Seeds and the Art of Genome Maintenance

Successful germination represents a crucial developmental transition in the plant lifecycle and is important both for crop yields and plant survival in natural ecosystems. However, germination potential decreases during storage and seed longevity is a key determinant of crop production. Decline in germination vigor is initially manifest as an increasing delay to radicle emergence and the completion of germination and eventually culminating in loss of seed viability. The molecular mechanisms that determine seed germination vigor and viability remain obscure, although deterioration in seed quality is associated with the accumulation of damage to cellular structures and macromolecules including lipids, protein, and nucleic acids. In desiccation tolerant seeds, desiccation/rehydration cycles and prolonged periods in the dry quiescent state are associated with remarkable levels of stress to the embryo genome which can result in mutagenesis of the genetic material, inhibition of transcription and replication and delayed growth and development. An increasing number of studies are revealing DNA damage accumulated in the embryo genome, and the repair capacity of the seed to reverse this damage, as major factors that determine seed vigor and viability. Recent findings are now establishing important roles for the DNA damage response in regulating germination, imposing a delay to germination in aged seed to minimize the deleterious consequences of DNA damage accumulated in the dry quiescent state. Understanding the mechanistic basis of seed longevity will underpin the directed improvement of crop varieties and support preservation of plant genetic resources in seed banks

Hormone replacement therapy after surgery for stage 1 or 2 cutaneous melanoma

A total of 206 women were followed for a minimum of 5 years after primary melanoma surgery to establish if hormone replacement therapy (HRT) adversely affected prognosis. In all, 123 had no HRT and 22 have died of melanoma; 83 had HRT for varying periods and one has died of melanoma. After controlling for known prognostic factors, we conclude that HRT after melanoma does not adversely affect prognosis

Nature vs. Nurture: Dynamical Evolution in Disordered Ising Ferromagnets

We study the predictability of zero-temperature Glauber dynamics in various models of disordered ferromagnets. This is analyzed using two independent dynamical realizations with the same random initialization (called twins). We derive, theoretically and numerically, trajectories for the evolution of the normalized magnetization and twin overlap as the system size tends to infinity. The systems we treat include mean-field ferromagnets with light-tailed and heavy-tailed coupling distributions, as well as highly-disordered models with a variety of other geometries. In the mean-field setting with light-tailed couplings, the disorder averages out and the limiting trajectories of the magnetization and twin overlap match those of the homogenous Curie--Weiss model. On the other hand, when the coupling distribution has heavy tails, or the geometry changes, the effect of the disorder persists in the thermodynamic limit. Nonetheless, qualitatively all such random ferromagnets share a similar time evolution for their twin overlap, wherein the two twins initially decorrelate, before either partially or fully converging back together due to the ferromagnetic drift.Comment: 16 pages, 7 figure

Not a nurse but more than a mother: The practices of mothering children with complex health care needs

This paper reports on the analysis of parent-recorded video diaries from a parent-driven campaign, #notanurse_but, supported by the charity WellChild. The campaign reveals the challenges that parents (predominantly mothers) face providing high level, ongoing clinical care for a son or daughter who has complex care needs. A team of four researchers analysed 30 videos from the WellChild website, WellChild Facebook page, a dedicated #notanurse_but campaign Facebook page, YouTube and Twitter. An interpretative, inductive qualitative analytical approach was utilised. This paper reflects on the portrayal of mothering (it was predominantly mothers who produced campaign videos) a child with complex health care needs. In particular, this paper considers the competing identities of mother and nurse that these mothers fulfil as part of their daily regimes in ‘being mum’. This paper also contributes to geographical discussions concerning methods and ethics of online data collection and the use of secondary online material

phyloXML: XML for evolutionary biology and comparative genomics

<p>Abstract</p> <p>Background</p> <p>Evolutionary trees are central to a wide range of biological studies. In many of these studies, tree nodes and branches need to be associated (or annotated) with various attributes. For example, in studies concerned with organismal relationships, tree nodes are associated with taxonomic names, whereas tree branches have lengths and oftentimes support values. Gene trees used in comparative genomics or phylogenomics are usually annotated with taxonomic information, genome-related data, such as gene names and functional annotations, as well as events such as gene duplications, speciations, or exon shufflings, combined with information related to the evolutionary tree itself. The data standards currently used for evolutionary trees have limited capacities to incorporate such annotations of different data types.</p> <p>Results</p> <p>We developed a XML language, named phyloXML, for describing evolutionary trees, as well as various associated data items. PhyloXML provides elements for commonly used items, such as branch lengths, support values, taxonomic names, and gene names and identifiers. By using "property" elements, phyloXML can be adapted to novel and unforeseen use cases. We also developed various software tools for reading, writing, conversion, and visualization of phyloXML formatted data.</p> <p>Conclusion</p> <p>PhyloXML is an XML language defined by a complete schema in XSD that allows storing and exchanging the structures of evolutionary trees as well as associated data. More information about phyloXML itself, the XSD schema, as well as tools implementing and supporting phyloXML, is available at <url>http://www.phyloxml.org</url>.</p

Background risk of breast cancer and the association between physical activity and mammographic density

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Mosquito Abundance, Bed net Coverage and Other Factors Associated with Variations in Sporozoite Infectivity Rates in Four Villages of Rural Tanzania.

Entomological surveys are of great importance in decision-making processes regarding malaria control strategies because they help to identify associations between vector abundance both species-specific ecology and disease intervention factors associated with malaria transmission. Sporozoite infectivity rates, mosquito host blood meal source, bed net coverage and mosquito abundance were assessed in this study. A longitudinal survey was conducted in four villages in two regions of Tanzania. Malaria vectors were sampled using the CDC light trap and pyrethrum spray catch methods. In each village, ten paired houses were selected for mosquitoes sampling. Sampling was done in fortnight case and study was undertaken for six months in both Kilimanjaro (Northern Tanzania) and Dodoma (Central Tanzania) regions. A total of 6,883 mosquitoes were collected including: 5,628 (81.8%) Anopheles arabiensis, 1,100 (15.9%) Culex quinquefasciatus, 89 (1.4%) Anopheles funestus, and 66 (0.9%) Anopheles gambiae s.s. Of the total mosquitoes collected 3,861 were captured by CDC light trap and 3,022 by the pyrethrum spray catch method. The overall light trap: spray catch ratio was 1.3:1. Mosquito densities per room were 96.5 and 75.5 for light trap and pyrethrum spray catch respectively. Mosquito infectivity rates between villages that have high proportion of bed net owners and those without bed nets was significant (P < 0.001) and there was a significant difference in sporozoite rates between households with and without bed nets in these four villages (P < 0.001). Malaria remains a major problem in the study areas characterized as low transmission sites. Further studies are required to establish the annual entomological inoculation rates and to observe the annual parasitaemia dynamics in these communities. Outdoor mosquitoes collection should also be considered

The translation, validity and reliability of the German version of the Fremantle Back Awareness Questionnaire

Background: The Fremantle Back Awareness Questionnaire (FreBAQ) claims to assess disrupted self-perception of the back. The aim of this study was to develop a German version of the Fre-BAQ (FreBAQ-G) and assess its test-retest reliability, its known-groups validity and its convergent validity with another purported measure of back perception. Methods: The FreBaQ-G was translated following international guidelines for the transcultural adaptation of questionnaires. Thirty-five patients with non-specific CLBP and 48 healthy participants were recruited. Assessor one administered the FreBAQ-G to each patient with CLBP on two separate days to quantify intra-observer reliability. Assessor two administered the FreBaQ-G to each patient on day 1. The scores were compared to those obtained by assessor one on day 1 to assess inter-observer reliability. Known-groups validity was quantified by comparing the FreBAQ-G score between patients and healthy controls. To assess convergent validity, patient\u27s FreBAQ-G scores were correlated to their two-point discrimination (TPD) scores. Results: Intra- and Inter-observer reliability were both moderate with ICC3.1 = 0.88 (95%CI: 0.77 to 0.94) and 0.89 (95%CI: 0.79 to 0.94), respectively. Intra- and inter-observer limits of agreement (LoA) were 6.2 (95%CI: 5.0±8.1) and 6.0 (4.8±7.8), respectively. The adjusted mean difference between patients and controls was 5.4 (95%CI: 3.0 to 7.8, p\u3c0.01). Patient\u27s FreBAQ-G scores were not associated with TPD thresholds (Pearson\u27s r = -0.05, p = 0.79). Conclusions: The FreBAQ-G demonstrated a degree of reliability and known-groups validity. Interpretation of patient level data should be performed with caution because the LoA were substantial. It did not demonstrate convergent validity against TPD. Floor effects of some items of the FreBAQ-G may have influenced the validity and reliability results. The clinimetric properties of the FreBAQ-G require further investigation as a simple measure of disrupted self-perception of the back before firm recommendations on its use can be made

Changes in rod and frame test scores recorded in schoolchildren during development--a longitudinal study.

The Rod and Frame Test has been used to assess the degree to which subjects rely on the visual frame of reference to perceive vertical (visual field dependence-independence perceptual style). Early investigations found children exhibited a wide range of alignment errors, which reduced as they matured. These studies used a mechanical Rod and Frame system, and presented only mean values of grouped data. The current study also considered changes in individual performance. Changes in rod alignment accuracy in 419 school children were measured using a computer-based Rod and Frame test. Each child was tested at school Grade 2 and retested in Grades 4 and 6. The results confirmed that children displayed a wide range of alignment errors, which decreased with age but did not reach the expected adult values. Although most children showed a decrease in frame dependency over the 4 years of the study, almost 20% had increased alignment errors suggesting that they were becoming more frame-dependent. Plots of individual variation (SD) against mean error allowed the sample to be divided into 4 groups; the majority with small errors and SDs; a group with small SDs, but alignments clustering around the frame angle of 18°; a group showing large errors in the opposite direction to the frame tilt; and a small number with large SDs whose alignment appeared to be random. The errors in the last 3 groups could largely be explained by alignment of the rod to different aspects of the frame. At corresponding ages females exhibited larger alignment errors than males although this did not reach statistical significance. This study confirms that children rely more heavily on the visual frame of reference for processing spatial orientation cues. Most become less frame-dependent as they mature, but there are considerable individual differences

Percentile reference values for anthropometric body composition indices in European children from the IDEFICS study

INTRODUCTION: To characterise the nutritional status in children with obesity or wasting conditions, European anthropometric reference values for body composition measures beyond the body mass index (BMI) are needed. Differentiated assessment of body composition in children has long been hampered by the lack of appropriate references. OBJECTIVES: The aim of our study is to provide percentiles for body composition indices in normal weight European children, based on the IDEFICS cohort (Identification and prevention of Dietary-and lifestyle-induced health Effects in Children and infantS). METHODS: Overall 18 745 2.0-10.9-year-old children from eight countries participated in the study. Children classified as overweight/obese or underweight according to IOTF (N = 5915) were excluded from the analysis. Anthropometric measurements (BMI (N = 12 830); triceps, subscapular, fat mass and fat mass index (N = 11 845-11 901); biceps, suprailiac skinfolds, sum of skinfolds calculated from skinfold thicknesses (N = 8129-8205), neck circumference (N = 12 241); waist circumference and waist-to-height ratio (N = 12 381)) were analysed stratified by sex and smoothed 1st, 3rd, 10th, 25th, 50th, 75th, 90th, 97th and 99th percentile curves were calculated using GAMLSS. RESULTS: Percentile values of the most important anthropometric measures related to the degree of adiposity are depicted for European girls and boys. Age-and sex-specific differences were investigated for all measures. As an example, the 50th and 99th percentile values of waist circumference ranged from 50.7-59.2 cm and from 51.3-58.7 cm in 4.5-to < 5.0-year-old girls and boys, respectively, to 60.6-74.5 cm in girls and to 59.9-76.7 cm in boys at the age of 10.5-10.9 years. CONCLUSION: The presented percentile curves may aid a differentiated assessment of total and abdominal adiposity in European children