Geographically weighted correspondence matrices for local error reporting and change analyses: mapping the spatial distribution of errors and change

This letter describes and applies generic methods for generating local measures from the correspondence table. These were developed by integrating the functionality of two existing R packages: gwxtab and diffeR. They demonstrate how spatially explicit accuracy and error measures can be generated from local geographically weighted correspondence matrices, for example to compare classified and reference data (predicted and observed) for error analyses, and classes at times t1 and t2 for change analyses. The approaches in this letter extend earlier work that considered the measures derived from correspondence matrices in the context of generalized linear models and probability. Here the methods compute local, geographically weighted correspondence matrices, from which local statistics are directly calculated. In this case a selection of the overall and categorical difference measures proposed by Pontius and Milones (2011) and Pontius and Santacruz (2014), as well as spatially distributed estimates of kappa coefficients, User and Producer accuracies. The discussion reflects on the use of the correspondence matrix in remote sensing research, the philosophical underpinnings of local rather than global approaches for modelling landscape processes and the potential for policy and scientific benefits that local approaches support

RNA Docking and Local Translation Regulate Site-Specific Axon Remodeling In Vivo

Nascent proteins can be positioned rapidly at precise subcellular locations by local protein synthesis (LPS) to facilitate localized growth responses. Axon arbor architecture, a major determinant of synaptic connectivity, is shaped by localized growth responses, but it is unknown whether LPS influences these responses in vivo. Using high-resolution live imaging, we examined the spatiotemporal dynamics of RNA and LPS in retinal axons during arborization in vivo. Endogenous RNA tracking reveals that RNA granules dock at sites of branch emergence and invade stabilized branches. Live translation reporter analysis reveals that de novo ß-actin hotspots colocalize with docked RNA granules at the bases and tips of new branches. Inhibition of axonal ß-actin mRNA translation disrupts arbor dynamics primarily by reducing new branch emergence and leads to impoverished terminal arbors. The results demonstrate a requirement for LPS in building arbor complexity and suggest a key role for pre-synaptic LPS in assembling neural circuits.This work was supported by Cambridge Trust, Croucher Foundation, Sir Edward Youde Memorial Fund (H.H.-W.W.), Gates Cambridge (J.Q.L.), Fundac¸ a˜ o para a Cieˆ ncia e Tecnologia (C.M.R.), Wellcome Trust Senior Investigator Award (100329/Z/ 12/Z) (W.A.H.), EPSRC Grant (EP/H018301/1), MRC Grant (MR/K015850/1 and MR/K02292X/1), Wellcome Trust (089703/Z/09/Z) (C.F.K.), Wellcome Trust Programme Grant (085314/Z/08/Z), and ERC Advanced Grant (322817) (C.E.H.)

On the origin of utility, weighting, and discounting functions: How they get their shapes and how to change their shapes

We present a theoretical account of the origin of the shapes of utility, probability weighting, and temporal discounting functions. In an experimental test of the theory, we systematically change the shape of revealed utility, weighting, and discounting functions by manipulating the distribution of monies, probabilities, and delays in the choices used to elicit them. The data demonstrate that there is no stable mapping between attribute values and their subjective equivalents. Expected and discounted utility theories, and also their descendants such as prospect theory and hyperbolic discounting theory, simply assert stable mappings to describe choice data and offer no account of the instability we find. We explain where the shape of the mapping comes from and, in describing the mechanism by which people choose, explain why the shape depends on the distribution of gains, losses, risks, and delays in the environment

Scattering AMplitudes from Unitarity-based Reduction Algorithm at the Integrand-level

SAMURAI is a tool for the automated numerical evaluation of one-loop corrections to any scattering amplitudes within the dimensional-regularization scheme. It is based on the decomposition of the integrand according to the OPP-approach, extended to accommodate an implementation of the generalized d-dimensional unitarity-cuts technique, and uses a polynomial interpolation exploiting the Discrete Fourier Transform. SAMURAI can process integrands written either as numerator of Feynman diagrams or as product of tree-level amplitudes. We discuss some applications, among which the 6- and 8-photon scattering in QED, and the 6-quark scattering in QCD. SAMURAI has been implemented as a Fortran90 library, publicly available, and it could be a useful module for the systematic evaluation of the virtual corrections oriented towards automating next-to-leading order calculations relevant for the LHC phenomenology.Comment: 35 pages, 7 figure

Building development and roads: implications for the distribution of stone curlews across the Brecks

Background: Substantial new housing and infrastructure development planned within England has the potential to conflict with the nature conservation interests of protected sites. The Breckland area of eastern England (the Brecks) is designated as a Special Protection Area for a number of bird species, including the stone curlew (for which it holds more than 60% of the UK total population). We explore the effect of buildings and roads on the spatial distribution of stone curlew nests across the Brecks in order to inform strategic development plans to avoid adverse effects on such European protected sites. Methodology: Using data across all years (and subsets of years) over the period 1988 – 2006 but restricted to habitat areas of arable land with suitable soils, we assessed nest density in relation to the distances to nearest settlements and to major roads. Measures of the local density of nearby buildings, roads and traffic levels were assessed using normal kernel distance-weighting functions. Quasi-Poisson generalised linear mixed models allowing for spatial auto-correlation were fitted. Results: Significantly lower densities of stone curlew nests were found at distances up to 1500m from settlements, and distances up to 1000m or more from major (trunk) roads. The best fitting models involved optimally distance-weighted variables for the extent of nearby buildings and the trunk road traffic levels. Significance : The results and predictions from this study of past data suggests there is cause for concern that future housing development and associated road infrastructure within the Breckland area could have negative impacts on the nesting stone curlew population. Given the strict legal protection afforded to the SPA the planning and conservation bodies have subsequently agreed precautionary restrictions on building development within the distances identified and used the modelling predictions to agree mitigation measures for proposed trunk road developments

Project20: interpreter services for pregnant women with social risk factors in England: what works, for whom, in what circumstances, and how?

Background: Black and minority ethnic women and those with social risk factors such as deprivation, refugee and asylum seeker status, homelessness, mental health issues and domestic violence are at a disproportionate risk of poor birth outcomes. Language barriers further exacerbate this risk, with women struggling to access, engage with maternity services and communicate concerns to healthcare professionals. To address the language barrier, many UK maternity services offer telephone interpreter services. This study explores whether or not women with social risk factors find these interpreter services acceptable, accessible and safe, and to suggest solutions to address challenges. Methods: Realist methodology was used to refine previously constructed programme theories about how women with language barriers access and experience interpreter services during their maternity care. Twenty-one longitudinal interviews were undertaken during pregnancy and the postnatal period with eight non-English speaking women and their family members. Interviews were analysed using thematic framework analysis to confirm, refute or refine the programme theories and identify specific contexts, mechanisms and outcomes relating to interpreter services. Results: Women with language barriers described difficulties accessing maternity services, a lack of choice of interpreter, suspicion around the level of confidentiality interpreter services provide, and questioned how well professional interpreters were able to interpret what they were trying to relay to the healthcare professional during appointments. This resulted in many women preferring to use a known and trusted family member or friend to interpret for them where possible. Their insights provide detailed insight into how poor-quality interpreter services impact on their ability to disclose risk factors and communicate concerns effectively with their healthcare providers. A refined programme theory puts forward mechanisms to improve their experiences and safety such as regulated, high-quality interpreter services throughout their maternity care, in which women have choice, trust and confidence. Conclusions: The findings of this study contribute to concerns highlighted in previous literature around interpreter services in the wider healthcare arena, particularly around the lack of regulation and access to high-quality interpretation. This is thought to have a significant effect on pregnant women who are living socially complex lives as they are not able to communicate their concerns and access support. This not only impacts on their safety and pregnancy outcomes, but also their wider holistic needs. The refined program theory developed in this study offers insights into the mechanisms of equitable access to appropriate interpreter services for pregnant women with language barriers

Gamma-rays from millisecond pulsars in Globular Clusters

Globular clusters (GCs) with their ages of the order of several billion years contain many final products of evolution of stars such as: neutron stars, white dwarfs and probably also black holes. These compact objects can be at present responsible for the acceleration of particles to relativistic energies. Therefore, gamma-ray emission is expected from GCs as a result of radiation processes occurring either in the inner magnetosperes of millisecond pulsars or in the vicinity of accreting neutron stars and white dwarfs or as a result of interaction of particles leaving the compact objects with the strong radiation field within the GC. Recently, GeV gamma-ray emission has been detected from several GCs by the new satellite observatory Fermi. Also Cherenkov telescopes reported interesting upper limits at the TeV energies which start to constrain the content of GCs. We review the results of these gamma-ray observations in the context of recent scenarios for their origin.Comment: 20 pages, 9 figures, will be published in Astrophysics and Space Science Series (Springer), eds. N. Rea and D.F. Torre

Annotations for Rule-Based Models

The chapter reviews the syntax to store machine-readable annotations and describes the mapping between rule-based modelling entities (e.g., agents and rules) and these annotations. In particular, we review an annotation framework and the associated guidelines for annotating rule-based models of molecular interactions, encoded in the commonly used Kappa and BioNetGen languages, and present prototypes that can be used to extract and query the annotations. An ontology is used to annotate models and facilitate their description

Spina bifida-predisposing heterozygous mutations in Planar Cell Polarity genes and Zic2 reduce bone mass in young mice

Fractures are a common comorbidity in children with the neural tube defect (NTD) spina bifida. Mutations in the Wnt/planar cell polarity (PCP) pathway contribute to NTDs in humans and mice, but whether this pathway independently determines bone mass is poorly understood. Here, we first confirmed that core Wnt/PCP components are expressed in osteoblasts and osteoclasts in vitro. In vivo, we performed detailed µCT comparisons of bone structure in tibiae from young male mice heterozygous for NTD-associated mutations versus WT littermates. PCP signalling disruption caused by Vangl2 (Vangl2Lp/+) or Celsr1 (Celsr1Crsh/+) mutations significantly reduced trabecular bone mass and distal tibial cortical thickness. NTD-associated mutations in non-PCP transcription factors were also investigated. Pax3 mutation (Pax3Sp2H/+) had minimal effects on bone mass. Zic2 mutation (Zic2Ku/+) significantly altered the position of the tibia/fibula junction and diminished cortical bone in the proximal tibia. Beyond these genes, we bioinformatically documented the known extent of shared genetic networks between NTDs and bone properties. 46 genes involved in neural tube closure are annotated with bone-related ontologies. These findings document shared genetic networks between spina bifida risk and bone structure, including PCP components and Zic2. Genetic variants which predispose to spina bifida may therefore independently diminish bone mass

Quantum Zeno Effect and Light-Dark Periods for a Single Atom

The quantum Zeno effect (QZE) predicts a slow-down of the time development of a system under rapidly repeated ideal measurements, and experimentally this was tested for an ensemble of atoms using short laser pulses for non-selective state measurements. Here we consider such pulses for selective measurements on a single system. Each probe pulse will cause a burst of fluorescence or no fluorescence. If the probe pulses were strictly ideal measurements, the QZE would predict periods of fluorescence bursts alternating with periods of no fluorescence (light and dark periods) which would become longer and longer with increasing frequency of the measurements. The non-ideal character of the measurements is taken into account by incorporating the laser pulses in the interaction, and this is used to determine the corrections to the ideal case. In the limit, when the time between the laser pulses goes to zero, no freezing occurs but instead we show convergence to the familiar macroscopic light and dark periods of the continuously driven Dehmelt system. An experiment of this type should be feasible for a single atom or ion in a trapComment: 16 pages, LaTeX, a4.sty; to appear in J. Phys.