The Overlap Package

Camera traps - cameras linked to detectors so that they fire when an animal is present - are a major source of information on the abundance and habitat preferences of rare or shy forest animals. Modern cameras record the time of the photo, and the use of this to investigate diel activity patterns was immediately recognised (Gri?ffiths and van Schaik, 1993). Initially this resulted in broad classfication of taxa as diurnal, nocturnal, crepuscular, or cathemeral (van Schaik and Gri?ths, 1996). More recently, researchers have compared activity patterns among species to see how overlapping patterns may relate to competition or predation (Linkie and Ridout, 2011; Carver et al., 2011; Ramesh et al., 2012; Carter et al., 2012; Kamler et al., 2012; Ross et al., 2013). Ridout and Linkie (2009) presented methods to fit kernel density functions to times of observations of animals and to estimate the coe?cient of overlapping, a quantitative measure ranging from 0 (no overlap) to 1 (identical activity patterns). The code they used forms the basis of the overlap package. Although motivated by the analysis of camera trap data, overlap could be applied to data from other sources such as data loggers, provided data collection is carried out around the clock. Nor is it limited to diel cycles: tidal cycles or seasonal cycles, such as plant flowering or fruiting or animal breeding seasons could also be investigated

Level-Screening Designs for factors with many levels

We consider designs for f factors each at m levels, where f is small but m is large. Main effect designs with mf experimental points are presented. For two factors, two types of designs are investigated, termed sawtooth and dumbbell designs, based on a graphical representation. For three factors, cyclic sawtooth designs are considered. The paper seeks optimal and near optimal designs which involve factors with many levels but few observations. It also investigates issues of robustness when as much as one third of the data is structurally missing. An important area of application is in screening for drug discovery and we compare our designs with others using a published data set with two factors each with fifty levels, where the dumbbell design outperforms others and is an example of an inherently unbalanced design dominating more balanced designs

Presentations of Wess-Zumino-Witten Fusion Rings

The fusion rings of Wess-Zumino-Witten models are re-examined. Attention is drawn to the difference between fusion rings over Z (which are often of greater importance in applications) and fusion algebras over C. Complete proofs are given characterising the fusion algebras (over C) of the SU(r+1) and Sp(2r) models in terms of the fusion potentials, and it is shown that the analagous potentials cannot describe the fusion algebras of the other models. This explains why no other representation-theoretic fusion potentials have been found. Instead, explicit generators are then constructed for general WZW fusion rings (over Z). The Jacobi-Trudy identity and its Sp(2r) analogue are used to derive the known fusion potentials. This formalism is then extended to the WZW models over the spin groups of odd rank, and explicit presentations of the corresponding fusion rings are given. The analogues of the Jacobi-Trudy identity for the spinor representations (for all ranks) are derived for this purpose, and may be of independent interest.Comment: 32 pages, 3 figures, added references, minor additions to text. To be published in Rev. Math. Phy

Arctic sea surface height variability and change from satellite radar altimetry and GRACE, 2003–2014

Arctic sea surface height (SSH) is poorly observed by radar altimeters due to the poor coverage of the polar oceans provided by conventional altimeter missions and because large areas are perpetually covered by sea ice, requiring specialized data processing. We utilize SSH estimates from both the ice-covered and ice-free ocean to present monthly estimates of Arctic Dynamic Ocean Topography (DOT) from radar altimetry south of 81.5°N and combine this with GRACE ocean mass to estimate steric height. Our SSH and steric height estimates show good agreement with tide gauge records and geopotential height derived from Ice-Tethered Profilers. The large seasonal cycle of Arctic SSH (amplitude ∼5 cm) is dominated by seasonal steric height variation associated with seasonal freshwater fluxes, and peaks in October–November. Overall, the annual mean steric height increased by 2.2 ± 1.4 cm between 2003 and 2012 before falling to circa 2003 levels between 2012 and 2014 due to large reductions on the Siberian shelf seas. The total secular change in SSH between 2003 and 2014 is then dominated by a 2.1 ± 0.7 cm increase in ocean mass. We estimate that by 2010, the Beaufort Gyre had accumulated 4600 km3 of freshwater relative to the 2003–2006 mean. Doming of Arctic DOT in the Beaufort Sea is revealed by Empirical Orthogonal Function analysis to be concurrent with regional reductions in the Siberian Arctic. We estimate that the Siberian shelf seas lost ∼180 km3 of freshwater between 2003 and 2014, associated with an increase in annual mean salinity of 0.15 psu yr−1. Finally, ocean storage flux estimates from altimetry agree well with high-resolution model results, demonstrating the potential for altimetry to elucidate the Arctic hydrological cycle

An On-Farm experimental philosophy for farmer-centric digital innovation

In this paper, we review learnings gained from early On-Farm Experiments (OFE) conducted in the broad acre Australian grain industry from the 1990s to the present day. Although the initiative was originally centered around the possibilities of new data and analytics in precision agriculture, we discovered that OFEs could represent a platform for engaging farmers around digital technologies and innovation. Insight from interacting closely with farmers and advisors leads us to argue for a change in the ways we approach OFE research. Acknowledging that conditions have changed and drawing from business and social sciences, we suggest that OFE approaches today should develop aspects related to skill development, value generation and value sharing, the social dimension of change, and a renewed focus on farmer-centric research to better bridge industry requirements and scientist inputs

Combining qualitative and quantitative operational research methods to inform quality improvement in pathways that span multiple settings

BACKGROUND: Improving integration and continuity of care across sectors within resource constraints is a priority in many health systems. Qualitative operational research methods of problem structuring have been used to address quality improvement in services involving multiple sectors but not in combination with quantitative operational research methods that enable targeting of interventions according to patient risk. We aimed to combine these methods to augment and inform an improvement initiative concerning infants with congenital heart disease (CHD) whose complex care pathway spans multiple sectors. METHODS: Soft systems methodology was used to consider systematically changes to services from the perspectives of community, primary, secondary and tertiary care professionals and a patient group, incorporating relevant evidence. Classification and regression tree (CART) analysis of national audit datasets was conducted along with data visualisation designed to inform service improvement within the context of limited resources. RESULTS: A 'Rich Picture' was developed capturing the main features of services for infants with CHD pertinent to service improvement. This was used, along with a graphical summary of the CART analysis, to guide discussions about targeting interventions at specific patient risk groups. Agreement was reached across representatives of relevant health professions and patients on a coherent set of targeted recommendations for quality improvement. These fed into national decisions about service provision and commissioning. CONCLUSIONS: When tackling complex problems in service provision across multiple settings, it is important to acknowledge and work with multiple perspectives systematically and to consider targeting service improvements in response to confined resources. Our research demonstrates that applying a combination of qualitative and quantitative operational research methods is one approach to doing so that warrants further consideration

A critical reflection on the development of the Participatory Autism Research Collective (PARC)

Purpose The Participatory Autism Research Collective (PARC) was initially set up with the purpose of bringing autistic people, including scholars and activists (but not exclusively), together with early career researchers and practitioners who work with autistic people, with the aim being to build a community where those who wished to see more significant involvement of autistic people in autism research could share knowledge and expertise. Approach This article explores the development of the PARC network, reflecting upon its activities and ethos within current Higher Education (HE) practices and structures. Findings In supporting autistic individuals in their attempts to establish themselves within academic systems that may not always be considerate or accommodating, the existence of PARC creates a structure with which autistic people can influence social change. PARC serves as a network of support, strengthening the presence of autistic scholars in academia. It also provides a structure through which autistic people are able to demonstrate helpful practices with which to engage more broadly. Value The PARC network is the first autistic-led venture of its kind in the UK to have a sustained impact. PARC is growing to become an important element in the field of autism studies both by supporting the emerging autistic academics and by promoting ethical and participatory research methods and practices

Identifying improvements to complex pathways: evidence synthesis and stakeholder engagement in infant congenital heart disease

OBJECTIVES: Many infants die in the year following discharge from hospital after surgical or catheter intervention for congenital heart disease (3–5% of discharged infants). There is considerable variability in the provision of care and support in this period, and some families experience barriers to care. We aimed to identify ways to improve discharge and postdischarge care for this patient group. DESIGN: A systematic evidence synthesis aligned with a process of eliciting the perspectives of families and professionals from community, primary, secondary and tertiary care. SETTING: UK. RESULTS: A set of evidence-informed recommendations for improving the discharge and postdischarge care of infants following intervention for congenital heart disease was produced. These address known challenges with current care processes and, recognising current resource constraints, are targeted at patient groups based on the number of patients affected and the level and nature of their risk of adverse 1-year outcome. The recommendations include: structured discharge documentation, discharging certain high-risk patients via their local hospital, enhanced surveillance for patients with certain (high-risk) cardiac diagnoses and an early warning tool for parents and community health professionals. CONCLUSIONS: Our recommendations set out a comprehensive, system-wide approach for improving discharge and postdischarge services. This approach could be used to address challenges in delivering care for other patient populations that can fall through gaps between sectors and organisations

Methylation of the Leukocyte Glucocorticoid Receptor Gene Promoter in Adults: Associations with Early Adversity and Depressive, Anxiety and Substance-Use Disorders

Early adversity increases risk for developing psychopathology. Epigenetic modification of stress reactivity genes is a likely mechanism contributing to this risk. The glucocorticoid receptor (GR) gene is of particular interest because of the regulatory role of the GR in hypothalamic–pituitary–adrenal (HPA) axis function. Mounting evidence suggests that early adversity is associated with GR promoter methylation and gene expression. Few studies have examined links between GR promoter methylation and psychopathology, and findings to date have been mixed. Healthy adult participants (N = 340) who were free of psychotropic medications reported on their childhood experiences of maltreatment and parental death and desertion. Lifetime depressive and anxiety disorders and past substance-use disorders were assessed using the Structured Clinical Interview for the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition. Methylation of exon 1F of the GR gene (NR3C1) was examined in leukocyte DNA via pyrosequencing. On a separate day, a subset of the participants (n = 231) completed the dexamethasone/corticotropin- releasing hormone (Dex/CRH) test. Childhood adversity and a history of past substance-use disorder and current or past depressive or anxiety disorders were associated with lower levels of NR3C1 promoter methylation across the region as a whole and at individual CpG sites (Po0.05). The number of adversities was negatively associated with NR3C1 methylation in participants with no lifetime disorder (P = 0.018), but not in those with a lifetime disorder. GR promoter methylation was linked to altered cortisol responses to the Dex/CRH test (Po0.05). This study presents evidence of reduced methylation of NR3C1 in association with childhood maltreatment and depressive, anxiety and substance-use disorders in adults. This finding stands in contrast to our prior work, but is consistent with emerging findings, suggesting complexity in the regulation of this gene

Abelian Sandpile Model on the Honeycomb Lattice

We check the universality properties of the two-dimensional Abelian sandpile model by computing some of its properties on the honeycomb lattice. Exact expressions for unit height correlation functions in presence of boundaries and for different boundary conditions are derived. Also, we study the statistics of the boundaries of avalanche waves by using the theory of SLE and suggest that these curves are conformally invariant and described by SLE2.Comment: 24 pages, 5 figure