Research note: Urban street tree density and antidepressant prescription rates—A cross-sectional study in London, UK

This is the author’s version of a work that was accepted for publication in Landscape and Urban Planning. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published at doi:10.1016/j.landurbplan.2014.12.005.Abstract: Growing evidence suggests an association between access to urban greenspace and mental health and wellbeing. Street trees may be an important facet of everyday exposure to nature in urban environments, but there is little evidence regarding their role in influencing population mental health. In this brief report, we raise the issue of street trees in the nature-health nexus, and use secondary data sources to examine the association between the density of street trees (trees/km street) in London boroughs and rates of antidepressant prescribing. After adjustment for potential confounders, and allowing for unmeasured area-effects using Bayesian mixed effects models, we find an inverse association, with a decrease of 1.18 prescriptions per thousand population per unit increase in trees per km of street (95% credible interval 0.00, 2.45). This study suggests that street trees may be a positive urban asset to decrease the risk of negative mental health outcomes.European Regional Development Fund Programme 2007 to 2013 and European Social Fund Convergence Programme for Cornwall and the Isles of Scill

What accounts for ‘England’s green and pleasant land’? A panel data analysis of mental health and land cover types in rural England

This is the author’s version of a work that was accepted for publication in Landscape and Urban Planning. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published at doi:10.1016/j.landurbplan.2015.05.008.Exposure to green space is associated with a variety of positive health states. Research to date has focused primarily on ‘generic’ green space in urban areas, where green space is relatively scarce and where it is dominated by playing fields and parks. The current research adds to our understanding with an examination of relationships between different types of green space and mental health in rural areas in England (approximate rural population = 4 million). The aggregate land cover classes of Land Cover Map 2007 were linked to rural residential areas (Lower-level Super Output Areas) and then linked to rural participants (n = 2020) in the 18-year longitudinal British Household Panel Survey. Random effects regression of mental health (as measured by GHQ12 scores) against land cover enabled effects to be simultaneously estimated from both mean between-individual differences and from within-individual differences over time. The nine natural land cover classes (Broadleaved woodland; Coniferous woodland; Arable; Improved grassland; Semi-natural grassland; Mountain, heath and bog; Saltwater; Freshwater; Coastal) were not significantly associated with differences in mental health between individuals. However, significant relationships were observed between some types of land cover and within-individual change in mental health amongst individuals who relocated during the 18 annual waves of the panel. These findings indicate the presence of important health related ecosystem services from different land cover types that have not previously been investigated and which help more effective spatial planning and land use management.Economic and Social Research CouncilNational Institute for Health Research Health Protection Research Unit (NIHR HPRU

Beyond greenspace: an ecological study of population general health and indicators of natural environment type and quality.

This is a freely-available open access publication. Please cite the published version which is available via the DOI link in this record.BACKGROUND: Many studies suggest that exposure to natural environments ('greenspace') enhances human health and wellbeing. Benefits potentially arise via several mechanisms including stress reduction, opportunity and motivation for physical activity, and reduced air pollution exposure. However, the evidence is mixed and sometimes inconclusive. One explanation may be that "greenspace" is typically treated as a homogenous environment type. However, recent research has revealed that different types and qualities of natural environments may influence health and wellbeing to different extents. METHODS: This ecological study explores this issue further using data on land cover type, bird species richness, water quality and protected or designated status to create small-area environmental indicators across Great Britain. Associations between these indicators and age/sex standardised prevalence of both good and bad health from the 2011 Census were assessed using linear regression models. Models were adjusted for indicators of socio-economic deprivation and rurality, and also investigated effect modification by these contextual characteristics. RESULTS: Positive associations were observed between good health prevalence and the density of the greenspace types, "broadleaf woodland", "arable and horticulture", "improved grassland", "saltwater" and "coastal", after adjusting for potential confounders. Inverse associations with bad health prevalence were observed for the same greenspace types, with the exception of "saltwater". Land cover diversity and density of protected/designated areas were also associated with good and bad health in the predicted manner. Bird species richness (an indicator of local biodiversity) was only associated with good health prevalence. Surface water quality, an indicator of general local environmental condition, was associated with good and bad health prevalence contrary to the manner expected, with poorer water quality associated with better population health. Effect modification by income deprivation and urban/rural status was observed for several of the indicators. CONCLUSIONS: The findings indicate that the type, quality and context of 'greenspace' should be considered in the assessment of relationships between greenspace and human health and wellbeing. Opportunities exist to further integrate approaches from ecosystem services and public health perspectives to maximise opportunities to inform policies for health and environmental improvement and protection.Economic and Social Research CouncilEuropean Regional Development Fund Programme 2007 to 2013 and European Social Fund Convergence Programme for Cornwall and the Isles of Scill

Mapping the root systems of individual trees in a natural community using genotyping-by-sequencing

•The architecture of root systems is an important driver of plant fitness, competition and ecosystem processes. However, the methodological difficulty of mapping roots hampers the study of these processes. Existing approaches to match individual plants to belowground samples are low throughput and species specific. Here, we developed a scalable sequencing-based method to map the root systems of individual trees across multiple species. We successfully applied it to a tropical dry forest community in the Brazilian Caatinga containing 14 species. • We sequenced all 42 individual shrubs and trees in a 14 × 14 m plot using double-digest restriction site-associated sequencing (ddRADseq). We identified species-specific markers and individual-specific haplotypes from the data. We matched these markers to the ddRADseq data from 100 mixed root samples from across the centre (10 × 10 m) of the plot at four different depths using a newly developed R package. • We identified individual root samples for all species and all but one individual. There was a strong significant correlation between belowground and aboveground size measurements, and we also detected significant species-level root-depth preference for two species. • The method is more scalable and less labour intensive than the current techniques and is broadly applicable to ecology, forestry and agricultural biology

Argumentation in school science : Breaking the tradition of authoritative exposition through a pedagogy that promotes discussion and reasoning

The value of argumentation in science education has become internationally recognised and has been the subject of many research studies in recent years. Successful introduction of argumentation activities in learning contexts involves extending teaching goals beyond the understanding of facts and concepts, to include an emphasis on cognitive and metacognitive processes, epistemic criteria and reasoning. The authors focus on the difficulties inherent in shifting a tradition of teaching from one dominated by authoritative exposition to one that is more dialogic, involving small-group discussion based on tasks that stimulate argumentation. The paper builds on previous research on enhancing the quality of argument in school science, to focus on how argumentation activities have been designed, with appropriate strategies, resources and modelling, for pedagogical purposes. The paper analyses design frameworks, their contexts and lesson plans, to evaluate their potential for enhancing reasoning through foregrounding the processes of argumentation. Examples of classroom dialogue where teachers adopt the frameworks/plans are analysed to show how argumentation processes are scaffolded. The analysis shows that several layers of interpretation are needed and these layers need to be aligned for successful implementation. The analysis serves to highlight the potential and limitations of the design frameworks

Performing and Visualizing Temporal Analysis of Large Text Data Issued for Open Sources: Past and Future Methods

International audienceIn this paper we first propose a state of the art on the methods for the visualization and the interpretation of textual data, in particular of scientific data. We then shortly present our contributions to this field in the form of original methods for the automatic classification of documents and easy interpretation of their content through characteristic keywords and classes created by our algorithms. In a second step, we focus our analysis on the data evolving over time. We detail our di-achronic approach, especially suitable for the detection and visualization of topic changes. This allows us to conclude with Diachronic'Explorer, our upcoming tool for visual exploration of evolutionary data

Mapping the root systems of individual trees in a natural community using genotyping-by-sequencing.

This is the final version. Available from Wiley via the DOI in this record.The architecture of root systems is an important driver of plant fitness, competition and ecosystem processes. However, the methodological difficulty of mapping roots hampers the study of these processes. Existing approaches to match individual plants to belowground samples are low throughput and species specific. Here, we developed a scalable sequencing-based method to map the root systems of individual trees across multiple species. We successfully applied it to a tropical dry forest community in the Brazilian Caatinga containing 14 species. We sequenced all 42 individual shrubs and trees in a 14 × 14 m plot using double-digest restriction site-associated sequencing (ddRADseq). We identified species-specific markers and individual-specific haplotypes from the data. We matched these markers to the ddRADseq data from 100 mixed root samples from across the centre (10 × 10 m) of the plot at four different depths using a newly developed R package. We identified individual root samples for all species and all but one individual. There was a strong significant correlation between belowground and aboveground size measurements, and we also detected significant species-level root-depth preference for two species. The method is more scalable and less labour intensive than the current techniques and is broadly applicable to ecology, forestry and agricultural biology.Natural Environment Research Council (NERC)Natural Environment Research Council (NERC)Fundação de Amparo à Pesquisa do Estado de São Paul

The role of multiple marks in epigenetic silencing and the emergence of a stable bivalent chromatin state

We introduce and analyze a minimal model of epigenetic silencing in budding yeast, built upon known biomolecular interactions in the system. Doing so, we identify the epigenetic marks essential for the bistability of epigenetic states. The model explicitly incorporates two key chromatin marks, namely H4K16 acetylation and H3K79 methylation, and explores whether the presence of multiple marks lead to a qualitatively different systems behavior. We find that having both modifications is important for the robustness of epigenetic silencing. Besides the silenced and transcriptionally active fate of chromatin, our model leads to a novel state with bivalent (i.e., both active and silencing) marks under certain perturbations (knock-out mutations, inhibition or enhancement of enzymatic activity). The bivalent state appears under several perturbations and is shown to result in patchy silencing. We also show that the titration effect, owing to a limited supply of silencing proteins, can result in counter-intuitive responses. The design principles of the silencing system is systematically investigated and disparate experimental observations are assessed within a single theoretical framework. Specifically, we discuss the behavior of Sir protein recruitment, spreading and stability of silenced regions in commonly-studied mutants (e.g., sas2, dot1) illuminating the controversial role of Dot1 in the systems biology of yeast silencing.Comment: Supplementary Material, 14 page

HER2 and ESR1 mRNA expression levels and response to neoadjuvant trastuzumab plus chemotherapy in patients with primary breast cancer

Introduction: Recent data suggest that benefit from trastuzumab and chemotherapy might be related to expression of HER2 and estrogen receptor (ESR1). Therefore, we investigated HER2 and ESR1 mRNA levels in core biopsies of HER2-positive breast carcinomas from patients treated within the neoadjuvant GeparQuattro trial. Methods: HER2 levels were centrally analyzed by immunohistochemistry (IHC), silver in-situ hybridization (SISH) and qRT-PCR in 217 pretherapeutic formalin-fixed, paraffin-embedded (FFPE) core biopsies. All tumors had been HER2-positive by local pathology and had been treated with neoadjuvant trastuzumab/ chemotherapy in GeparQuattro. Results: Only 73% of the tumors (158 of 217) were centrally HER2-positive (cHER2-positive) by IHC/SISH, with cHER2-positive tumors showing a significantly higher pCR rate (46.8% vs. 20.3%, p<0.0005). HER2 status by qRT-PCR showed a concordance of 88.5% with the central IHC/SISH status, with a low pCR rate in those tumors that were HER2-negative by mRNA analysis (21.1% vs. 49.6%, p<0.0005). The level of HER2 mRNA expression was linked to response rate in ESR1-positive tumors, but not in ESR1-negative tumors. HER2 mRNA expression was significantly associated with pCR in the HER2-positive/ESR1-positive tumors (p=0.004), but not in HER2-positive/ESR1-negative tumors. Conclusions: Only patients with cHER2-positive tumors - irrespective of the method used - have an increased pCR rate with trastuzumab plus chemotherapy. In patients with cHER2-negative tumors the pCR rate is comparable to the pCR rate in the non-trastuzumab treated HER-negative population. Response to trastuzumab is correlated to HER2 mRNA levels only in ESR1-positive tumors. This study adds further evidence to the different biology of both subsets within the HER2-positive group