WETLAND OCCUPANCY OF POND-BREEDING AMPHIBIANS IN YOSEMITE NATIONAL PARK, USA

We estimated wetland occupancy and population trends for three species of pond-breeding anurans in Yosemite National Park from 2007 – 2011. We used a double survey technique in which two observers independently surveyed each site on the same day. Double surveys allowed us to calculate detectability for the three most common anurans within the park: Rana sierrae, Anaxyrus canorus, and Pseudacris regilla. Annual estimates of detectability were generally high; mean detectability ranged from 73.7% + 0.6 (SE) for any life history stage of A. canorus to 86.7% + 0.7 for sites with P. regilla reproduction (eggs or larvae present). Detectability was most variable for Anaxyrus canorus, which ranged from 45.9% to 99.7%. The probability of occupancy for R. sierrae was highest in larger, low-elevation wetlands that lacked fish. Anaxyrus canorus were more common in shallow high-elevation ponds; their occurrence was minimally impacted by the presence of fish. Finally, occurrence of P. regilla was largely unrelated to wetland size and elevation, but like R. sierrae, they were less likely to occupy sites with fish. Occupancy showed no trend over the five years of our study for R. sierrae or A. canorus when considering either sites with any life stage or only sites with reproduction. However, P. regilla showed a modest downward trend for sites with any life stage and sites with reproduction. Our results for R. sierrae run counter to expectations given recent concern about the decline of this species, while our findings for P. regilla raise concerns for this widespread and generally common species

Multi-generational oxidation model to simulate secondary organic aerosol in a 3-D air quality model

Multi-generational gas-phase oxidation of organic vapors can influence the abundance, composition and properties of secondary organic aerosol (SOA). Only recently have SOA models been developed that explicitly represent multi-generational SOA formation. In this work, we integrated the statistical oxidation model (SOM) into SAPRC-11 to simulate the multi-generational oxidation and gas/particle partitioning of SOA in the regional UCD/CIT (University of California, Davis/California Institute of Technology) air quality model. In the SOM, evolution of organic vapors by reaction with the hydroxyl radical is defined by (1) the number of oxygen atoms added per reaction, (2) the decrease in volatility upon addition of an oxygen atom and (3) the probability that a given reaction leads to fragmentation of the organic molecule. These SOM parameter values were fit to laboratory smog chamber data for each precursor/compound class. SOM was installed in the UCD/CIT model, which simulated air quality over 2-week periods in the South Coast Air Basin of California and the eastern United States. For the regions and episodes tested, the two-product SOA model and SOM produce similar SOA concentrations but a modestly different SOA chemical composition. Predictions of the oxygen-to-carbon ratio qualitatively agree with those measured globally using aerosol mass spectrometers. Overall, the implementation of the SOM in a 3-D model provides a comprehensive framework to simulate the atmospheric evolution of organic aerosol

Simulating secondary organic aerosol in a regional air quality model using the statistical oxidation model – Part 1: Assessing the influence of constrained multi-generational ageing

Multi-generational oxidation of volatile organic compound (VOC) oxidation products can significantly alter the mass, chemical composition and properties of secondary organic aerosol (SOA) compared to calculations that consider only the first few generations of oxidation reactions. However, the most commonly used state-of-the-science schemes in 3-D regional or global models that account for multi-generational oxidation (1) consider only functionalization reactions but do not consider fragmentation reactions, (2) have not been constrained to experimental data and (3) are added on top of existing parameterizations. The incomplete description of multi-generational oxidation in these models has the potential to bias source apportionment and control calculations for SOA. In this work, we used the statistical oxidation model (SOM) of Cappa and Wilson (2012), constrained by experimental laboratory chamber data, to evaluate the regional implications of multi-generational oxidation considering both functionalization and fragmentation reactions. SOM was implemented into the regional University of California at Davis / California Institute of Technology (UCD/CIT) air quality model and applied to air quality episodes in California and the eastern USA. The mass, composition and properties of SOA predicted using SOM were compared to SOA predictions generated by a traditional two-product model to fully investigate the impact of explicit and self-consistent accounting of multi-generational oxidation. Results show that SOA mass concentrations predicted by the UCD/CIT-SOM model are very similar to those predicted by a two-product model when both models use parameters that are derived from the same chamber data. Since the two-product model does not explicitly resolve multi-generational oxidation reactions, this finding suggests that the chamber data used to parameterize the models captures the majority of the SOA mass formation from multi-generational oxidation under the conditions tested. Consequently, the use of low and high NOx yields perturbs SOA concentrations by a factor of two and are probably a much stronger determinant in 3-D models than multi-generational oxidation. While total predicted SOA mass is similar for the SOM and two-product models, the SOM model predicts increased SOA contributions from anthropogenic (alkane, aromatic) and sesquiterpenes and decreased SOA contributions from isoprene and monoterpene relative to the two-product model calculations. The SOA predicted by SOM has a much lower volatility than that predicted by the traditional model, resulting in better qualitative agreement with volatility measurements of ambient OA. On account of its lower-volatility, the SOA mass produced by SOM does not appear to be as strongly influenced by the inclusion of oligomerization reactions, whereas the two-product model relies heavily on oligomerization to form low-volatility SOA products. Finally, an unconstrained contemporary hybrid scheme to model multi-generational oxidation within the framework of a two-product model in which ageing reactions are added on top of the existing two-product parameterization is considered. This hybrid scheme formed at least 3 times more SOA than the SOM during regional simulations as a result of excessive transformation of semi-volatile vapors into lower volatility material that strongly partitions to the particle phase. This finding suggests that these hybrid multi-generational schemes should be used with great caution in regional models

Performance of the Xpert HPV assay in women attending for cervical screening

© 2015 The Authors. Objectives: This study evaluated the Xpert HPV Assay in women attending screening in general practice by comparing Xpert with two established HPV tests, cytology and histology. Methods: A prospective study in women aged 20-60 years attending screening in Bristol, Edinburgh and London using residual Preservcyt cytology samples. Sample order was randomised between Roche cobas4800 and Cepheid Xpert assays with Qiagen hc2 third. Results: 3408 cases were included in the primary analysis. Positivity for Xpert was 19.6%, cobas 19.2% and hc2 19.9% with high concordance (kappa=86.8% vs cobas, 81.55 vs hc2). Xpert, cobas and hc2 showed similar sensitivity (98.7%, 97.5%, 98.7%) for CIN2+. All pairwise comparisons had high concordance (Kappa ≥0.78 with any abnormal cytology. Xpert and hc2 were positive for all cases of ≥moderate dyskaryosis ( N=63)), cobas was negative in two. Histology was available for 172 participants. 79 reported CIN2+, 47 CIN3+. All CIN3+ was positive on Xpert and hc2 and one case negative for cobas. One case of CIN2 was negative for all assays. Conclusions: The performance of Xpert HPV Assay in a general screening population is comparable to established HPV tests. It offers simplicity of testing, flexibility with non-batching of individual samples and rapid turnaround time

Modeling the Atmospheric Concentrations of Individual Gas-Phase and Particle-Phase Organic Compounds

An Eulerian photochemical airshed model is adapted to track the concentrations of individual vapor-phase, semivolatile, and particle-phase compounds over the carbon number range from C_1 to C_(34). The model incorporates primary emissions of organic gases and particles from sources based on recent source tests. These emissions are processed through a photochemical airshed model whose chemical mechanism has been expanded to explicitly follow the reaction or formation of 125 individual vapor-phase organic compounds plus 11 lumped vapor-phase compound groups. Primary organic compounds in the particle phase can be disaggregated at will from a lumped primary organic compound mass category; in the present model application, 31 individual primary particulate organic compounds are tracked as they are transported from sources to receptor air monitoring sites. The model is applied to study air quality relationships for organics in California's South Coast Air Basin that surrounds Los Angeles during the severe photochemical smog episode that occurred on September 8−9, 1993. The ambient concentra tions of all normal alkanes and most aromatic hydrocarbons are predicted within the correct order of magnitude over 6 orders of magnitude concentration change from most abundant gas phase to least abundant particulate species studied. A formal evaluation of model performance shows that, with the exception of a few outliers, the concentrations of over 100 organic compounds studied were reproduced with an average absolute bias of ±47% and with roughly equal numbers of compounds underpredicted (58) versus overpredicted (46). The time series of observed aromatic hydrocarbons concentrations are reproduced closely, production of methylglyoxal from aromatic precursors is tracked, and the predicted olefinic hydrocarbon concentrations decline dramatically in concentration due to chemical reaction and dilution during downwind transport as is observed in the ambient monitoring database. This ability to simultaneously account for the concentrations of individual gas-phase and particulate organic compounds lays a foundation for future calculations of secondary organic aerosol formation and gas/particle repartitioning in the atmosphere

Early Neutrophilia Marked by Aerobic Glycolysis Sustains Host Metabolism and Delays Cancer Cachexia

An elevated neutrophil–lymphocyte ratio negatively predicts the outcome of patients with cancer and is associated with cachexia, the terminal wasting syndrome. Here, using murine model systems of colorectal and pancreatic cancer we show that neutrophilia in the circulation and multiple organs, accompanied by extramedullary hematopoiesis, is an early event during cancer progression. Transcriptomic and metabolic assessment reveals that neutrophils in tumor-bearing animals utilize aerobic glycolysis, similar to cancer cells. Although pharmacological inhibition of aerobic glycolysis slows down tumor growth in C26 tumor-bearing mice, it precipitates cachexia, thereby shortening the overall survival. This negative effect may be explained by our observation that acute depletion of neutrophils in pre-cachectic mice impairs systemic glucose homeostasis secondary to altered hepatic lipid processing. Thus, changes in neutrophil number, distribution, and metabolism play an adaptive role in host metabolic homeostasis during cancer progression. Our findings provide insight into early events during cancer progression to cachexia, with implications for therapy