bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fire persistence traits can be used to predict vegetation response to changing fire regimes at expansive landscape scales – an Australian example
Authors: Russell‐Smith Jeremy , Gardener Mark R. , Brock Chris , Brennan Kym , Yates Cameron P. , Grace Blair 
Published: June 2012

AbstractAim  Building on a substantial literature addressing the fire responses of woody plants, particularly under mediterranean climates, we assess the extent to which fire persistence traits can be used to predict vegetation responses to fire regime changes in fire‐prone arid and savanna landscape settings.Location  Australia, applying data from arid central to monsoonal northern regions (11–26° S, 129–138° E).Methods  With reference to a substantial sub‐continental floristics dataset, we first assigned the fire response (obligate seeder, resprouter) and seedbank persistence (transient, dormant) of rapid and longer‐maturing (> 3 years) woody taxa. Using logistic regression, we then modelled the proportions of taxa possessing these traits as a function of mean annual rainfall (highly correlated with fire frequency) and terrain roughness (a measure of topographic variability) in 0.25° × 0.25° and 1° × 1° grid cells. Separate assessments were undertaken with datasets for 1264 sclerophyll and 236 rain forest taxa.Results  This woody flora is characterized by taxa exhibiting mostly resprouting and dormant seedbank traits that promote site persistence. While numbers of obligate seeder and resprouter taxa were related positively to both rainfall and roughness, the relative abundance of both sclerophyll and rain forest obligate seeders decreased significantly with rainfall. The relative abundance of sclerophyll (especially long‐lived) obligate seeders alone increased with topographic roughness. The proportion of taxa with transient seedbanks increased with rainfall in resprouters generally, and in rain forest obligate seeders alone.Main conclusions  We find that resprouters are favoured on more productive, fire‐prone sites, and obligate seeders are favoured in less productive, more fire‐protected settings. Seedbank persistence responses are more variable. These findings concur generally with theoretical constructs, and support comparable assessments in Australian and other fire‐prone systems ranging from mediterranean to boreal environments. Our observations illustrate that resprouting and obligate seeding syndromes, but not necessarily seedbank persistence, are useful predictors of vegetation responses to changing fire regime conditions at large landscape scales.
Serious games as new educational tools: how effective are they? A meta‐analysis of recent studies
Authors: Girard C. , Ecalle J. , Magnan A. 
Published: June 2012

AbstractComputer‐assisted learning is known to be an effective tool for improving learning in both adults and children. Recent years have seen the emergence of the so‐called ‘serious games (SGs)’ that are flooding the educational games market. In this paper, the term ‘serious games’ is used to refer to video games (VGs) intended to serve a useful purpose. The objective was to review the results of experimental studies designed to examine the effectiveness of VGs and SGs on players' learning and engagement. After pointing out the varied nature of the obtained results and the impossibility of reaching any reliable conclusion concerning the effectiveness of VGs and SGs in learning, we stress the limitations of the existing literature and make a number of suggestions for future studies.
Hospital patients' reports of medical errors and undesirable events in their health care
Authors: Davis Rachel E. , Sevdalis Nick , Neale Graham , Massey Rachel , Vincent Charles A. 
Published: June 2012

AbstractObjective  To investigate hospital patients' reports of undesirable events in their health care.Design  Cross‐sectional mixed methods design.Participants  A total of 80 medical and surgical patients (mean age 58, 56 male).Intervention  Patients were interviewed post‐discharge using a survey to assess patient reports of errors or problems in their care. Patients' medical records and notes were also reviewed.Main outcome measures  Frequency of health care process problems, medical complications and interpersonal problems, and patient willingness to report an undesirable event in their care.Results  In total, 258 undesirable events were reported (rate of 3.2 per person), including 136 interpersonal problems, 90 medical complications and 32 health care process problems. Patients identified a number of events that were reported in the medical records (30 out of 36). In addition, patients reported events that were not recorded in the medical records. Patients were more willing (P < 0.05) to report undesirable events to a researcher (as in the present case) than to a local or national reporting system.Conclusion  Patients appear able to report undesirable events that occur in their health care management over and above those that are recorded in their medical records. However, patients appear more willing to report these incidents for the purpose of a study rather than to an established incident reporting system. Interventions aimed at educating and encouraging patients about incident reporting systems need to be developed in order to enhance this important contribution patients could make to improving patient safety.
Effects of linseeds on the symptoms of irritable bowel syndrome: a pilot randomised controlled trial
Authors: Cockerell K. M. , Watkins A. S. M. , Reeves L. B. , Goddard L. , Lomer M. C. E. 
Published: June 2012

AbstractBackground:  Manipulation of dietary fibre intake represents a longstanding treatment for patients with irritable bowel syndrome (IBS), particularly for those with constipation. Linseeds are often recommended by both clinicians and dietitians as a source of dietary fibre to alleviate symptoms. Recent guidance on the management of irritable bowel syndrome (IBS) advises that linseeds may reduce wind and bloating, although there is limited clinical evidence to support this recommendation. The present pilot study aimed to compare the clinical effectiveness of: (i) whole linseeds versus ground linseeds; (ii) whole linseeds versus no linseeds; and (iii) ground linseeds versus no linseeds in the management of IBS symptoms.Methods:  In an open randomised controlled trial, subjects with IBS (n = 40) were allocated to one of three intervention groups: two tablespoons of whole linseeds per day (n = 14), two tablespoons of ground linseeds per day (n = 13) and no linseeds as controls (n = 13). Symptom severity (primary outcome) and bowel habit were assessed before and after a 4‐week intervention and statistical differences between the groups were compared.Results:  Thirty‐one subjects completed the present study. Between‐group analysis comparing the improvement in symptom severity did not reach statistical significance for whole linseeds (n = 11) versus ground linseeds (n = 11; P = 0.62), whole linseeds versus controls (n = 9; P = 0.12) and ground linseeds versus controls (P = 0.10). There were no significant changes in stool frequency or stool consistency for any of the groups.Conclusions:  Linseeds may be useful in relief of IBS symptoms. Further research is needed to detect clear differences between the effects of whole and ground linseeds.
Recurrent gene deletions and the evolution of adaptive cyanogenesis polymorphisms in white clover (Trifolium repens L.)
Authors: OLSEN KENNETH M. , KOOYERS NICHOLAS J. , SMALL LINDA L. 
Published: June 2012

AbstractUnderstanding the molecular evolution of genes that underlie intraspecific polymorphisms can provide insights into the process of adaptive evolution. For adaptive polymorphisms characterized by gene presence/absence (P/A) variation, underlying loci commonly show signatures of long‐term balancing selection, with gene‐presence and gene‐absence alleles maintained as two divergent lineages. We examined the molecular evolution of two unlinked P/A polymorphisms that underlie a well‐documented adaptive polymorphism for cyanogenesis (hydrogen cyanide release with tissue damage) in white clover. Both cyanogenic and acyanogenic plants occur in this species, and the ecological forces that maintain this chemical defence polymorphism have been studied for several decades. Using a sample of 65 plants, we investigated the molecular evolution of sequences flanking the two underlying cyanogenesis genes: Ac/ac (controlling the presence/absence of cyanogenic glucosides) and Li/li (controlling the presence/absence of their hydrolysing enzyme, linamarase). A combination of genome walking, PCR assays, DNA sequence analysis and Southern blotting was used to test whether these adaptive P/A polymorphisms show evidence of long‐term balancing selection, or whether gene‐absence alleles have evolved repeatedly through independent deletion events. For both loci, we detect no signatures of balancing selection in the closest flanking genomic sequences. Instead, we find evidence for variation in the size of the deletions characterizing gene‐absence alleles. These observations strongly suggest that both of these polymorphisms have been evolving through recurrent gene deletions over time. We discuss the genetic mechanisms that could account for this surprising pattern and the implications of these findings for mechanisms of rapid adaptive evolution in white clover.
The structure of the NasR transcription antiterminator reveals a one‐component system with a NIT nitrate receptor coupled to an ANTAR RNA‐binding effector
Authors: Boudes Marion , Lazar Noureddine , Graille Marc , Durand Dominique , Gaidenko Tatiana A. , Stewart Valley , van Tilbeurgh Herman 
Published: June 2012

SummaryThe nitrate‐ and nitrite‐sensing NIT domain is present in diverse signal‐transduction proteins across a wide range of bacterial species. NIT domain function was established through analysis of the Klebsiella oxytoca NasR protein, which controls expression of the nasF operon encoding enzymes for nitrite and nitrate assimilation. In the presence of nitrate or nitrite, the NasR protein inhibits transcription termination at the factor‐independent terminator site in the nasF operon transcribed leader region. We present here the crystal structure of the intact NasR protein in the apo state. The dimeric all‐helical protein contains a large amino‐terminal NIT domain that associates two four‐helix bundles, and a carboxyl‐terminal ANTAR (AmiR and NasR transcription antitermination regulator) domain. The analysis reveals unexpectedly that the NIT domain is structurally similar to the periplasmic input domain of the NarX two‐component sensor that regulates nitrate and nitrite respiration. This similarity suggests that the NIT domain binds nitrate and nitrite between two invariant arginyl residues located on adjacent alpha helices, and results from site‐specific mutagenesis showed that these residues are critical for NasR function. The resulting structural movements in the NIT domain would provoke an active configuration of the ANTAR domains necessary for specific leader mRNA binding.
Identification of two small regulatory RNAs linked to virulence in Brucella abortus 2308
Authors: Caswell Clayton C. , Gaines Jennifer M. , Ciborowski Pawel , Smith Derek , Borchers Christoph H. , Roux Christelle M. , Sayood Khalid , Dunman Paul M. , Roop II R. Martin 
Published: June 2012

SummaryHfq is an RNA‐binding protein that functions in post‐transcriptional gene regulation by mediating interactions between mRNAs and small regulatory RNAs (sRNAs). Two proteins encoded by BAB1_1794 and BAB2_0612 are highly over‐produced in a Brucella abortus hfq mutant compared with the parental strain, and recently, expression of orthologues of these proteins in Agrobacterium tumefaciens was shown to be regulated by two sRNAs, called AbcR1 and AbcR2. Orthologous sRNAs (likewise designated AbcR1 and AbcR2) have been identified in B. abortus 2308. In Brucella, abcR1 and abcR2 single mutants are not defective in their ability to survive in cultured murine macrophages, but an abcR1 abcR2 double mutant exhibits significant attenuation in macrophages. Additionally, the abcR1 abcR2 double mutant displays significant attenuation in a mouse model of chronic Brucella infection. Quantitative proteomics and microarray analyses revealed that the AbcR sRNAs predominantly regulate genes predicted to be involved in amino acid and polyamine transport and metabolism, and Northern blot analyses indicate that the AbcR sRNAs accelerate the degradation of the target mRNAs. In an Escherichia coli two‐plasmid reporter system, overexpression of either AbcR1 or AbcR2 was sufficient for regulation of target mRNAs, indicating that the AbcR sRNAs from B. abortus 2308 perform redundant regulatory functions.
Aberrant temporal growth pattern and morphology of root and shoot caused by a defective circadian clock in Arabidopsis thaliana
Authors: Ruts Tom , Matsubara Shizue , Wiese‐Klinkenberg Anika , Walter Achim 
Published: June 2012

SummaryCircadian clocks synchronized with the environment allow plants to anticipate recurring daily changes and give a fitness advantage. Here, we mapped the dynamic growth phenotype of leaves and roots in two lines of Arabidopsis thaliana with a disrupted circadian clock: the CCA1 over‐expressing line (CCA1ox) and the prr9 prr7 prr5 (prr975) mutant. We demonstrate leaf growth defects due to a disrupted circadian clock over a 24 h time scale. Both lines showed enhanced leaf growth compared with the wild‐type during the diurnal period, suggesting increased partitioning of photosynthates for leaf growth. Nocturnal leaf growth was reduced and growth inhibition occurred by dawn, which may be explained by ineffective starch degradation in the leaves of the mutants. However, this growth inhibition was not caused by starch exhaustion. Overall, these results are consistent with the notion that the defective clock affects carbon and energy allocation, thereby reducing growth capacity during the night. Furthermore, rosette morphology and size as well as root architecture were strikingly altered by the defective clock control. Separate analysis of the primary root and lateral roots revealed strong suppression of lateral root formation in both CCA1ox and prr975, accompanied by unusual changes in lateral root growth direction under light–dark cycles and increased lateral extension of the root system. We conclude that growth of the whole plant is severely affected by improper clock regulation in A. thaliana, resulting not only in altered timing and capacity for growth but also aberrant development of shoot and root architecture.
Fine‐scale genetic analysis of species‐specific female preference in Drosophila simulans
Authors: Laturney M. , Moehring A. J. 
Published: June 2012

AbstractBehavioural differences are thought to be the first components to contribute to species isolation, yet the precise genetic basis of behavioural isolation remains poorly understood. Here, we used a combination of behaviour assays and genetic mapping to provide the first refined map locating candidate genes for interspecific female preference isolating Drosophila simulans from D. melanogaster. First, we tested whether two genes identified as affecting D. melanogaster female intraspecific mate choice also affect interspecific mate choice; neither of these genes was found to contribute to species‐specific female preference. Next, we used deficiency mapping to locate genes on the right arm of the third chromosome for species‐specific female preference and identified five small significant regions that contain candidate genes contributing to behavioural isolation. All five regions were located in areas that would have low interspecific recombination, which mirrors the results of other behavioural isolation studies that used quantitative trait locus (QTL) mapping, but without the potential concern of bias towards regions of low recombination that QTL mapping may have. As this model system may be refined to the individual gene level using the same methodology, this initial map we provide may potentially serve as a ready template for the identification and characterization of the first behavioural isolation genes.
Evolution of maternal care in diploid and haplodiploid populations
Authors: GARDNER A. 
Published: June 2012

AbstractMaternal care has been suggested to evolve more readily in haplodiploid populations. Because maternal care appears to have been a prerequisite for the evolution of eusociality, this effect potentially explains the apparent preponderance of haplodiploidy among eusocial taxa. Here, I use a kin selection approach to model the evolution of maternal care in diploid and haplodiploid populations. In contrast to previous suggestions, I find that haplodiploidy may inhibit as well as promote the evolution of maternal care. Moreover, I find that the haplodiploidy effect vanishes in outbred populations if gene effects average rather than add together. I confirm these analytical results using numerical simulation of an explicit population genetics model. This analysis casts doubt upon the idea that haplodiploidy has promoted the evolution of maternal care and, consequently, the evolution of eusociality.
Effect of pencil grasp on the speed and legibility of handwriting after a 10‐minute copy task in Grade 4 children
Authors: Schwellnus Heidi , Carnahan Heather , Kushki Azadeh , Polatajko Helene , Missiuna Cheryl , Chau Tom 
Published: June 2012

AimTo investigate the impact of common pencil grasp patterns on the speed and legibility of handwriting after a 10‐minute copy task, intended to induce muscle fatigue, in typically developing children and in those non‐proficient in handwriting.MethodsA total of 120 Grade 4 students completed a standardised handwriting assessment before and after a 10‐minute copy task. The students indicated the perceived difficulty of the handwriting task at baseline and after 10 minutes. The students also completed a self‐report questionnaire regarding their handwriting proficiency upon completion.ResultsThe majority of the students rated higher effort after the 10‐minute copy task than at baseline (rank sum: P = 0.00001). The effort ratings were similar for the different grasp patterns (multiple linear regression: F = 0.37, P = 0.895). For both typically developing children and those with handwriting issues, the legibility of the writing samples decreased after the 10‐minute copy task but the speed of writing increased.Conclusions and Significance of the StudyThe quality of the handwriting decreased after the 10‐minute copy task; however, there was no difference in the quality or speed scores among the different pencil grasps before and after the copy task. The dynamic tripod pencil grasp did not offer any advantage over the lateral tripod or the dynamic or lateral quadrupod pencil grasps in terms of quality of handwriting after a 10‐minute copy task. These four pencil grasp patterns performed equivalently. Our findings question the practice of having students adopt the dynamic tripod pencil grasp.
Hiatal hernia and the risk of Barrett's esophagus
Authors: Andrici Juliana , Tio Martin , Cox Michael R , Eslick Guy D 
Published: June 2012

AbstractBackground and Aim:  Barrett's esophagus has been associated with the presence of hiatal hernia; however, to date no meta‐analysis of the relationship has been performed. We aimed to conduct a systematic review and meta‐analysis, providing a quantitative estimate of the increased risk of Barrett's esophagus associated with hiatal hernia.Methods:  A search was conducted through four electronic databases (Medline, PubMed, Embase, and Current Contents Connect) to 4 April 2012, for observational studies of Barrett's esophagus patients. We calculated pooled odds ratios and 95% confidence intervals using a random effects model for the association of hiatal hernia with any length Barrett's esophagus, as well as with short segment Barrett's esophagus and long segment Barrett's esophagus. 33 studies comprising 4390 Barrett's esophagus patients were eligible for the meta‐analysis.Results:  Hiatal hernia was associated with an increased risk of Barrett's esophagus of any length (odds ratio 3.94; 95% confidence interval 3.02–5.13). Heterogeneity was present (I2 = 82.03%, P < 0.001), and the Egger test for publication bias was significant (P = 0.0005). The short segment Barrett's esophagus subgroup analysis likewise showed an increased risk (odds ratio 2.87; 95% confidence interval 1.75–4.70). The strongest association was between hiatal hernia and long segment Barrett's esophagus (odds ratio 12.67; 95% confidence interval 8.33–19.25). The increased risk was present even after adjusting for reflux and body mass index.Conclusions:  The presence of hiatal hernia was associated with an increased risk of Barrett's esophagus, even after adjusting for clinically significant confounders. The strongest association was found between hiatal hernia and long segment Barrett's esophagus.
Hepatitis B virus infection increases the risk of cholangiocarcinoma: A meta‐analysis and systematic review
Authors: Li Min , Li Jinzheng , Li Peizhi , Li Hongyang , Su Tianyi , Zhu Rongtao , Gong Jianping 
Published: June 2012

AbstractBackground and Aim:  A number of studies have shown that hepatitis virus infections may be associated with cholangiocarcinoma (CC). However, the relationship between hepatitis B virus (HBV) infection and CC, especially intrahepatic cholangiocarcinoma (ICC), is still controversial.Methods:  Relevant studies were identified by searching PUBMED, EMBASE and Web of Science Datebases up to September 2011. Pooled risk estimates were calculated using a random‐effects model. Potential sources of heterogeneity were performed by subgroup analyses. A total of 18 papers were included in this meta‐analysis.Results:  The pooled risk estimate of all studies showed a statistically significant increased risk of CC among individuals with HBV infection (rate ratio [RR]: 2.66; 95% confidence interval [CI]: 1.97, 3.60). Compared with those without HBV infection, persons with HBV infection had an increased risk of intra‐CC (ICC) (RR: 3.42; 95% CI: 2.46, 43.74), extrahepatic CC (OR: 1.46; 95% CI: 0.98, 2.17), and CC (OR: 2.03; 95% CI: 1.15, 3.56). In a subgroup analysis of HBV infection and risk of ICC, the pooled risk estimate of studies in Asians (RR: 3.63; 95% CI: 2.56, 5.13) was higher than that in non‐Asians (RR: 1.93; 95% CI: 0.78, 4.76). A Begg funnel plot and Egger test revealed no evidence for publication bias.Conclusions:  This meta‐analysis shows that HBV is associated with increased risk of CC, especially for ICC. Further investigation is needed to focus on the mechanism by which HBV may be involved in the pathogenesis of CC.