS JONATHAN M. , RUBINSTEIN SAMARA , JACKSON SCOTT A. , PURUGGANAN MICHAEL D. , SCHAAL BARBARA A. 
Published: May 2012

AbstractAsian wild rice (Oryza rufipogon) that ranges widely across the eastern and southern part of Asia is recognized as the direct ancestor of cultivated Asian rice (O. sativa). Studies of the geographic structure of O. rufipogon, based on chloroplast and low‐copy nuclear markers, reveal a possible phylogeographic signal of subdivision in O. rufipogon. However, this signal of geographic differentiation is not consistently observed among different markers and studies, with often conflicting results. To more precisely characterize the phylogeography of O. rufipogon populations, a genome‐wide survey of unlinked markers, intensively sampled from across the entire range of O. rufipogon is critical. In this study, we surveyed sequence variation at 42 genome‐wide sequence tagged sites (STS) in 108 O. rufipogon accessions from throughout the native range of the species. Using Bayesian clustering, principal component analysis and amova, we conclude that there are two genetically distinct O. rufipogon groups, Ruf‐I and Ruf‐II. The two groups exhibit a clinal variation pattern generally from north‐east to south‐west. Different from many earlier studies, Ruf‐I, which is found mainly in China and the Indochinese Peninsula, shows genetic similarity with one major cultivated rice variety, O. satvia indica, whereas Ruf‐II, mainly from South Asia and the Indochinese Peninsula, is not found to be closely related to cultivated rice varieties. The other major cultivated rice variety, O. sativa japonica, is not found to be similar to either O. rufipogon groups. Our results support the hypothesis of a single origin of the domesticated O. sativa in China. The possible role of palaeoclimate, introgression and migration–drift balance in creating this clinal variation pattern is also discussed.
Cell division and DNA segregation inStreptomyces: how to build a septum in the middle of nowhere?
Authors: Jakimowicz Dagmara , van Wezel Gilles P. 
Published: May 2012

SummaryStreptomycetes are antibiotic‐producing filamentous microorganisms that have a mycelial life style. In many ways streptomycetes are the odd ones out in terms of cell division. While the basic components of the cell division machinery are similar to those found in rod‐shaped bacteria such asEscherichia coliandBacillus subtilis, many aspects of the control of cell division and its co‐ordination with chromosome segregation are remarkably different. The rather astonishing fact that cell division is not essential for growth makes these bacteria unique. The fundamental difference between the cross‐walls produced during normal growth and sporulation septa formed in aerial hyphae, and the role of the divisome in their formation are discussed. We then take a closer look at the way septum site localization is regulated in the long and multinucleoidStreptomyceshyphae, with particular focus on actinomycete‐specific proteins and the role of nucleoid segregation and condensation.
Allosteric mutants show that PrfA activation is dispensable for vacuole escape but required for efficient spread and Listeria survival in vivo
Authors: Deshayes Caroline , Bielecka Magdalena K. , Cain Robert J. , Scortti Mariela , de las Heras Aitor , Pietras Zbigniew , Luisi Ben F. , Núñez Miguel Ricardo , Vázquez‐Boland José A. 
Published: May 2012

SummaryThe transcriptional regulator PrfA controls key virulence determinants of the facultative intracellular pathogen Listeria monocytogenes. PrfA‐dependent gene expression is strongly induced within host cells. While the basis of this activation is unknown, the structural homology of PrfA with the cAMP receptor protein (Crp) and the finding of constitutively activated PrfA* mutants suggests it may involve ligand‐induced allostery. Here, we report the identification of a solvent‐accessible cavity within the PrfA N‐terminal domain that may accommodate an activating ligand. The pocket occupies a similar position to the cAMP binding site in Crp but lacks the cyclic nucleotide‐anchoring motif and has its entrance on the opposite side of the β‐barrel. Site‐directed mutations in this pocket impaired intracellular PrfA‐dependent gene activation without causing extensive structural/functional alterations to PrfA. Two substitutions, L48F and Y63W, almost completely abolished intracellular virulence gene induction and thus displayed the expected phenotype for allosteric activation‐deficient PrfA mutations. Neither PrfAallo substitution affected vacuole escape and initial intracellular growth of L. monocytogenes in epithelial cells and macrophages but caused defective cell‐to‐cell spread and strong attenuation in mice. Our data support the hypothesis that PrfA is allosterically activated during intracellular infection and identify the probable binding site for the effector ligand. They also indicate that PrfA allosteric activation is not required for early intracellular survival but is essential for full Listeria virulence and colonization of host tissues.
Is home management of fevers a cost‐effective way of reducing under‐five mortality in Africa? The case of a rural Ghanaian District
Authors: Nonvignon Justice , Chinbuah Margaret A. , Gyapong Margaret , Abbey Mercy , Awini Elizabeth , Gyapong John O. , Aikins Moses 
Published: May 2012

AbstractObjective To assess the cost‐effectiveness of two strategies of home management of under‐five fevers in Ghana – treatment using antimalarials only (artesunate–amodiaquine – AAQ) and combined treatment using antimalarials and antibiotics (artesunate–amodiaquine plus amoxicillin – AAQ + AMX).Methods We assessed the costs and cost‐effectiveness of AAQ and AAQ + AMX compared with a control receiving standard care. Data were collected as part of a cluster randomised controlled trial with a step‐wedged design. Approximately, 12 000 children aged 2–59 months in Dangme West District in southern Ghana were covered. Community health workers delivered the interventions. Costs were analysed from societal perspective, using anaemia cases averted, under‐five deaths averted and disability‐adjusted life years (DALYs) averted as effectiveness measures.Results Total economic costs for the interventions were US$ 204 394.72 (AAQ) and US$ 260 931.49 (AAQ + AMX). Recurrent costs constituted 89% and 90% of the total direct costs of AAQ and AAQ + AMX, respectively. Deaths averted were 79.1 (AAQ) and 79.9 (AAQ + AMX), with DALYs averted being 2264.79 (AAQ) and 2284.57 (AAQ + AMX). The results show that cost per anaemia case averted were US$ 150.18 (AAQ) and US$ 227.49 (AAQ + AMX) and cost per death averted was US$ 2585.58 for AAQ and US$ 3272.20 for AAQ + AMX. Cost per DALY averted were US$ 90.25 (AAQ) and US$ 114.21 (AAQ + AMX).Conclusion Both AAQ and AAQ + AMX approaches were cost‐effective, each averting one DALY at less than the standard US$ 150 threshold recommended by the World Health Organisation. However, AAQ was more cost‐effective. Home management of under‐five fevers in rural settings is cost‐effective in reducing under‐five mortality.
Flowering dynamics and pollination system of the sedge Rhynchospora ciliata (Vahl) Kükenth (Cyperaceae): does ambophily enhance its reproductive success?
Authors: Costa A. C. G. , Machado I. C. 
Published: May 2012

AbstractCyperaceae are characteristically anemophilous, but there are some reports of species re‐adapted to entomophily, such as Rhynchospora ciliata. Our objective was to investigate: (1) the distribution pattern of flowers in inflorescences of Rhynchospora ciliata; (2) the dynamics of its anthesis; and (3) whether R. ciliata is pollinated by bees, by wind or by both. Additionally, we tested the hypotheses: (i) the hypsophylls and/or anthers attract pollinators, and (ii) biotic vectors enhance the reproductive success of R. ciliata. We analysed floral biology, dynamics of anthesis, frequency and behaviour of insects visiting flowers; we also carried out experiments on flower attractiveness, pollination by wind and reproductive success. Rhynchospora ciliata has flowers with anemophilous attributes, including anthers exposed during anthesis; however, the anthers (here considered a mixed trait) together with the white hypsophylls can be considered as attributes that favour entomophily. Both wind and four species of bee were considered as pollen vectors of R. ciliata. Through flower attractiveness tests, we observed that the hypsophylls do not affect the frequency of pollinating bees and that the absence of exposed anthers affects the average number of visits, probably because pollen is the only floral resource. Reproductive tests indicate that R. ciliata is self‐incompatible and that ambophily enhances its reproductive success.
Effects of fire on grass‐layer savanna macroinvertebrates as key food resources for insectivorous vertebrates in northern Australia
Authors: RADFORD IAN J. , ANDERSEN ALAN N. 
Published: May 2012

AbstractThis paper documents the effects of fire on grass‐layer invertebrates in tropical savannas of the Kimberley region of north‐western Australia, in the context of resource availability for consumers. Inappropriate fire regimes have been identified as a factor threatening a number of vertebrate groups, including small mammals, across northern Australia, and a possible mechanism might be through the effects of individual fires or fire regimes on food availability. We test for a fire effect on grass‐layer invertebrate resources, which may affect insectivorous savanna vertebrates. Wet season sweep‐net invertebrate samples were taken in two tropical savanna habitats, with contrasting laterite and sandstone substrates, in 2008, 2009 and 2010. Sites were stratified by post‐fire interval to analyse invertebrate successional change after fire. In addition, experimental burns were implemented in 2010 to investigate immediate post‐fire invertebrate responses. Total invertebrate numbers declined by 80–90% immediately (1 week) following fire, reflecting the loss of grass‐layer habitat. Of the commonly sampled invertebrate groups, Araneae, Coleoptera, Hempitera, Lepidoptera, Formicidae and Diptera were all reduced in numbers immediately post‐fire, whereas Orthoptera showed no immediate post‐fire decline. Invertebrate numbers were rapidly restored to pre‐fire levels by the first wet season after fire, and no detectible change was observed in numbers or composition from 1 to 3–4 years post‐fire (the longest post‐fire interval available). This suggests that the effects of individual fires on grass‐layer invertebrates are very short‐lived. Such short‐lived post‐fire responses among grass‐layer invertebrates, plus evidence that most ground‐layer invertebrate groups are fire‐resilient, suggest that food resource limitation is not a tenable explanation for fire‐related declines among insectivorous savanna vertebrates. However, wet season burning could result in significant invertebrate resource depletion in highly flammable habitats (Triodia and Sorghum spp. savannas) during important vertebrate breeding/recruitment periods, if burning is extensive and if grass‐layer invertebrates do not recover within a few weeks of fire.
Increase in nephrology advanced trainee numbers in Australia and associated reduction in clinical exposure over the past decade
Authors: Amos L. , Toussaint N. D. , Phoon R. K. , Elias T. J. , Levidiotis V. , Campbell S. B. , Walker A. M. , Harrex C. 
Published: May 2012

AbstractBackgroundAdvanced training in nephrology should provide broad experience in all aspects of nephrology. In Australia, the Specialist Advisory Committee in Nephrology oversees nephrology training, and recent increases in advanced trainee numbers have led to concern about dilution of training experience. No study has examined variations in clinical exposure for nephrology trainees in Australia.AimTo assess the changes in nephrology advanced training in Australia with respect to trainee numbers and exposure to patients and procedures over the past 10 years.MethodsA retrospective study was performed by obtaining all available Royal Australasian College of Physician supervisor reports from 2000 to 2010 to determine differences in clinical exposure and procedures performed by nephrology trainees.ResultsFive hundred and forty‐two reports were reviewed involving 208 nephrology trainees in Australia across 53 different training sites. In 2000, 22 trainees were undertaking a core clinical year of training. Trainee numbers have steadily risen from 33 in 2004 to 84 in 2010. The greatest increases have occurred in New South Wales, Victoria and Queensland (sixfold, threefold and fivefold increases respectively). Trainee exposure to dialysis patients has gradually decreased in the past decade. The average number per trainee per year in 2000 compared with 2010 were 66 versus 43 (P = 0.02) and 28 versus 16 (P = 0.01) for haemodialysis and peritoneal dialysis respectively. Acute kidney injury cases per trainee showed a gradual nonsignificant reduction over time and average procedural numbers per trainee decreased significantly from 2000 to 2010 with fewer temporary dialysis catheters inserted per year (39 vs 10, P < 0.01) and fewer renal biopsies performed per year (65 vs 41, P < 0.01). The proportion of trainees working in a hospital that does not provide exposure to acute transplantation has steadily increased from 15% in 2003 to 44% in 2010.ConclusionsThere has been a dramatic and significant increase in nephrology advanced trainee numbers over the past decade at a more rapid rate than the growth in dialysis and transplant patient numbers. This study suggests that training experience has diminished over the past decade and supports a 3‐year core clinical nephrology training programme in Australia.
Clinical model for ethical cardiopulmonary resuscitation decision‐making
Authors: Hayes B. 
Published: May 2012

AbstractBackgroundDecisions to withhold cardiopulmonary resuscitation (CPR) for future cardiac arrest continue to be problematic, with a lack of consistency in how doctors approach this decision.AimsTo develop a clinical model that can be used in education to improve consistency inCPRdecision‐making.MethodsA qualitative study, using semistructured interviews with a total of 33 senior doctors, junior doctors and nurses from twoMelbourne hospitals explored how decisions to withholdCPRare made. Interviews explored: issues arising; how doctors learn to make these decisions; how they deal with disagreement and their experiences of performingCPR. The transcripts were coded and analysed thematically.ResultsThree major themes were identified:CPRas a life‐and‐death decision; good and bad dying; and trust. The research also defined the two elements to aCPRdecision: (i) technical and (ii) ethical.ConclusionsApplying ethical principles commonly used in medicine, a model for ethicalCPRdecision‐making has been developed that identifies four patient groups, each with a different discussion aim. This approach simplifies the complexities of theCPRdecision, providing a structured way to teachCPRdecision‐making to doctors and thereby achieve greater consistency in the decisions made.
Spin density projection‐assisted R2 magnetic resonance imaging of the liver in the management of body iron stores in patients receiving multiple red blood cell transfusions: an audit and retrospective study in South Australia
Authors: Brown G. C. , Patton W. N. , Tapp H. E. , Taylor D. J. , St Pierre T. G. 
Published: May 2012

AbstractAim:  To assess the impact of non‐invasive monitoring of liver iron concentration (LIC) on management of body iron stores in patients receiving multiple blood transfusions.Method:  A retrospective audit was conducted on clinical data from 40 consecutive subjects with haemolytic anaemias or ineffective haematopoiesis who had been monitored non‐invasively for LIC over a period of at least 1 year. LIC was measured with spin density projection‐assisted proton transverse relaxation rate‐magnetic resonance imaging.Results:  Nineteen clinical decisions were explicitly documented in the case notes as being based on LIC results. Decisions comprised initiation of chelation therapy, increasing chelator dose, decreasing chelator dose and change of mode of delivery of deferioxamine from subcutaneous to intravenous. The geometrical mean LIC for the cohort dropped significantly (P= 0.008) from 6.8 mg Fe/g dry tissue at initial measurement to 4.8 mg Fe/g dry tissue at final measurement. The proportion of subjects with LIC in the range associated with greatly increased risk of cardiac disease and death (>15 mg Fe/g dry tissue) dropped significantly (P= 0.01) from 14 of 40 subjects at initial measurement to 5 of 40 subjects at final measurement. No significant changes in the geometrical mean of serum ferritin or the proportion of subjects with serum ferritin above 2500 or 1500 µg/L were observed.Conclusions:  The data are consistent with previous observations that introduction of non‐invasive monitoring of LIC can contribute to a decreased body iron burden through improved clinical decision making and improved feedback to patients and hence improved adherence to chelation therapy.
POLG mutations in Australian patients with mitochondrial disease
Authors: Woodbridge P. , Liang C. , Davis R. L. , Vandebona H. , Sue C. M. 
Published: May 2012

AbstractBackground/AimThe nuclear POLG gene encodes the catalytic subunit of DNA polymerase gamma (polγ), the only polymerase involved in the replication and proofreading of mitochondrial DNA. As a consequence, POLG mutations can cause disease through impaired replication of mitochondrial DNA. To date, over 150 different mutations have been identified, with a growing number of associated phenotypes described. The aim of this study was to determine the prevalence of POLG mutations in an adult population of Australian patients with mitochondrial disease, displaying symptoms commonly associated with POLG‐related diseases.MethodsThe clinical presentations of 322 patients from a specialist adult mitochondrial disease clinic were reviewed. Nineteen exhibited a cluster of three or more predefined clinical manifestations suggestive of POLG‐related disease: progressive external ophthalmoplegia, seizures and/or an abnormal electroencephalogram, neuropathy, ataxia, liver function abnormalities, migraine or dysphagia/dysarthria. Patients were screened for mutations by direct nucleotide sequencing of the coding and exon‐flanking intronic regions of POLG.ResultsFive of the 19 patients (26%) displaying a phenotype suggestive of POLG‐related disease were found to have informative POLG coding mutations (p.T851A, p.N468D, p.Y831C, p.G517V and novel p.P163S variant). Literature and analysis of these mutations revealed that two of these patients had pathogenic mutations known to cause POLG‐related disease (patient #1: p.T851A and p.P163S; patient #2: p.T851A and p.N468D).ConclusionsWe conclude that the prevalence of pathogenic POLG mutations in our selected adult Australian cohort with suggestive clinical manifestations was 10%. A further 16% of patients had POLG variants but are unlikely to be responsible for causing their disease.
Awareness and opinions of non‐alcoholic fatty liver disease by hospital specialists
Authors: Bergqvist C.‐J. , Skoien R. , Horsfall L. , Clouston A. D. , Jonsson J. R. , Powell E. E. 
Published: May 2012

AbstractBackground/AimSubjects with metabolic risk factors for non‐alcoholic fatty liver disease (NAFLD) are commonly seen by hospital specialists other than gastroenterologists/hepatologists. The aim of this study was to assess the awareness of NAFLD and opinions regarding management among non‐hepatologists at two major tertiary hospitals in Brisbane.MethodsA face‐to‐face questionnaire assessing current beliefs and practices regarding NAFLD was administered to specialists and specialists‐in‐training across six specialties (internal medicine, cardiology/cardiac surgery, endocrinology, thoracic medicine, rheumatology and nephrology).ResultsOne hundred clinicians were surveyed with 99% returning completed questionnaires (>89% questions answered). The majority of respondents (75%) believe the prevalence of NAFLD in the general population to be ≤10%, although two‐thirds feel that its incidence will rise markedly. The vast majority (>90%) appreciate that traditional cardiovascular risk factors (obesity, hypertriglyceridaemia and diabetes) are risk factors for NAFLD and acknowledge that these are common in non‐hepatology patients. Despite this, most believe that NAFLD is uncommon in their own patients (89% indicated a prevalence ≤30%). The vast majority (93%) agree that non‐alcoholic steatohepatitis (NASH) is associated with increased overall mortality, but 60% also believe that simple steatosis confers increased liver‐related mortality. Most (74%) agree that a diagnosis of NASH cannot be made using liver enzymes, but 67% support 6‐monthly liver function tests as the most effective way to monitor progression of NAFLD. Most respondents (71%) make no referrals to hepatology for suspected NAFLD.ConclusionsNon‐hepatologists appreciate the seriousness of NAFLD but appear to underestimate its prevalence, especially among their own patients despite known risk factors. Attitudes regarding simple steatosis versus NASH and appropriate monitoring of suspected NAFLD suggest that more can be done to improve the understanding of this disease among non‐hepatologists. This has implications for targeting ‘at‐risk’ populations and appropriate referral of patients to hepatology clinics.
A trait‐based approach for modelling microbial litter decomposition
Authors: Allison S. D. 
Published: May 2012

AbstractTrait‐based models are an emerging tool in ecology with the potential to link community dynamics, environmental responses and ecosystem processes. These models represent complex communities by defining taxa with trait combinations derived from prior distributions that may be constrained by trade‐offs. Herein I develop a model that links microbial community composition with physiological and enzymatic traits to predict litter decomposition rates. This approach allows for trade‐offs among traits that represent alternative microbial strategies for resource acquisition. The model predicts that optimal strategies depend on the level of enzyme production in the whole community, which determines resource availability and decomposition rates. There is also evidence for facilitation and competition among microbial taxa that co‐occur on decomposing litter. These interactions vary with community investment in extracellular enzyme production and the magnitude of trade‐offs affecting enzyme biochemical traits. The model accounted for 69% of the variation in decomposition rates of 15 Hawaiian litter types and up to 26% of the variation in enzyme activities. By explicitly representing diversity, trait‐based models can predict ecosystem processes based on functional trait distributions in a community. The model developed herein illustrates that traits influencing microbial enzyme production are some of the key controls on litter decomposition rates.