Multi-year (2004–2008) record of nonmethane hydrocarbons and halocarbons in New England: seasonal variations and regional sources

Multi-year time series records of C<sub>2</sub>-C<sub>6</sub> alkanes, C<sub>2</sub>-C<sub>4</sub> alkenes, ethyne, isoprene, C<sub>6</sub>-C<sub>8</sub> aromatics, trichloroethene (C<sub>2</sub>HCl<sub>3</sub>), and tetrachloroethene (C<sub>2</sub>Cl<sub>4</sub>) from canister samples collected during January 2004–February 2008 at the University of New Hampshire (UNH) AIRMAP Observatory at Thompson Farm (TF) in Durham, NH are presented. The objectives of this work are to identify the sources of nonmethane hydrocarbons (NMHCs) and halocarbons observed at TF, characterize the seasonal and interannual variability in ambient mixing ratios and sources, and estimate regional emission rates of NMHCs. Analysis of correlations and comparisons with emission ratios indicated that a ubiquitous and persistent mix of emissions from several anthropogenic sources is observed throughout the entire year. The highest C<sub>2</sub>-C<sub>8</sub> anthropogenic NMHC mixing ratios were observed in mid to late winter. Following the springtime minimums, the C<sub>3</sub>-C<sub>6</sub> alkanes, C<sub>7</sub>-C<sub>8</sub> aromatics, and C<sub>2</sub>HCl<sub>3</sub> increased in early to mid summer, presumably reflecting enhanced evaporative emissions. Mixing ratios of C<sub>2</sub>Cl<sub>4</sub> and C<sub>2</sub>HCl<sub>3</sub> decreased by 0.7±0.2 and 0.3±0.05 pptv/year, respectively, which is indicative of reduced usage and emissions of these halogenated solvents. Emission rates of C<sub>3</sub>-C<sub>8</sub> NMHCs were estimated to be 10<sup>9</sup> to 10<sup>10</sup> molecules cm<sup>−2</sup> s<sup>−1</sup> in winter 2006. The emission rates extrapolated to the state of New Hampshire and New England were ~2–60 Mg/day and ~12–430 Mg/day, respectively. Emission rates of benzene, toluene, ethylbenzene, xylenes, and ethyne in the 2002 and 2005 EPA National Emissions Inventories were within ±50% of the TF emission rates

Combining cytotoxicity assessment and Xenopus laevis phenotypic abnormality assay as a predictor of nanomaterial safety

The African clawed frog, Xenopus laevis, has been used as an efficient pre-clinical screening tool to predict drug safety during the early stages of the drug discovery process. X. laevis is a relatively inexpensive model that can be used in whole organism high-throughput assays whilst maintaining a high degree of homology to the higher vertebrate models often used in scientific research. Despite an ever-increasing volume of biomedical nanoparticles (NPs) in development, their unique physico-chemical properties challenge the use of standard toxicology assays. Here, we present a protocol that directly compares the sensitivity of X. laevis development as a tool to assess potential NP toxicity by observation of embryo phenotypic abnormalities/lethality after NP exposure to in vitro cytotoxicity obtained using mammalian cell lines. In combination with conventional cytotoxicity assays, the X. laevis phenotypic assay provides accurate data to efficiently assess the safety of a novel biomedical NP

Extensive alternative polyadenylation during zebrafish development

The post-transcriptional fate of messenger RNAs (mRNAs) is largely dictated by their 3′ untranslated regions (3′ UTRs), which are defined by cleavage and polyadenylation (CPA) of pre-mRNAs. We used poly(A)-position profiling by sequencing (3P-seq) to map poly(A) sites at eight developmental stages and tissues in the zebrafish. Analysis of over 60 million 3P-seq reads substantially increased and improved existing 3′ UTR annotations, resulting in confidently identified 3′ UTRs for >79% of the annotated protein-coding genes in zebrafish. mRNAs from most zebrafish genes undergo alternative CPA, with those from more than a thousand genes using different dominant 3′ UTRs at different stages. These included one of the poly(A) polymerase genes, for which alternative CPA reinforces its repression in the ovary. 3′ UTRs tend to be shortest in the ovaries and longest in the brain. Isoforms with some of the shortest 3′ UTRs are highly expressed in the ovary, yet absent in the maternally contributed RNAs of the embryo, perhaps because their 3′ UTRs are too short to accommodate a uridine-rich motif required for stability of the maternal mRNA. At 2 h post-fertilization, thousands of unique poly(A) sites appear at locations lacking a typical polyadenylation signal, which suggests a wave of widespread cytoplasmic polyadenylation of mRNA degradation intermediates. Our insights into the identities, formation, and evolution of zebrafish 3′ UTRs provide a resource for studying gene regulation during vertebrate development.National Institutes of Health (U.S.) (Grant GM067031)

A gas chromatographic instrument for measurement of hydrogen cyanide in the lower atmosphere

A gas-chromatographic (GC) instrument was developed for measuring hydrogen cyanide (HCN) in the lower atmosphere. The main features of the instrument are (1) a cryogen-free cooler for sample dehumidification and enrichment, (2) a porous polymer PLOT column for analyte separation, (3) a flame thermionic detector (FTD) for sensitive and selective detection, and (4) a dynamic dilution system for calibration. We deployed the instrument for a ∼4 month period from January–June, 2010 at the AIRMAP atmospheric monitoring station Thompson Farm 2 (THF2) in rural Durham, NH. A subset of measurements made during 3–31 March is presented here with a detailed description of the instrument features and performance characteristics. The temporal resolution of the measurements was ~20 min, with a 75 s sample capture time. The 1σ measurement precision was <10% and the instrument response linearity was excellent on a calibration scale of 0.10–0.75 ppbv (±5%). The estimated method detection limit (MDL) and accuracy were 0.021 ppbv and 15%, respectively. From 3–31 March 2010, ambient HCN mixing ratios ranged from 0.15–1.0 ppbv (±15%), with a mean value of 0.36 ± 0.16 ppbv (1σ). The approximate mean background HCN mixing ratio of 0.20 ± 0.04 ppbv appeared to agree well with tropospheric column measurements reported previously. The GC-FTD HCN measurements were strongly correlated with acetonitrile (CH<sub>3</sub>CN) measured concurrently with a proton transfer-reaction mass spectrometer (PTR-MS), as anticipated given our understanding that the nitriles share a common primary biomass burning source to the global atmosphere. The nitriles were overall only weakly correlated with carbon monoxide (CO), which is reasonable considering the greater diversity of sources for CO. However, strong correlations with CO were observed on several nights under stable atmospheric conditions and suggest regional combustion-based sources for the nitriles. These results demonstrate that the GC-FTD instrument is capable of making long term, in-situ measurements of HCN in the lower atmosphere. To date, similar measurements have not been performed, yet they are critically needed to (1) better evaluate the regional scale distribution of HCN in the atmosphere and (2) discern the influence of biomass burning on surface air composition in remote regions

Tropospheric methanol observations from space: retrieval evaluation and constraints on the seasonality of biogenic emissions

Methanol retrievals from nadir-viewing space-based sensors offer powerful new information for quantifying methanol emissions on a global scale. Here we apply an ensemble of aircraft observations over North America to evaluate new methanol measurements from the Tropospheric Emission Spectrometer (TES) on the Aura satellite, and combine the TES data with observations from the Infrared Atmospheric Sounding Interferometer (IASI) on the MetOp-A satellite to investigate the seasonality of methanol emissions from northern midlatitude ecosystems. Using the GEOS-Chem chemical transport model as an intercomparison platform, we find that the TES retrieval performs well when the degrees of freedom for signal (DOFS) are above 0.5, in which case the model : TES regressions are generally consistent with the model : aircraft comparisons. Including retrievals with DOFS below 0.5 degrades the comparisons, as these are excessively influenced by the a priori. The comparisons suggest DOFS > 0.5 as a minimum threshold for interpreting retrievals of trace gases with a weak tropospheric signal. We analyze one full year of satellite observations and find that GEOS-Chem, driven with MEGANv2.1 biogenic emissions, underestimates observed methanol concentrations throughout the midlatitudes in springtime, with the timing of the seasonal peak in model emissions 1-2 months too late. We attribute this discrepancy to an underestimate of emissions from new leaves in MEGAN, and apply the satellite data to better quantify the seasonal change in methanol emissions for midlatitude ecosystems. The derived parameters (relative emission factors of 11.0, 1.0, 0.05 and 8.6 for new, growing, mature, and old leaves, respectively, plus a leaf area index activity factor of 0.75 for expanding canopies with leaf area index < 2.0) provide a more realistic simulation of seasonal methanol concentrations in midlatitudes on the basis of IASI, TES, and ground-based measurements

Using stable isotopes of hydrogen to quantify biogenic and thermogenic atmospheric methane sources: A case study from the Colorado Front Range

Global atmospheric concentrations of methane (CH4), a powerful greenhouse gas, are increasing, but because there are many natural and anthropogenic sources of CH4, it is difficult to assess which sources may be increasing in magnitude. Here we present a data set of δ2H-CH4 measurements of individual sources and air in the Colorado Front Range, USA. We show that δ2H-CH4, but not δ13C, signatures are consistent in air sampled downwind of landfills, cattle feedlots, and oil and gas wells in the region. Applying these source signatures to air in ground and aircraft samples indicates that at least 50% of CH4 emitted in the region is biogenic, perhaps because regulatory restrictions on leaking oil and natural gas wells are helping to reduce this source of CH4. Source apportionment tracers such as δ2H may help close the gap between CH4 observations and inventories, which may underestimate biogenic as well as thermogenic sources

Total Observed Organic Carbon (TOOC): A synthesis of North American observations

Measurements of organic carbon compounds in both the gas and particle phases measured upwind, over and downwind of North America are synthesized to examine the total observed organic carbon (TOOC) over this region. These include measurements made aboard the NOAA WP-3 and BAe-146 aircraft, the NOAA research vessel Ronald H. Brown, and at the Thompson Farm and Chebogue Point surface sites during the summer 2004 ICARTT campaign. Both winter and summer 2002 measurements during the Pittsburgh Air Quality Study are also included. Lastly, the spring 2002 observations at Trinidad Head, CA, surface measurements made in March 2006 in Mexico City and coincidentally aboard the C-130 aircraft during the MILAGRO campaign and later during the IMPEX campaign off the northwestern United States are incorporated. Concentrations of TOOC in these datasets span more than two orders of magnitude. The daytime mean TOOC ranges from 4.0 to 456 μgC m^−3 from the cleanest site (Trinidad Head) to the most polluted (Mexico City). Organic aerosol makes up 3–17% of this mean TOOC, with highest fractions reported over the northeastern United States, where organic aerosol can comprise up to 50% of TOOC. Carbon monoxide concentrations explain 46 to 86% of the variability in TOOC, with highest TOOC/CO slopes in regions with fresh anthropogenic influence, where we also expect the highest degree of mass closure for TOOC. Correlation with isoprene, formaldehyde, methyl vinyl ketene and methacrolein also indicates that biogenic activity contributes substantially to the variability of TOOC, yet these tracers of biogenic oxidation sources do not explain the variability in organic aerosol observed over North America. We highlight the critical need to develop measurement techniques to routinely detect total gas phase VOCs, and to deploy comprehensive suites of TOOC instruments in diverse environments to quantify the ambient evolution of organic carbon from source to sink

A comparison of GC-FID and PTR-MS toluene measurements in ambient air under conditions of enhanced monoterpene loading

Toluene was measured using both a gas chromatographic system (GC), with a flame ionization detector (FID), and a proton transfer reaction-mass spectrometer (PTR-MS) at the AIRMAP atmospheric monitoring station Thompson Farm (THF) in rural Durham, NH during the summer of 2004. Simultaneous measurements of monoterpenes, including &amp;alpha;- and &amp;beta;-pinene, camphene, &amp;Delta; &lt;sup&gt;3&lt;/sup&gt;-carene, and &lt;i&gt;d&lt;/i&gt;-limonene, by GC-FID demonstrated large enhancements in monoterpene mixing ratios relative to toluene, with median and maximum enhancement ratios of ~2 and ~30, respectively. A detailed comparison between the GC-FID and PTR-MS toluene measurements was conducted to test the specificity of PTR-MS for atmospheric toluene measurements under conditions often dominated by biogenic emissions. We derived quantitative estimates of potential interferences in the PTR-MS toluene measurements related to sampling and analysis of monoterpenes, including fragmentation of the monoterpenes and some of their primary carbonyl oxidation products via reactions with H&lt;sub&gt;3&lt;/sub&gt;O&lt;sup&gt;+&lt;/sup&gt;, O&lt;sub&gt;2&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt; and NO&lt;sup&gt;+&lt;/sup&gt; in the PTR-MS drift tube. The PTR-MS and GC-FID toluene measurements were in good quantitative agreement and the two systems tracked one another well from the instrumental limits of detection to maximum mixing ratios of ~0.5 ppbv. A correlation plot of the PTR-MS versus GC-FID toluene measurements was described by the least squares regression equation &lt;i&gt;y&lt;/i&gt;=(1.13&amp;plusmn; 0.02)&lt;i&gt;x&lt;/i&gt;&amp;minus;(0.008&amp;plusmn;0.003) ppbv, suggesting a small ~13% positive bias in the PTR-MS measurements. The bias corresponded with a ~0.055 ppbv difference at the highest measured toluene level. The two systems agreed quantitatively within the combined 1&amp;sigma; measurement precisions for 60% of the measurements. Discrepancies in the measured mixing ratios were not well correlated with enhancements in the monoterpenes. Better quantitative agreement between the two systems was obtained by correcting the PTR-MS measurements for contributions from monoterpene fragmentation in the PTR-MS drift tube; however, the improvement was minor (&lt;10%). Interferences in the PTR-MS measurements from fragmentation of the monoterpene oxidation products pinonaldehyde, caronaldehyde and &amp;alpha;-pinene oxide were also likely negligible. A relatively large and variable toluene background in the PTR-MS instrument likely drove the measurement bias; however, the precise contribution was difficult to accurately quantify and thus was not corrected for in this analysis. The results from THF suggest that toluene can be reliably quantified by PTR-MS using our operating conditions (drift tube pressure, temperature and voltage of 2.0 mbar, 45 °C and 600 V, respectively) under the ambient compositions probed. This work extends the range of field conditions under which PTR-MS validation studies have been conducted

Double sampling of a faecal immunochemical test is not superior to single sampling for detection of colorectal neoplasia: a colonoscopy controlled prospective cohort study

<p>Abstract</p> <p>Background</p> <p>A single sampled faecal immunochemical test (FIT) has moderate sensitivity for colorectal cancer and advanced adenomas. Repeated FIT sampling could improve test sensitivity. The aim of the present study is to determine whether any of three different strategies of double FIT sampling has a better combination of sensitivity and specificity than single FIT sampling.</p> <p>Methods</p> <p>Test performance of single FIT sampling in subjects scheduled for colonoscopy was compared to double FIT sampling intra-individually. Test positivity of double FIT sampling was evaluated in three different ways: 1) "one of two FITs+" when at least one out of two measurements exceeded the cut-off value, 2) "two of two FITs+" when both measurements exceeded the cut-off value, 3) "mean of two FITs+" when the geometric mean of two FITs exceeded the cut-off value. Receiver operator curves were calculated and sensitivity of single and the three strategies of double FIT sampling were compared at a fixed level of specificity.</p> <p>Results</p> <p>In 124 of 1096 subjects, screen relevant neoplasia (SRN) were found (i.e. early stage CRC or advanced adenomas). At any cut-off, "two of two FITs+" resulted in the lowest and "one of two FITs+" in the highest sensitivity for SRN (range 35-44% and 42%-54% respectively). ROC's of double FIT sampling were similar to single FIT sampling. At specificities of 85/90/95%, sensitivity of any double FIT sampling strategy did not differ significantly from single FIT (p-values 0.07-1).</p> <p>Conclusion</p> <p>At any cut off, "one of two FITs+" is the most sensitive double FIT sampling strategy. However, at a given specificity level, sensitivity of any double FIT sampling strategy for SRN is comparable to single FIT sampling at a different cut-off value. None of the double FIT strategies has a superior combination of sensitivity and specificity over single FIT.</p