3,115 research outputs found
Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-seq and ESTs
The reference annotations made for a genome sequence provide the framework
for all subsequent analyses of the genome. Correct annotation is particularly
important when interpreting the results of RNA-seq experiments where short
sequence reads are mapped against the genome and assigned to genes according to
the annotation. Inconsistencies in annotations between the reference and the
experimental system can lead to incorrect interpretation of the effect on RNA
expression of an experimental treatment or mutation in the system under study.
Until recently, the genome-wide annotation of 3-prime untranslated regions
received less attention than coding regions and the delineation of intron/exon
boundaries. In this paper, data produced for samples in Human, Chicken and A.
thaliana by the novel single-molecule, strand-specific, Direct RNA Sequencing
technology from Helicos Biosciences which locates 3-prime polyadenylation sites
to within +/- 2 nt, were combined with archival EST and RNA-Seq data. Nine
examples are illustrated where this combination of data allowed: (1) gene and
3-prime UTR re-annotation (including extension of one 3-prime UTR by 5.9 kb);
(2) disentangling of gene expression in complex regions; (3) clearer
interpretation of small RNA expression and (4) identification of novel genes.
While the specific examples displayed here may become obsolete as genome
sequences and their annotations are refined, the principles laid out in this
paper will be of general use both to those annotating genomes and those seeking
to interpret existing publically available annotations in the context of their
own experimental dataComment: 44 pages, 9 figure
Direct observation of the injection dynamics of a laser wakefield accelerator using few-femtosecond shadowgraphy
International audienceWe present few-femtosecond shadowgraphic snapshots taken during the non-linear evolution of the plasma wave in a laser wakefield accelerator with transverse synchronized few-cycle probe pulses. These snapshots can be directly associated with the electron density distribution within the plasma wave and give quantitative information about its size and shape. Our results show that self-injection of electrons into the first plasma wave period is induced by a lengthening of the first plasma period. Three dimensional particle in cell simulations support our observations
Prevalence and predictors of video game addiction: a study based on a national representative sample of gamers
Video gaming has become a popular leisure activity in many parts of the world, and an increasing number of empirical studies examine the small minority that appears to develop problems as a result of excessive gaming. This study investigated prevalence rates and predictors of video game addiction in a sample of gamers, randomly selected from the National Population Registry of Norway (N =3389). Results showed there were 1.4 % addicted gamers, 7.3 % problem gamers, 3.9 % engaged gamers, and 87.4 % normal gamers. Gender (being male) and age group (being young) were positively associated with addicted-, problem-, and engaged gamers. Place of birth (Africa, Asia, South- and Middle America) were positively associated with addicted- and problem gamers. Video game addiction was negatively associated with conscientiousness and positively associated with neuroticism. Poor psychosomatic health was positively associated with problem- and engaged gaming. These factors provide insight into the field of video game addiction, and may help to provide guidance as to how individuals that are at risk of becoming addicted gamers can be identified
Serotonin tranporter methylation and response to cognitive behaviour therapy in children with anxiety disorders
Anxiety disorders that are the most commonly occurring psychiatric disorders in childhood, are associated with a range of social and educational impairments and often continue into adulthood. Cognitive behaviour therapy (CBT) is an effective treatment option for the majority of cases, although up to 35-45% of children do not achieve remission. Recent research suggests that some genetic variants may be associated with a more beneficial response to psychological therapy. Epigenetic mechanisms such as DNA methylation work at the interface between genetic and environmental influences. Furthermore, epigenetic alterations at the serotonin transporter (SERT) promoter region have been associated with environmental influences such as stressful life experiences. In this study, we measured DNA methylation upstream of SERT in 116 children with an anxiety disorder, before and after receiving CBT. Change during treatment in percentage DNA methylation was significantly different in treatment responders vs nonresponders. This effect was driven by one CpG site in particular, at which responders increased in methylation, whereas nonresponders showed a decrease in DNA methylation. This is the first study to demonstrate differences in SERT methylation change in association with response to a purely psychological therapy. These findings confirm that biological changes occur alongside changes in symptomatology following a psychological therapy such as CBT
Eating patterns and overweight in 9- to 10-year-old children in Telemark County, Norway: a cross-sectional study
Background/Objectives: Increasing prevalence of overweight in children is a growing health problem. The aim of this study was to describe the eating patterns of 9-to 10-year-old schoolchildren, and to investigate the relationship between overweight and eating patterns. Subjects/Methods: We recruited 1045 children for a cross-sectional study in Telemark County, Norway. The children's food, snacking and meal frequencies were reported by their parents using a retrospective food frequency questionnaire. Height and weight were measured by health professionals, and body mass index categories were calculated using international standard cutoff points (International Obesity Task Force values). Complete data were obtained for 924 children. Four distinct eating patterns were identified using principal component analysis. We used multiple logistic regression and calculated odds ratios (ORs) with 95% confidence intervals (CIs) for being overweight, and adjusted for parental characteristics and physical activity levels of the children (aORs). Results: Parental characteristics and physical activity were associated with both obesity and eating patterns. Children adhering to a 'junk/convenient' eating pattern had a significantly lower likelihood of being overweight (aOR: 0.6; 95% CI: 0.4, 0.9), whereas children adhering to a 'varied Norwegian' or a 'dieting' eating pattern had a significantly higher likelihood of being overweight (respective values: aOR: 2.1; 95% CI: 1.3, 3.2; aOR: 2.2; 95% CI: 1.4, 3.4). No association with overweight was seen for a 'snacking pattern'. Conclusions: The main finding was that, although family characteristics influenced both the prevalence of overweight and overall dietary behaviour, independent associations were evident between eating patterns and overweight, indicating parental modification of the diets of overweight children
Genetic Markers of Obesity Risk: Stronger Associations with Body Composition in Overweight Compared to Normal-Weight Children
Genetic factors are important determinants of overweight. We examined whether there are differential effect sizes depending on children's body composition.
We analysed data of n = 4,837 children recorded in the Avon Longitudinal Study of Parents and Children (ALSPAC), applying quantile regression with sex- and age-specific standard deviation scores (SDS) of body mass index (BMI) or with body fat mass index and fat-free mass index at 9 years as outcome variables and an "obesity-risk-allele score" based on eight genetic variants known to be associated with childhood BMI as the explanatory variable.
The quantile regression coefficients increased with increasing child's BMI-SDS and fat mass index percentiles, indicating larger effects of the genetic factors at higher percentiles. While the associations with BMI-SDS were of similar size in medium and high BMI quantiles (40th percentile and above), effect sizes with fat mass index increased over the whole fat mass index distribution. For example, the fat mass index of a normal-weight (50th percentile) child was increased by 0.13 kg/m(2) (95% confidence interval (CI): 0.09, 0.16) per additional allele, compared to 0.24 kg/m(2) per allele (95% CI: 0.15, 0.32) in children at the 90th percentile. The genetic associations with fat-free mass index were weaker and the quantile regression effects less pronounced than those on fat mass index.
Genetic risk factors for childhood overweight appear to have greater effects on fatter children. Interaction of known genetic factors with environmental or unknown genetic factors might provide a potential explanation of these findings
Body composition and body fat distribution are related to cardiac autonomic control in non-alcoholic fatty liver disease patients
BACKGROUND/OBJECTIVES: Heart rate recovery (HRR), a cardiac autonomic control marker, was shown to be related to body composition (BC), yet this was not tested in non-alcoholic fatty liver disease (NAFLD) patients. The aim of this study was to determine if, and to what extent, markers of BC and body fat (BF) distribution are related to cardiac autonomic control in NAFLD patients. SUBJECTS/METHODS: BC was assessed with dual-energy X-ray absorptiometry in 28 NAFLD patients (19 men, 51±13 years, and 9 women, 47±13 years). BF depots ratios were calculated to assess BF distribution. Subjects’ HRR was recorded 1 (HRR1) and 2 min (HRR2) immediately after a maximum graded exercise test.
RESULTS: BC and BF distribution were related to HRR; particularly weight, trunk BF and trunk BF-to-appendicular BF ratio showed a negative relation with HRR1 (r 1⁄4 0.613, r 1⁄4 0.597 and r 1⁄4 0.547, respectively, Po0.01) and HRR2 (r 1⁄4 0.484, r 1⁄4 0.446, Po0.05, and r 1⁄4 0.590, Po0.01, respectively). Age seems to be related to both HRR1 and HRR2 except when controlled for BF distribution. The preferred model in multiple regression should include trunk BF-to-appendicular BF ratio and BF to predict HRR1 (r2 1⁄4 0.549; Po0.05), and trunk BF-to-appendicular BF ratio alone to predict HRR2 (r2 1⁄4 0.430; Po0.001).
CONCLUSIONS: BC and BF distribution were related to HRR in NAFLD patients. Trunk BF-to-appendicular BF ratio was the best independent predictor of HRR and therefore may be best related to cardiovascular increased risk, and possibly act as a mediator in age-related cardiac autonomic control variation.info:eu-repo/semantics/publishedVersio
Body image, body dissatisfaction and weight status in south asian children: a cross-sectional study
Background
Childhood obesity is a continuing problem in the UK and South Asian children represent a group that are particularly vulnerable to its health consequences. The relationship between body dissatisfaction and obesity is well documented in older children and adults, but is less clear in young children, particularly South Asians. A better understanding of this relationship in young South Asian children will inform the design and delivery of obesity intervention programmes. The aim of this study is to describe body image size perception and dissatisfaction, and their relationship to weight status in primary school aged UK South Asian children.
Methods
Objective measures of height and weight were undertaken on 574 predominantly South Asian children aged 5-7 (296 boys and 278 girls). BMI z-scores, and weight status (underweight, healthy weight, overweight or obese) were calculated based on the UK 1990 BMI reference charts. Figure rating scales were used to assess perceived body image size (asking children to identify their perceived body size) and dissatisfaction (difference between perceived current and ideal body size). The relationship between these and weight status were examined using multivariate analyses.
Results
Perceived body image size was positively associated with weight status (partial regression coefficient for overweight/obese vs. non-overweight/obese was 0.63 (95% CI 0.26-0.99) and for BMI z-score was 0.21 (95% CI 0.10-0.31), adjusted for sex, age and ethnicity). Body dissatisfaction was also associated with weight status, with overweight and obese children more likely to select thinner ideal body size than healthy weight children (adjusted partial regression coefficient for overweight/obese vs. non-overweight/obese was 1.47 (95% CI 0.99-1.96) and for BMI z-score was 0.54 (95% CI 0.40-0.67)).
Conclusions
Awareness of body image size and increasing body dissatisfaction with higher weight status is established at a young age in this population. This needs to be considered when designing interventions to reduce obesity in young children, in terms of both benefits and harms
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