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Isoprene oxidation schemes vary greatly among gas-phase chemical mechanisms, with potentially significant ramifications for air quality modeling and interpretation of satellite observations in biogenic-rich regions. In this study, in situ observations from the 2013 SENEX mission are combined with a constrained 0-D photochemical box model to evaluate isoprene chemistry among five commonly used gas-phase chemical mechanisms: CB05, CB6r2, MCMv3.2, MCMv3.3.1, and a recent version of GEOS-Chem. Mechanisms are evaluated and inter-compared with respect to formaldehyde (HCHO), a high-yield product of isoprene oxidation. Though underestimated by all considered mechanisms, observed HCHO mixing ratios are best reproduced by MCMv3.3.1 (normalized mean bias = −15%), followed by GEOS-Chem (−17%), MCMv3.2 (−25%), CB6r2 (−32%) and CB05 (−33%). Inter-comparison of HCHO production rates reveals that major restructuring of the isoprene oxidation scheme in the Carbon Bond mechanism increases HCHO production by only ∼5% in CB6r2 relative to CB05, while further refinement of the complex isoprene scheme in the Master Chemical Mechanism increases HCHO production by ∼16% in MCMv3.3.1 relative to MCMv3.2. The GEOS-Chem mechanism provides a good approximation of the explicit isoprene chemistry in MCMv3.3.1 and generally reproduces the magnitude and source distribution of HCHO production rates. We analytically derive improvements to the isoprene scheme in CB6r2 and incorporate these changes into a new mechanism called CB6r2-UMD, which is designed to preserve computational efficiency. The CB6r2-UMD mechanism mimics production of HCHO in MCMv3.3.1 and demonstrates good agreement with observed mixing ratios from SENEX (−14%). Improved simulation of HCHO also impacts modeled ozone: at ∼0.3 ppb NO, the ozone production rate increases ∼3% between CB6r2 and CB6r2-UMD, and rises another ∼4% when HCHO is constrained to match observations.

The Framework for 0-D Atmospheric Modeling (F0AM) is a flexible and user-friendly MATLAB-based platform for simulation of atmospheric chemistry systems. The F0AM interface incorporates front-end configuration of observational constraints and model setup, making it readily adaptable to simulation of photochemical chambers, Lagrangian plumes, and steady-state or time-evolving solar cycles. Six different chemical mechanisms and three options for calculation of photolysis frequencies are currently available. Example simulations are presented to illustrate model capabilities and, more generally, highlight some of the advantages and challenges of 0-D box modeling.

The chemical link between isoprene and formaldehyde (HCHO) is a strong, nonlinear function of NOx (i.e., NO + NO2). This relationship is a linchpin for top-down isoprene emission inventory verification from orbital HCHO column observations. It is also a benchmark for overall photochemical mechanism performance with regard to VOC oxidation. Using a comprehensive suite of airborne in situ observations over the southeast US, we quantify HCHO production across the urban–rural spectrum. Analysis of isoprene and its major first-generation oxidation products allows us to define both a "prompt" yield of HCHO (molecules of HCHO produced per molecule of freshly emitted isoprene) and the background HCHO mixing ratio (from oxidation of longer-lived hydrocarbons). Over the range of observed NOx values (roughly 0.1–2 ppbv), the prompt yield increases by a factor of 3 (from 0.3 to 0.9 ppbv ppbv−1), while background HCHO increases by a factor of 2 (from 1.6 to 3.3 ppbv). We apply the same method to evaluate the performance of both a global chemical transport model (AM3) and a measurement-constrained 0-D steady-state box model. Both models reproduce the NOx dependence of the prompt HCHO yield, illustrating that models with updated isoprene oxidation mechanisms can adequately capture the link between HCHO and recent isoprene emissions. On the other hand, both models underestimate background HCHO mixing ratios, suggesting missing HCHO precursors, inadequate representation of later-generation isoprene degradation and/or underestimated hydroxyl radical concentrations. Detailed process rates from the box model simulation demonstrate a 3-fold increase in HCHO production across the range of observed NOx values, driven by a 100 % increase in OH and a 40 % increase in branching of organic peroxy radical reactions to produce HCHO.

The chemical link between isoprene and formaldehyde (HCHO) is a strong, non-linear function of NOx (= NO + NO2). This relationship is a linchpin for top-down isoprene emission inventory verification from orbital HCHO column observations. It is also a benchmark for overall photochemical mechanism performance with regard to VOC oxidation. Using a comprehensive suite of airborne in situ observations over the Southeast U.S., we quantify HCHO production across the urban-rural spectrum. Analysis of isoprene and its major first-generation oxidation products allows us to define both a “prompt” yield of HCHO (molecules of HCHO produced per molecule of freshly-emitted isoprene) and the background HCHO mixing ratio (from oxidation of longer-lived hydrocarbons). Over the range of observed NOx values (roughly 0.1 – 2 ppbv), the prompt yield increases by a factor of 3 (from 0.3 to 0.9 ppbv ppbv−1), while background HCHO increases by a factor of 2 (from 1.6 to 3.3 ppbv). We apply the same method to evaluate the performance of both a global chemical transport model (AM3) and a measurement-constrained 0-D steady state box model. Both models reproduce the NOx dependence of the prompt HCHO yield, illustrating that models with updated isoprene oxidation mechanisms can adequately capture the link between HCHO and recent isoprene emissions. On the other hand, both models under-estimate background HCHO mixing ratios, suggesting missing HCHO precursors, inadequate representation of later-generation isoprene degradation and/or under-estimated hydroxyl radical concentrations. Detailed process rates from the box model simulation demonstrate a 3-fold increase in HCHO production across the range of observed NOx values, driven by a 100% increase in OH and a 40% increase in branching of organic peroxy radical reactions to produce HCHO.

Atmospheric composition is governed by the interplay of emissions, chemistry, deposition, and transport. Substantial questions surround each of these processes, especially in forested environments with strong biogenic emissions. Utilizing aircraft observations acquired over a forest in the southeast U.S., we calculate eddy covariance fluxes for a suite of reactive gases and apply the synergistic information derived from this analysis to quantify emission and deposition fluxes, oxidant concentrations, aerosol uptake coefficients, and other key parameters. Evaluation of results against state-of-the-science models and parameterizations provides insight into our current understanding of this system and frames future observational priorities. As a near-direct measurement of fundamental process rates, airborne fluxes offer a new tool to improve biogenic and anthropogenic emissions inventories, photochemical mechanisms, and deposition parameterizations.

Previous work has demonstrated that cell-mediated immune function in rats is better preserved after laparoscopic than open surgery. We have also shown that tumors are more easily established in mice and grow larger after sham laparotomy than after pneumoperitoneum. The purpose of this study is to determine if the functional status of the cell-mediated immune system influences postoperative tumor growth.Immunocompetent (study 1) and T-cell deficient athymic (study 2) mice were injected with mouse mammary carcinoma cells in the dorsal skin. Mice then underwent either no procedure, midline laparotomy, or carbon dioxide pneumoperitoneum. Tumor masses on postoperative day 12 were compared.In immunocompetent mice, laparotomy group tumors were nearly twice as large as laparoscopy group tumors (p0.02), which were 1.5 times as large as control group tumors (NS). In the athymic model, however, differences between the sham laparotomy and pneumoperitoneum groups were lost (p0.5). Tumors grew much larger in the athymic control mice than in the immunocompetent control mice (p0.01).We conclude that T-cell function plays a significant role in host containment of mouse mammary carcinoma and in the mechanism of differences in tumor growth observed after laparotomy and pneumoperitoneum.

Surgery can suppress immune function and facilitate tumor growth. Several studies have demonstrated better preservation of immune function following laparoscopic procedures. Our laboratory has also shown that tumors are more easily established and grow larger after sham laparotomy than after pneumoperitoneum in mice. The purpose of this study was to determine if the previously reported differences in tumor establishment and growth would persist in the setting of an intraabdominal manipulation.Syngeneic mice received intradermal injections of tumor cells and underwent either an open or laparoscopic cecal resection. In study 1, the incidence of tumor development was observed after a low dose inoculum; whereas in study 2, tumor mass was compared on postoperative day 12 after a high-dose inoculum.In study 1, tumors were established in 5% of control mice, 30% of laparoscopy mice, and 83% of open surgery mice (p0.01 for all comparisons). In study 2, open surgery group tumors were 1.5 times as large as laparoscopy group tumors (p0.01), which were 1.5 times as large as control group tumors (p0.02).We conclude that tumors are more easily established and grow larger after open laparoscopic bowel resection in mice.

Even though the small intestine contains 90% of the gastrointestinal tract mucosa and is located between the stomach and large intestine, two organs with a high cancer incidence, adenocarcinoma of the small intestine is 1/50th as common as adenocarcinoma of the large bowel. In several other respects, small-intestinal adenocarcinoma resembles large bowel adenocarcinoma; eg, it arises from adenomatous polyps, co-occurs in the same individuals, and has a similar pattern of incidence rates by country. Small-intestinal adenocarcinoma is diagnosed prior to surgery in only about 50% of cases and often occurs in conjunction with small bowel obstruction. The mainstay of treatment is surgery; prognosis depends on stage at presentation. Little is known about the use of radiotherapy and chemotherapy in this malignancy, but most physicians utilize therapeutic strategies modeled on the management of large-intestinal adenocarcinoma. Clarification of the reason for the low incidence of small-intestinal adenocarcinoma could lead to new interventions for the prevention of colorectal cancer.