Economic Impacts of Aquatic Vegetation to Angling in Two South Carolina Reservoirs

Angler creel surveys and economic impact models were used to evaluate potential expansion of aquatic vegetation in Lakes Murray and Moultrie, South Carolina. (PDF contains 4 pages.

Nocturnal Copulation in Glaucous-winged Gulls Larus glaucescens

Gulls (Laridae) are primarily diurnal, although many species forage opportunistically at night, and several species copulate at night. We used trail cameras to study time-of-day variation in the rate of copulation by Glaucous-winged Gulls Larus glaucescens in a breeding colony (1500+ pairs) at Protection Island, Washington, USA, from 31 May to 07 June 2018. Copulations (n = 353) occurred at a significantly higher rate during the day (0.82/camera-h) than at night (0.51/camera-h), with 76.3 % of copulations during the day and 23.7 % at night (daylight comprised 66.1 % and darkness comprised 33.9 % of the study period). The copulation rate peaked shortly before and after dawn, with a second peak before sunset. Copulation rate was lowest during the middle of the day and middle of the night. Glaucous-winged Gulls sleep intermittently during both day and night and have sufficient energy to sustain sporadic copulations during the night, which appears to be a normal part of their reproductive behavior. The most likely advantage of this pattern is an increased opportunity for fertilization with a mate

JCoDA: a tool for detecting evolutionary selection

<p>Abstract</p> <p>Background</p> <p>The incorporation of annotated sequence information from multiple related species in commonly used databases (Ensembl, Flybase, Saccharomyces Genome Database, Wormbase, etc.) has increased dramatically over the last few years. This influx of information has provided a considerable amount of raw material for evaluation of evolutionary relationships. To aid in the process, we have developed JCoDA (Java Codon Delimited Alignment) as a simple-to-use visualization tool for the detection of site specific and regional positive/negative evolutionary selection amongst homologous coding sequences.</p> <p>Results</p> <p>JCoDA accepts user-inputted unaligned or pre-aligned coding sequences, performs a codon-delimited alignment using ClustalW, and determines the dN/dS calculations using PAML (Phylogenetic Analysis Using Maximum Likelihood, yn00 and codeml) in order to identify regions and sites under evolutionary selection. The JCoDA package includes a graphical interface for Phylip (Phylogeny Inference Package) to generate phylogenetic trees, manages formatting of all required file types, and streamlines passage of information between underlying programs. The raw data are output to user configurable graphs with sliding window options for straightforward visualization of pairwise or gene family comparisons. Additionally, codon-delimited alignments are output in a variety of common formats and all dN/dS calculations can be output in comma-separated value (CSV) format for downstream analysis. To illustrate the types of analyses that are facilitated by JCoDA, we have taken advantage of the well studied sex determination pathway in nematodes as well as the extensive sequence information available to identify genes under positive selection, examples of regional positive selection, and differences in selection based on the role of genes in the sex determination pathway.</p> <p>Conclusions</p> <p>JCoDA is a configurable, open source, user-friendly visualization tool for performing evolutionary analysis on homologous coding sequences. JCoDA can be used to rapidly screen for genes and regions of genes under selection using PAML. It can be freely downloaded at <url>http://www.tcnj.edu/~nayaklab/jcoda</url>.</p

A novel cellular pathway of antigen presentation and CD4 T cell activation in vivo

Dendritic cell activation of CD4 T cells in the lymph node draining a site of infection or vaccination is widely considered the central event in initiating adaptive immunity. The accepted dogma is that this occurs by stimulating local activation and antigen acquisition by dendritic cells, with subsequent lymph node migration, however the generalizability of this mechanism is unclear. Here we show that in some circumstances antigen can bypass the injection site inflammatory response, draining freely and rapidly to the lymph nodes where it interacts with subcapsular sinus (SCS) macrophages resulting in their death. Debris from these dying SCS macrophages is internalized by monocytes recruited from the circulation. This coordinated response leads to antigen presentation by monocytes and interactions with naïve CD4 T cells that can drive the initiation of T cell and B cell responses. These studies demonstrate an entirely novel pathway leading to initiation of adaptive immune responses in vivo

Air pollution, deprivation and health: Understanding relationships to add value to local air quality management policy and practice in Wales, UK

© The Author 2016. Published by Oxford University Press on behalf of Faculty of Public Health. All rights reserved. Background Air pollution exposure reduces life expectancy. Air pollution, deprivation and poor-health status combinations can create increased and disproportionate disease burdens. Problems and solutions are rarely considered in a broad public health context, but doing so can add value to air quality management efforts by reducing air pollution risks, impacts and inequalities. Methods An ecological study assessed small-area associations between air pollution (nitrogen dioxide and particulate matter), deprivation status and health outcomes in Wales, UK. Results Air pollution concentrations were highest in 'most' deprived areas. When considered separately, deprivation-health associations were stronger than air pollution-health associations. Considered simultaneously, air pollution added to deprivation-health associations; interactions between air pollution and deprivation modified and strengthened associations with all-cause and respiratory disease mortality, especially in 'most' deprived areas where most-vulnerable people lived and where health needs were greatest. Conclusion There is a need to reduce air pollution-related risks for all. However, it is also the case that greater health gains can result from considering local air pollution problems and solutions in the context of wider health-determinants and acting on a better understanding of relationships. Informed and co-ordinated air pollution mitigation and public health action in high deprivation and pollution areas can reduce risks and inequalities. To achieve this, greater public health integration and collaboration in local air quality management policy and practice is needed

Progress with air quality management in the 60 years since the UK clean air act, 1956. Lessons, failures, challenges and opportunities

© 2016 WIT Press, www.witpress.com. This paper explores the challenges, opportunities and progress made with managing air quality since the United Kingdom parliament passed the Clean Air Act, 1956. It seeks to identify the factors contributing to successful management of air quality and the factors that have acted, or continue to do so, as barriers to progress. The public health catastrophe of the 1952 London Smog created the political momentum for the 1956 Act to be passed. The nature of the contemporary air pollution challenge is reviewed in terms of the public health burden, the economic cost and the governmental response. The contemporary response is considered inadequate for the scale and intensity of the problem

Simulating Radiating and Magnetized Flows in Multi-Dimensions with ZEUS-MP

This paper describes ZEUS-MP, a multi-physics, massively parallel, message- passing implementation of the ZEUS code. ZEUS-MP differs significantly from the ZEUS-2D code, the ZEUS-3D code, and an early "version 1" of ZEUS-MP distributed publicly in 1999. ZEUS-MP offers an MHD algorithm better suited for multidimensional flows than the ZEUS-2D module by virtue of modifications to the Method of Characteristics scheme first suggested by Hawley and Stone (1995), and is shown to compare quite favorably to the TVD scheme described by Ryu et. al (1998). ZEUS-MP is the first publicly-available ZEUS code to allow the advection of multiple chemical (or nuclear) species. Radiation hydrodynamic simulations are enabled via an implicit flux-limited radiation diffusion (FLD) module. The hydrodynamic, MHD, and FLD modules may be used in one, two, or three space dimensions. Self gravity may be included either through the assumption of a GM/r potential or a solution of Poisson's equation using one of three linear solver packages (conjugate-gradient, multigrid, and FFT) provided for that purpose. Point-mass potentials are also supported. Because ZEUS-MP is designed for simulations on parallel computing platforms, considerable attention is paid to the parallel performance characteristics of each module. Strong-scaling tests involving pure hydrodynamics (with and without self-gravity), MHD, and RHD are performed in which large problems (256^3 zones) are distributed among as many as 1024 processors of an IBM SP3. Parallel efficiency is a strong function of the amount of communication required between processors in a given algorithm, but all modules are shown to scale well on up to 1024 processors for the chosen fixed problem size.Comment: Accepted for publication in the ApJ Supplement. 42 pages with 29 inlined figures; uses emulateapj.sty. Discussions in sections 2 - 4 improved per referee comments; several figures modified to illustrate grid resolution. ZEUS-MP source code and documentation available from the Laboratory for Computational Astrophysics at http://lca.ucsd.edu/codes/currentcodes/zeusmp2