The 5'-3' exoribonuclease Pacman (Xrn1) regulates expression of the heat shock protein Hsp67Bc and the microRNA miR-277-3p in Drosophila wing imaginal discs

Pacman/Xrn1 is a highly conserved exoribonuclease known to play a critical role in gene regulatory events such as control of mRNA stability, RNA interference and regulation via miRNAs. Although Pacman has been well studied in Drosophila tissue culture cells, the biologically relevant cellular pathways controlled by Pacman in natural tissues are unknown. This study shows that a hypomorphic mutation in pacman (pcm5) results in smaller wing imaginal discs. These tissues, found in the larva, are known to grow and differentiate to form wing and thorax structures in the adult fly. Using microarray analysis, followed by quantitative RT-PCR, we show that eight mRNAs were increased in level by >2 fold in the pcm5 mutant wing discs compared to the control. The levels of pre mRNAs were tested for five of these mRNAs; four did not increase in the pcm5 mutant, showing that they are regulated at the post-transcriptional level and therefore could be directly affected by Pacman. These transcripts include one that encodes the heat-shock protein Hsp67Bc, which is upregulated 11.9-fold at the post-transcriptional level and 2.3-fold at the protein level. One miRNA, miR-277-3p, is 5.6-fold downregulated at the post-transcriptional level in mutant discs, suggesting that Pacman affects its processing in this tissue. Together, these data show that a relatively small number of mRNAs and miRNAs substantially change in abundance in pacman mutant wing imaginal discs. Since Hsp67Bc is known to regulate autophagy and protein synthesis, it is possible that Pacman may control the growth of wing imaginal discs by regulating these processes

Natural selection towards wild-type in composite cross populations of winter wheat

Most of our crops are grown in monoculture with single genotypes grown over wide acreage. An alternative approach, where segregating populations are used as crops, is an exciting possibility, but outcomes of natural selection upon this type of crop are not well understood. We tracked allelic frequency changes in evolving composite cross populations of wheat grown over ten generations under organic and conventional farming. At three generations, each population was genotyped with 19 SSR and 8 SNP markers. The latter were diagnostic for major functional genes. Gene diversity was constant at SSR markers but decreased over time for SNP markers. Population differentiation between the four locations could not be detected, suggesting that organic vs. non-organic crop management did not drive allele frequency changes. However, we did see changes for genes controlling plant height and phenology in all populations independently and consistently. We interpret these changes as the result of a consistent natural selection towards wild-type. Independent selection for alleles that are associated with plant height suggests that competition for light was central, resulting in the predominance of stronger intraspecific competitors, and highlighting a potential trade-off between individual and population performanc

K-Space at TRECVID 2008

In this paper we describe K-Space’s participation in TRECVid 2008 in the interactive search task. For 2008 the K-Space group performed one of the largest interactive video information retrieval experiments conducted in a laboratory setting. We had three institutions participating in a multi-site multi-system experiment. In total 36 users participated, 12 each from Dublin City University (DCU, Ireland), University of Glasgow (GU, Scotland) and Centrum Wiskunde and Informatica (CWI, the Netherlands). Three user interfaces were developed, two from DCU which were also used in 2007 as well as an interface from GU. All interfaces leveraged the same search service. Using a latin squares arrangement, each user conducted 12 topics, leading in total to 6 runs per site, 18 in total. We officially submitted for evaluation 3 of these runs to NIST with an additional expert run using a 4th system. Our submitted runs performed around the median. In this paper we will present an overview of the search system utilized, the experimental setup and a preliminary analysis of our results

Weeds in Organic Fertility-Building Leys: Aspects of Species Richness and Weed Management

Legume-based leys (perennial sod crops) are an important component of fertility management in organic rotations in many parts of Europe. Despite their importance, however, relatively little is known about how these leys affect weed communities or how the specific composition of leys may contribute to weed management. To determine whether the choice of plant species in the ley affects weeds, we conducted replicated field trials at six locations in the UK over 24 months, measuring weed cover and biomass in plots sown with monocultures of 12 legume and 4 grass species, and in plots sown with a mixture of 10 legume species and 4 grass species. Additionally, we monitored weed communities in leys on 21 organic farms across the UK either sown with a mixture of the project species or the farmers’ own species mix. In total, 63 weed species were found on the farms, with the annuals Stellaria media, Sonchus arvensis, and Veronica persica being the most frequent species in the first year after establishment of the ley, while Stellaria media and the two perennials Ranunculus repens and Taraxacum officinale dominated the weed spectrum in the second year. Our study shows that organic leys constitute an important element of farm biodiversity. In both replicated and on-farm trials, weed cover and species richness were significantly lower in the second year than in the first, owing to lower presence of annual weeds in year two. In monocultures, meadow pea (Lathyrus pratensis) was a poor competitor against weeds, and a significant increase in the proportion of weed biomass was observed over time, due to poor recovery of meadow pea after mowing. For red clover (Trifolium pratense), we observed the lowest proportion of weed biomass in total biomass among the tested legume species. Crop biomass and weed biomass were negatively correlated across species. Residuals from the linear regression between crop biomass and weed biomass indicated that at similar levels of crop biomass, grasses had lower weed levels than legumes. We conclude that choice of crop species is an important tool for weed management in leys

User-defined challenges and desiderata for robotics and autonomous systems in health and social care settings

We report the needs and challenges identified by health and social care professionals and service users for robotics and autonomous systems that are of importance to researchers and policymakers. To this end, we held eight workshops in different locations across Cornwall (UK) in which we raised awareness of the applications and opportunities of assistive robots. The 223 participants could interact physically with four robots, watched a multimedia presentation including video and use-case scenarios and then took part in 33 focus groups. Content analysis was carried out based on summaries written by facilitators during the focus groups. The focus groups produced 163 challenges that may have digital solutions including 78 suitable for robotic assistive technology, in three main areas: maintaining independence at home, social isolation, and rurality. Although further research is needed with technology and its implementation, this study shows that health and social care professionals, patients, carers, and students are willing to consider using robotics and autonomous systems in health and social care settings

Financial burden of men with localized prostate cancer: a process paper

BackgroundMany individuals undergoing cancer treatment experience substantial financial hardship, often referred to as financial toxicity (FT). Those undergoing prostate cancer treatment may experience FT and its impact can exacerbate disparate health outcomes. Localized prostate cancer treatment options include: radiation, surgery, and/or active surveillance. Quality of life tradeoffs and costs differ between treatment options. In this project, our aim was to quantify direct healthcare costs to support patients and clinicians as they discuss prostate cancer treatment options. We provide the transparent steps to estimate healthcare costs associated with treatment for localized prostate cancer among the privately insured population using a large claims dataset.MethodsTo quantify the costs associated with their prostate cancer treatment, we used data from the Truven Health Analytics MarketScan Commercial Claims and Encounters, including MarketScan Medicaid, and peer reviewed literature. Strategies to estimate costs included: (1) identifying the problem, (2) engaging a multidisciplinary team, (3) reviewing the literature and identifying the database, (4) identifying outcomes, (5) defining the cohort, and (6) designing the analytic plan. The costs consist of patient, clinician, and system/facility costs, at 1-year, 3-years, and 5-years following diagnosis.ResultsWe outline our specific strategies to estimate costs, including: defining complex research questions, defining the study population, defining initial prostate cancer treatment, linking facility and provider level related costs, and developing a shared understanding of definitions on our research team.Discussion and next stepsAnalyses are underway. We plan to include these costs in a prostate cancer patient decision aid alongside other clinical tradeoffs

Changes in Exposure to Neighborhood Characteristics are Associated with Sexual Network Characteristics in a Cohort of Adults Relocating from Public Housing

Ecologic and cross-sectional multilevel analyses suggest that characteristics of the places where people live influence their vulnerability to HIV and other sexually-transmitted infections (STIs). Using data from a predominately substance-misusing cohort of African-American adults relocating from US public housing complexes, this multilevel longitudinal study tested the hypothesis that participants who experienced greater post-relocation improvements in economic disadvantage, violent crime, and male:female sex ratios would experience greater reductions in perceived partner risk and in the odds of having a partner who had another partner (i.e., indirect concurrency). Baseline data were collected from 172 public housing residents before relocations occurred; three waves of post-relocation data were collected every nine months. Participants who experienced greater improvements in community violence and in economic conditions experienced greater reductions in partner risk. Reduced community violence was associated with reduced indirect concurrency. Structural interventions that decrease exposure to violence and economic disadvantage may reduce vulnerability to HIV/STIs

Is there sufficient Ensifer and Rhizobium species diversity in UK farmland soils to support red clover (Trifolium pratense), white clover (T. repens), lucerne (Medicago sativa) and black medic (M. lupulina)?

Rhizobia play important roles in agriculture owing to their ability to fix nitrogen through a symbiosis with legumes. The specificity of rhizobia-legume associations means that underused legume species may depend on seed inoculation with their rhizobial partners. For black medic (Medicago lupulina) and lucerne (Medicago sativa) little is known about the natural prevalence of their rhizobial partner Ensifer meliloti in UK soils, so that the need for inoculating them is unclear. We analysed the site-dependence of rhizobial seed inoculation effects on the subsequent ability of rhizobial communities to form symbioses with four legume species (Medicago lupulina, M. sativa, Trifolium repens and T. pratense). At ten organic farms across the UK, a species-diverse legume based mixture (LBM) which included these four species was grown. The LBM seed was inoculated with a mix of commercial inocula specific for clover and lucerne. At each site, soil from the LBM treatment was compared to the soil sampled prior to the sowing of the LBM (the control). From each site and each of the two treatments, a suspension of soils was applied to seedlings of the four legume species and grown in axenic conditions for six weeks. Root nodules were counted and their rhizobia isolated. PCR and sequencing of a fragment of the gyrB gene from rhizobial isolates allowed identification of strains. The number of nodules on each of the four legume species was significantly increased when inoculated with soil from the LBM treatment compared to the control. Both the proportion of plants forming nodules and the number of nodules formed varied significantly by site, with sites significantly affecting the Medicago species but not the Trifolium species. These differences in nodulation were broadly reflected in plant biomass where site and treatment interacted; at some sites there was a significant advantage from inoculation with the commercial inoculum but not at others. In particular, this study has demonstrated the commercial merit of inoculation of lucerne with compatible rhizobia

New insights into the classification and nomenclature of cortical GABAergic interneurons.

A systematic classification and accepted nomenclature of neuron types is much needed but is currently lacking. This article describes a possible taxonomical solution for classifying GABAergic interneurons of the cerebral cortex based on a novel, web-based interactive system that allows experts to classify neurons with pre-determined criteria. Using Bayesian analysis and clustering algorithms on the resulting data, we investigated the suitability of several anatomical terms and neuron names for cortical GABAergic interneurons. Moreover, we show that supervised classification models could automatically categorize interneurons in agreement with experts' assignments. These results demonstrate a practical and objective approach to the naming, characterization and classification of neurons based on community consensus

Author correction : Divergence across mitochondrial genomes of sympatric members of the 'Schistosoma indicum' group and clues into the evolution of 'Schistosoma spindale'

An amendment to this paper has been published and can be accessed via a link at the top of the paper