The bench scientist\u27s guide to statistical analysis of RNA-Seq data

RNA sequencing (RNA-Seq) is emerging as a highly accurate method to quantify transcript abundance. However, analyses of the large data sets obtained by sequencing the entire transcriptome of organisms have generally been performed by bioinformatics specialists. Here we provide a step-by-step guide and outline a strategy using currently available statistical tools that results in a conservative list of differentially expressed genes. We also discuss potential sources of error in RNA-Seq analysis that could alter interpretation of global changes in gene expression

Measuring the Contribution and Complexity of Nurse and Physiotherapy Consultants: A Feasibility Study

Advanced practice roles in nursing and other health professions have become integral to a range of healthcare services world-wide providing experienced practitioners with the opportunity to extend their roles and influence decision making whilst maintaining patient contact. However, there has been limited research to evaluate the impact on health services of these advanced practice roles

Variation in acclimation of photosynthesis in Trifolium repens after eight years of exposure to Free Air CO2 Enrichment (FACE)

The initial stimulation of photosynthesis observed on elevation of [CO2] in grasslands has been predicted to be a transient phenomenon constrained by the loss of photosynthetic capacity due to other limitations, notably nutrients and sinks for carbohydrates. Legumes might be expected partially to escape these feedbacks through symbiotic N2 fixation. The Free‐Air Carbon dioxide Enrichment (FACE) experiment at Eschikon, Switzerland, has been the longest running investigation of the effects of open‐air elevation of [CO2] on vegetation. The prediction of a long‐term loss of photosynthetic capacity was tested by analysing photosynthesis in Trifolium repens L. (cv. Milkanova) in the spring and autumn of the eighth, ninth and tenth years of treatment. A high and low N treatment also allowed a test of the significance of exogenous N‐supply in maintaining a stimulation of photosynthetic capacity in the long‐term. Prior work in this Free Air CO2 Enrichment (FACE) experiment has revealed that elevated [CO2] increased both vegetative and reproductive growth of T. repens independent of N treatment. It is shown here that the photosynthetic response of T. repens was also independent of N fertilization under both current ambient and elevated (600 µmol mol-1) [CO2]. There was a strong effect of season on photosynthesis, with light‐saturated rates (Asat) 37% higher in spring than in autumn. Higher Asat in the spring was supported by higher maximum Rubisco carboxylation rates (Vc,max) and maximum rates of electron transport (Jmax) contributing to RuBP regeneration. Elevated [CO2] increased Asat by 37% when averaged across all measurement periods and both N fertilization levels, and decreased stomatal conductance by 25%. In spring, there was no effect of elevated [CO2] on photosynthetic capacity of leaves, but in autumn both Vc,max and Jmax were reduced by approximately 20% in elevated [CO2]. The results show that acclimation of photosynthetic capacity can occur in a nitrogen‐fixing species, in the field where there are no artificial restrictions on sink capacity. However, even with acclimation there was a highly significant increase in photosynthesis at elevated [CO2

Genetic strategies for improving crop yields.

The current trajectory for crop yields is insufficient to nourish the world's population by 20501. Greater and more consistent crop production must be achieved against a backdrop of climatic stress that limits yields, owing to shifts in pests and pathogens, precipitation, heat-waves and other weather extremes. Here we consider the potential of plant sciences to address post-Green Revolution challenges in agriculture and explore emerging strategies for enhancing sustainable crop production and resilience in a changing climate. Accelerated crop improvement must leverage naturally evolved traits and transformative engineering driven by mechanistic understanding, to yield the resilient production systems that are needed to ensure future harvests

A revised diet matrix to improve the parameterization of a West Florida Shelf Ecopath model for understanding harmful algal bloom impacts

Harmful algal blooms (HABs) are a growing concern in the West Florida Shelf (WFS) region. An Ecopath with Ecosim (EwE) model of the WFS explicitly simulating HABs was previously developed to illuminate the potential impacts of blooms of the dinoflagellate Karenia brevis (colloquially referred to as “red tides”) on the WFS ecosystem. However, the diet matrix of the Ecopath component of this EwE model (referred to as “WFS-HAB Ecopath”) was based largely on sparse, cursory information and not on local survey data. Here, we revise the diet matrix of the WFS-HAB Ecopath model using predictions of a robust statistical model that incorporates local survey data and employs the Dirichlet distribution and maximum likelihood estimation. The relative impacts of both the revised diet matrix and red tide mortality scenarios on model structure are explored by comparing four alternative WFS-HAB Ecopath models: (i) the base model; (ii) a model employing the revised diet matrix; (iii) a model with elevated red tide mortality; and (iv) a model with both the revised diet matrix and elevated red tide mortality. Incorporating the revised diet matrix into the WFS-HAB Ecopath model had a relatively large impact on ecosystem structure (i.e., trophic organization, mortality rates, trophic interaction strengths, and omnivory). Elevated red tide mortality had virtually no impact on ecosystem structure aside from altering the contribution of fishing, natural, and red tide mortalities to the total mortality of functional groups; however, elevated red tide mortality might have meaningful implications in dynamic simulations, which should be explored in future studies. Collectively, results showed that incorporating the revised diet matrix into WFS-HAB Ecopath, which revealed a number of new predator-prey linkages, led to a more complex and interconnected food web. Specifically, prey items were generally consumed by a broader variety of predators, which contrasts with the base WFS-HAB Ecopath model where many prey, particularly juvenile fishes, were subjected to exceedingly high predation mortality rates from specific predators. The incorporation of the revised diet matrix into the WFS-HAB Ecopath model discussed herein is a fundamental step towards increasing the realism of trophic interactions in the model, which is particularly important as these trophic interactions define starting conditions for dynamic simulations.publishedVersio

Supplementary materials for "Understanding University Student Priorities for Mental Health and Well-being Support: A Mixed-Methods Exploration using the Person-Based Approach"

These supplementary materials comprise some of the study materials used in a mixed-methods exploration of student engagement with and priorities for well-being and mental health support at university. They include the content of an online survey instrument (part 1, quantitative), the focus group discussion schedule (part 2, qualitative), and anonymised data from the survey and focus groups. Research took place in the summer of 2020; the participants were students of the University of Bath at that time.Full details of the methodology may be found in the associated paper. The survey instrument and focus group schedule are included in the dataset.The data archived here has been anonymised in line with the nature of informed consent obtained from participants.Transcripts and descriptively analysed survey data are in MS Word (docx) format. Anonymised and pre-processed survey data are in MS Excel (xlsx) format. The qualitative analysis was conducted in NVivo.The online survey was open between 25th June and 5th August 2020. The three focus groups took place in July 2020

Shifts in microbial communities in soil, rhizosphere and roots of two major crop systems under elevated CO2 and O3

Rising atmospheric concentrations of CO2 and O3 are key features of global environmental change. To investigate changes in the belowground bacterial community composition in response to elevated CO2 and O3 (eCO2 and eO3) the endosphere, rhizosphere and soil were sampled from soybeans under eCO2 and maize under eO3. The maize rhizosphere and endosphere α-diversity was higher than soybean, which may be due to a high relative abundance of Rhizobiales. Only the rhizosphere microbiome composition of the soybeans changed in response to eCO2, associated with an increased abundance of nitrogen fixing microbes. In maize, the microbiome composition was altered by the genotype and linked to differences in root exudate profiles. The eO3 treatment did not change the microbial communities in the rhizosphere, but altered the soil communities where hybrid maize was grown. In contrast to previous studies that focused exclusively on the soil, this study provides new insights into the effects of plant root exudates on the composition of the belowground microbiome in response to changing atmospheric conditions. Our results demonstrate that plant species and plant genotype were key factors driving the changes in the belowground bacterial community composition in agroecosystems that experience rising levels of atmospheric CO2 and O3

Pragmatic cluster randomised controlled trial of contextualised grammar teaching and small group teaching to improve the writing skills of 11 year old children

Introduction: We evaluated two interventions: a contextualised grammar teaching intervention – Grammar for Writing - to assess whether it improved 11 year old children’s writing skills; and a small group literacy intervention to assess whether or not this was effective. Design and method: We used a pragmatic cluster randomised trial with partial split plot design. Independent concealed randomisation was undertaken at the class level, and, within the intervention group, children were also individually randomised to receive the whole class intervention plus a small group intervention or to receive the intervention in a whole class setting only. The main outcomes were writing and reading assessed by the Progress in English 11 (Long Form) test (GL Assessment). Results: In 2013, 55 schools in England, each with two classes, were recruited and randomised. Within each school, the two classes were randomly allocated to receive either the intervention or the control condition. After randomisation, 2 schools withdrew, leaving 53 schools, 106 classes and 2510 pupils. We observed an effect size (ES) of 0.10 favouring the Grammar for Writing classes; however, this was not statistically significant (95% confidence interval (CI) -0.10 to 0.31). Pupils randomised to the small groups had an increased literacy score when compared with the control classes (ES = 0.24, 95% CI 0.00 to 0.49) and when compared with the intervention children taught in the whole class (ES = 0.21, 95% CI 0.04 to 0.38). Conclusion: There is little evidence that this form of contextualised grammar teaching had an effect on 11 year old children’s writing skills. There was some evidence of an effect for small group teaching