bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk factors for burns at home in Kurdish preschool children: a case-control study
Authors: Othman Nasih , Kendrick Denise 
Published: October 2012

BackgroundIt is globally reported that young children are at a higher risk of burns but little is known about the individual risk factors. This study was undertaken in 2008 to investigate factors associated with burn injuries in children aged 0–5 years.MethodsThis was a case-control study with cases recruited prospectively from children attending hospital for a new burn injury and controls recruited from children admitted for other conditions.ResultsA total of 248 cases and 248 controls were recruited. Cases included scalds (79%), contact burns (17%) and flame injuries (4%). Burns were most commonly caused by tea utensils (42%) and kerosene stoves (36%). Multivariable analyses found that a poor living standard (OR 5.4, 95% CI 2.6 to 11.7), having a child with a higher activity score (OR 5.3, 95% CI 3.4 to 8.5), having a history of burns in other family members (OR 2.8, 95% CI 1.5 to 5.2) and a higher number of home hazards (OR for a one unit increase in hazards score 1.32, 95% CI 1.02 to 1.70) were all associated with a significant increase in the odds of a burn injury. The presence of a second carer (OR 0.42, 95% CI 0.2 to 0.7) and having disability (OR 0.14, 95% CI 0.03 to 0.6) were protective factors.ConclusionsThis information about risk factors for burn injuries can be used to target preventive interventions towards families at the greatest risk of injury.
Changing associations between partnership history and risk of accidents, violence and suicides
Authors: Silventoinen Karri , Moustgaard Heta , Peltonen Riina , Martikainen Pekka 
Published: October 2012

BackgroundLower mortality has been systematically found in married when compared with non-married, especially in men, but little is known about marital status differences in mortality from external causes. Furthermore, the role of cohabitation and partnership history in the formation of these differences and how they have been changed over time are poorly understood.MethodsThe incidence of fatal and non-fatal cases of accidents, violence and suicides by partnership history was analysed during 1991–1997 and 2001–2007 in a representative sample of the Finnish population aged 26–59 years. HRs were calculated using Cox proportional hazards models.ResultsIncidence rates in accidents, violence and suicides were generally lower in men and women living with a partner than those living alone. Current cohabitation and previous divorce increased the risk of all of these outcomes when compared with married without previous divorce. Higher incidence rates were found in men who had divorced 3 years ago or earlier when compared with those who had divorced later. Generally, these differences were larger in fatal than in non-fatal cases and significantly larger in men. There was little change in these differences between 1991–1997 and 2001–2007. These differences were partly explained by socioeconomic factors but remained statistically significant also after these adjustments.ConclusionsCurrently living without a partner and cohabitation and previous divorce increased the risk of accidents, violence and suicides. This indicates that also other mechanisms than immediate support from a partner are important in the formation of marital status differences in mortality.
Sensitivity, specificity and likelihood ratios of PCR in the diagnosis of syphilis: a systematic review and meta-analysis
Authors: Gayet-Ageron Angèle , Lautenschlager Stephan , Ninet Béatrice , Perneger Thomas V , Combescure Christophe 
Published: October 2012

ObjectiveTo systematically review and estimate pooled sensitivity and specificity of the polymerase chain reaction (PCR) technique compared to recommended reference tests in the diagnosis of suspected syphilis at various stages and in various biological materials.DesignSystematic review and meta-analysis.Data sourcesSearch of three electronic bibliographic databases from January 1990 to January 2012 and the abstract books of five congresses specialized in the infectious diseases' field (1999–2011). Search key terms included syphilis,Treponema pallidumor neurosyphilis and molecular amplification, polymerase chain reaction or PCR.Review methodsWe included studies that used both reference tests to diagnose syphilis plus PCR and we presented pooled estimates of PCR sensitivity, specificity, and positive and negative likelihood ratios (LR) per syphilis stages and biological materials.ResultsOf 1160 identified abstracts, 69 were selected and 46 studies used adequate reference tests to diagnose syphilis. Sensitivity was highest in the swabs from primary genital or anal chancres (78.4%; 95% CI: 68.2–86.0) and in blood from neonates with congenital syphilis (83.0%; 55.0–95.2). Most pooled specificities were ∼95%, except those in blood. A positive PCR is highly informative with a positive LR around 20 in ulcers or skin lesions. In the blood, the positive LR was <10.ConclusionsThe pooled values of LR showed thatT. pallidumPCR was more efficient to confirm than to exclude syphilis diagnosis in lesions. PCR is a useful diagnostic tool in ulcers, especially when serology is still negative and in medical settings with a high prevalence of syphilis.
Chlamydia screening, retesting and repeat diagnoses in Cornwall, UK 2003–2009
Authors: Turner Katy M E , Horner Paddy J , Trela-Larsen Lea , Sharp Matt , May Margaret 
Published: October 2012

ObjectivesThis study aims to describe the patterns of testing and retesting for chlamydia in Cornwall during the first 5 years of the National Chlamydia Screening Programme. We evaluate the factors associated with retesting and estimate the incidence of chlamydia diagnosis and repeat diagnosis.MethodsStudy design: Secondary database analysis. Selection criteria: men and women tested for chlamydia between March 2003 and January 2009 in Cornwall, aged ≥12 years and ≤25 years at the first test. The factors associated with retesting in those with at least one known test result and at least 14 days follow-up time were analysed using Cox regression and the incidence of diagnosis and repeat diagnosis were calculated.ResultsThe final dataset consisted of 71 066 records from 49 941 individuals; of whom 59.0% were female and 75.4% were only tested once. There were 48 375 individuals with at least one known test result (negative or positive) and at least 14 days follow-up, included in the Cox regression analysis. Factors associated with testing more than once were (adjusted HR, 95% CI): being female (2.24; 2.14 to 2.34) and initially testing positive (1.43; 1.35 to 1.51). The positivity at first episode declined from 13.2% (1077 cases) in 2003/2004 to 5.8% (843 cases) in 2008/2009. The incidence of diagnosis at the second test was 5.9 per 100 person years in those testing negative at the first test compared with 18.1 per 100 person years in those initially positive.DiscussionMost individuals in this analysis were tested only once, but the testing volume and proportion of repeat tests were highest at the end of the study period. As the testing rate stabilises to 30% coverage, maintaining retesting rates in those previously tested and especially in those previously diagnosed with chlamydia will be necessary for the sustainability of the screening programme.ConclusionsA key feature of the next 5 years of the screening programme will be to maintain screening and rescreening.
Contrasted patterns of selective pressure in three recent paralogous gene pairs in the Medicagogenus (L.)
Authors: Ho-Huu Joan , Ronfort Joëlle , De Mita Stéphane , Bataillon Thomas , Hochu Isabelle , Weber Audrey , Chantret Nathalie 
Published: October 2012

Abstract

Background
Gene duplications are a molecular mechanism potentially mediating generation of functional novelty. However, the probabilities of maintenance and functional divergence of duplicated genes are shaped by selective pressures acting on gene copies immediately after the duplication event. The ratio of non-synonymous to synonymous substitution rates in protein-coding sequences provides a means to investigate selective pressures based on genic sequences. Three molecular signatures can reveal early stages of functional divergence between gene copies: change in the level of purifying selection between paralogous genes, occurrence of positive selection, and transient relaxed purifying selection following gene duplication. We studied three pairs of genes that are known to be involved in an interaction with symbiotic bacteria and were recently duplicated in the history of the Medicago genus (Fabaceae). We sequenced two pairs of polygalacturonase genes (Pg11-Pg3 and Pg11a-Pg11c) and one pair of auxine transporter-like genes (Lax2-Lax4) in 17 species belonging to the Medicago genus, and sought for molecular signatures of differentiation between copies.

Results
Selective histories revealed by these three signatures of molecular differentiation were found to be markedly different between each pair of paralogs. We found sites under positive selection in the Pg11 paralogs while Pg3 has mainly evolved under purifying selection. The most recent paralogs examined Pg11a and Pg11c, are both undergoing positive selection and might be acquiring new functions. Lax2 and Lax4 paralogs are both under strong purifying selection, but still underwent a temporary relaxation of purifying selection immediately after duplication.

Conclusions
This study illustrates the variety of selective pressures undergone by duplicated genes and the effect of age of the duplication. We found that relaxation of selective constraints immediately after duplication might promote adaptive divergence.
Genome-wide metabolic (re-) annotation of Kluyveromyces lactis
Authors: Dias Oscar , Gombert Andreas K , Ferreira Eugénio C , Rocha Isabel 
Published: October 2012

Abstract

Background
Even before having its genome sequence published in 2004, Kluyveromyces lactis had long been considered a model organism for studies in genetics and physiology. Research on Kluyveromyces lactis is quite advanced and this yeast species is one of the few with which it is possible to perform formal genetic analysis. Nevertheless, until now, no complete metabolic functional annotation has been performed to the proteins encoded in the Kluyveromyces lactis genome.

Results
In this work, a new metabolic genome-wide functional re-annotation of the proteins encoded in the Kluyveromyces lactis genome was performed, resulting in the annotation of 1759 genes with metabolic functions, and the development of a methodology supported by merlin (software developed in-house). The new annotation includes novelties, such as the assignment of transporter superfamily numbers to genes identified as transporter proteins. Thus, the genes annotated with metabolic functions could be exclusively enzymatic (1410 genes), transporter proteins encoding genes (301 genes) or have both metabolic activities (48 genes). The new annotation produced by this work largely surpassed the Kluyveromyces lactis currently available annotations. A comparison with KEGG’s annotation revealed a match with 844 (~90%) of the genes annotated by KEGG, while adding 850 new gene annotations. Moreover, there are 32 genes with annotations different from KEGG.

Conclusions
The methodology developed throughout this work can be used to re-annotate any yeast or, with a little tweak of the reference organism, the proteins encoded in any sequenced genome. The new annotation provided by this study offers basic knowledge which might be useful for the scientific community working on this model yeast, because new functions have been identified for the so-called metabolic genes. Furthermore, it served as the basis for the reconstruction of a compartmentalized, genome-scale metabolic model of Kluyveromyces lactis, which is currently being finished.
Virulence of the Pseudomonas fluorescens clinical strain MFN1032 towards Dictyostelium discoideumand macrophages in relation with type III secretion system
Authors: Sperandio Daniel , Decoin Victorien , Latour Xavier , Mijouin Lily , Hillion Mélanie , Feuilloley Marc G J , Orange Nicole , Merieau Annabelle 
Published: October 2012

Abstract

Background

Pseudomonas fluorescens biovar I MFN1032 is a clinical isolate able to grow at 37°C. This strain displays secretion-mediated hemolytic activity involving phospholipase C and cyclolipopeptides, and a cell-associated hemolytic activity distinct from the secreted hemolytic activity. Cell-associated hemolysis is independent of biosurfactant production and remains in a gacA mutant. Disruption of the hrpU-like operon (the basal part of type III secretion system from rhizospheric strains) suppresses this activity. We hypothesized that this phenotype could reflect evolution of an ancestral mechanism involved in the survival of this species in its natural niche. In this study, we evaluated the hrpU-like operon’s contribution to other virulence mechanisms using a panel of Pseudomonas strains from various sources.

Results
We found that MFN1032 inhibited the growth of the amoebae Dictyostelium discoideum and that this inhibition involved the hrpU-like operon and was absent in a gacA mutant. MFN1032 was capable of causing macrophage lysis, if the hrpU-like operon was intact, and this cytotoxicity remained in a gacA mutant. Cell-associated hemolytic activity and macrophage necrosis were found in other P. fluorescens clinical isolates, but not in biocontrol P. fluorescens strains harbouring hrpU-like operon. The growth of Dictyostelium discoideum was inhibited to a different extent by P. fluorescens strains without correlation between this inhibition and hrpU-like operon sequences.

Conclusions
In P. fluorescens MFN1032, the basal part of type III secretion system plays a role in D. discoideum growth inhibition and macrophage necrosis. The inhibition of D. discoideum growth is dependent on the GacS/GacA system, while cell-associated hemolytic activity and macrophage lysis are not. Virulence against eukaryotic cells based on the hrpU-like operon may be more than just a stochastic evolution of a conserved system dedicated to survival in competition with natural predators such as amoebae. It may also mean that there are some important modifications of other type III secretion system components, which remain unknown. Cell-associated hemolysis might be a good indicator of the virulence of Pseudomonas fluorescens strain.
Transcriptomic and metabolomic analysis of Yukon Thellungiella plants grown in cabinets and their natural habitat show phenotypic plasticity
Authors: Guevara David R , Champigny Marc J , Tattersall Ashley , Dedrick Jeff , Wong Chui E , Li Yong , Labbe Aurelie , Ping Chien-Lu , Wang Yanxiang , Nuin Paulo , Golding G Brian , McCarry Brian E , Summers Peter S , Moffatt Barbara A , Weretilnyk Elizabeth A 
Published: October 2012

Abstract

Background

Thellungiella salsuginea is an important model plant due to its natural tolerance to abiotic stresses including salt, cold, and water deficits. Microarray and metabolite profiling have shown that Thellungiella undergoes stress-responsive changes in transcript and organic solute abundance when grown under controlled environmental conditions. However, few reports assess the capacity of plants to display stress-responsive traits in natural habitats where concurrent stresses are the norm.

Results
To determine whether stress-responsive changes observed in cabinet-grown plants are recapitulated in the field, we analyzed leaf transcript and metabolic profiles of Thellungiella growing in its native Yukon habitat during two years of contrasting meteorological conditions. We found 673 genes showing differential expression between field and unstressed, chamber-grown plants. There were comparatively few overlaps between genes expressed under field and cabinet treatment-specific conditions. Only 20 of 99 drought-responsive genes were expressed both in the field during a year of low precipitation and in plants subjected to drought treatments in cabinets. There was also a general pattern of lower abundance among metabolites found in field plants relative to control or stress-treated plants in growth cabinets. Nutrient availability may explain some of the observed differences. For example, proline accumulated to high levels in cold and salt-stressed cabinet-grown plants but proline content was, by comparison, negligible in plants at a saline Yukon field site. We show that proline accumulated in a stress-responsive manner in Thellungiella plants salinized in growth cabinets and in salt-stressed seedlings when nitrogen was provided at 1.0 mM. In seedlings grown on 0.1 mM nitrogen medium, the proline content was low while carbohydrates increased. The relatively higher content of sugar-like compounds in field plants and seedlings on low nitrogen media suggests that Thellungiella shows metabolic plasticity in response to environmental stress and that resource availability can influence the expression of stress tolerance traits under field conditions.

Conclusion
Comparisons between Thellungiella plants responding to stress in cabinets and in their natural habitats showed differences but also overlap between transcript and metabolite profiles. The traits in common offer potential targets for improving crops that must respond appropriately to multiple, concurrent stresses.
FILAMENTOUS FLOWER controls lateral organ development by acting as both an activator and a repressor
Authors: Bonaccorso Oliver , Lee Joanne E , Puah Libby , Scutt Charles P , Golz John F 
Published: October 2012

Abstract

Background
The YABBY (YAB) family of transcription factors participate in a diverse range of processes that include leaf and floral patterning, organ growth, and the control of shoot apical meristem organisation and activity. How these disparate functions are regulated is not clear, but based on interactions with the LEUNIG-class of co-repressors, it has been proposed that YABs act as transcriptional repressors. In the light of recent work showing that DNA-binding proteins associated with the yeast co-repressor TUP1 can also function as activators, we have examined the transcriptional activity of the YABs.

Results
Of the four Arabidopsis YABs tested in yeast, only FILAMENTOUS FLOWER (FIL) activated reporter gene expression. Similar analysis with Antirrhinum YABs identified the FIL ortholog GRAMINIFOLIA as an activator. Plant-based transactivation assays not only confirmed the potential of FIL to activate transcription, but also extended this property to the FIL paralog YABBY3 (YAB3). Subsequent transcriptomic analysis of lines expressing a steroid-inducible FIL protein revealed groups of genes that responded either positively or negatively to YAB induction. Included in the positively regulated group of genes were the polarity regulators KANADI1 (KAN1), AUXIN RESPONSE FACTOR 4 (ARF4) and ASYMMETRIC LEAVES1 (AS1). We also show that modifying FIL to function as an obligate repressor causes strong yab loss-of-function phenotypes.

Conclusions
Collectively these data show that FIL functions as a transcriptional activator in plants and that this activity is involved in leaf patterning. Interestingly, our study also supports the idea that FIL can act as a repressor, as transcriptomic analysis identified negatively regulated FIL-response genes. To reconcile these observations, we propose that YABs are bifunctional transcription factors that participate in both positive and negative regulation. These findings fit a model of leaf development in which adaxial/abaxial patterning is maintained by a regulatory network consisting of positive feedback loops.
Patients with chronic kidney disease are at an elevated risk of dementia: A population-based cohort study in Taiwan
Authors: Cheng Kao-Chi , Chen Yu-Lung , Lai Shih-Wei , Mou Chih-Hsin , Tsai Pang-Yao , Sung Fung-Chang 
Published: October 2012

Abstract

Background
Chronic kidney disease (CKD) is more prevalent in Taiwan than in most countries. This population-based cohort study evaluated the dementia risk associated with CKD.

Methods
Using claims data of 1,000,000 insured residents covered in the universal health insurance of Taiwan, we selected 37049 adults with CKD newly diagnosed from 2000–2006 as the CKD cohort. We also randomly selected 74098 persons free from CKD and other kidney diseases, frequency matched with age, sex and the date of CKD diagnosed. Incidence and hazard ratios (HRs) of dementia were evaluated by the end of 2009.

Results
Subjects in the CKD cohort were more prevalent with comorbidities than those in the non-CKD cohort (p <0.0001). The dementia incidence was higher in the CKD cohort than in the non-CKD cohort (9.30 vs. 5.55 per 1,000 person-years), with an overall HR of 1.41 (95% confidence interval (CI), 1.32-1.50), controlling for sex, age, comorbidities and medicaitions. The risk was similar in men and women but increased sharply with age to an HR of 133 (95% CI, 68.9-256) for the elderly. However, the age-specific CKD cohort to non-CKD cohort incidence rate ratio decreased with age, with the highest ratio of 16.0 (95% CI, 2.00-128) in the youngest group. Among comorbidities and medications, alcoholism and taking benzodiazepines were also associated with dementia with elevated adjusted HRs of 3.05 (95% CI 2.17-4.28) and 1.23 (95% CI 1.14-1.32), respectively.

Conclusions
Patients with CKD could have an elevated dementia risk. CKD patients with comorbidity deserve attention to prevent dementia.
Effect of a family focused active play intervention on sedentary time and physical activity in preschool children
Authors: O’Dwyer Mareesa V , Fairclough Stuart J , Knowles Zoe , Stratton Gareth 
Published: October 2012

Abstract

Background
Early childhood provides a window of opportunity for the promotion of physical activity. Given the limited effectiveness of interventions to date, new approaches are needed. Socio-ecological models suggest that involving parents as intervention targets may be effective in fostering healthier lifestyles in children. This study describes the effectiveness of a family-focused ‘Active Play’ intervention in decreasing sedentary time and increasing total physical activity in preschool children.

Method
Seventy-seven families were recruited from 8 randomly selected SureStart children’s centres in the North West of England. Centres were randomly assigned to either an intervention (n = 4) or a comparison group (n = 4). Parents and children in the intervention group received a 10-week active play programme delivered by trained active play professionals; this included an activity and educational component. Families in the comparison group were asked to maintain their usual routine. Each participating parent and child wore a uni-axial accelerometer for 7 days at baseline and post-test. Week and weekend day sedentary time and total physical activity adjusted for child- and home- level covariates were analysed using multilevel analyses.

Results
Significant intervention effects were observed for sedentary time and physical activity for both week and weekend days. Children in the intervention group engaged in 1.5% and 4.3% less sedentary time during week and weekend days, respectively and 4.5% and 13.1% more physical activity during week and weekend days, respectively than children in the comparison group. Parent’s participation in sport and their physical activity levels, child’s sex, availability of media in the home and attendance at organised activities were significant predictors of sedentary time and physical activity in this age group.

Conclusion
A 10-week family focused active play intervention produced positive changes in sedentary time and total physical activity levels in preschool children. Specific covariates were identified as having a significant effect on the outcome measures. Moreover, children whose parents were active engaged in less sedentary time and more physical activity suggesting that parent’s activity habits are mediators of physical activity engagement in this age group.