Evaluation of the impact of a school gardening intervention on children's fruit and vegetable intake: a randomised controlled trial.

Background: Current academic literature suggests that school gardening programmes can provide an interactive environment with the potential to change children’s fruit and vegetable intake. This is the first cluster randomised controlled trial (RCT) designed to evaluate whether a school gardening programme can have an effect on children’s fruit and vegetable intake. Methods: The trial included children from 23 schools; these schools were randomised into two groups, one to receive the Royal Horticultural Society (RHS)-led intervention and the other to receive the less involved Teacher-led intervention. A 24-hour food diary (CADET) was used to collect baseline and follow-up dietary intake 18 months apart. Questionnaires were also administered to evaluate the intervention implementation. Results: A total of 641 children completed the trial with a mean age of 8.1 years (95% CI: 8.0, 8.4). The unadjusted results from multilevel regression analysis revealed that for combined daily fruit and vegetable intake the Teacher-led group had a higher daily mean change of 8 g (95% CI: −19, 36) compared to the RHS-led group -32 g (95% CI: −60, −3). However, after adjusting for possible confounders this difference was not significant (intervention effect: −40 g, 95% CI: −88, 1; p = 0.06). The adjusted analysis of process measures identified that if schools improved their gardening score by 3 levels (a measure of school gardening involvement - the scale has 6 levels from 0 ‘no garden’ to 5 ‘community involvement’), irrespective of group allocation, children had, on average, a daily increase of 81 g of fruit and vegetable intake (95% CI: 0, 163; p = 0.05) compared to schools that had no change in gardening score. Conclusions: This study is the first cluster randomised controlled trial designed to evaluate a school gardening intervention. The results have found very little evidence to support the claims that school gardening alone can improve children’s daily fruit and vegetable intake. However, when a gardening intervention is implemented at a high level within the school it may improve children’s daily fruit and vegetable intake by a portion. Improving children’s fruit and vegetable intake remains a challenging task

Measuring diet in primary school children aged 8-11 years: validation of the Child and Diet Evaluation Tool (CADET) with an emphasis on fruit and vegetable intake.

Background/Objectives:The Child And Diet Evaluation Tool (CADET) is a 24-h food diary that measures the nutrition intake of children aged 3-7 years, with a focus on fruit and vegetable consumption. Until now CADET has not been used to measure nutrient intake of children aged 8-11 years. To ensure that newly assigned portion sizes for this older age group were valid, participants were asked to complete the CADET diary (the school and home food diary) concurrently with a 1-day weighed record. Subjects/Methods:A total of 67 children with a mean age of 9.3 years (s.d.: ± 1.4, 51% girls) participated in the study. Total fruit and vegetable intake in grams and other nutrients were extracted to compare the mean intakes from the CADET diary and Weighed record using t-tests and Pearson's r correlations. Bland-Altman analysis was also conducted to assess the agreement between the two methods. Results: Correlations comparing the CADET diary to the weighed record were high for fruit, vegetables and combined fruit and vegetables (r=0.7). The results from the Bland-Altman plots revealed a mean difference of 54 g (95% confidence interval: -88, 152) for combined fruit and vegetables intake. CADET is the only tool recommended by the National Obesity Observatory that has been validated in a UK population and provides nutrient level data on children's diets. Conclusions:The results from this study conclude that CADET can provide high-quality nutrient data suitable for evaluating intervention studies now for children aged 3-11 years with a focus on fruit and vegetable intake

Pilot Validation Study of Inertial Measurement Units and Markerless Methods for 3D Neck and Trunk Kinematics during a Simulated Surgery Task

Surgeons are at high risk for developing musculoskeletal symptoms (MSS), like neck and back pain. Quantitative analysis of 3D neck and trunk movements during surgery can help to develop preventive devices such as exoskeletons. Inertial Measurement Units (IMU) and markerless motion capture methods are allowed in the operating room (OR) and are a good alternative for bulky optoelectronic systems. We aim to validate IMU and markerless methods against an optoelectronic system during a simulated surgery task. Intraclass correlation coefficient (ICC (2,1)), root mean square error (RMSE), range of motion (ROM) difference and Bland–Altman plots were used for evaluating both methods. The IMU-based motion analysis showed good-to-excellent (ICC 0.80–0.97) agreement with the gold standard within 2.3 to 3.9 degrees RMSE accuracy during simulated surgery tasks. The markerless method shows 5.5 to 8.7 degrees RMSE accuracy (ICC 0.31–0.70). Therefore, the IMU method is recommended over the markerless motion capture

Biomechanical Load of Neck and Lumbar Joints in Open-Surgery Training

The prevalence of musculoskeletal symptoms (MSS) like neck and back pain is high among open-surgery surgeons. Prolonged working in the same posture and unfavourable postures are biomechanical risk factors for developing MSS. Ergonomic devices such as exoskeletons are possible solutions that can reduce muscle and joint load. To design effective exoskeletons for surgeons, one needs to quantify which neck and trunk postures are seen and how much support during actual surgery is required. Hence, this study aimed to establish the biomechanical profile of neck and trunk postures and neck and lumbar joint loads during open surgery (training). Eight surgical trainees volunteered to participate in this research. Neck and trunk segment orientations were recorded using an inertial measurement unit (IMU) system during open surgery (training). Neck and lumbar joint kinematics, joint moments and compression forces were computed using OpenSim modelling software and a musculoskeletal model. Histograms were used to illustrate the joint angle and load distribution of the neck and lumbar joints over time. During open surgery, the neck flexion angle was 71.6% of the total duration in the range of 10~40 degrees, and lumbar flexion was 68.9% of the duration in the range of 10~30 degrees. The normalized neck and lumbar flexion moments were 53.8% and 35.5% of the time in the range of 0.04~0.06 Nm/kg and 0.4~0.6 Nm/kg, respectively. Furthermore, the neck and lumbar compression forces were 32.9% and 38.2% of the time in the range of 2.0~2.5 N/kg and 15~20 N/kg, respectively. In contrast to exoskeletons used for heavy lifting tasks, exoskeletons designed for surgeons exhibit lower support torque requirements while additional degrees of freedom (DOF) are needed to accommodate combinations of neck and trunk postures.</p

Augmenting Basin-Hopping With Techniques From Unsupervised Machine Learning: Applications in Spectroscopy and Ion Mobility

Published by 'Frontiers in Chemistry' at 10.3389/fchem.2019.00519.Evolutionary algorithms such as the basin-hopping (BH) algorithm have proven to be useful for difficult non-linear optimization problems with multiple modalities and variables. Applications of these algorithms range from characterization of molecular states in statistical physics and molecular biology to geometric packing problems. A key feature of BH is the fact that one can generate a coarse-grained mapping of a potential energy surface (PES) in terms of local minima. These results can then be utilized to gain insights into molecular dynamics and thermodynamic properties. Here we describe how one can employ concepts from unsupervised machine learning to augment BH PES searches to more efficiently identify local minima and the transition states connecting them. Specifically, we introduce the concepts of similarity indices, hierarchical clustering, and multidimensional scaling to the BH methodology. These same machine learning techniques can be used as tools for interpreting and rationalizing experimental results from spectroscopic and ion mobility investigations (e.g., spectral assignment, dynamic collision cross sections). We exemplify this in two case studies: (1) assigning the infrared multiple photon dissociation spectrum of the protonated serine dimer and (2) determining the temperature-dependent collision cross-section of protonated alanine tripeptide.WH acknowledges funding from the Natural Sciences and Engineering Research Council (NSERC) of Canada in the form of a Discovery Grant and from the Province of Ontario in the form of an Early Researcher Award (ERA). CI acknowledges funding from NSERC in the form of a post graduate scholarship

Beyond Repair Foci: DNA Double-Strand Break Repair in Euchromatic and Heterochromatic Compartments Analyzed by Transmission Electron Microscopy

DNA double-strand breaks (DSBs) generated by ionizing radiation pose a serious threat to the preservation of genetic and epigenetic information. The known importance of local chromatin configuration in DSB repair raises the question of whether breaks in different chromatin environments are recognized and repaired by the same repair machinery and with similar efficiency. An essential step in DSB processing by non-homologous end joining is the high-affinity binding of Ku70-Ku80 and DNA-PKcs to double-stranded DNA ends that holds the ends in physical proximity for subsequent repair.Using transmission electron microscopy to localize gold-labeled pKu70 and pDNA-PKcs within nuclear ultrastructure, we monitored the formation and repair of actual DSBs within euchromatin (electron-lucent) and heterochromatin (electron-dense) in cortical neurons of irradiated mouse brain.While DNA lesions in euchromatin (characterized by two pKu70-gold beads, reflecting the Ku70-Ku80 heterodimer) are promptly sensed and rejoined, DNA packaging in heterochromatin appears to retard DSB processing, due to the time needed to unravel higher-order chromatin structures. Complex pKu70-clusters formed in heterochromatin (consisting of 4 or ≥ 6 gold beads) may represent multiple breaks in close proximity caused by ionizing radiation of highly-compacted DNA. All pKu70-clusters disappeared within 72 hours post-irradiation, indicating efficient DSB rejoining. However, persistent 53BP1 clusters in heterochromatin (comprising ≥ 10 gold beads), occasionally co-localizing with γH2AX, but not pKu70 or pDNA-PKcs, may reflect incomplete or incorrect restoration of chromatin structure rather than persistently unrepaired DNA damage.Higher-order organization of chromatin determines the accessibility of DNA lesions to repair complexes, defining how readily DSBs are detected and processed. DNA lesions in heterochromatin appear to be more complex, with multiple breaks in spatial vicinity inducing severe chromatin disruptions. Imperfect restoration of chromatin configurations may leave DSB-induced epigenetic memory of damage with potentially pathological repercussions

Differential Dynamics of Transposable Elements during Long-Term Diploidization of Nicotiana Section Repandae (Solanaceae) Allopolyploid Genomes

PubMed ID: 23185607This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

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

The Effect of Pre-Injury Anti-Platelet Therapy on the Development of Complications in Isolated Blunt Chest Wall Trauma: A Retrospective Study

INTRODUCTION: The difficulties in the management of the blunt chest wall trauma patient in the Emergency Department due to the development of late complications are well recognised in the literature. Pre-injury anti-platelet therapy has been previously investigated as a risk factor for poor outcomes following traumatic head injury, but not in the blunt chest wall trauma patient cohort. The aim of this study was to investigate pre-injury anti-platelet therapy as a risk factor for the development of complications in the recovery phase following blunt chest wall trauma. METHODS: A retrospective study was completed in which the medical notes were analysed of all blunt chest wall trauma patients presenting to a large trauma centre in Wales in 2012 and 2013. Using univariate and multivariable logistic regression analysis, pre-injury platelet therapy was investigated as a risk factor for the development of complications following blunt chest wall trauma. Previously identified risk factors were included in the analysis to address the influence of confounding. RESULTS: A total of 1303 isolated blunt chest wall trauma patients presented to the ED in Morriston Hospital in 2012 and 2013 with complications recorded in 144 patients (11%). On multi-variable analysis, pre-injury anti-platelet therapy was found to be a significant risk factor for the development of complications following isolated blunt chest wall trauma (odds ratio: 16.9; 95% confidence intervals: 8.2-35.2). As in previous studies patient age, number of rib fractures, chronic lung disease and pre-injury anti-coagulant use were also found to be significant risk factors. CONCLUSIONS: Pre-injury anti-platelet therapy is being increasingly used as a first line treatment for a number of conditions and there is a concurrent increase in trauma in the elderly population. Pre-injury anti-platelet therapy should be considered as a risk factor for the development of complications by clinicians managing blunt chest wall trauma

Alternative processing of human HTT mRNA with implications for Huntington's disease therapeutics

Huntington disease is caused by a CAG repeat expansion in exon 1 of the huntingtin gene (HTT) that is translated into a polyglutamine stretch in the huntingtin protein (HTT). We previously showed that HTT mRNA carrying an expanded CAG repeat was incompletely spliced to generate HTT1a, an exon 1 only transcript, which was translated to produce the highly aggregation-prone and pathogenic exon 1 HTT protein. This occurred in all knock-in mouse models of Huntington's disease and could be detected in patient cell lines and post-mortem brains. To extend these findings to a model system expressing human HTT, we took advantage of YAC128 mice that are transgenic for a yeast artificial chromosome carrying human HTT with an expanded CAG repeat. We discovered that the HTT1a transcript could be detected throughout the brains of YAC128 mice. We implemented RNAscope to visualise HTT transcripts at the single molecule level and found that full-length HTT and HTT1a were retained together in large nuclear RNA clusters, as well as being present as single transcripts in the cytoplasm. Homogeneous time-resolved fluorescence analysis demonstrated that the HTT1a transcript had been translated to produce the exon 1 HTT protein. The levels of exon 1 HTT in YAC128 mice, correlated with HTT aggregation, supportive of the hypothesis that exon 1 HTT initiates the aggregation process. Huntingtin-lowering strategies are a major focus of therapeutic development for Huntington's disease. These approaches often target full-length HTT alone and would not be expected to reduce pathogenic exon 1 HTT levels. We have established YAC128 mouse embryonic fibroblast lines and shown that, together with our QuantiGene multiplex assay, these provide an effective screening tool for agents that target HTT transcripts. The effects of current targeting strategies on nuclear RNA clusters are unknown, structures that may have a pathogenic role, or alternatively could be protective by retaining HTT1a in the nucleus and preventing it from being translated. In light of recently halted antisense oligonucleotide trials, it is vital that agents targeting HTT1a are developed, and that the effects of HTT-lowering strategies on the subcellular levels of all HTT transcripts and their various HTT protein isoforms are understood