Data Visualization for Network Simulations

As many other kinds of simulation experiments, simulations of computer networks tend to generate high volumes of output data. While the collection and the statistical processing of these data are challenges in and of themselves, creating meaningful visualizations from them is as much an art as it is a science. A sophisticated body of knowledge in information design and data visualization has been developed and continues to evolve. However, many of the visualizations created by the network simulation community tend to be less than optimal at creating compelling, informative narratives from experimental output data. The primary contribution of this paper is to explore some of the design dimensions in visualization and some advances in the field that are applicable to network simulation. We also discuss developments in the creation of the visualization subsystem in the Simulation Automation Framework for Experiments (SAFE) in the context of best practices for data visualization

Vector competence of Aedes aegypti, Culex tarsalis, and Culex quinquefasciatus from California for Zika virus.

Zika virus (ZIKV) has emerged since 2013 as a significant global human health threat following outbreaks in the Pacific Islands and rapid spread throughout South and Central America. Severe congenital and neurological sequelae have been linked to ZIKV infections. Assessing the ability of common mosquito species to transmit ZIKV and characterizing variation in mosquito transmission of different ZIKV strains is important for estimating regional outbreak potential and for prioritizing local mosquito control strategies for Aedes and Culex species. In this study, we evaluated the laboratory vector competence of Aedes aegypti, Culex quinquefasciatus, and Culex tarsalis that originated in areas of California where ZIKV cases in travelers since 2015 were frequent. We compared infection, dissemination, and transmission rates by measuring ZIKV RNA levels in cohorts of mosquitoes that ingested blood meals from type I interferon-deficient mice infected with either a Puerto Rican ZIKV strain from 2015 (PR15), a Brazilian ZIKV strain from 2015 (BR15), or an ancestral Asian-lineage Malaysian ZIKV strain from 1966 (MA66). With PR15, Cx. quinquefasciatus was refractory to infection (0%, N = 42) and Cx. tarsalis was infected at 4% (N = 46). No ZIKV RNA was detected in saliva from either Culex species 14 or 21 days post feeding (dpf). In contrast, Ae. aegypti developed infection rates of 85% (PR15; N = 46), 90% (BR15; N = 20), and 81% (MA66; N = 85) 14 or 15 dpf. Although MA66-infected Ae. aegypti showed higher levels of ZIKV RNA in mosquito bodies and legs, transmission rates were not significantly different across virus strains (P = 0.13, Fisher's exact test). To confirm infectivity and measure the transmitted ZIKV dose, we enumerated infectious ZIKV in Ae. aegypti saliva using Vero cell plaque assays. The expectorated plaque forming units PFU varied by viral strain: MA66-infected expectorated 13±4 PFU (mean±SE, N = 13) compared to 29±6 PFU for PR15-infected (N = 13) and 35±8 PFU for BR15-infected (N = 6; ANOVA, df = 2, F = 3.8, P = 0.035). These laboratory vector competence results support an emerging consensus that Cx. tarsalis and Cx. quinquefasciatus are not vectors of ZIKV. These results also indicate that Ae. aegypti from California are efficient laboratory vectors of ancestral and contemporary Asian lineage ZIKV

Effects of Nitrogen and Planting Seed Size on Cotton Growth, Development, and Yield

A standardized experiment was conducted during 2009 and 2010 at 20 location-years across U.S. cotton (Gossypium hirsutum L.)-producing states to compare the N use requirement of contemporary cotton cultivars based on their planting seed size. Treatments consisted of three cotton varieties with planting seed of different numbers of seed per kg and N rates of 0, 45, 90, and 134 kg ha⁻¹. Soil at each trial location was sampled and tested for nitrate presence. High levels of soil nitrate (>91 N-NO₃⁻kg ha⁻¹) were found in Arizona and western Texas, and soil nitrate in the range of 45 to 73 kg N-NO₃⁻ ha⁻¹ was found at locations in the central United States. Cotton lint yield responded to applied N at 11 of 20 locations. Considering only sites that responded to applied N, highest lint yields were achieved with 112 to 224 kg ha⁻¹of applied plus pre-plant residual soil NO₃—translating to an optimal N requirement of 23 kg ha⁻¹ per 218 kg bale of lint produced. Among the varieties tested those with medium-sized seed produced higher yields in response to N than did larger and smaller seeded varieties. Varieties with larger seed had longer and stronger fibers, higher fiber length uniformity than small seeded varieties and decreased micronaire. Seed protein and oil increased and decreased slightly in response to increasing amounts of soil nitrate plus applied N, respectively

The Bolocam Galactic Plane Survey IV: 1.1 and 0.35 mm Dust Continuum Emission in the Galactic Center Region

The Bolocam Galactic Plane Survey (BGPS) data for a six square degree region of the Galactic plane containing the Galactic center is analyzed and compared to infrared and radio continuum data. The BGPS 1.1 mm emission consists of clumps interconnected by a network of fainter filaments surrounding cavities, a few of which are filled with diffuse near-IR emission indicating the presence of warm dust or with radio continuum characteristic of HII regions or supernova remnants. New 350 {\mu}m images of the environments of the two brightest regions, Sgr A and B, are presented. Sgr B2 is the brightest mm-emitting clump in the Central Molecular Zone and may be forming the closest analog to a super star cluster in the Galaxy. The Central Molecular Zone (CMZ) contains the highest concentration of mm and sub-mm emitting dense clumps in the Galaxy. Most 1.1 mm features at positive longitudes are seen in silhouette against the 3.6 to 24 {\mu}m background observed by the Spitzer Space Telescope. However, only a few clumps at negative longitudes are seen in absorption, confirming the hypothesis that positive longitude clumps in the CMZ tend to be on the near-side of the Galactic center, consistent with the suspected orientation of the central bar in our Galaxy. Some 1.1 mm cloud surfaces are seen in emission at 8 {\mu}m, presumably due to polycyclic aromatic hydrocarbons (PAHs). A ~0.2\degree (~30 pc) diameter cavity and infrared bubble between l \approx 0.0\degree and 0.2\degree surrounds the Arches and Quintuplet clusters and Sgr A. The bubble contains several clumpy dust filaments that point toward Sgr A\ast; its potential role in their formation is explored. [abstract truncated]Comment: 76 pages, 22 figures, published in ApJ: http://iopscience.iop.org/0004-637X/721/1/137

Effectiveness of a biopsychosocial e-learning intervention on the clinical judgements of medical students and GP trainees regarding future risk of disability in patients with chronic lower back pain: study protocol for a randomised controlled trial

Introduction Chronic lower back pain (CLBP) is a major healthcare problem with wide ranging effects. It is a priority for appropriate management of CLBP to get individuals back to work as early as possible. Interventions that identify biopsychosocial barriers to recovery have been observed to lead to successfully reduced pain-related work absences and increased return to work for individuals with CLBP. Modern conceptualisations of pain adopt a biopsychosocial approach, such as the flags approach. Biopsychosocial perspectives have been applied to judgements about future adjustment, recovery from pain and risk of long-term disability; and provide a helpful model for understanding the importance of contextual interactions between psychosocial and biological variables in the experience of pain. Medical students and general practitioner (GP) trainees are important groups to target with education about biopsychosocial conceptualisations of pain and related clinical implications. Aim The current study will compare the effects of an e-learning intervention that focuses on a biopsychosocial model of pain, on the clinical judgements of medical students and trainees. Methods and analysis Medical student and GP trainee participants will be randomised to 1 of 2 study conditions: (1) a 20 min e-learning intervention focused on the fundamentals of the flags approach to clinical judgement-making regarding risk of future pain-related disability; compared with a (2) wait-list control group on judgement accuracy and weighting (ie, primary outcomes); flags approach knowledge, attitudes and beliefs towards pain, judgement speed and empathy (ie, secondary outcomes). Participants will be assessed at preintervention and postintervention. Ethics and dissemination The study will be performed in agreement with the Declaration of Helsinki and is approved by the National University of Ireland Galway Research Ethics Committee. The results of the trial will be published according to the CONSORT statement and will be presented at conferences and reported in peer-reviewed journals

Aboveground biomass density models for NASA's Global Ecosystem Dynamics Investigation (GEDI) lidar mission

NASA's Global Ecosystem Dynamics Investigation (GEDI) is collecting spaceborne full waveform lidar data with a primary science goal of producing accurate estimates of forest aboveground biomass density (AGBD). This paper presents the development of the models used to create GEDI's footprint-level (similar to 25 m) AGBD (GEDI04_A) product, including a description of the datasets used and the procedure for final model selection. The data used to fit our models are from a compilation of globally distributed spatially and temporally coincident field and airborne lidar datasets, whereby we simulated GEDI-like waveforms from airborne lidar to build a calibration database. We used this database to expand the geographic extent of past waveform lidar studies, and divided the globe into four broad strata by Plant Functional Type (PFT) and six geographic regions. GEDI's waveform-to-biomass models take the form of parametric Ordinary Least Squares (OLS) models with simulated Relative Height (RH) metrics as predictor variables. From an exhaustive set of candidate models, we selected the best input predictor variables, and data transformations for each geographic stratum in the GEDI domain to produce a set of comprehensive predictive footprint-level models. We found that model selection frequently favored combinations of RH metrics at the 98th, 90th, 50th, and 10th height above ground-level percentiles (RH98, RH90, RH50, and RH10, respectively), but that inclusion of lower RH metrics (e.g. RH10) did not markedly improve model performance. Second, forced inclusion of RH98 in all models was important and did not degrade model performance, and the best performing models were parsimonious, typically having only 1-3 predictors. Third, stratification by geographic domain (PFT, geographic region) improved model performance in comparison to global models without stratification. Fourth, for the vast majority of strata, the best performing models were fit using square root transformation of field AGBD and/or height metrics. There was considerable variability in model performance across geographic strata, and areas with sparse training data and/or high AGBD values had the poorest performance. These models are used to produce global predictions of AGBD, but will be improved in the future as more and better training data become available

Basic science232. Certolizumab pegol prevents pro-inflammatory alterations in endothelial cell function

Background: Cardiovascular disease is a major comorbidity of rheumatoid arthritis (RA) and a leading cause of death. Chronic systemic inflammation involving tumour necrosis factor alpha (TNF) could contribute to endothelial activation and atherogenesis. A number of anti-TNF therapies are in current use for the treatment of RA, including certolizumab pegol (CZP), (Cimzia ®; UCB, Belgium). Anti-TNF therapy has been associated with reduced clinical cardiovascular disease risk and ameliorated vascular function in RA patients. However, the specific effects of TNF inhibitors on endothelial cell function are largely unknown. Our aim was to investigate the mechanisms underpinning CZP effects on TNF-activated human endothelial cells. Methods: Human aortic endothelial cells (HAoECs) were cultured in vitro and exposed to a) TNF alone, b) TNF plus CZP, or c) neither agent. Microarray analysis was used to examine the transcriptional profile of cells treated for 6 hrs and quantitative polymerase chain reaction (qPCR) analysed gene expression at 1, 3, 6 and 24 hrs. NF-κB localization and IκB degradation were investigated using immunocytochemistry, high content analysis and western blotting. Flow cytometry was conducted to detect microparticle release from HAoECs. Results: Transcriptional profiling revealed that while TNF alone had strong effects on endothelial gene expression, TNF and CZP in combination produced a global gene expression pattern similar to untreated control. The two most highly up-regulated genes in response to TNF treatment were adhesion molecules E-selectin and VCAM-1 (q 0.2 compared to control; p > 0.05 compared to TNF alone). The NF-κB pathway was confirmed as a downstream target of TNF-induced HAoEC activation, via nuclear translocation of NF-κB and degradation of IκB, effects which were abolished by treatment with CZP. In addition, flow cytometry detected an increased production of endothelial microparticles in TNF-activated HAoECs, which was prevented by treatment with CZP. Conclusions: We have found at a cellular level that a clinically available TNF inhibitor, CZP reduces the expression of adhesion molecule expression, and prevents TNF-induced activation of the NF-κB pathway. Furthermore, CZP prevents the production of microparticles by activated endothelial cells. This could be central to the prevention of inflammatory environments underlying these conditions and measurement of microparticles has potential as a novel prognostic marker for future cardiovascular events in this patient group. Disclosure statement: Y.A. received a research grant from UCB. I.B. received a research grant from UCB. S.H. received a research grant from UCB. All other authors have declared no conflicts of interes