Extending Continuum Models for Atom Probe Simulation

This work describes extensions to existing level-set algorithms developed for application within the field of Atom Probe Tomography (APT). We present a new simulation tool for the simulation of 3D tomographic volumes, using advanced level set methods. By combining narrow-band, B-Tree and particle-tracing approaches from level-set methods, we demonstrate a practical tool for simulating shape changes to APT samples under applied electrostatic fields, in three dimensions. This work builds upon our previous studies by allowing for non-axially symmetric solutions, with minimal loss in computational speed, whilst retaining numerical accuracy

Timing of poverty in childhood and adolescent health: Evidence from the US and UK

Childhood poverty is associated with poorer adolescent health and health behaviours, but the importance of the timing of poverty remains unclear. There may be critical or sensitive periods in early life or early adolescence, or poverty may have cumulative effects throughout childhood. Understanding when poverty is most important can support efficient timing of interventions to raise family income or buffer against the effects of low income, but answers may vary across social contexts. The US and the UK are a useful comparison with similar liberal approaches to cash transfers, but very different approaches to healthcare provision. Utilising data from large population studies in the US (n = 9408; born 1979–1996) and UK (n = 1204; born 1991–1997), this study employs a structured life course approach to compare competing hypotheses about the importance of the timing or pattern of childhood exposure to poverty in predicting adolescent health limitations, symptoms of psychiatric distress, and smoking at age 16 (age 15/16 in US). Household income histories identified experience of poverty (measured as <60% of the national median equivalised income for a given year) in early life (ages 0–5), mid-childhood (ages 6–10) and early adolescence (ages 11–15). The Bayesian Information Criterion (BIC) compared fit across models with variables representing different life course patterns of exposure to poverty. Adolescent distress was not associated with poverty in either country. In both countries, however, variables representing cumulative or persistent experiences of poverty exhibited optimal fit of all poverty exposure variables in predicting adolescent smoking and health limitations. There was also evidence of an early life sensitive period for smoking in the US. Poverty was more persistent in the US, but associations between poverty and outcomes were consistent across countries. Although poverty can have cumulative effects on health and behaviour, early interventions may offer the best long-term protection

DF-Fit : A robust algorithm for detection of crystallographic information in Atom Probe Tomography data

We report on a new algorithm for detection of crystallographic information in 3D, as retained in Atom Probe Tomography (APT), with improved robustness and signal detection performance. The algorithm is underpinned by 1D distribution functions, as per existing algorithms, but eliminates an unnecessary parameter as compared to current methods. By examining traditional distribution functions in an automated fashion in real space, rather than using Fourier transform approaches, we utilise an error metric based upon the expected value for a spatially random distribution for detecting crystallography. We show cases where the metric is able to successfully obtain orientation information, and show that it can function with high levels of additive and displacive background noise. We additionally compare this metric to Fourier transform methods, showing fewer artefacts when examining simulated datasets. An extension of the approach is used to aid the automatic detection of high-quality data regions within an entire dataset, albeit with a large increase in computational cost. This extension is demonstrated on acquired Aluminium and Tungsten APT datasets, and shown to be able to discern regions of the data which have relatively improved spatial data quality. Finally, this program has been made available for use in other laboratories undertaking their own analyses

Central Executive Dysfunction and Deferred Prefrontal Processing in Veterans with Gulf War Illness.

Gulf War Illness is associated with toxic exposure to cholinergic disruptive chemicals. The cholinergic system has been shown to mediate the central executive of working memory (WM). The current work proposes that impairment of the cholinergic system in Gulf War Illness patients (GWIPs) leads to behavioral and neural deficits of the central executive of WM. A large sample of GWIPs and matched controls (MCs) underwent functional magnetic resonance imaging during a varied-load working memory task. Compared to MCs, GWIPs showed a greater decline in performance as WM-demand increased. Functional imaging suggested that GWIPs evinced separate processing strategies, deferring prefrontal cortex activity from encoding to retrieval for high demand conditions. Greater activity during high-demand encoding predicted greater WM performance. Behavioral data suggest that WM executive strategies are impaired in GWIPs. Functional data further support this hypothesis and suggest that GWIPs utilize less effective strategies during high-demand WM

Efficacy, Safety, and Timing of Anticoagulant Thromboprophylaxis for the Prevention of Venous Thromboembolism in Patients With Acute Spinal Cord Injury: A Systematic Review

Study Design: Systematic review. Objectives: The objective of this study was to answer 5 key questions: What is the comparative effectiveness and safety of (1a) anticoagulant thromboprophylaxis compared to no prophylaxis, placebo, or another anticoagulant strategy for preventing deep vein thrombosis (DVT) and pulmonary embolism (PE) after acute spinal cord injury (SCI)? (1b) Mechanical prophylaxis strategies alone or in combination with other strategies for preventing DVT and PE after acute SCI? (1c) Prophylactic inferior vena cava filter insertion alone or in combination with other strategies for preventing DVT and PE after acute SCI? (2) What is the optimal timing to initiate and/or discontinue anticoagulant, mechanical, and/or prophylactic inferior vena cava filter following acute SCI? (3) What is the cost-effectiveness of these treatment options? Methods: A systematic literature search was conducted to identify studies published through February 28, 2015. We sought randomized controlled trials evaluating efficacy and safety of antithrombotic strategies. Strength of evidence was evaluated using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) system. Results: Nine studies satisfied inclusion criteria. We found a trend toward lower risk of DVT in patients treated with enoxaparin. There were no significant differences in rates of DVT, PE, bleeding, and mortality between patients treated with different types of low-molecular-weight heparin or between low-molecular-weight heparin and unfractionated heparin. Combined anticoagulant and mechanical prophylaxis initiated within 72 hours of SCI resulted in lower risk of DVT than treatment commenced after 72 hours of injury. Conclusion: Prophylactic treatments can be used to lower the risk of venous thromboembolic events in patients with acute SCI, without significant increase in risk of bleeding and mortality and should be initiated within 72 hours. © 2017, © The Author(s) 2017

Perceived role of the veterinarian in promoting dairy cattle welfare

Improving the lives of animals in agricultural systems has primarily focused on minimizing negative experiences. Research is needed on the promotion of positive experiences (pleasure, enjoyment, play, choice, happiness) for animals and the role of veterinarians in their promotion. Our aims were to describe how Canadian bovine veterinarians and veterinary students perceive the role of a veterinarian in positive vs. negative experiences for dairy cows and to analyze the rationale provided to explain their answers. Canadian veterinary practitioners (n = 78) and veterinary students (n = 148) responded to an online cross-sectional survey and were asked, on a 7-point scale, how important the role of a veterinarian is to promote practices that influence the experience of dairy cows. We used qualitative description to analyse participants’ open-ended text responses. Practices to minimize negative experiences were most important (mean ± SE; 6.8 ± 0.03), a balance of positive and negative experiences was less important (6.4 ± 0.05), and encouragement of positive experiences scored lowest (6.0 ± 0.06), although all scored highly. Four themes were identified to explain participants’ reasoning regarding their perceived role of a veterinarian in the promotion of dairy cattle welfare, centered on: the animal, the producer, the veterinarian, and society. Participants indicated that promoting positive experiences was less important than decreasing negative experiences (5.9 ± 0.09). There were four themes identified to explain participants’ reasoning regarding the relative importance of promotion of positive experiences versus decreasing negative experiences which centered on: frameworks to compare positive and negative experiences, impacts on the animal, the participant’s view of their role, and the practicality of implementation. These results indicate modest differences in valuing avoidance of negative vs. promotion of positive welfare. There were no differences in the quantitative analyses between veterinarians and veterinary students. We conclude that veterinarians are favorably disposed to positive aspects of welfare for dairy cows but may be more focussed on avoidance of negative aspects of welfare

Long serial analysis of gene expression for gene discovery and transcriptome profiling in the widespread marine coccolithophore Emiliania huxleyi

Author Posting. © American Society for Microbiology, 2006. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 72 (2006): 252-260, doi:10.1128/AEM.72.1.252-260.2006.The abundant and widespread coccolithophore Emiliania huxleyi plays an important role in mediating CO2 exchange between the ocean and the atmosphere through its impact on marine photosynthesis and calcification. Here, we use long serial analysis of gene expression (SAGE) to identify E. huxleyi genes responsive to nitrogen (N) or phosphorus (P) starvation. Long SAGE is an elegant approach for examining quantitative and comprehensive gene expression patterns without a priori knowledge of gene sequences via the detection of 21-bp nucleotide sequence tags. E. huxleyi appears to have a robust transcriptional-level response to macronutrient deficiency, with 42 tags uniquely present or up-regulated twofold or greater in the N-starved library and 128 tags uniquely present or up-regulated twofold or greater in the P-starved library. The expression patterns of several tags were validated with reverse transcriptase PCR. Roughly 48% of these differentially expressed tags could be mapped to publicly available genomic or expressed sequence tag (EST) sequence data. For example, in the P-starved library a number of the tags mapped to genes with a role in P scavenging, including a putative phosphate-repressible permease and a putative polyphosphate synthetase. In short, the long SAGE analyses have (i) identified many new differentially regulated gene sequences, (ii) assigned regulation data to EST sequences with no database homology and unknown function, and (iii) highlighted previously uncharacterized aspects of E. huxleyi N and P physiology. To this end, our long SAGE libraries provide a new public resource for gene discovery and transcriptional analysis in this biogeochemically important marine organism.This work was supported by the Woods Hole Oceanographic Institution Ocean Life Institute, the J. Lamar Worzel Assistant Scientist Fund, and the Frank and Lisina Hoch Endowed Fund. A.G.M., S.R.B., and M.J.C. were supported in part by the Marine Biological Laboratory's Program in Global Infectious Diseases, funded by the Ellison Medical Foundation. Computational resources were provided by the Josephine Bay Paul Center for Comparative Molecular Biology and Evolution (Marine Biological Laboratory) through funds provided by the W. M. Keck Foundation and the G. Unger Vetlesen Foundation

Distribution of \u3ci\u3eBaylisascaris procyonis\u3c/i\u3e in Raccoons (\u3ci\u3eProcyon lotor\u3c/i\u3e) in Florida, USA

Baylisascaris procyonis, or raccoon roundworm, is an intestinal nematode parasite of raccoons (Procyon lotor) that is important to public and wildlife health. Historically, the parasite was uncommon in the southeastern US; however, the range of B. procyonis has expanded to include Florida, US. From 2010 to 2016, we opportunistically sampled 1,030 raccoons statewide. The overall prevalence was 3.7% (95% confidence interval=2.5–4.8%) of sampled individuals, and infection intensity ranged from 1 to 48 (mean±standard deviation 9.9±4.0). We found raccoon roundworm in 9/56 (16%) counties sampled, and the percent positive ranged from 1.1% to 13.3% of specimens collected per county. Including previously published data, B. procyonis was detected in 11 Florida counties. We used logistic regression to estimate the contribution of raccoon demographic variables and the presence of the endoparasite Macracanthorhynchus ingens to B. procyonis detection in Florida. Following the model selection process we found housing density, M. ingens presence, and urbanicity to be predictive of raccoon roundworm presence. We also found substantial among-county variation. Raccoon sex and age were not useful predictors. Public health officials, wildlife rehabilitators, wildlife managers, and others should consider any Florida raccoon to be potentially infected with B. procyonis, particularly in areas where housing density is high