125 research outputs found
Recommended from our members
Global tropospheric halogen (Cl, Br, I) chemistry and its impact on oxidants
We present an updated mechanism for tropospheric halogen (Cl + Br + I) chemistry in the GEOS-Chem global atmospheric chemical transport model and apply it to investigate halogen radical cycling and implications for tropospheric oxidants. Improved representation of HOBr heterogeneous chemistry and its pH dependence in our simulation leads to less efficient recycling and mobilization of bromine radicals and enables the model to include mechanistic sea salt aerosol debromination without generating excessive BrO. The resulting global mean tropospheric BrO mixing ratio is 0.19 ppt (parts per trillion), lower than previous versions of GEOS-Chem. Model BrO shows variable consistency and biases in comparison to surface and aircraft observations in marine air, which are often near or below the detection limit. The model underestimates the daytime measurements of Cl2 and BrCl from the ATom aircraft campaign over the Pacific and Atlantic, which if correct would imply a very large missing primary source of chlorine radicals. Model IO is highest in the marine boundary layer and uniform in the free troposphere, with a global mean tropospheric mixing ratio of 0.08 ppt, and shows consistency with surface and aircraft observations. The modeled global mean tropospheric concentration of Cl atoms is 630 cm−3, contributing 0.8 % of the global oxidation of methane, 14 % of ethane, 8 % of propane, and 7 % of higher alkanes. Halogen chemistry decreases the global tropospheric burden of ozone by 11 %, NOx by 6 %, and OH by 4 %. Most of the ozone decrease is driven by iodine-catalyzed loss. The resulting GEOS-Chem ozone simulation is unbiased in the Southern Hemisphere but too low in the Northern Hemisphere.
Full List of Authors:
Xuan Wang1,2, Daniel J. Jacob3, William Downs3, Shuting Zhai4, Lei Zhu5, Viral Shah3, Christopher D. Holmes6, Tomás Sherwen7,8, Becky Alexander4, Mathew J. Evans7,8, Sebastian D. Eastham9, J. Andrew Neuman10,11, Patrick R. Veres10, Theodore K. Koenig11,12, Rainer Volkamer11,12, L. Gregory Huey13, Thomas J. Bannan14, Carl J. Percival14,a, Ben H. Lee4, and Joel A. Thornton4
1School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
2City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
3School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
4Department of Atmospheric Sciences, University of Washington, Seattle, Washington, USA
5School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China
6Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, Florida, USA
7Wolfson Atmospheric Chemistry Laboratories, Department of Chemistry, University of York, York, UK
8National Centre for Atmospheric Science, University of York, York, UK
9Laboratory for Aviation and the Environment, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
10NOAA Chemical Sciences Laboratory (CSL), Boulder, Colorado, USA
11Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
12Department of Chemistry, University of Colorado, Boulder, Colorado, USA
13School of Earth and Atmospheric Science, Georgia Institute of Technology, Atlanta, Georgia, USA
14School of Earth, Atmospheric and Environmental Sciences, University of Manchester, Manchester, UK
anow at: Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
</p
Recommended from our members
The proteome of the infectious bronchitis virus Beau-R Virion
Infectious bronchitis is a highly contagious respiratory disease of poultry caused by the coronavirus IBV. It was thought that coronavirus virions were composed of three major viral structural proteins, until investigations of other coronaviruses showed that coronavirus virions also include viral non-structural and group specific proteins as well as host cell proteins. To study the proteome of IBV virions, virus was grown in embryonated chicken eggs and purified by sucrose gradient ultracentrifugation and analysed by mass spectrometry proteomic. Analysis of three preparations of purified IBV yielded the three expected structural proteins plus thirty-five additional virion-associated host proteins. Virion-associated host proteins had a diverse range of functional attributions, being involved in cytoskeleton formation, RNA binding and protein folding pathways. Some of these proteins were unique to this study, whilst others were found to be orthologous to proteins identified in SARS-CoV virions, and also virions from a number of other RNA and DNA viruses. Together these results demonstrate that coronaviruses have the capacity to incorporate a substantial variety of host protein, which may have implications for the disease process
Directed assembly of optically bound matter
We present a study of optically bound matter formation in a counter-propagating evanescent field, exploiting total internal reflection on a prism surface. Small ensembles of silica microspheres are assembled in a controlled manner using optical tweezers. The structures and dynamics of the resulting optically bound chains are interpreted using a simulation implementing generalized Lorentz-Mie theory. In particular, we observe enhancement of the scattering force along the propagation direction of the optically bound colloidal chains leading to a microscopic analogue of a driven pendulum which, at least superficially, resembles Newtonās cradle
Characteristics of tropospheric ozone depletion events in the Arctic spring: analysis of the ARCTAS, ARCPAC, and ARCIONS measurements and satellite BrO observations
Arctic ozone depletion events (ODEs) are caused by halogen catalyzed ozone loss. In situ chemistry, advection of ozone-poor air mass, and vertical mixing in the lower troposphere are important factors affecting ODEs. To better characterize the ODEs, we analyze the combined set of surface, ozonesonde, and aircraft in situ measurements of ozone and bromine compounds during the Arctic Research of the Composition of the Troposphere from Aircraft and Satellites (ARCTAS), the Aerosol, Radiation, and Cloud Processes affecting Arctic Climate (ARCPAC), and the Arctic Intensive Ozonesonde Network Study (ARCIONS) experiments (April 2008). Tropospheric BrO columns retrieved from satellite measurements and back trajectory calculations are also used to investigate the characteristics of observed ODEs. In situ observations from these field experiments are inadequate to validate tropospheric BrO columns derived from satellite measurements. In view of this difficulty, we construct an ensemble of tropospheric column BrO estimates from two satellite (OMI and GOME-2) measurements and with three independent methods of calculating stratospheric BrO columns. Furthermore, we select analysis methods that do not depend on the absolute magnitude of column BrO, such as time-lagged correlation analysis of ozone and tropospheric column BrO, to understand characteristics of ODEs. Time-lagged correlation analysis between in situ (surface and ozonesonde) measurements of ozone and satellite derived tropospheric BrO columns indicates that the ODEs are due to either local halogen-driven ozone loss or short-range (ā¼1 day) transport from nearby regions with ozone depletion. The effect of in situ ozone loss is also evident in the diurnal variation difference between low (10th and 25th percentiles) and higher percentiles of surface ozone concentrations at Alert, Canada. Aircraft observations indicate low-ozone air mass transported from adjacent high-BrO regions. Correlation analyses of ozone with potential temperature and time-lagged tropospheric BrO column show that the vertical extent of local ozone loss is surprisingly deep (1ā2 km) at Resolute and Churchill, Canada. The unstable boundary layer during ODEs at Churchill could potentially provide a source of free-tropospheric BrO through convective transport and explain the significant negative correlation between free-tropospheric ozone and tropospheric BrO column at this site
Recommended from our members
Temperature-dependent sensitivity of iodide chemical ionization mass spectrometers
Iodide chemical ionization mass spectrometry (CIMS) is a common analytical tool used in both laboratory and field experiments to measure a large suite of atmospherically relevant compounds. Here, we describe a systematic ion molecule reactor (IMR) temperature dependence of iodide CIMS analyte sensitivity for a wide range of analytes in laboratory experiments. Weakly bound iodide clusters, such as HCl, HONO, HCOOH, HCN, phenol, 2-nitrophenol, and acyl peroxynitrate (PAN) detected via the peroxy radical cluster, all exhibit strong IMR temperature dependence of sensitivity ranging from −3.4 % āC−1 to 5.9 % āC−1 (from 37 to 47 āC). Strongly bound iodide clusters, such as Br2, N2O5, ClNO2, and PAN detected via the carboxylate anion, all exhibit little to no IMR temperature dependence ranging from 0.2 % āC−1 to −0.9 % āC−1 (from 37 to 47 āC). The IMR temperature relationships of weakly bound clusters provide an estimate of net reaction enthalpy, and comparison with database values indicates that these clusters are in thermal equilibrium. Ground site HCOOH data collected in the summer of 2021 in Pasadena (CA) are corrected and show a reversal in the diel cycle, emphasizing the importance of this correction (35±6 % during the day,  % at night). Finally, we recommend two approaches to minimize this effect in the field, namely heating or cooling the IMR; the latter technique has the added benefit of improving absolute sensitivity.</p
Recommended from our members
On the sources and sinks of atmospheric VOCs: an integrated analysis of recent aircraft campaigns over North America
We apply a high-resolution chemical transport model (GEOS-Chem CTM) with updated treatment of volatile organic compounds (VOCs) and a comprehensive suite of airborne datasets over North America to (i) characterize the VOC budget and (ii) test the ability of current models to capture the distribution and reactivity of atmospheric VOCs over this region. Biogenic emissions dominate the North American VOC budget in the model, accounting for 70 % and 95 % of annually emitted VOC carbon and reactivity, respectively. Based on current inventories anthropogenic emissions have declined to the point where biogenic emissions are the dominant summertime source of VOC reactivity even in most major North American cities. Methane oxidation is a 2× larger source of nonmethane VOCs (via production of formaldehyde and methyl hydroperoxide) over North America in the model than are anthropogenic emissions. However, anthropogenic VOCs account for over half of the ambient VOC loading over the majority of the region owing to their longer aggregate lifetime. Fires can be a significant VOC source episodically but are small on average. In the planetary boundary layer (PBL), the model exhibits skill in capturing observed variability in total VOC abundance (R2=0.36) and reactivity (R2=0.54). The same is not true in the free troposphere (FT), where skill is low and there is a persistent low model bias (∼ 60 %), with most (27 of 34) model VOCs underestimated by more than a factor of 2. A comparison of PBL : FT concentration ratios over the southeastern US points to a misrepresentation of PBL ventilation as a contributor to these model FT biases. We also find that a relatively small number of VOCs (acetone, methanol, ethane, acetaldehyde, formaldehyde, isoprene + oxidation products, methyl hydroperoxide) drive a large fraction of total ambient VOC reactivity and associated model biases; research to improve understanding of their budgets is thus warranted. A source tracer analysis suggests a current overestimate of biogenic sources for hydroxyacetone, methyl ethyl ketone and glyoxal, an underestimate of biogenic formic acid sources, and an underestimate of peroxyacetic acid production across biogenic and anthropogenic precursors. Future work to improve model representations of vertical transport and to address the VOC biases discussed are needed to advance predictions of ozone and SOA formation.
</div
High throughput analysis of epistasis in genome-wide association studies with BiForce
Motivation: Geneāgene interactions (epistasis) are thought to be important in shaping complex traits, but they have been under-explored in genome-wide association studies (GWAS) due to the computational challenge of enumerating billions of single nucleotide polymorphism (SNP) combinations. Fast screening tools are needed to make epistasis analysis routinely available in GWAS. Results: We present BiForce to support high-throughput analysis of epistasis in GWAS for either quantitative or binary disease (caseācontrol) traits. BiForce achieves great computational efficiency by using memory efficient data structures, Boolean bitwise operations and multithreaded parallelization. It performs a full pair-wise genome scan to detect interactions involving SNPs with or without significant marginal effects using appropriate Bonferroni-corrected significance thresholds. We show that BiForce is more powerful and significantly faster than published tools for both binary and quantitative traits in a series of performance tests on simulated and real datasets. We demonstrate BiForce in analysing eight metabolic traits in a GWAS cohort (323 697 SNPs, >4500 individuals) and two disease traits in another (>340 000 SNPs, >1750 cases and 1500 controls) on a 32-node computing cluster. BiForce completed analyses of the eight metabolic traits within 1 day, identified nine epistatic pairs of SNPs in five metabolic traits and 18 SNP pairs in two disease traits. BiForce can make the analysis of epistasis a routine exercise in GWAS and thus improve our understanding of the role of epistasis in the genetic regulation of complex traits. Availability and implementation: The software is free and can be downloaded from http://bioinfo.utu.fi/BiForce/. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online
Speech Perception Changes in the Acoustically Aided, Nonimplanted Ear after Cochlear Implantation: A Multicenter Study
In recent years there has been an increasing percentage of cochlear implant (CI) users who have usable residual hearing in the contralateral, nonimplanted ear, typically aided by acoustic amplification. This raises the issue of the extent to which the signal presented through the cochlear implant may influence how listeners process information in the acoustically stimulated ear. This multicenter retrospective study examined pre- to postoperative changes in speech perception in the nonimplanted ear, the implanted ear, and both together. Results in the latter two conditions showed the expected increases, but speech perception in the nonimplanted ear showed a modest yet meaningful decrease that could not be completely explained by changes in unaided thresholds, hearing aid malfunction, or several other demographic variables. Decreases in speech perception in the nonimplanted ear were more likely in individuals who had better levels of speech perception in the implanted ear, and in those who had better speech perception in the implanted than in the nonimplanted ear. This raises the possibility that, in some cases, bimodal listeners may rely on the higher quality signal provided by the implant and may disregard or even neglect the input provided by the nonimplanted ear
- ā¦